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Carbohydrate utilization

The Haemophilus somnus 129Pt genome encoded genes involved in the utilization of glucose,

ribose, xylose, fucose, galactitol, glucitol/sorbitol, mannose and mannitol (Table S5), while H.

ducreyi 35000HP had genes involved in glucose and mannose utilization. The H. influenzae Rd

genome contained genes involved in the utilization of glucose, ribose, xylose, fucose, glycerol,

fructose and galactose (15, 27).

        The most interesting aspect of carbohydrate utilization involved the genes for glucose and

fructose transport. H. influenzae Rd has the enzyme I (ptsI, HI1712), Hpr (ptsH, HI1713) and

glucose specific IIA (crr, HI1711) genes for the glucose phosphotransferase system (PTS), but

not the gene encoding membrane bound glucose-specific enzyme II (ptsG) (Fleischmann et al,

1995). Both H. somnus 129Pt and H. ducreyi 350HP had the ptsI (HS_1097, HD0228), ptsH

(HS_1098, HD0229) and crr (IIAGlc, HS_1096, HD0227) genes and, like H. influenzae, lacked

ptsG.

        We found that H. somnus 129Pt and H. ducreyi 35000HP, like H. influenzae Rd (15),

lacked genes encoding the membrane-bound glucose specific enzyme IIBC (ptsG) of the glucose

PTS, indicating that they did not have a functional glucose PTS for glucose transport. Therefore,

instead of being involved in glucose utilization, the product of the crr gene may be involved in

regulation of carbon metabolism and stress response in these Haemophilus strains, as has been

proposed for S. coelicolor (22) and P. multocida (4). If this is true, how do these organisms take

up glucose? A previous study of H. influenzae suggests that it takes up glucose via a non-PTS

permease (26). We did find one gene in H. somnus 129Pt that encoded a sodium/glucose

symporter (HS_0338). However, this gene was not present in H. influenzae Rd or H. ducreyi




                                                 1
35000HP. Glucose may enter these organisms via an unidentified permease, an ABC transport

system or may be transported by a permease that is specific to another sugar (26). Another option

for H. ducreyi 35000HP and H. somnus 129Pt is that they may be able to transport glucose via a

mannose PTS, as has been described for P. multocida (4), since they both had genes encoding

the mannose PTS. Further evidence in support of this option was our finding that H. ducreyi

35000HP had no genes with sequence similarity to known glucokinase genes. However, it is

possible that H. ducreyi 35000HP contains a functional homolog with no sequence similarity to

other glucokinase/hexokinase genes. As an alternative to glycolysis, P. multocida may use the

pentose phosphate pathway to process glucose (4). This may also be the case for H. somnus

129Pt, H. ducreyi 35000HP and H. influenzae Rd, which all have the complete set of pentose

phosphate pathway genes.

       H. influenzae had the fruBKA operon (HI0446 – HI0448) encoding components of the

fructose PTS, consisting of the fruB gene encoding the protein FPr, fruK (1-

phosphofructokinase), and fruA, encoding the fructose-specific IIBC component. Neither H.

somnus 129Pt nor H. ducreyi 35000HP had these genes. The closest relative to the fructose PTS

is the mannitol PTS (35), which only H somnus 129Pt had. This is interesting in light of evidence

that H. somnus can ferment fructose in culture (16). It is possible H. somnus takes up fructose via

either a mannose or mannitol PTS, which it encodes, or by an unidentified permease. Both H

somnus 129Pt and H. influenzae Rd had genes that were similar to the E. coli mak gene

(HS_1253; HI1082), which encodes cryptic manno(fructo)kinase that converts fructose to

fructose-6-phosphate, as well as pfkA (6-phosphofructokinase 1; HS_0485; HI0982) and fbaA

(fructose bisphosphate aldolase class II; HS_0206; HI0524), all of which are part of the fructose

degradation pathway. H. ducreyi 35000HP had homologs of pfkA (HD0465) and fbaA (HD0864)




                                                2
but not mak. H. somnus 129Pt also had a gene that encodes a possible fructose bisphosphate

aldolase class I (HS_0055).

       In H. influenzae, the galactose utilization genes galMKTR (HI0818 – HI0821) are located

together, while galU (HI0812) and galE (HI0351) are not (28). Like H. influenzae Rd, H. somnus

129Pt had the genes galK, galM, galU and galE, but only galK (HS_0235) and galM (HS_0236)

were located next to each other (Table S5). It did not have galT, which encodes galactose-1-

phosphate uridylyltransferase or galR, the galactose operon repressor. H. ducreyi had only galU

(HD1431) and galE (HD0829). GalE is required for the biosynthesis of extracellular

polysaccharide materials such as lipopolysaccharide (LPS) and capsule (36). galU is an essential

virulence gene that is critical in generating sugar precursors needed for polysaccharide formation

and LOS outer core synthesis (49). The unlinked location of galE relative to the other gal operon

genes in H. somnus 129Pt and H. influenzae Rd is also seen in Pasteurella (Mannheimia)

haemolytica A1; the separation of galE from the rest of the gal operon may have resulted from a

transposition event (36). P. haemolytica A1 is normally found inside its bovine host, and

therefore may not need a catabolic gal operon, since it probably does not have to grow on

galactose as its sole source of carbon (36). Since they are missing some or many of the gal

operon genes, and can use other sugars, this may also be the case for H. somnus 129Pt.

       Both H. somnus 129Pt and H. influenzae Rd had the ribose operon genes. The H.

influenzae rbs genes were organized in an operon, in the same order as in E. coli (3). In contrast,

the H. somnus 129Pt rbs operon genes were present in 4 locations around the genome: 1) rbsD,

rbsK and rbsR (HS_0223 – HS_0227), HS_0224 and HS_0224a were possible transposases; 2)

rbsACB (HS_0763-HS_0765); 3) and 4) H. somnus 129Pt had 1 extra copy of rbsA (HS_0768)

and 2 extra copies of rbsC (HS_0769 and HS_1580).




                                                 3
       H. somnus 129Pt and H. influenzae Rd both had genes involved in D-xylose and xylitol

degradation (Table S5). The genes for D-xylose degradation to D-xylulose 5-phosphate, xylA

(HS_0587, HI1112) and xylB (HS_0588, HI1113), were not present in H. ducreyi 35000HP. H.

somnus 129Pt and H. influenzae Rd also had most of the components of the xylitol degradation

pathway, which converts xylitol to xylulose 5-phosphate. The first step in this pathway, the

conversion of xylitol to L-xylulose, is catalyzed by a xylitol 4-dehydrogenase/L-xylulose

reductase, which exists in Erwinia uredovora (10) and many eukaryotes. However, there were no

gene or protein sequences available from E. uredovora to use in blast searches. Blastx of the L-

xylulose reductase gene sequence from Trichoderma reesei (Hypocrea jecorina) hit

reductase/dehydrogenase proteins in H. somnus 129Pt (HS_0167), H. ducreyi 35000HP

(HD0708) and H. influenzae Rd (HI0155) at 29% – 30% amino acid identity. So, the xylitol 4-

dehydrogenase activity may be present in these organisms. The next reaction, conversion of L-

xylulose to L-xylulose 5-phosphate is catalyzed by L-xylulokinase (9), which was present in H.

somnus 129Pt (HS_0770) and H. influenzae Rd (HI1027), but not in H. ducreyi 35000HP.

However, H. somnus 129Pt, H. ducreyi 35000HP and H. influenzae Rd all had rpe (HS_0175,

HS_0057, HD1929, HI0566), encoding ribulose phosphate 3-epimerase, which converts D- and

L-xylulose 5-phosphate to D- or L-ribulose 5-phosphate (42). There was a cluster of genes in H.

somnus 129Pt (HS_0763 to HS_0773) involved in ribose and xylitol metabolism. Although H.

influenzae Rd had all of these genes, they were not organized on the chromosome in the same

way. As mentioned above, H. influenzae Rd had only 1 copy of the rbs operon (HI0501 –

HI0506), which was not adjacent to the sgbK/lyx, sgbH, sgbU and araD genes (HI1024 –

HI1027), as one set of rbs genes was in H. somnus 129Pt.




                                                4
       Like H. influenzae Rd, H. somnus 129Pt had the fuc operon (HS_1446 – HS_1451;

HI0610 – HI0615), so it can probably metabolize fucose. H. ducreyi 35000HP did not have these

genes. Both H. influenzae Rd and H. somnus 129Pt had an extra copy of the fucA gene

(HS_0014, HI1012), which encodes fucose-1-P aldolase. Both H. somnus 129Pt and H. ducreyi

35000HP had the mannose utilization genes manAZYX (HS_0605 – HS_0609; HD0765 –

HD0768), while H. influenzae Rd did not. However, the genes that flanked the mannose

utilization genes in H. somnus 129Pt and H. ducreyi 35000HP were different. H. ducreyi

35000HP had a complete set of genes encoding the mannose PTS and mannose 6-phosphate

isomerase (HD0765-HD0768).

       H. somnus 129Pt had the galactitol utilization operon (HS_1140 – HS_1146), but H.

influenzae Rd and H. ducreyi 35000HP did not. H. influenzae Rd and H. ducreyi 35000HP did

have the pflA and pflB genes that flanked the galactitol operon in H. somnus 129Pt, although they

were on the opposite strand in reverse order. H. somnus 129Pt had the glucitol/sorbitol utilization

operon (HS_0675 – HS_0679) flanked by genes purE (opposite strand HS_0672) and pepP

(HS_0682), H. ducreyi 35000HP had the flanking genes on opposite strands with other genes in-

between (HD1419 – HD1423; aspC, hypothetical, purK, hypothetical, purK). H. influenzae Rd

had purE, purK, aspC in a row (HI1615 – HI1617), but pepP (HI0816) was located

approximately 800 genes away.

       H. somnus 129Pt had a mannitol utilization operon consisting of mtlADR (HS_1250 –

HS_1252). This was like the mtl operon in E. coli, which consists of the mtlA, mtlR, and mtlD

genes that encode the mannitol transporter (enzyme IICBAmtl), a transcriptional regulator, and

mannitol-1-phosphate dehydrogenase (46). H. ducreyi 35000HP and H.influenzae Rd did not




                                                5
have these genes. HD1859 may be a mannitol/fructose specific IIA component of a PTS, but H.

somnus 129Pt did not have it.

       H. somnus 129Pt had a gene that was similar to E. coli celB (HS_0437), which encodes a

cellobiose-specific IIC component, but did not have genes encoding the complete cellobiose

PTS. H. ducreyi 35000HP and H. influenzae Rd did not have any cellobiose PTS genes.

Because H. somnus in culture has been reported to use trehalose and maltose (16), we looked for

genes involved in trehalose and maltose uptake and degradation. The enzyme II of the trehalose

PTS (encoded by treB) can function with the rest of the glucose PTS (crr, HPr, EI) (1, 34).

However, H. somnus 129Pt, H. ducreyi 35000HP and H. influenzae Rd did not have treB. None

of the organisms had treC, enoding the trehalose 6-P hydrolase or treA, encoding the periplasmic

trehalase. So trehalose probably does not enter the cell via the PTS or follow the trehalose I

degradation pathway. The genomes of H. somnus 129Pt, H. ducreyi 35000HP and H. influenzae

Rd also didn’t have a gene encoding trehalose-6-phosphate phosphorylase (trePP) or treF,

encoding cytoplasmic trehalase, which is part of the trehalose degradation II pathway. Trehalose

can also enter cells via a permease (34), followed by trehalose phosphorylase conversion of

trehalose to glucose-1-P. However, none of these organisms had genes encoding trehalose

phosphorylase. With regard to maltose, H. influenzae Rd, H. somnus 129Pt and H. ducreyi

35000HP were missing all of the key E. coli genes involved in maltose uptake and degradation

(malT, malS, malE, malF, malG, malK, malP, malZ) (5). H. somnus 129Pt and H. influenzae Rd

did have malQ, which is necessary for maltose metabolism in E. coli (5).




                                                 6
Amino acid metabolism

A common feature between H. somnus129Pt and H. influenzae Rd was the possession of the

gdhA (glutamate dehydrogenase) gene, which H. ducreyi 35000HP did not have (Table S6).

Glutamate dehydrogenase aids in ammonia assimilation by catalyzing the conversion of

ammonium and alpha-ketoglutarate to glutamate (32). Glutamate and glutamine are the primary

products of ammonia assimilation (38), and these amino acids donate nitrogen that is used in

biosynthetic reactions (14, 32). The main bacterial pathway for the incorporation of nitrogen into

glutamate and glutamine is the glutamine synthetase (glnA)/glutamate synthetase (gltB,D)

pathway (32). H. somnus 129Pt, H. influenzae Rd and H. ducreyi 35000HP all had glnA,

encoding glutamine synthetase, which converts glutamate to glutamine. However, H. somnus

129Pt, H. influenzae Rd and H. ducreyi 35000HP were all missing the gltB,D genes, encoding

glutamate synthetase, which produces two molecules of glutamate from glutamine. Glutamate

can also be derived from glutamine by the action of glutaminase (19), but none of the organisms

had any genes with similarity to known glutaminases. Klebsiella aerogenes mutants lacking

gltB,D and glutamate dehydrogenase genes require a source of glutamate, compounds that can be

degraded to glutamate, or compounds that can donate an amino group for the transamination of

alpha-ketoglutarate to form glutamate (7, 17). It appears that the latter process may occur in H.

somnus 129Pt, H. influenzae Rd and H. ducreyi 35000HP, as they all had aspartate

aminotransferase (encoded by aspC), which catalyzes the transfer of an amino group from

aspartate to alpha-ketoglutarate, forming oxaloacetate and glutamate.

       Also common among H. somnus 129Pt, H. ducreyi 35000HP and H. influenzae Rd (Table

S6) were the cysE and K genes required to synthesize L-cysteine from L-serine, as well as the

cysZ gene, encoding a sulfate transporter; all three organisms had the complete pathway for L-




                                                 7
lysine synthesis and the genes required to interconvert L-glutamate and L-aspartate, L-aspartate

and L-fumarate, and to convert L-aspartate to L-asparagine and L-aspartate to L-lysine. All had

the gene encoding alanine dehydrogenase, and none had a complete pathway for arginine

degradation; they also lacked the cysA, C, D, G, H, I, J, and M genes for sulfate assmilation, as

well as the gltB,D, asnB, rpoN, and ntrB,C genes involved in the regulation of nitrogen

assimilation (43). All were missing the complete pathway to make L-methionine from L-

aspartate, although they did have the metK gene, which converts L-methionine to S-adenosyl-L-

methionine. None had the genes to convert L-valine to L-alanine; they also did not have all genes

required to make alanine, phenylalanine or tyrosine. Finally, none of these organisms contained a

complete pathway for arginine, asparagine, histidine, leucine, isoleucine, valine, proline or

phenylalanine degradation; some of these results have been reported previously for H. influenzae

(29). We also noted differences among the organisms. H. somnus 129Pt had pathways for lysine

and tryptophan degradation, while H. ducreyi and H. influenzae Rd did not. Only H. ducreyi had

the complete pathway for arginine biosynthesis from L-glutamate; However, H. somnus and H.

influenzae did have argG and argH, encoding arginosuccinate synthase and arginosuccinate

lyase, which should enable them to make L-arginine from citrulline. Although all three

organisms had the asnA gene (encoding aspartate-ammonia ligase) needed to synthesize L-

asparagine from L-aspartate, only H. ducreyi 35000HP had ansA (asparaginase), which converts

L-asparagine to L-aspartate. H. influenzae Rd had all of the essential genes for histidine and

tryptophan biosynthesis, while H. somnus 129Pt and H. ducreyi 35000HP did not. H. somnus

129Pt did not have the gene encoding L-serine deaminase, which is responsible for the

degradation of L-serine to pyruvate, but H. ducreyi 35000HP and H. influenzae Rd did. H.

ducreyi 35000HP lacked the tnaA and metC genes for L-cysteine degradation to pyruvate, as




                                                 8
well as the genes needed to make L-threonine from L-aspartate; H. ducreyi 35000HP also did not

have any of the genes to make L-proline from alpha-ketoglutarate or L-glutamate. Only H.

somnus 129Pt and H. influenzae Rd contained the complete biosynthetic pathways for serine,

glycine, proline, threonine, leucine, valine and isoleucine.



Arginine metabolism

Like H. influenzae Rd (43), H. somnus 129Pt was missing the genes encoding the enzymes for

five initial steps of arginine biosynthesis (argA, argB, argC, argD, and argE), and in addition

was missing argI, which is present in H. influenzae Rd (43). H. ducreyi 35000HP had all of the

genes necessary for arginine biosynthesis (Table S6). Also like H. influenzae Rd (43), both H.

somnus 129Pt and H. ducreyi 35000HP were missing the spe genes, speA, speB, speC, speD and

speE, which are involved in polyamine biosynthesis from arginine and S-adenosyl methionine.

We could not find any genes for arginine degradation in the genome of H. somnus 129Pt;

however, it did contain speF encoding ornithine decarboxylase (HS_1573), which converts

ornithine to putrescene. H. influenzae Rd also had a speF homolog, but H. ducreyi did not. In

fact, none of these organisms contained a complete pathway for arginine degradation.



Sulfate assimilation and cysteine metabolism

As in H. influenzae Rd (43), both H. somnus 129Pt and H. ducreyi 35000HP had genes encoding

the enzymes that convert L-serine to cysteine (cysE; cysK), as well as a sulfate transporter (cysZ).

Also like H. influenzae Rd, both H. somnus 129Pt and H. ducreyi 35000HP lacked the

cysA,C,D,G,H,I,J,M genes for sulfate assimilation. H. somnus 129Pt had both tnaA (HS_0801)




                                                 9
and metC (HS_0475) genes involved in cysteine degradation, H. influenzae Rd had metC

(HI0122), and H. ducreyi 35000HP did not have these genes.



Lysine, threonine and methionine

The pathway from L-aspartate to L-lysine was complete in all three organisms, H. influenzae Rd

and H. somnus 129Pt had all of the components to make L-threonine from L-aspartate, and none

of the three organisms had all of the components to make S-adenosyl-L-methionine from L-

aspartate (Table S6). In E. coli, thrA, metL, and lysC encode similar aspartokinase isozymes that

show feedback inhibition by threonine, methionine, and lysine, respectively (23). metL was

missing in H. influenzae Rd, H. somnus 129Pt and H. ducreyi 35000HP. H. ducreyi 35000HP

had a lysC homolog (HD1375), which encodes lysine-sensitive aspartokinase III, but H.

influenzae Rd and H. somnus 129Pt had genes that were similar to E. coli thrA (HS_1214 63%

amino acid identity; HI0089 62% amino acid identity), which encodes a bifunctional protein

containing aspartokinase I (N-terminal) and homoserine dehydrogenase I (C-terminal). Only H.

somnus 129Pt had cadB and cadA, involved in lysine degradation. In E. coli, CadB exhibits

cadaverine uptake activity and cadaverine excretion activity, acting as a cadaverine-lysine

antiporter. cadA encodes lysine decarboxylase (41). H. somnus 129Pt and H. influenzae Rd had

ilvA (HS_0183; HI0738a), encoding threonine deaminase. Both H. somnus 129Pt and H.

influenzae Rd had metB (HS_1345; HI0086), encoding cystathionine gamma-synthase. H.

influenzae Rd, H. somnus 129Pt and H. ducreyi 35000HP all had genes encoding formate

acetyltransferase (HS_1136; HD0990; HI0180) and propionate kinase (HS_0803; HD1456;

HI1204), which comprise the branch of threonine metabolism leading to propionate. H.

influenzae Rd, H. somnus 129Pt and H. ducreyi 35000HP all had metK, which would allow them




                                                10
to convert L-methionine to S-adenosyl-L-methionine (8). H. somnus 129Pt also had a gene

encoding DNA-cytosine methyltransferase, which forms S-adenosyl-homocysteine from S-

adenosyl-L-methionine (8).



Leucine, isoleucine and valine

H. influenzae Rd and H. somnus 129Pt had genes encoding components of the pathways for

leucine, isoleucine and valine synthesis. H. ducreyi 35000HP was missing all of the components

of these pathways except sdaA, which encodes L-threonine deaminase I / L-serine ammonia-

lyase. The first three steps for degradation of leucine, isoleucine and valine are the same (8), and

H. influenzae Rd and H. somnus 129Pt had the gene ilvE, encoding branched-chain amino acid

transaminase that performs the first step, but did not have the rest of the pathway genes.



Histidine, glycine, serine, alanine, proline, phenylalanine, tyrosine, tryptophan

As reported previously, H. influenzae Rd has homologs of all of the essential E. coli genes for

the metabolism of histidine, glycine, serine, alanine, proline, phenylalanine, tyrosine and

tryptophan (43). H. ducreyi 35000HP did not have any of the genes for histidine biosynthesis,

and H. somnus 129Pt was missing all of the histidine biosynthesis genes except hisC. H. ducreyi

35000HP was also missing glyA and serA, which are involved in glycine and serine biosynthesis,

respectively (8). None of the three organisms had the gene avtA, whose product converts L-

valine to L-alanine (47). H. ducreyi 35000HP also did not have the genes to make proline from

alpha-ketoglutarate or L-glutamate. All three of the organisms had the pheA and tyrA genes

involved in both phenylalanine and tyrosine biosynthesis, but none of them had the tyrB gene,

which is involved in the synthesis of L-tyrosine (8). In terms of tryptophan biosynthesis, H.




                                                 11
influenzae Rd had genes encoding all of the components of the pathway from chorismate to L-

tryptophan, while H. somnus 129Pt and H. ducreyi 35000HP each had one copy of trpG, which

converts chorismate to anthranilate (8), and H. influenzae Rd had two copies of trpG.



Energy Metabolism

Based on the TCA cycle genes that they do have, H. somnus 129Pt and H. influenzae Rd should

be able to generate alpha-ketoglutarate by the reductive branch, from oxaloacetate through

malate, fumarate, succinate and succinyl-CoA to alpha-ketoglutarate. Because H. ducreyi

35000HP was also missing the gene encoding succinyl-CoA synthetase (converts succinate to

succinyl-CoA), it apparently can only generate alpha-ketoglutarate (within the context of the

TCA cycle) by the action of aspartate aminotransferase, encoded by aspC. Aspartate

aminotransferase also appeared to be a key enzyme for H. ducreyi production of glutamate, as it

did not have the complete glutamine synthetase/glutamate synthetase pathway, or glutamate

dehydrogenase (Table S8). However, it is likely that H. ducreyi can generate alpha-ketoglutarate

by some other reactions that are not tied to the TCA cycle. For example, alpha-ketoglutarate is a

by-product of the action of dTDP-4-oxo-6-deoxy-D-glucose transaminase, encoded by

wecE(rffA) (30), which H. ducreyi did have. H. somnus 129Pt was unlike H. influenzae Rd and

H. ducreyi 35000HP, in that it was only missing isocitrate dehydrogenase. Since H. somnus

129Pt had gltA and acnB, it should be able to make isocitrate from oxaloacetate, but it did not

have icd, so it probably cannot convert isocitrate to alpha-ketoglutarate.

       Like H. influenzae Rd (43), both H. somnus 129Pt and H. ducreyi 35000HP were missing

the aerobic respiratory nitrate reductases 1 (narGHJI) and 2 (narZYWV), formate hydrogen lyase

(hyc), hydrogenase 1 (hya), and hydrogenase 2 (hyb, hyp).




                                                 12
LOS biosynthesis

The H. ducreyi 35000HP genome contained unique genes (not found in H. influenzae Rd or H.

somnus 129Pt) that could be involved in LOS biosynthesis. These genes included a possible beta

galactoside alpha-2,6-sialyltransferase (HD0053), probable glycosyltransferases (HD0375,

HD0884), and a cluster of genes (HD1833-HD1843) corresponding to the wec(rff) locus of E.

coli, which is involved in enterobacterial common antigen biosynthesis (13, 31).

H. influenzae Rd and H. somnus 129Pt contained the licABCD genes, which encode the enzymes

necessary for adding phosphocholine to LOS. However it appears that in H. somnus 129Pt licA is

non-functional due to interruption of the gene with an insertion sequence at its 5’ end. H. somnus

129Pt had HS_0727, an extra copy of licD, which contained a frameshift. H. ducreyi 35000HP

had HD1021, which corresponded to the C-terminal region of licA, and did not have the licBCD

genes. The licA genes of 129Pt and H. influenzae Rd did not have CAAT repeats in the coding

sequence, as does the licA gene from pathogenic H. influenzae strains (21). Instead, the region

upstream of the H. influenzae Rd gene (HI1537) contained an alternative start followed by 17

CAAT repeats; this region was out of frame with the actual gene start. The H. somnus 129Pt licA

gene (and the upstream region) had no repeats at all.

       H. ducreyi 35000HP contains two sialyltransferase genes, neuA (HD0685) and lst

(HD0686) (Bozue et al, 1999). neuA was also present in H. somnus 129Pt (HS_0706) and H.

influenzae Rd (HI1279). We found that the H. somnus 129Pt neuA gene was truncated, as

described previously (M. D. Howard, A. J. Duncan, A. D. Cox, W.Wakarchuk, and T. J. Inzana,

Abstr.103rd Gen. Meeting Am. Soc. Microbiol., abstr. Z-003, 2003). H. influenzae Rd contains a




                                                13
gene (HI0871) (6) that had 45% amino acid identity to the H. ducreyi lst gene, but H. somnus

129Pt did not have this gene.

       Bacteria may gain access to these iron sources by secreting hemolysin (44) or cytotoxin

(37) to lyse the host cells and release the heme-containing compounds. H. somnus 129Pt, H.

ducreyi 35000HP and H. influenzae Rd had three hemolysin genes in common

(HS_0237/HD1145/HI0301; HS_0737/HD0800/HI1658; HS_1429/HD0770/HI0107; Table

S14). In addition, H. ducreyi 35000HP had two genes (HD1326 hhdB, pore-forming component,

and HD1327 hhdA, secreted hemolysin) that were not present in H. somnus 129Pt or H.

influenzae. Only H. ducreyi has genes encoding cytolethal distending toxin (HD0902 - HD0904),

which is not found in other Haemophilus species (37). H. somnus 129Pt also had a gene

(HS_0842), originally identified in H. somnus 8025 (48), encoding a bi-functional protein that

has hemolysin activity in the N-terminal part, while the C-terminal is similar to OmpA of H.

influenzae and H. ducreyi. However, among these three organisms, only H. ducreyi is reported

to be hemolytic (24, 33, 44).



Exopolysaccharide

H. somnus produces an exopolysaccharide that contains mannose and galactose, whose

production is upregulated when the bacteria are grown anaerobically and in high salt (T.J.

Inzana, A. Cox, and G. Glindemann, Abstr. 102nd General Meeting of the American Society for

Microbiology, abstr. Z-26, 2002) (40). We found in H. somnus 129Pt all but one of the genes

involved in the pathways leading to GDP-D-mannose and GDP-D-galactose (Table S16), which

are incorporated into the exopolysaccharide of Burkholderia cepacia (39). The genes necessary

for GDP-D-galactose synthesis included phosphoglucomutase (HS_0730), UDP-glucose




                                               14
pyrophosphorylase (galU; HS_1117) and UDP-glucose epimerase (galE; HS_0789). For GDP-

D-mannose synthesis, the genes that were present in H. somnus 129Pt included phosphoglucose

isomerase (pgi; HS_0938), phosphomannose isomerase/mannose-6-phosphate isomerase (manA;

HS_0605) and phosphomannomutase (manB; HS_1118 and HS_1670). Missing from H. somnus

129Pt was the manC gene encoding GDP-D-mannose-pyrophosphorylase, which catalyzes the

last step in the formation of GDP-D-mannose, the conversion of mannose-1-phosphate to GDP-

D-mannose.



Haemophilus-specific uptake sequences

The H. influenzae DNA uptake signal sequence is overrepresented in H. ducreyi and H. somnus

(2). Bakkali et al. (2) report 41 Haemophilus-specific uptake sequences (hUSs) in H. ducreyi,

most of which cluster in 2 islands of bacteriophage genes. We found the H. influenzae consensus

of “AAGTGCGGT” (and its reverse complement “ACCGCACTT”) in 37 locations throughout

the H. ducreyi 35000HP genome, and in agreement with the previous report, most of these were

in areas containing bacteriophage genes. In addition, 32 (87%) of the consensus sequence

locations in H. ducreyi 35000HP were in CDSs. Bakkali et al. (2) also reported that the

unfinished sequence of H. somnus 129Pt has 1205 hUSs. We found that the finished genome

sequence of H. somnus 129Pt had approximately 1244 potential hUSs. 62% (776) of these sites

were within coding sequences and the rest were in intergenic regions. H. somnus 129Pt, H.

ducreyi 35000HP and H. influenzae Rd all had genes involved in DNA uptake and

transformation (11, 12, 45)(Table S13).



Restriction modification systems




                                               15
As shown in Table S15, H. somnus 129Pt had genes encoding components of type I and the BcgI

restriction-modification systems. H. ducreyi 35000HP had one gene encoding a possible type I

methytransferase protein(HD0914), as well as genes encoding a type III system and possibly the

BcgI system. H. influenzae Rd had genes encoding components of type I, II and III systems, but

not BcgI. In terms of type I systems, H. somnus 129Pt had hsdS (HS_0556) and an hsdR gene

(HS_0559) that was also present in H. influenzae Rd (HI1285). H. somnus 129Pt had a second

hsdS (HS_0560), but not hsdM. H. influenzae Rd had one complete type I system composed of

the genes HI1285 – HI1287 (hsdR, hsdS and hsdM). Another type I system in H. influenzae Rd

consisted of HI0215 (hsdM, which contained a frameshift), HI0216 (hsdS) and hsdR (HI0218).

Neither H. somnus 129Pt nor H. ducreyi 35000HP had any type II system genes. H. influenzae

Rd had three complete type II systems, encoded by HI0512 and HI0513, HI1040 and HI1041,

HI1393 and HI1392. H. somnus 129Pt did not have any type III restriction-modification system

genes. H. influenzae Rd had a type III methylase gene (HI1056), while H. ducreyi 35000HP had

a complete type III system (HD1690 to HD1693).

       There is evidence supporting the hypothesis that restriction modification systems may

move between and within genomes and may cause evolutionary changes in genomes (25). This

evidence includes observations of the proximity of mobile genetic elements to restriction

modification gene complexes. Our results indicated that all of the restriction modification system

gene complexes in H. somnus 129Pt were in the vicinity of mobile elements, including putative

prophage regions and transposases (Table 15). Also, as the H. influenzae DNA uptake signal

sequence is overrepresented in H. somnus (2), mobile elements may not be necessary for the

movement of restriction modification gene complexes. Several of the restriction-modification




                                               16
genes either contain the H. influenzae DNA uptake signal sequence or are close to H. influenzae

DNA uptake signal sequences, so they may have been acquired by DNA uptake.




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                                             20
Table S1. Candidate prophages and phage-related genes

Gene                           H. somnus 129Pt    H. ducreyi 35000HP   H. influenzae Rd

Region 1*

conserved hypothetical         HS_0423            no                   no

protein; possible phage-

related protein

phage integrase                HS_0424            no                   no

hypothetical protein           HS_0425            no                   no

possible phage DNA-            HS_0426            no                   no

polymerase or DNA-

primase

conserved hypothetical         HS_0427            no                   no

protein; possible virulence-

associated protein E

conserved hypothetical         HS_0428            no                   no

protein

conserved hypothetical         HS_0429            no                   no

protein

bcgIA                          HS_0430            maybe HD0293         no

bifunctional protein: site-

specific DNA-

methyltransferase (adenine-




                                             21
specific); restriction

enzyme, alpha subunit

bcgIB                           HS_0431        maybe HD0294   no

restriction enzyme, beta

subunit

bcgIB                           HS_0432        no             no

restriction enzyme, beta

subunit, C-terminal

conserved hypothetical          HS_0433        no             no

protein

transposase fragment            HS_0434        no             no

transposase                     HS_0486        no             no

HflK protein; phage lambda      HS_0487        HD1809         HI0151

CII stabilizer; possible CII-

specific protease

HflC protein; protease          HS_0488        HD1808         HI0150

specific for phage lambda

CII repressor

Region 2

phage integrase intA            HS_0519        no             no

hypothetical                    HS_0520        no             no

hypothetical                    HS_0521        no             no

conserved hypothetical;         HS_0522        no             no




                                          22
possible phage

transcriptional regulator

conserved hypothetical      HS_0523        no       no

hypothetical                HS_0524        no       no

conserved hypothetical      HS_0525        no       no

hypothetical                HS_0526        no       no

hypothetical                HS_0527        no       no

conserved hypothetical      HS_0528        no       no

hypothetical                HS_0529        no       no

hypothetical                HS_0530        no       no

hypothetical                HS_0531        no       no

conserved hypothetical      HS_0532        no       no

phage DNA primase-like      HS_0533        no       no

protein

conserved hypothetical      HS_0534        no       no

conserved hypothetical      HS_0535        no       no

protein; possible

transcriptional regulator

conserved hypothetical      HS_0536        no       no

conserved hypothetical      HS_0537        HD1614   no

conserved hypothetical      HS_0538        no       no

hypothetical                HS_0539        no       no

hypothetical                HS_0540        no       no




                                      23
conserved hypothetical        HS_0541           no   no

Region 3

phage integrase               HS_0555           no   no

conserved hypothetical,       HS_0556

possible restriction

endonuclease

phage P1-related protein      HS_0557           no   no

enterobacteria phage P1       HS_0558           no   no

Region 4

hypothetical                  HS_1331           no   no

hypothetical                  HS_1332           no   no

phage terminase, small        HS_1333           no   no

subunit

conserved hypothetical        HS_1334           no   HI1411

protein; possible terminase

small subunit

conserved hypothetical        HS_1335           no   no

protein; possible prophage

CP4-57 regulatory protein

hypothetical                  HS_1336           no   no

integrase                     HS_1337           no   no

Region 5

conserved hypothetical        HS_1365 to



                                           24
proteins and Haemophilus-    HS_1371

specific proteins,

uncharacterized

conserved hypothetical       HS_1372        no   no

protein; possible phage-

related protein

conserved hypothetical       HS_1372        no   no

protein; possible phage-

related tail fiber protein

Haemophilus-specific         HS_1373        no   no

protein, uncharacterized

Haemophilus-specific         HS_1374        no   no

protein, uncharacterized

Haemophilus-specific         HS_1375        no   no

protein, uncharacterized

Haemophilus-specific         HS_1376        no   no

protein, uncharacterized

conserved hypothetical       HS_1377        no   no

protein might be a coat

protein

conserved hypothetical       HS_1378        no   no

protein

Haemophilus-specific         HS_1379        no   no




                                       25
protein, uncharacterized

possible transcription        HS_1380        no   no

regulator

conserved hypothetical        HS_1381        no   no

protein

conserved hypothetical        HS_1382        no   HI1412

protein; possible phage-

related protein

hypothetical protein          HS_1383        no   no

Haemophilus-specific          HS_1384        no   no

protein, uncharacterized

conserved hypothetical        HS_1385        no   no

protein (possible phage

terminase)

conserved hypothetical        HS_1386        no   no

protein; possible terminase

small subunit

conserved hypothetical        HS_1387        no   no

protein

lysozyme, possible phage-     HS_1388        no   no

related lysozyme

Haemophilus-specific          HS_1389        no   no

protein, uncharacterized




                                        26
transposase                  HS_1390        no   no

transposase                  HS_1391        no   no

conserved hypothetical       HS_1392        no   no

protein

conserved hypothetical       HS_1393        no   HI1421

protein

Bacteriophage Lambda         HS_1394        no   no

NinG recombination protein

conserved hypothetical       HS_1395        no   no

protein

conserved hypothetical       HS_1396        no   no

protein

conserved hypothetical       HS_1397        no   no

protein

conserved hypothetical       HS_1398        no   HI1418

protein; possible prophage

antirepressor

conserved hypothetical       HS_1399        no   no

protein

conserved hypothetical       HS_1400        no   no

protein; possible DNA

methylase

conserved hypothetical       HS_1401        no   no




                                       27
protein; possible replication

protein P

conserved hypothetical          HS_1402        no   no

protein

conserved hypothetical          HS_1403        no   no

protein

conserved hypothetical          HS_1404        no   no

protein

conserved hypothetical          HS_1405        no   no

protein

conserved hypothetical          HS_1406        no   no

protein; possible repressor

protein

Haemophilus-specific            HS_1407        no   no

protein, uncharacterized

Haemophilus-specific            HS_1408        no   no

protein, uncharacterized

Haemophilus-specific            HS_1409        no   no

protein, uncharacterized

Haemophilus-specific            HS_1410        no   no

protein, uncharacterized

hypothetical protein            HS_1411        no   no

Haemophilus -specific           HS_1412        no   no




                                          28
protein, uncharacterized

conserved hypothetical     HS_1413        no   no

protein

hypothetical protein       HS_1414        no   no

conserved hypothetical     HS_1415        no   no

protein; possible phage-

related protein

Haemophilus -specific      HS_1416        no   no

protein, uncharacterized

Haemophilus -specific      HS_1417        no   no

protein, uncharacterized

Haemophilus -specific      HS_1418        no   no

protein, uncharacterized

conserved hypothetical     HS_1419        no   no

protein; possible phage

recombinase

conserved hypothetical     HS_1420        no   no

protein

conserved hypothetical     HS_1421        no   no

protein

DNA-cytosine               HS_1422        no   no

methyltransferase

Haemophilus -specific      HS_1423        no   no




                                     29
protein, uncharacterized

conserved hypothetical         HS_1424              no                      no

protein; possible

transcriptional regulator

integrase                      HS_1425              no                      no

*Region 1 may be a decaying prophage that has had stretches of functional genes inserted into it.




                                               30
Table S2. Pseudogenes in H. somnus 129Pt

Gene                             H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

H. somnus 129Pt

tbpA                             HS_0097           no                   HI0661 full length

transferrin-binding protein A,

C-terminal region

tbpA                             HS_0098           no                   HI0994 full length

transferrin-binding protein A,

central fragment

tbpA                             HS_0102           no                   HI1565 full length

transferrin-binding protein A,

N-terminal region

transposase fragment             HS_0434           no                   no

conserved hypothetical           HS_0619a          no                   no

protein; possible transposase

fragment

lob2C                            HS_0636a          HD0466 lgtA full     HI1578 full length

glucosyltransferase; involved                      length

in LOS biosynthesis, N-

terminal

hgbA                             HS_0720           HD2025 full length   HI1567 full length

hemoglobin-binding protein,




                                             31
C-terminal

hgbA                             HS_0721         HD2025 full length   HI0712 full length

hemoglobin binding protein                                            HI0635?

A, N-terminal                                                         HI0661?

                                                                      HI1565?

conserved hypothetical           HS_1066a        no                   no

protein, fragment

IS1016                           HS_1462         no                   HI1328.1

insertion sequence, C-terminal

IS1016                           HS_1463         no                   no

insertion sequence, N-

terminal

H+/gluconate symporter, N-       HS_1522         no                   HI0092 full length

terminal

H+/gluconate symporter, C-       HS_1523         no                   HI0092 full length

terminal

restriction-modification         HS_1525         no                   no

system methyltransferase, N-

terminal

restriction-modification         HS_1526         no                   no

system methyltransferase, C-

terminal




                                            32
Table S3. IS elements excluding prophage transposases

IS Family/Gene        H. somnus 129Pt       H. ducreyi 35000HP H. influenzae Rd

IS1

insB                  no                    HD1970              no

insA                  no                    HD1971              no

IS150

                      no                    no                  HI1721

IS200/IS605

                      HS_0224               no                  no

                      HS_0486               no                  no

                      HS_0583               no                  no

                      HS_0666               no                  no

                      HS_0667               no                  no

                      HS_0668               no                  no

                      HS_0716               no                  no

                      HS_0717               no                  no

                      HS_1390               no                  no

                      HS_1391               no                  no

IS1016

IS1016C2              HS_0642               no                  no




                                             33
                     HS_0324               no       no

                     HS_0434 fragment      no       no

                     HS_1116               no       no

                     HS_1462               no       no



                     HS_1463               no       no

                     HS_1679               no       no

                     HS_1709               HD1616   HI1328.1

IS1016V6             no                    no       HI1577

                     no                    no       HI1329

                     similarity to above            HI1018

                     genes

ISNCY

                     HS_0445               HD0908   no

Other transposases

                     HS_0224a              no       no

                     HS_0619a              no       no

                     no                    HD0290   no

                     no                    HD0291   no

                     no                    HD0295   no




                                            34
                      no                    HD1612                 no

                      no                    HD1689                 no

                      no                    HD1695                 no

                      no                    HD1696                 no

The genes in H. somnus 129Pt that were in the neighborhood of the complete IS1016 elements

included iron transporter and pyrimidine metabolism genes (HS_0642), iron transporter genes

(HS_0324), DNA, amino acid and carbohydrate metabolism genes (HS_1116), succinate-

semialdehyde dehydrogenase (HS_1679) and DNA gyrase and helicase (HS_1709).




                                              35
Table S4. Unique genes in H. somnus 129Pt, excluding genes annotated as hypothetical and

conserved hypothetical.

Function                                             Locus Tag   Definition

Anion transport                                      HS_1426     sulfate transporter

Biosynthesis of cofactors, prosthetic groups, and    HS_1540     uroporphyrinogen decarboxylase

carriers; Heme, porphyrin, and cobalamin

Biosynthesis of cofactors, prosthetic groups, and    HS_0150     4-hydroxybenzoate synthetase

carriers; Menaquinone and ubiquinone                             (chorismate--pyruvate lyase)

                                                     HS_0544     ubiquinone biosynthesis protein

                                                     HS_0681     2-octaprenyl-6-methoxyphenol

                                                                 hydroxylase

                                                     HS_0915     3-octaprenyl-4-hydroxybenzoate

                                                                 carboxy-lyase

Biosynthesis of cofactors, prosthetic groups, and    HS_0925     4-hydroxythreonine-4-phosphate

carriers; Pyridoxine                                             dehydrogenase

Biosynthesis of cofactors, prosthetic groups, and    HS_0902     thiamine biosynthesis protein

carriers; Thiamine

Butanoate metabolism                                 HS_0407     succinate-semialdehyde

Glutamate metabolism                                             dehydrogenase (NAD(P)+)

Tyrosine metabolism

Carbohydrate utilization                             HS_0030     sugar ABC transporter, sugar-

                                                                 binding protein



                                                36
     HS_0050   transcriptional regulator, possible

               sorbitol operon regulator

     HS_0054   ABC transporter, solute-binding,

               sugar transport

     HS_0437   PTS system, cellobiose-specific IIC

               component

     HS_0607   mannose-specific

               phosphotransferase system IID

               component

     HS_0607   mannose-specific

               phosphotransferase system IID

               component

     HS_0608   mannose-specific

               phosphotransferase system IIC

               component

     HS_0609   phosphotransferase system

               mannose/fructose-specific IIA

               component

     HS_0675   glucitol operon activator

     HS_0677   PTS system, glucitol/sorbitol-

               specific IIA component

     HS_0678   PTS system, glucitol/sorbitol-

               specific IIBC component




37
                        HS_0679   PTS system, glucitol/sorbitol-

                                  specific IIC2 component

                        HS_0765   ABC-type sugar-binding

                                  periplasmic protein

                        HS_0843   conserved hypothetical protein;

                                  possible fructosamine kinase family

                                  enzyme

                        HS_1142   PTS system, galactitol-specific IIC

                                  component

                        HS_1143   PTS system, galactitol-specific IIB

                                  component

                        HS_1144   PTS system, galactitol-specific IIA

                                  component

                        HS_1145   tagatose 6-phosphate kinase

                        HS_1146   tagatose 1,6-diphosphate aldolase

                        HS_1250   mannitol operon repressor

                        HS_1251   mannitol 1-phosphate 5-

                                  dehydrogenase

                        HS_1330   beta-glucuronidase

                        HS_1601   glucuronide permease

                        HS_1602   glucuronate isomerase

Cation transport        HS_0343   calcium/proton antiporter

                        HS_0375   potassium uptake protein; K+




                   38
                                                             transporter

                                                   HS_0376   potassium uptake protein

                                                   HS_0647   sodium-dependent transporter

                                                   HS_0652   Na+/H+ antiporter

                                                   HS_1078   possible sodium/calcium exchange

                                                             protein

                                                   HS_1101   ammonium transporter

                                                   HS_1517   copper homeostasis protein

Cell envelope                                      HS_0625   membrane protein; possible

                                                             tellurium resistance protein

                                                   HS_1254   lytic murein transglycosylase A

                                                   HS_1265   outer membrane protein precursor

Cellular processes; Adaptations to atypical        HS_0633   stress response protein; tellurium

conditions                                                   resistance protein

                                                   HS_0634   stress response protein; tellurium

                                                             resistance protein

                                                   HS_0635   stress response protein; tellurium

                                                             resistance protein

Cellular processes; Cell division                  HS_0441   cell filamentation-like protein

                                                   HS_1346   chromosome partitioning-related

                                                             protein

                                                   HS_1719   chromosome partitioning-related

                                                             protein




                                              39
Citrate cycle (TCA cycle)                         HS_0960   citrate synthase

Glyoxylate and dicarboxylate metabolism

                                                  HS_1641   isocitrate dehydrogenase

Degradation of proteins, peptides, and            HS_0572   possible regulator of membrane

glycopeptides                                               protease activity

DNA replication, recombination, and repair        HS_1009   chromosome initiation inhibitor

                                                  HS_1639   possible NTP

                                                            pyrophosphohydrolase, MutT/Nudix

                                                            family

DNA methylation                                   HS_1422   DNA-cytosine methyltransferase

Electron transport                                HS_1156   possible 2-octaprenyl-3-methyl-6-

                                                            methoxy-1,4-benzoquinol

                                                            hydroxylase

                                                  HS_1225   possible flavin:NADH reductase

                                                  HS_1674   possible chaperone protein

Fatty acid and phospholipid metabolism            HS_0111   acyl carrier protein

                                                  HS_0113   conserved hypothetical protein;

                                                            possible 3-hydroxymyristoyl/3-

                                                            hydroxydecanoyl-[acyl-carrier-

                                                            protein] dehydratase

                                                  HS_0164   possible fatty acid/phospholipid

                                                            synthesis protein

Fermentation                                      HS_1681   NAD-dependent aldehyde



                                             40
                                                          dehydrogenase

                                                HS_1682   aldehyde dehydrogenase, possible

                                                          succinate-semialdehyde

                                                          dehydrogenase [NAD(P)]

Glutamate metabolism                            HS_0287   glutamate--cysteine ligase

Glutathione metabolism

Glycerolipid metabolism                         HS_0110   1-acyl-sn-glycerol-3-phosphate

                                                          acyltransferase

Glycine, serine and threonine metabolism        HS_1718   D-serine dehydratase

Glycoconjugate degradation                      HS_0435   alpha-L-fucosidase

Iron and heme metabolism                        HS_0069   iron-regulated outer membrane

                                                          protein

Inositol metabolism                             HS_1576   dehydrogenase; possible myo-

                                                          inositol 2-dehydrogenase

                                                HS_1577   myo-inositol catabolism protein

                                                HS_1587   conserved hypothetical protein;

                                                          possible myo-inositol catabolism

                                                          protein

LOS biosynthesis                                HS_0116   glycosyl transferase, group 2 family

                                                          protein

                                                HS_0275   conserved hypothetical protein;

                                                          possible glycosyltransferase

                                                HS_0700   possible N-acylneuraminate



                                           41
                                                       cytidylyltransferase

Nitrogen metabolism                          HS_0801   tryptophanase

Tryptophan metabolism

                                             HS_0810   glutamyl-tRNA reductase

Pentose phosphate pathway                    HS_0379   gluconokinase (gluconate kinase)

Phage-related functions and prophages        HS_0424   phage integrase



                                             HS_0426   possible phage DNA-polymerase or

                                                       DNA-primase

                                             HS_0519   phage integrase

                                             HS_0533   phage DNA primase-like protein

                                             HS_0555   phage integrase

                                             HS_0557   phage P1-related protein

                                             HS_0558   enterobacteria phage P1

                                             HS_1228   integrase

                                             HS_1335   conserved hypothetical protein;

                                                       possible prophage CP4-57

                                                       regulatory protein

                                             HS_1337   integrase

                                             HS_1388   lysozyme, possible phage-related

                                                       lysozyme

                                             HS_1400   conserved hypothetical protein;

                                                       possible DNA methylase




                                        42
                                            HS_1401   conserved hypothetical protein;

                                                      possible replication protein P

                                            HS_1406   conserved hypothetical protein;

                                                      possible repressor protein

                                            HS_1415   conserved hypothetical protein;

                                                      possible phage-related protein

                                            HS_1425   integrase

Porphyrin and chlorophyll metabolism        HS_0044   hydroxymethylbilane synthase

                                                      (porphobilinogen deaminase, PGB)

Purine metabolism                           HS_0964   dGTP triphosphohydrolase

Regulatory functions                        HS_0817   possible low molecular weight

                                                      protein-tyrosine-phosphatase

Restriction and modification                HS_0560   type I restriction enzyme,

                                                      specificity subunit

Transcription                               HS_0422   transcriptional regulator

                                            HS_0757   NagC-like transcriptional regulator

Transport and binding proteins              HS_1233   membrane protein; possible

                                                      multiple antibiotic resistance protein

                                            HS_1567   permease, possible drug/metabolite

                                                      transporter superfamily

                                            HS_1586   permease, possible MFS

                                                      superfamily

Transport and binding proteins; ABC         HS_0849   ABC-type multidrug transport



                                       43
Superfamily                                                     system, permease component

Transport and binding proteins; Carbohydrates,        HS_0924   possible 2-keto-3-deoxygluconate

organic alcohols, and acids                                     permease



Transposase                                           HS_0434   transposase fragment

                                                      HS_0486   transposase

                                                      HS_0583   transposase

                                                      HS_0666   transposase

                                                      HS_0667   transposase

                                                      HS_0668   transposase

                                                      HS_0716   transposase

                                                      HS_0717   transposase

                                                      HS_1463   IS1016 related transposase,

                                                                possible protein V6

Unassigned                                            HS_0442   resolvase/integrase-like protein

                                                      HS_0443   ParA-like protein

                                                      HS_0632   serine/threonine kinase-like protein

                                                      HS_0680   VisC protein, monooxygenase

                                                                family

                                                      HS_0808   possible SAM-dependent

                                                                methyltransferase

                                                      HS_0898   tetrathionate reductase, subunit C

                                                      HS_1584   NAD-dependent aldehyde




                                                 44
                         dehydrogenase

Unknown        HS_0019   permease, major facilitator

                         superfamily

               HS_0100   conserved hypothetical protein;

                         possible transcriptional regulator

               HS_0106   conserved hypothetical protein;

                         possible dehydratase

               HS_0117   conserved hypothetical protein;

                         possible acyltransferase

               HS_0119   conserved thioesterase

               HS_0121   conserved membrane protein

               HS_0277   conserved hypothetical protein;

                         possible SAM-dependent

                         methyltransferase

               HS_0297   conserved hypothetical protein;

                         possible hydrolase

               HS_0380   conserved hypothetical protein;

                         possible periplasmic-binding protein

               HS_0427   conserved hypothetical protein;

                         possible virulence-associated

                         protein E

               HS_0478   conserved hypothetical protein;

                         possible cell-surface large adhesin




          45
     HS_0589    conserved hypothetical protein;

                possible adhesin

     HS_0619a   conserved hypothetical protein;

                possible transposase fragment

     HS_0628    conserved hypothetical protein, with

                von Willebrand factor (vWF)

                domain

     HS_0630    conserved hypothetical protein, with

                von Willebrand factor (vWF)

                domain

     HS_0660    possible membrane protein

     HS_0686    conserved hypothetical protein;

                possible aphA-like regulator

     HS_0723    HugX protein

     HS_0766    conserved hypothetical protein;

                possible gluconolactonase precursor

     HS_1046    conserved hypothetical protein;

                possible permease

     HS_1183    conserved hypothetical protein;

                possible permease

     HS_1234    conserved hypothetical protein;

                possible large adhesin

     HS_1247    conserved hypothetical protein;




46
               possible autotransporter protein

               YapE

     HS_1424   conserved hypothetical protein;

               possible transcriptional regulator

     HS_1428   possible permease

     HS_1480   conserved hypothetical protein;

               possible permease

     HS_1543   conserved hypothetical protein;

               possible outer membrane protein

     HS_1583   conserved hypothetical protein;

               possible dehydrogenase

     HS_1615   conserved hypothetical protein;

               possible dehydrogenase

     HS_1616   conserved hypothetical protein;

               possible large adhesin

     HS_1675   conserved hypothetical protein;

               possible histone acetyltransferase




47
Table S5. Carbohydrate metabolism

A. Galactitol

Gene                                    H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

HIT like protein (flanking gene same    HS_1134           HD1023               HI0961

strand)

pflB(flanking gene opp strand)          HS_1136           HD0990               HI0180

conserved hypothetical (opp strand)     HS_1137           no                   HI1602

conserved hypothetical (opp strand)     HS_1138           no                   HI1600



conserved hypothetical (opp strand)     HS_1139           no                   HI1599



gatR                                    HS_1140           no                   no

gatD                                    HS_1141           no                   no

gatC                                    HS_1142           no                   no

gatB                                    HS_1143           no                   no

gatA                                    HS_1144           no                   no

gatZ                                    HS_1145           no                   no

lacD (gatY)                             HS_1146           no                   no

pflA (flanking gene opp strand)         HS_1147           HD0989               HI0179



conserved hypothetical (flanking gene   HS_1155           HD0226               HI0019

same strand)




                                            48
mfd (same strand)                   HS_1161           HD0975               HI1258




B. Glucitol/sorbitol

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

tyrA (flanking gene, same strand)   HS_0671           HD0443               HI1290

purE (flanking gene, opp strand)    HS_0672           HD1424               HI1615

srlR/gutR                           HS_0673           HD1863               HI1009

conserved phosphatase               HS_0674           HD0176               HI0488

gutM                                HS_0675           no                   no

srlD/gutD                           HS_0676           HD0708               HI0155

srlB/gutB                           HS_0677           no                   no

srlE/gutE                           HS_0678           no                   no

srlA/gutA                           HS_0679           no                   no

visC (flanking gene)                HS_0680           HD0582               no

ubiH/visB                           HS_0681           HD0579               no

pepP                                HS_0682           HD1418               HI0816



C. Mannose

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

ampG                                HS_0600           HD0827               HI0350



conserved hypothetical              HS_0602           no                   no



                                        49
dnaQ (same strand) this is a second      HS_0603           HD0223               no

copy of dnaQ in 129Pt

ribonuclease H (flanking gene, opp       HS_0604           no                   no

strand)

manA                                     HS_0605           HD0765               no

conserved hypothetical                   HS_0606           no                   no

manZ                                     HS_0607           HD0766               no

manY                                     HS_0608           HD0767               no

manX                                     HS_0609           HD0768               no

conserved hypothetical (flanking gene)   HS_0610           HD1377               HI1168



serC (opp strand)                        HS_0611           HD1382               HI1167



conserved hypothetical protein (same     HS_0616           HD1854               HI0282

strand)                                                    (55% identity)       (55% identity)

menD                                     HS_0617           HD1853               HI0283




D. Cellobiose

Gene                                     H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

celA                                     no                no                   no

cellobiose-specific IIB

celB                                     HS_0437           no                   no




                                              50
cellobiose-specific IIC

celC                                     no                no                   no

cellobiose-specific IIA

celD                                     no                no                   no

celF                                     no                no                   no



E. Glucose

Gene                                     H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

crr                                      HS_1096           HD0227               HI1711

glucose-specific IIA component

ptsI                                     HS_1097           HD0228               HI1712

ptsH                                     HS_1098           HD0229               HI1713

ptsG                                     no                no                   no

glucose-specific IICB component

phosphotransferase system (PTS)          no                no                   no

glucose-specific enzyme IICBA

component



F. Mannitol

Gene                                     H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

fbp                                      HS_1248           HD0702               HI1645

(flanking gene, same strand) fructose-

1,6-bisphosphatase



                                              51
mpl                                        HS_1249         HD0703                HI0121

(flanking gene, opp strand)

mtlR                                       HS_1250         no                    no

mannitol operon repressor

mtlD                                       HS_1251         no                    no

mannitol 1-phosphate 5-dehydrogenase

mtlA                                       HS_1252         no                    no

mannitol-specific IIABC component

cons hypo (flanking gene, opp strand)      HS_1253         no                    HI0182?



valS (flanking gene)                       HS_1259         HD0669                HI1391




G. Unidentified substrate sugar permease

Gene                                    H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

sgaH                                    HS_0771           HD1857               HI1024

hexulose-6-phosphate synthase

PTS system Enzyme II-A permease         no                HD1859               HI0448?

component

sgaT                                    no                HD1860               no

carbohydrate transport protein SGAT




                                              52
H. Galactose

Gene                        H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

galK galactokinase          HS_0235           no                   HI0819

galM                        HS_0236           no                   HI0818

aldose 1-epimerase

galU                        HS_1117           HD1431               HI0812

galE                        HS_0789           HD0829               HI0351

UDP-galactose 4-epimerase

galT                        no                no                   HI0820

galactose-1-phosphate

uridylyltransferase

galR                        no                no                   HI0821



I. Fucose

Gene                        H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

gmd                         no                no                   no

GDP-D-mannose dehydratase

fucR                        HS_1446           no                   HI0615

fucP                        HS_1447           no                   HI0610

fucose permease

fucP                        HS_0750           no                   no

fucose permease

fucI                        HS_1448           no                   HI0614




                                  53
L-fucose isomerase

fucK fucokinase, L-fuculose kinase    HS_1449           no                    HI0613

fucU                                  HS_1450           no                    HI0612

fucA                                  HS_1451           no                    HI0611

fucose-1-P aldolase

fucA                                  HS_0014           no                    HI1012

fucose-1-P aldolase

L-1,2-propanediol oxidoreductase      no                no                    no

lactaldehyde dehydrogenase            no                no                    no




J. Ribose

Gene                                 H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

rbsD                                 HS_0223           no                   HI0501

high affinity ribose transport

protein

poss transposase                     HS_0224           no                   no

poss transposase                     HS_0224a          no                   no

rbsK                                 HS_0225           no                   HI0505

rbsR                                 HS_0226           no                   HI0506

rbsA                                 HS_0763           no                   HI0502

ribose ABC transporter, ATP-

binding protein




                                            54
rbsC                                 HS_0764      no   HI0503

ribose ABC transporter, permease

rbsB                                 HS_0765      no   HI0504

ABC-type sugar-binding

periplasmic protein

cons hypo poss gluconolactonase      HS_0766      no   no

precursor

sugar ABC transporter, periplasmic   HS_0767      no   no

sugar-binding protein                opp strand

rbsA                                 HS_0768      no   HI1110

ribose ABC transporter, ATP-

binding protein

rbsC                                 HS_0769      no   HI0503

ribose transport system permease

rbsC                                 HS_1579      no   HI0503

ABC transporter, possible ribose

permease

sugar ABC transporter, ATP-          HS_1580      no   HI0823

binding protein

ABC transporter, periplasmic         HS_1581      no   HI0504

sugar-binding protein



K. Xylose




                                             55
Gene                                 H. somnus 129Pt    H. ducreyi 35000HP    H. influenzae Rd

xylH                                 HS_0584            no                    HI1109

D-xylose ABC transporter, permease

xylG                                 HS_0585            no                    HI1110

D-xylose ABC transporter, ATP-

binding protein

xylF                                 HS_0586            no                    HI1111

D-xylose ABC transporter,

periplasmic sugar-binding protein

xylA                                 HS_0587            no                    HI1112

xylose isomerase

xylB                                 HS_0588            no                    HI1113

xylulokinase

xylR                                 HS_0794            no                    HI1106



L. Xylulose

Gene                                  H. somnus 129Pt    H. ducreyi 35000HP     H. influenzae Rd

NAD(P)H-dependent xylose reductase    no                 no                     no

xdh                                   no                 no                     no

xylitol dehydrogenase

zinc-binding xylitol/sorbitol         no                 no                     no

dehydrogenase

xylitol (sorbitol) dehydrogenase      no                 no                     no




                                           56
D-xylulose reductase (EC 1.1.1.9)      no                no                    no

(Xylitol dehydrogenase) (XDH)



L-xylulose reductase (EC 1.1.1.10)     no                no                    no

(XR)



sgbK/lyxK                              HS_0770           no                    HI1027

L-xylulokinase

sgbH                                   HS_0771           HD1857                HI1024

3-hexulose-6-phosphate synthase

sgbU                                   HS_0772           HD1864                HI1026

hexulose-6-phosphate isomerase

L-arabinitol 4-dehydrogenase (LAD1)    no                no                    no

araD                                   HS_0773           HD1866                HI1025

ribulose phosphate 4-epimerase



M. Trehalose (pathways from MetaCyc (8))

Gene                                  H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

trehalose degradation I

treC                                  no                no                   no

trehalose 6-P hydrolase

trehalose degradation II

treA                                  no                no                   no




                                            57
trehalase, periplasmic

treF                                 no                no                   no

trehalase, cytoplasmic

trehalose degradation III

trePP/otsB                           no                no                   no

trehalose-6-phosphate phosphatase

trehalose degradation IV and V

trehalose phosphorylase 2.4.1.64     no                no                   no

synthesis

otsA                                 no                no                   no

trehalose-6-phosphate synthase

transport

treB/treP                            no                no                   no

PTS family enzyme IIBC,

trehalose(maltose)-specific

regulation

treR                                 no                no                   no

repressor of treA,B,C




N. Fructose

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

mak                                 HS_1041           no                   HI0182




                                           58
Cryptic manno(fructo)kinase

pfkB                                 no                 no                    no

6-phosphofructokinase II

pfkA                                 HS_0485            HD0465                HI0982

6-phosphofructokinase I

fbaA                                 HS_0206            HD0864                HI0524

fructose-bisphosphate aldolase,

class II

fbaB                                 possibly           no                    no

fructose-bisphosphate aldolase class HS_0055

I

fruA                                 no                 no                    HI0446

PTS system, fructose-specific IIBC

component

fruK                                 no                 no                    HI0447

1-phosphofructokinase

fruB                                 no                 no                    HI0448

PTS system, fructose-specific

IIA/FPr component



O. Maltose

Gene                                  H. somnus 129Pt    H. ducreyi 35000HP    H. influenzae Rd

malT                                  no                 no                    no




                                                59
transcriptional regulator necessary for

transcription of mal genes except

malIXY

malQ                                      HS_0890   no   HI1356

amylomaltase

malE                                      no        no   no

malF                                      no        no   no

maltose transport protein (ABC

superfamily, membrane)

malG                                      no        no   no

maltose transport protein (ABC

superfamily, membrane)

malK                                      no        no   no

malP                                      no        no   no

maltodextrin phosphorylase

malS                                      no        no   no

alpha-amylase

lamB                                      no        no   no

maltodextrin pore

malX                                      no        no   no

PTS family enzyme IIC (N-terminal);

enzyme IIB (C-terminal)

malZ                                      no        no   no




                                               60
maltodextrin glucosidase

maltose phosphorylase      no        no   no

Beta-phosphoglucomutase    no        no   no




                                61
Table S6. Amino acid metabolism

A. Arginine and polyamine biosynthesis

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

argA                                no                HD1384               no

N-acetylglutamate synthase

argB                                no                HD0891               no

N-acetylglutamate kinase

argC                                no                HD0890               no

N-acetylglutamyl phosphate

reductase

argD                                no                HD0892               no

acetylornithine transaminase

argE                                no                HD0566               no

acetylornithine deacetylase

astC                                no                no                   no

acetylornithine transaminase,

catabolic

argI                                no                HD0232               HI0596

ornithine carbamoyltransferase

argF                                no                no                   no

ornithine carbamoyltransferase

argG                                HS_1362           HD1204               HI1727




                                           62
arginosuccinate synthase

argH                                  HS_0692    HD1033   HI0811

arginosuccinate lyase

argJ                                  no         no       no

Glutamate N-acetyltransferase

(Ornithine acetyltransferase)

argR                                  HS_1056    HD0262   HI1209

arginine repressor

speA                                  no         no       no

arginine decarboxylase,

biosynthetic

adiA                                  no         no       no

arginine decarboxylase, degradative

speB                                  no         no       no

agmatinase

speC                                  HS_1573    no       HI0591

ornithine

decarboxylase, biosynthetic

speF                                  HS_1573    no       HI0591

ornithine

decarboxylase, degradative

speD                                  no         no       no

S-adenosylmethionine




                                            63
decarboxylase

speE                                  no                no                   no

spermidine synthase

carB                                  no                HD0233               no

carbamoyl phosphate synthetase

carA                                  no                HD0235               no

carbamoyl phosphate synthetase



B. Cysteine biosynthesis and sulfate assimilation

Gene                                  H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

cysE                                  HS_0154           HD0659               HI0606

serine acetyltransferase

cysM                                  no                no                   no

O-acetylserine (thiol)-lyase B

cysK                                  HS_0369           HD0896               HI1103

O-acetylserine (thiol)-lyase A

cysZ                                  HS_0370           HD0832               HI1102

cysteine biosynthesis protein

cysQ                                  HS_1650           HD0840               HI0559

cysA                                  no                no                   no

ATP-binding component of sulfate

permease A protein; chromate

resistance




                                               64
cysC                                 no                 no                   no

adenosine 5'-phosphosulfate kinase

cysD                                 no                 no                   no

ATP-sulfurylase, subunit 2

cysG                                 no                 no                   no

siroheme synthase

cysH                                 no                 no                   no

3'-phosphoadenosine 5'-

phosphosulfate (PAPS) reductase

cysI                                 no                 no                   no

sulfite reductase, alpha subunit

cysJ                                 no                 no                   no

sulfite reductase (NADPH),

flavoprotein beta subunit

cysN                                 no                 no                   no

ATP-sulfurylase (ATP:sulfate

adenylyltransferase), subunit 1,

probably a GTPase



C. Glutamate, Glutamine, Aspartate and Asparagine biosynthesis

Gene                                 H. somnus 129Pt    H. ducreyi 35000HP   H. influenzae Rd

Glutamate and glutamine

gltB                                 no                 no                   no




                                             65
glutamate synthase, large subunit

gltD                                no         no       no

glutamate synthase, small subunit

gdhA                                HS_1339    no       HI0189

glutamate dehydrogenase, NADP-

specific

glnA                                HS_0418    HD0750   HI0865

glutamine synthetase

glnB                                HS_1355    HD0062   HI0337

nitrogen regulatory protein p-II

glnD                                HS_0829    HD1497   HI1719

uridylyltransferase                            HD1496

glnE                                HS_1218    HD1709   HI0069

glutamate-ammonia-ligase

adenylyltransferase

Aspartate and asparagine

aspA                                HS_0466    HD0564   HI0534

aspartate ammonia-lyase

asnA                                HS_1440    HD1913   HI0564

asparagine synthetase

asnB                                no         no       no

asparagine synthetase B

aspC                                HS_0838    HD1419   HI1617




                                          66
aspartate aminotransferase

ansB                                  no                HD0372               no

periplasmic L-asparaginase II

NP_417432



ansA                                  no                no                   no

cytoplasmic L-asparaginase I

asparaginase                          no                no                   no

rpoN                                  no                no                   no

RNA polymerase, sigma(54 or 60)

factor

ntrB                                  no                no                   no

histidine protein kinase sensor for

GlnG regulator

ntrC                                  no                no                   no

response regulator for gln

serC                                  HS_0611           HD1382               HI1167

phosphoserine aminotransferase



D. Lysine, Threonine, Methionine biosynthesis

Gene                                  H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

Lysine

lysC                                  no                HD1375               no




                                                67
aspartokinase III

thrA                                 HS_1214    no       HI0089

aspartate kinase I



bifunctional: aspartokinase I (N-

terminal); homoserine

dehydrogenase I (C-terminal)

metL                                 no         no       no

aspartate kinase II



bifunctional: aspartokinase II and

homoserine dehydrogenase II

asd                                  HS_1552    HD0847   HI0646

aspartate semialdehyde

dehydrogenase

dapA                                 HS_0492    HD1107   HI0255

dihydrodipicolinate synthase

dapB                                 HS_0835    HD1398   HI1308

dihydrodipicolinate reductase

dapD                                 HS_0785    HD0630   HI1634

tetrahydrodipicolinate synthase

dapC                                 HS_0926    no       no

N-succinyldiaminopimelate-




                                           68
aminotransferase

dapE                               HS_0578    HD0642   HI0102

N-succinyl-L-diaminopimelic acid

desuccinylase

dapF                               HS_1610    HD0026   HI0750

diaminopimelate epimerase

lysA                               HS_1713    HD0036   HI0727

diaminopimelate decarboxylase

Threonine

thrA                               HS_1214    no       HI0089

homoserine dehydrogenase

thrB                               HS_1213    no       HI0088

homoserine kinase

thrC                               HS_1212    no       HI0087

threonine synthase

Methionine

metA                               no         no       no

homoserine O-succinyltransferase

metB                               HS_1345    no       HI0086

O-succinylhomoserine lyase

malY                               no         no       no

cystathionine beta-lyase

metC                               HS_0475    no       HI0122




                                         69
L-cysteine desulfhydrase /

cystathionine-beta-lyase

metH                                 no               no       no

Cobalamin-dependent

homocysteine transmethylase

metE                                 HS_1226          no       HI1702

Cobalamin-independent                HS_0824          no

homocysteine transmethylase



metK                                 HS_1623          HD0569   HI1172

methionine adenosyltransferase I

metF                                 HS_1130          no       HI1444

5,10-methylenetetrahydrofolate

reductase

metX                                 HS_1076          no       HI1263

homoserine O-acetyltransferase

metJ                                 HS_0469          HD0675   HI0294

met repressor

met2                                 no               no       no

Homoserine O-acetyltransferase

(EC 2.3.1.31)



E. Leucine, Isoleucine and Valine biosynthesis




                                                 70
Gene                                   H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

ilvA                                   HS_0183           no                   HI0738.1

threonine ammonia-lyase (threonine

dehydratase, threonine deaminase)

ilvB                                   no                no                   no

acetolactate synthase I, large

subunit, valine-sensitive

ilvC                                   HS_1671           no                   HI0682

ketol-acid reductoisomerase

ilvD                                   HS_0342           no                   HI0738

dihydroxy-acid dehydratase (DAD)

ilvE                                   HS_0494           no                   HI1193

branched-chain amino acid

transaminase

ilvG                                   HS_0147           no                   N-terminal of

acetohydroxy acid synthase II, large                                          HI0737

subunit

ilvH                                   no                no                   HI1584

acetolactate synthase III, small

subunit

ilvI                                   no                no                   HI1585

acetolactate synthase III, valine

sensitive, large subunit




                                              71
ilvM                                 HS_0148    no   C-terminal of

acetohydroxy acid synthase II,                       HI0737

small subunit

ilvN                                 no         no   no

acetolactate synthase I, small

subunit

leuA                                 HS_0392    no   HI0986

2-isopropylmalate synthase (alpha-

isopropylmalate synthetase)

leuB                                 HS_0391    no   HI0987

3-isopropylmalate dehydrogenase

leuC                                 HS_0390    no   HI0988

3-isopropylmalate dehydratase,

large subunit

leuD                                 HS_0389    no   HI0989

3-isopropylmalate dehydratase,

small subunit

avtA                                 no         no   no

alanine-alpha-ketoisovalerate (or

valine-pyruvate) transaminase,

transaminase C

tdcB                                 no         no   no

threonine deaminase, catabolic,




                                           72
PLP-dependent

NP_417587

sdaA                                   no                 HD1142                   HI0288

L-serine deaminase I

sdaB                                   no                 no                       no

L-serine deaminase 2

tyrB                                   no                 no                       no

tyrosine aminotransferase, tyrosine-

repressible,

PLP-dependent



F. Histidine, Glycine, Serine, Alanine, Proline, Phenylalanine, Tyrosine, Trptophan biosynthesis

Gene                                   H. somnus 129Pt    H. ducreyi 35000HP       H. influenzae Rd

Histidine

hisG                                   no                 no                       HI0468

ATP phosphoribosyltransferase

hisI                                   no                 no                       HI0475

bifunctional: phosphoribosyl-AMP

cyclohydrolase (N-terminal);

phosphoribosyl-ATP

pyrophosphatase (C-terminal)

hisA                                   no                 no                       HI0473

N-(5'-phospho-L-ribosyl-




                                               73
formimino)-5-amino-1- (5'-

phosphoribosyl)-4-

imidazolecarboxamide isomerase

hisF                                   no         no   HI0474

imidazole glycerol phosphate

synthase subunit in heterodimer

with HisH = imidazole glycerol

pHS_phate synthase holoenzyme

hisH                                   no         no   HI0472

glutamine amidotransferase subunit

of heterodimer with HisF =

imidazole glycerol phosphate

synthase holoenzyme

hisB                                   no         no   HI0471

bifunctional: histidinol-phosphatase

(N-terminal); imidazoleglycerol-

phosphate dehydratase (C-terminal)

hisC                                   HS_0612    no   HI0470

histidinol phosphate

aminotransferase

hisD                                   no         no   HI0469

L-histidinal:NAD+ oxidoreductase;

L-histidinol:NAD+ oxidoreductase




                                             74
Glycine and serine

glyA                                HS_1627    no       HI0889

glycine/serine

hydroxymethyltransferase

serA                                HS_0122    no       HI0465

phosphoglycerate dehydrogenase

(D-3-phosphoglycerate

dehydrogenase)

serC                                HS_0611    HD1382   HI1167

phosphoserine transaminase

(phosphoserine aminotransferase)

serB                                HS_0687    HD0207   HI1033

phosphoserine phosphatase

Alanine

ilvE                                HS_0494    no       HI1193

branched-chain amino acid

transaminase

avtA                                no         no       no

alanine-alpha-ketoisovalerate (or

valine-pyruvate) transaminase,

transaminase C

dadX                                HS_0939    HD0624   HI1575

alanine racemase 2, PLP-binding,




                                          75
catabolic

alr                                  HS_0939    HD0624   HI1575

alanine racemase

Proline

gdhA                                 HS_1339    no       HI0189

NADP-specific glutamate

dehydrogenase

proA                                 HS_0408    no       HI1239

glutamate-5-semialdehyde

dehydrogenase

proB                                 HS_0192    no       HI0900

glutamate 5-kinase (gamma-

glutamyl kinase)

proC                                 HS_1285    no       HI0307

pyrroline-5-carboxylate reductase

Phenylalanine and tyrosine

pheA                                 HS_0365    HD0873   HI1145

bifunctional P-protein: chorismate

mutase; prephenate dehydratase

tyrA                                 HS_0671    HD0443   HI1290

bifunctional protein: chorismate

mutase; prephenate dehydrogenase

tyrB                                 no         no       no




                                           76
tyrosine aminotransferase, tyrosine

repressible

Tryptophan

trpE                                  no         no       HI1387

anthranilate synthase component I



trpD/ trpGD                           no         no       HI1389

anthranilate synthase component II,

glutamine amidotransferase and

phosphoribosylanthranilate

transferase

trpG                                  HS_0130    HD0406   HI1171

anthranilate synthase component II                        HI1388

(para-aminobenzoate synthase

component II)

trpC                                  no         no       HI1389.1

N-(5-phosphoribosyl)anthranilate

isomerase and indole-3-

glycerolphosphate synthetase

trpA                                  no         no       HI1432

tryptophan synthase, alpha protein

trpB                                  no         no       HI1431

tryptophan synthase, beta




                                            77
G. Arginine degradation

Gene                              H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

E. coli ast pathway (arginine

degradation VI)

astA                              no                no                   no

arginine succinyltransferase

astB                              no                no                   no

succinylarginine dihydrolase

astC                              no                no                   no

acetylornithine delta-

aminotransferase

astD                              no                no                   no

succinylglutamic semialdehyde

dehydrogenase

astE                              no                no                   no

succinylglutamate desuccinylase

B. subtilis

arginase pathway (arginine

degradation I, IX, XIII, XII)

rocF                              no                no                   no

arginase

rocD                              no                no                   no




                                         78
ornithine aminotransferase

rocA                                  no        no       no

pyrroline-5 carboxylate

dehydrogenase

Pseudomonas aeruginosa arginine

deiminase (arginine degradation X

and XI)

arcA                                  no        no       no

arginine deiminase

arcB                                  no        HD0232   HI0596

ornithine carbamoyltransferase,

catabolic

arcC                                  no        no       HI0595

carbamate kinase

arginine degradation II and XII

Deinococcus radiodurans ,

Sulfolobus solfataricus, E.coli

speA                                  no        no       no

arginine decarboxylase,

biosynthetic

NP_417413

adiA                                  no        no       no

arginine decarboxylase, degradative




                                           79
NP_418541

speB                                no                no                   no

agmatinase

NP_417412

speC                                HS_1573           no                   HI0591

ornithine

decarboxylase, biosynthetic

arginine degradation V

Arginine 2-monooxygenase            no                no                   no

1.13.12.1

arginine degradation IV

Gamma-guanidinobutyraldehyde        no                no                   no

dehydrogenase 1.2.1.54



H. Cysteine degradation

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

tnaA                                HS_0801           no                   no

tryptophanase

metC                                HS_0475           no                   HI0122

cystathionine beta-lyase



I. Glutamate and Glutamine degradation

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd



                                           80
L-glutamate to fumarate

aspC                                 HS_0838    HD1419   HI1617

aspartate aminotransferase

aspA                                 HS_0466    HD0564   HI0534

aspartate ammonia-lyase

L-glutamate to alpha-ketoglutarate

gdhA                                 HS_1339    no       HI0189

glutamate dehydrogenase, NADP-

specific

L-glutamate to (2S, 3S)-3-

methylaspartate

glmE                                 no         no       no

glutamate mutase epsilon subunit

5.4.99.1

L-glutamate to L-glutamine

glnA                                 HS_0418    HD0750   HI0865

glutamine synthetase

L-glutamine to L-glutamate

glutaminase 3.5.1.2                  no         no       no

gltB                                 no         no       no

glutamate synthase, large subunit

gltD                                 no         no       no

glutamate synthase, small subunit



                                           81
J. Aspartate degradation

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

L-aspartate to NAD

nadA                                no                no                   no

quinolinate synthetase, A protein

nadE                                no                no                   no

NAD synthetase, prefers NH3 over

glutamine

nadB                                no                no                   no

quinolinate synthetase, B protein

nadC                                no                no                   no

quinolinate

phosphoribosyltransferase

nadD                                no                no                   no

NAMN adenylyltransferase

L-aspartate to beta-alanine

panD                                no                no                   no

Aspartate 1-decarboxylase



K.. Asparagine degradation

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

Asparagine to aspartate



                                           82
ansB                                   no                HD0372               no

periplasmic L-asparaginase II

ansA                                   no                no                   no

cytoplasmic L-asparaginase I




L. Lysine degradation

Gene                                   H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

lysine to cadaverine

ldcC                                   HS_1007           no                   no

lysine decarboxylase 2, constitutive

cadA                                   HS_1007           no                   no

lysine decarboxylase 1

cadB                                   HS_1006           no                   no

cadaverine/lysine antiporter



M. Threonine degradation

Gene                                   H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

threonine to glycine or

aminoacetone

tdh                                    no                no                   no

threonine dehydrogenase




                                              83
threonine to homoserine,

cystathione, o-succinyl-L-

homoserine, propionate

ilvA                                HS_0183           no                   HI0738.1

threonine deaminase (dehydratase)

L-cysteine desulfhydrase            no                no                   no

metB                                HS_1345           no                   HI0086

2.5.1.48

cystathionine gamma-synthase

2-oxobutanoate to propionate

pyruvate formate-lyase , formate    HS_1136           HD0990               HI0180

acetyltransferase

ackA                                HS_0803           HD1456               HI1204




N. Methionine degradation

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

metK see above                      yes               yes                  yes

DNA-cytosine methyltransferase      HS_1422           no                   no

2.1.1.37                            no                no                   HI1041

DNA (cytosine-5-)-

methyltransferase

3.3.1.1                             no                no                   no



                                           84
adenosyl homocysteinase

4.2.1.22                             no                     no                   no

serine sulfhydrolase




O. Leucine, Isoleucine and Valine degradation degradation

Gene                                 H. somnus 129Pt        H. ducreyi 35000HP   H. influenzae Rd

Common pathway

ilvE                                 HS_0494                no                   HI1193

branched-chain amino acid

transaminase

bfmBAA                               no                     no                   no

2-oxoisovalerate dehydrogenase

subunit alpha 1.2.4.4

bfmBAB                               no                     no                   no

2-oxoisovalerate dehydrogenase

subunit beta 1.2.4.4

2-methylacyl-CoA dehydrogenase       no                     no                   no

1.3.99.12

Leucine

3-methylcrotonyl-CoA carboxylase,    no                     no                   no

beta subunit



                                             85
6.4.1.4

3-methylglutaconyl-CoA hydratase      no                no                   no

4.2.1.18

Isoleucine

3-hydroxyacyl-CoA dehydrogenase       no                no                   no

1.1.1.178

Valine

3-hydroxyisobutyryl-CoA               no                no                   no

hydrolase 3.1.2.4



P. Histidine degradation

Gene                                  H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

hutH                                  no                no                   no

histidase (histidine ammonia lyase)

4.3.1.3

hutU                                  no                no                   no

urocanase (urocanate hydratase)

4.2.1.49

hutI                                  no                no                   no

imidazolonepropionase

3.5.2.7

hutF                                  no                no                   no

formiminoglutamate deiminase



                                             86
3.5.3.13



Q. Glycine degradation

Gene                              H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

gcv system

gcvP                              no                no                   no

glycine dehydrogenase

(decarboxylating) 1.4.4.2

lpdA                              HS_1093           HD1623               HI1231

dihydrolipoate dehydrogenase

gcvH                              no                no                   no

lipoyl protein

gcvT                              no                no                   no

aminomethyltransferase 2.1.2.10



R. Serine degradation

Gene                              H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

L-serine to pyruvate

sdaB                              no                HD1142               HI0288

L-serine deaminase 2 4.3.1.17

sdaA                              no                no                   no

L-serine deaminase 1

sdhY                              no                no                   no



                                         87
L-serine deaminase 3



S. Alanine degradation

Gene                                 H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

L-alanine to pyruvate

alanine dehydrogenase                HS_0232           HD1663               HI1362

1.4.1.1



T. Proline degradation

Gene                                 H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

L-proline to L-glutamate

putA                                 no                no                   no

proline dehydrogenase

1.5.99.8/Delta-1-pyrroline-5-

carboxylate dehydrogenase 1.5.1.12



U. Phenylalanine degradation

Gene                                 H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

L-phenylalanine to L-tyrosine

phhA phenylalanine-4-hydroxylase     no                no                   no

1.14.16.1



V. Tyrosine degradation



                                            88
Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

phhC/tyrB                           no                no                   no

tyrosine aminotransferase 2.6.1.5

hppD                                no                no                   no

4-hydroxyphenylpyruvate

dioxygenase 1.13.11.27



W.Tryptophan degradation

Gene                                H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

L-tryptophan to pyruvate

tnaA                                HS_0801           no                   no

tryptophanase

L-tryptophan to tryptamine

aromatic L-amino acid               no                no                   no

decarboxylase

L-tryptophan to indole-3-acetate

key enzyme: indolepyruvate          no                no                   no

carboxylase

L-tryptophan to anthranilate

tryptophan 2,3-dioxygenase          no                no                   no

1.13.11.11




                                           89
Table S7. Nucleotide metabolism

Gene                              H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

purA                              HS_1328           HD1807               HI1633

adenylosuccinate synthetase

purB                              HS_1593           HD1649               HI0639

adenylosuccinate lyase

purC                              HS_1364           HD0251N-terminal     HI1726

phosphoribosylaminoimidazole-                       HD0252 C-terminal

succinocarboxamide synthase

(SAICAR synthetase)

purD                              HS_1626           HD1042 C-terminal    HI0888

phosphoribosylamine--glycine                        HD1043 N-terminal

ligase

purE                              HS_0672           HD1424               HI1615

phosphoribosylaminoimidazole

carboxylase (AIR carboxylase)

purF                              HS_0916           HD1210 C-terminal    HI1207

amidophosphoribosyltransferase                      HD1209 N-terminal

purH                              HS_1625           HD1703 N-terminal    HI0887

phosphoribosylaminoimidazoleca                      HD1702 N-terminal

rboxamide formyltransferase

purK                              HS_0839           HD1421 C-terminal    HI1616




                                            90
phosphoribosylaminoimidazole                     HD1423 N-terminal

carboxylase, ATPase subunit

purL                              HS_1503        HD2008 N-terminal       HI0752

phosphoribosylformylglycinamidi                  HD2009 central region

ne synthase                                      HD2010 C-terminal

purM                              HS_1551        HD0561                  HI1429

phosphoribosylformylglycinamidi

ne cyclo-ligase

purN                              HS_0913        HD0548                  HI1428

phosphoribosylglycinamide

formyltransferase

purR                              HS_1032        HD1641                  HI1635

purine nucleotide synthesis

repressor

purT                              HS_0549        HD0548                  no – but this

phosphoribosylglycinamide                                                enzyme is

formyltransferase 2                                                      redundant with

                                                                         purN

purU                              HS_0786        no                      HI1588

formyltetrahydrofolate

deformylase

guaA                              HS_0421        HD1504                  HI0222

GMP synthase, glutamine-




                                            91
hydrolyzing (glutamine

amidotransferase)

guaB                               HS_0420        HD1503   HI0221

IMP dehydrogenase (inosine-5'-

monophosphate dehydrogenase)

guaC                               no             no       no

GMP reductase [Escherichia coli]

adk                                HS_0648        HD0826   HI0349

adenylate kinase

gmk                                HS_1457        HD1830   HI1743

guanylate kinase

ndk                                HS_0387        HD1053   HI0876

nucleoside-diphosphate kinase

nrdA                               HS_1196        HD1731   HI1659

ribonucleoside diphosphate

reductase 1, alpha subunit

nrdB                               HS_0961        HD1732   HI1660

ribonucleoside-diphosphate

reductase 1, beta subunit

nrdE                               no             no       no

ribonucleoside-diphosphate

reductase 2, alpha subunit

nrdF                               no             no       no




                                             92
ribonucleoside-diphosphate

reductase 2, beta subunit

carA/pyrA                           no             HD0235   no

carbamoyl phosphate synthetase,

glutamine amidotransferase small

subunit

carB                                no             HD0233   no

carbamoyl phosphate synthase,

large subunit

pyrB                                no             no       no

aspartate carbamoyltransferase,

catalytic subunit

pyrC                                no             no       no

dihydro-orotase

pyrD                                no             HD1626   HI1401

dihydroorotate dehydrogenase

pyrE                                no             HD1759   HI0272

orotate phosphoribosyltransferase

pyrF                                no             HD1356   HI1224

orotidine 5`-phosphate

decarboxylase

pyrG                                HS_0552        HD0373   HI1077

CTP synthase (UTP--ammonia




                                              93
ligase)

pyrH                              HS_0987        HD1597   HI1065

uridylate kinase

pyrI                              no             no       no

aspartate carbamoyltransferase,

regulatory subunit

pyrR                              HS_1561        HD1178   HI0459

pyrimidine operon regulatory                     HD1181

protein / uracil

phosphoribosyltransferase




                                            94
Table S8. Genes involved in TCA cycle, Embden-Meyerhof, pentose phosphate, Entner-

Doudoroff, ubiquinone/menaquinone biosynthesis and fermentation pathways in H. somnus

129Pt, H. ducreyi 35000HP and H. influenzae Rd.

 TCA cycle                        H. somnus 129Pt    H. ducreyi 35000HP   H. influenzae Rd

 aceE                             HS_1095            HD1625               HI1233

 pyruvate dehydrogenase E1

 component

 aceF                             HS_1094            HD1624               HI1232

 pyruvate dehydrogenase, E2

 complex

 lpdA                             HS_1093            HD1623               HI1231

 pyruvate dehydrogenase

 multienzyme complex, E3

 gltA                             HS_0960            no                   no

 citrate synthase

 acnA                             no                 no                   no

 aconitase

 acnB                             HS_1270            no                   no

 aconitate hydratase2

 icd                              no                 no                   no

 isocitrate dehydrogenase

 sucA                             HS_0959            HD1336               HI1662




                                            95
alpha ketoglutarate

dehydrogenase

sucB                            HS_0958        HD1334   HI1661

alpha ketoglutarate

dehydrogenase,

dihydrolipoamide

succinyltransferase component

sucC                            HS_0957        no       HI1196

succinyl-CoA synthetase beta

chain

sucD                            HS_0956        no       HI1197

succinyl-CoA synthetase alpha

chain

sdhA                            no             no       no

succinate dehydrogenase

flavoprotein subunit

sdhB                            no             no       no

succinate dehydrogenase iron-

sulfur protein

sdhC                            no             no       no

succinate dehydrogenase

cytochrome b-556 subunit

sdhD                            no             no       no




                                          96
succinate dehydrogenase

hydrophobic membrane anchor

protei

fumA                               no             no       no

fumarase

fumB                               no             no       no

fumarate hydratase class I,

anaerobic

fumC                               HS_1102        HD1986   HI1398

fumarate hydratase class II

mdh                                HS_1055        HD0264   HI1210

malate dehydrogenase

malate dehydrogenase,              no             HD0165   no

FAD/NAD(P)-binding domain

frdA                               HS_1277        HD0030   HI0835

fumarate reductase, flavoprotein

subunit

frdB                               HS_1278        HD0032   HI0834

fumarate reductase, iron-sulfur

protein

frdC                               HS_1279        HD0033   HI0833

fumarate reductase 15 kDa

hydrophobic protein




                                             97
frdD                             HS_1280        HD0034   HI0832

fumarate reductase, 13 kDa

hydrophobic protein

Embden-Meyerhof

glk                              HS_0379        no       no

hexokinase (glucokinase)

putative glucokinase from        no             no       HI0144

Streptomyces coelicolor A3

NP_624417

glucokinase from Streptomyces    HS_1041        no       HI0182

coelicolor A3                    ROK

NP_626383

pfkA                             HS_0485        HD0465   HI0982

6-phosphofructokinase I

pfkB                             no             no       no

6-phosphofructokinase II

fruK                             no             no       HI0447

1-phosphofructokinase

fba                              HS_0206        HD0864   HI0524

fructose bisphosphate aldolase

pgi                              HS_0938        HD0418   HI1576

glucose 6-phosphate isomerase

tpiA                             HS_1591        HD0762   HI0678




                                           98
triosephosphate isomerase

gap                            HS_1466        HD1291   HI0001

glyceraldehyde 3-phosphate

dehydrogenase

pgk                            HS_0207        HD0865   HI0525

phosphoglycerate kinase

gpmA                           HS_1445        HD1659   HI0757

phosphoglycerate mutase 1

gpmB                           HS_1664        no       no

phosphoglycerate mutase 2

eno                            HS_0561        HD0477   HI0932

enolase

pyk                            HS_1086        HD0446   HI1573

pyruvate kinase II

ldhA                           no             no       HI0085

fermentative D-lactate

dehydrogenase, NAD-dependent

dld                            HS_0784        no       HI1649

D-lactate dehydrogenase, FAD

protein, NADH independent

lldD/lctD                      no             HD0084   HI1739.1

L-lactate dehydrogenase

ptsG                           no             no       no




                                         99
PTS system, glucose-specific

IIABC component

crr                               HS_1096         HD0227   HI1711

PTS system, glucose-specific

enzyme II, A component

Pentose Phosphate

zwf                               HS_1651         HD0838   HI0558

glucose 6-phosphate 1-

dehydrogenase

pgl                               HS_1652         HD0836   HI0556

6-phosphogluconolactonase

gnd                               HS_1654         HD0833   HI0553

6-phosphogluconate

dehydrogenase, decarboxylating

rpiA                              HS_0123         HD0199   HI0464

ribose 5-phosphate isomerase A,

constitutive

rpiB                              no              no       no

ribose 5-phosphate isomerase B,

inducible

rpe                               HS_0175         HD1929   HI0566

ribulose phosphate 3-epimerase    HS_0057

tktA                              HS_0551         HD1723   HI1023




                                            100
transketolase I

tktB                             no              no       no

transketolase II

talA                             no              no       no

transaldolase A

talB                             HS_0204         HD0310   HI1125

transaldolase B

Entner-Doudoroff

edd                              HS_0342         no       HI0738

phosphogluconate dehydratase

eda                              HS_1603         no       HI0047

oxaloacetate decarboxylase

Ubiquinone biosynthesis

ubiA                             HS_0159         HD1647   no

4-hydroxybenzoate-

octaprenyltransferase

ubiB                             HS_0544         HD0717   no

NADPH:flavin oxidoreductase

ubiC                             HS_0150         no       no

chorismate lyase

ubiD                             HS_0474         HD0197   no

3-octaprenyl-4-hydroxybenzoate

carboxy-lyase




                                           101
ubiE                                HS_0542         HD0719   no

ubiquinone/menaquinone

biosynthesis methyltransferase

ubiH                                HS_0681         HD0579   no

2-octaprenyl-6-methoxyphenol

hydroxylase

ubiX                                HS_0915         HD1360   no

3-octaprenyl-4-hydroxybenzoate

carboxy-lyase

ubiG                                HS_1162         HD1750   no

3-demethylubiquinone 3-

methyltransferase / 2-octaprenyl-

6-hydroxyphenol methylase

ubiF                                HS_1156         HD1874   no

2-octaprenyl-3-methyl-6-

methoxy-1,4-benzoquinone

hydroxylase

menaquinone biosynthesis

menA                                HS_0221         HD0683   HI0509

1,4-dihydroxy-2-naphthoate

octaprenyltransferase

menB                                HS_0562         HD1925   HI0968

dihydroxynaphthoic acid




                                              102
synthase

menC                           HS_0563         HD1055   HI0969

o-succinylbenzoate-CoA

synthase (OSB synthase)

menD                           HS_0617         HD1853   HI0283

2-succinyl-6-hydroxy-2,4-

cyclohexadiene-1-carboxylate

synthase

menE                           HS_1207         HD1271   HI0194

O-succinylbenzoate-CoA

synthase

menF                           HS_0618         HD0621   HI0285

menaquinone-specific

isochorismate

entC                           no              no       no

isochorismate synthase,

enterobactin specific

menG                           HS_0220         HD0166   HI0508

S-adenosylmethionine:2-

demethylmenaquinone

methyltransferase

chorismate biosynthesis

(shikimate pathway)




                                         103
aroA                           HS_0613         HD1383   HI1589

3-phosphoshikimate-1-

carboxyvinyltransferase

aroB                           HS_1114         HD0422   HI0208

3-dehydroquinate synthase

aroC                           HS_1205         HD1274   HI0196

3-dehydroquinate dehydratase

(chorismate synthase)

aroD                           no              no       no

3-dehydroquinate dehydratase

aroE                           HS_0006         HD0415   HI0655

5-enolpyruvoylshikimate-3-                              HI0607

phosphate synthase

aroF                           no              HD0444   no

3-deoxy-D-

arabinoheptulosonate-7-

phosphate synthase (DAHP

synthetase)/

chorismate synthase

aroG                           HS_0941         HD1475   HI1547

2-dehydro-3-

deoxyphosphoheptonate

aldolase// 3-deoxy-D-




                                         104
arabinoheptulosonate-7-

phosphate synthase (DAHP

synthetase, phenylalanine

repressible)

aroH                              no              no       no

2-dehydro-3-

deoxyphosphoheptonate aldolase

aroK                              HS_1113         HD0423   HI0207

shikimate kinase I

aroL                              no              no       no

shikimate kinase II

Fermentation

pyruvate to D-lactate

ldhA                              HS_0945         no       HI0085

D-lactate dehydrogenase

dld                               HS_0784         no       HI1649

D-lactate dehydrogenase

pyruvate to L-lactate

lldD                              no              HD0084   HI1739.1

L-lactate dehydrogenase

pyruvate to formate and acetyl-

CoA

pflB                              HS_1136         HD0990   HI0180



                                            105
formate acetyltransferase 1



acetyl-CoA to acetate

pta                           HS_0802         HD1457   HI1203

phosphate acetyltransferase

ackA                          HS_0803         HD1456   HI1204

acetate kinase A

acetyl-CoA to ethanol

adhE                          no              no       no

acetaldehyde/alcohol

dehydrogenase




                                        106
Table S9. NAD biosynthesis and salvage

A. de novo pathway

 Gene                      H. somnus 129Pt         H. ducreyi 35000HP   H. influenzae Rd

 nadA                      no                      no                   no

 quinolinate synthetease

 A

 nadB                      no                      no                   no

 L-aspartate oxidase

 nadC                      no                      no                   no

 quinolinate

 phosphoribosyl

 transferase



 nadD                      no                      no                   no

 NAMN

 adenylyltransferase



 nadE                      no                      no                   no

 NAD synthetase,

 prefers NH3 over

 glutamine




                                             107
B. salvage pathway (from MetaCyc (8))

Gene                    H. somnus 129Pt   H. ducreyi 35000HP    H. influenzae Rd

NAD salvage

pathway II

nadR                    HS_0087           HD0274                HI0763

bifunctional protein:                     C-terminal fragment

NMN                                       HD0275

adenylyltransferase;                      N-terminal fragment

ribosylnicotinamide

kinase

NAD salvage

pathway I

NAD(+)                  no                no                    no

nucleosidase

3.2.2.5

nudC                    no                no                    possibly HI0432

NADH                                                            conserved

pyrophosphatase                                                 hypothetical protein

                                                                47% aa identity

pncA                    no                no                    no

nicotinamidase and

pyrazinamidase




                                          108
pncB                   no                   no                   no

nicotinate

phosphoribosyltransf

erase




C. Nicotinate phosphoribosyltransferase pathway:

Gene                   H. somnus 129Pt      H. ducreyi 35000HP   H. influenzae Rd

nadV                   HS_0002              HD1447               no

nicotinate

phosphoribosyltransf

erase

2.7.7.1                no                   no                   no

Nicotinamide-

nucleotide

adenylyltransferase




                                             109
Table S10. LOS biosynthesis genes

Genes identified in H. influenzae 86-028NP (18)

Gene                         H.           H. influenzae Rd H. somnus 129Pt H. ducreyi 35000HP
                             influenzae
                             86-028NP

kdsB                         NTHI0068 HI0058             HS_0658          HD0334

3-deoxy-D-manno-

octulosonate

cytidylyltransferase

lpxK                         NTHI0069 HI0059             HS_0656          HD0217

tetraacyldisaccharide-1-P

4'-kinase

msbA                         NTHI0072 HI0060             HS_1021          HD1630

Lipid A ABC transporter,

ATP-binding protein

msbB                         NTHI0296 HI0199             HS_1202          HD0404

lipid A biosynthesis

(kdo)2-(lauroyl)-lipid IVA

acyltransferase

lgtC                         NTHI0365 HI0258             HS_0636 lob2D HD1090

glycosyl transferase



repeats?                     GACA         GACA repeated CAGT repeated no repeats




                                                110
                              repeated 10 22 times in       19 times in the

                              times in      frame just after middle of the

                              frame         start codon     CDS

orfM                          NTHI0366 HI0260               HS_0125              HD1348

Xanthosine triphosphate

pyrophosphatase

kdkA                          NTHI0367 HI0260.1             no                   HD1101

3-deoxy-D-manno-

octulosonic acid kinase,

opsX/rfaC                     NTHI0368 HI0261               HS_1611              HD0445

ADP-heptose:LPS                                             lipopolysaccharid

heptosyltransferase I                                       e

                                                            heptosyltransferas

                                                            e-1

lpt6                          NTHI0383 HI0275               HS_0234              no

phosphorylethanolamine

transferase

galE                          NTHI0471 HI0351               HS_0789              HD0829

UDP-glucose 4-epimerase

lic3A                         NTHI0472 HI0352               no                   no

alpha-2,3-sialyltransferase

                              CAAT

                              repeated 18




                                                   111
                          times in

                          frame

possible acetyltransferase NTHI0512 HI0391            HS_0553            no



                          AGCA         no repeats     no repeats

                          repeated 8

                          times in

                          frame

waaQ                      NTHI0649 HI0523             no                 HD1202

ADP-heptose:LPS

heptosyltransferase III

lic2A                     NTHI0677 HI0550             HS_0637 lob2A Top hit is to lgtB

UDP galactose                                                            HD0472

lipooligosaccharide

galactosyltransferase

                          CAAT         CAAT repeated TGAT repeated       no repeats

                          repeated 14 21 times in     36 times in 300

                          times in     middle of CDS bases upstream of

                          frame                       CDS start

kdtA                      NTHI0772 HI0652             HS_1590            HD0454

3-deoxy-d-manno-

octulosonic-acid

transferase




                                              112
lgtF                       NTHI0773 HI0653              HS_0291           HD1201

UDP-glucose--

Lipooligosaccharide

glucosyltransferase



lpxH                       NTHI0892 HI0735              HS_0498           HD1938

UDP-2,3

diacylglucosamine

hydrolase



manB                       NTHI0899 HI0740              HS_1670           HD1507

phosphomannomutase

lex2B                      NTHI0913 top hit is HI1697 HS_0638 lob1        top hit is HD1721

UDP-glucose--              this is a   a family 25      glycosyltransferas a family 25

lipooligosaccharide        family 25   glycosyltransfera e, family 25     glycosyltransferase

glucosyltransferase        glycosyltran se

                           sferase

lic2B                      NTHI0926 HI0765              HS_0637 lob2A HD0472 lgtB is the top

glycosyltransferase lpsA                                is the top hit    hit

homolog

galU                       NTHI0976 HI0812              HS_1117           HD1431

glucosephosphate

uridylyltransferase




                                              113
lic3A2                   NTHI1034 HI0352                  no        no

CMP-neu5Ac--

lipooligosaccharide alpha CAAT       32 CAAT

2-3 sialyltransferase    repeated 18 repeats and an

                         times in    earlier start are

                         frame       317 bases

                                     upstream of the

                                     gene start. The

                                     earlier start and

                                     repeats are out of

                                     frame with the

                                     NTHI1034 gene.

rmlB/rffG                NTHI1037 HI0873                  HS_0707   HD0687

DTDP-glucose 4,6-

dehydratase

lpxD                     NTHI1082 HI0915                  HS_0978   HD1189

UDP-3-O-(3-

hydroxymyristoyl)-

glucosamine N-

acyltransferase

predicted PE--           NTHI1180 HI1005                  no        HD0371

lipooligosaccharide

phosphorylethanolamine




                                             114
transferase

lpxB                      NTHI1220 HI1060     HS_1358   HD0846

lipid-A-disaccharide

synthetase

lpxA                      NTHI1222 HI1061     HS_1359   HD1187

UDP-N-acetylglucosamine

acetyltransferase

predicted PE-             NTHI1224 HI1064     no        HD1598

lipooligosaccharide

phosphorylethanolamine

transferase

rfaF                      NTHI1272 HI1105     HS_1612   HD0653

ADP-heptose--LPS

heptosyltransferase II

rfaD                      NTHI1278 HI1114     HS_1613   HD1890

ADP-L-glycero-D-

mannoheptose-6-

epimerase

lpxC                      NTHI1312 HI1144     HS_0364   HD0816

UDP-3-0-(3-

hydroxymyristoyl) N-

acetylglucosamine

deacetylase




                                        115
lpcA/gmhA                    NTHI1350 HI1181             HS_1238       HD1228

phosphoheptose isomerase

lgtA                         NTHI1474 HI1578             no            HD0466

N-acetylglucosamine

glycosyltransferase

kdsA                         NTHI1576 HI1557             HS_0946       HD0857

2-dehydro-3-

deoxyphosphooctonate

aldolase

licD                         NTHI1594 HI1540             HS_1458       no

lipopolysaccharide choline                               HS_0727

phosphotransferase                                       fragment

licC                         NTHI1595 HI1539             HS_1459       no

CTP:phosphocholine

cytidylyltransferase

licB                         NTHI1596 HI1538             HS_1460       no

choline transporter

licA                         NTHI1597 HI1537             HS_1461       C-terminal only

phosphorylcholine kinase                                               HD1021

                             CAAT       alternative start no repeats   no repeats

                             repeated 15 and CAAT

                             times in   repeated 17

                             frame      times out of




                                               116
                                        frame prior to

                                        the gene start

htrB                      NTHI1606 HI1527                HS_0575           HD1106

lipid A biosynthesis

lauroyl acyltransferase

rfaE                      NTHI1607 HI1526                HS_0576           HD1182

ADP-heptose synthase

mrsA                      NTHI1664 HI1337                HS_0730           HD0201

Phosphomannomutase

glycosyltransferase       NTHI1750 HI0258 is top hit HS_0636 lob2D HD1090?

                                                         is top hit ~50%

                          GACA                           identity          no repeats

                          repeated 14

                          times in

                          frame

glycosyltransferase       NTHI1769 HI1386                no                HD0375 is top hit

                                                                           no repeats

                          CCAA          CCAA repeated

                          repeated 17 16 times in 300

                          times out of bases upstream

                          frame         of gene start

neuA                      NTHI1891 HI1279                HS_0706           HD0685

acylneuraminate




                                               117
cytidylyltransferase

Possible polysaccharide       NTHI1921 HI1244     no   HD1508

biosynthesis protein

lsgF                          NTHI2002 HI1695     no   HD0886

lipopolysaccharide

biosynthesis protein

lsgE                          NTHI2003 HI1696     no   HD0885

lipopolysaccharide

biosynthesis protein

lsgD                          NTHI2004 HI1697     no   HD0883

lipopolysaccharide

biosynthesis protein

lsgC                          NTHI2005 HI1698     no   no

lipopolysaccharide

biosynthesis protein,

putative



lsgB                          NTHI2006 HI1699     no   no

lipopolysaccharide

biosynthesis protein

beta-galactoside alpha-2,3-

sialyltransferase

lsgA                          NTHI2007 HI1700     no   HD0882




                                            118
lipopolysaccharide                      HI0867

biosynthesis protein

rfe/mraY/wecA                NTHI2025 HI1716            HS_0355            HD1844

undecaprenyl-phosphate

alpha-N-

acetylglucosaminyltransfer

ase



B. Genes identified in H. influenzae Rd (20) that are not included above

 Gene                      H. influenzae Rd   H. somnus 129Pt         H. ducreyi 35000HP

 kfiC                      HI0868             no                      HD0466

 beta-UDP-GlcA

 glycosyltransferase

 orfE                      HI0869             no                      no

 predicted

 glycosyltransferase

 orfO                      HI0870             no                      no

 possible

 glycosyltransferase

 orfY                      HI0871             no                      HD0466

 N-acetylneuraminic acid

 synthase-like protein

 rfbP                      HI0872             no                      no




                                              119
Genes identified in H. somnus 129Pt and H. ducreyi 35000HP

 Gene                    H. somnus 129Pt   H. ducreyi 35000HP   H. influenzae Rd

 glycosyl transferase,   HS_0116           no                   no

 group 2 family

 protein

 conserved               HS_0275           no                   no

 hypothetical protein;

 possible

 glycosyltransferase

 glmU                    HS_0333           HD1511               HI0642

 bifunctional protein:

 UDP-N-

 acetylglucosamine

 diphosphorylase;

 glucosamine-1-

 phosphate N-

 acetyltransferase

 murZ/murA               HS_1167           HD0253               HI1081

 UDP-N-

 acetylglucosamine 1-

 carboxyvinyltransfera

 se




                                           120
ftsI                     HS_0352   HD0241   HI1132

peptidoglycan

glycosyltransferase

(peptidoglycan

synthetase)

murG                     HS_0358   HD0824   HI1138

undecaprenyldiphosp

ho-

muramoylpentapeptid

e beta-N-

acetylglucosaminyltra

nsferase

malQ                     HS_0890   no       HI1356

4-alpha-

glucanotransferase

conserved                no        HD0375   no

hypothetical protein

(probable

glycosyltransferase)

lbgB                     no        HD1720   no

D-glycero-D-manno-

heptosyl

transferase/alpha-1,6-




                                   121
DD-

heptosyltransferase

lob1                    HS_0638            HD1721            no

                        36 CAAT repeats    no CAAT repeats

                        just after start

lob2A                   HS_0637            HD0472 lgtB       HI0550 lic2A

20 GA repeats in last   no more than 2                       22 CAAT repeats in the

third of the CDS        GA repeats in a                      first third of the CDS

(strain 738)            row

lob2B                   no                 HD0472 lgtB       no

                                           no GA repeats

lob2C                   HS_0636a           HD0466 lgtA       HI1578

lob2D                   HS_0636            HD1090            HI0258

                        29 CAGT repeats                      22 ACAG repeats just

                        in the middle of                     after the start

                        the CDS




                                           122
Table S11. Secretion systems, pili and adhesins

A. Secretion systems

1. General secretory (Sec) pathway for translocation of proteins across the inner membrane into

the periplasm

 Gene                          H. somnus 129Pt         H. ducreyi 35000HP   H. influenzae Rd

 Sec translocase

 secD                          HS_1313                 HD1752               HI0240

 secE                          HS_0194                 HD1886               HI0716

 secF                          HS_1312                 HD1753               HI0239

 secG                          HS_1311                 HD1277               HI0445

 secA                          HS_0990                 HD1788               HI0909

 secB                          HS_0156                 HD0661               HI0743

 yajC                          HS_1314                 HD1751               HI0241

 secY(prlA)                    HS_0080                 HD1957               HI0798

 Catalyze protein folding in

 periplasm

 dsbA                          HS_0308                 HD0638               HI0846

 thiol:disulfide interchange

 protein

 dsbA-like protein             HS_0624                 HD1729               HI0428

 dsbC                          HS_1475                 HD1340               HI1213

 thiol:disulfide interchange




                                                 123
 protein

 Signal peptidases

 lepB signal peptidase I   HS_1241                 HD1607                  HI0015

 lspA lipoprotein signal   HS_0185                 HD0063                  HI1006

 peptidase



2. Mechanisms for transport across the outer membrane – terminal branches of the general

secretory pathway

Gene                       H. somnus 129Pt         H. ducreyi 35000HP     H. influenzae Rd

Autotransporters

H. influenzae igA1         no                      no                     HI0990

protease

S. flexneri                no                      no                     no

icsA/virG

tsh                        no                      no                     no

possible large adhesin*    HS_0209                 no                     no

possible large adhesin*    HS_0383                 no                     no

possible large adhesin*    HS_0478                 no                     no

possible adhesin           HS_0589                 no                     no

possible adhesin           HS_0602                 no                     no

possible large adhesin*    HS_0790                 no                     no

possible large adhesin*    HS_1058                 no                     no

possible large adhesin*    HS_1085                 no                     no




                                             124
possible large adhesin*      HS_1154         no                no

possible large adhesin*      HS_1234         no                no

possible large adhesin*      HS_1616         no                no

possible large adhesin*      HS_1632         No                HI1718

Hia                          no              no                no

Hsf                          no              no                no

DsrA                         HS_1543         HD0769            no

NcaA                         no              HD1920            no

Chaperone/usher pathway

pap genes (E. coli)

involved in the biogenesis

of P pili



papC                         no              HD0283            no

                                             41% aa identity

papA                         no              HD0281            no

                                             32% aa identity

papD                         no              HD0284            no

                                             52% aa identity

papE                         no              no                no

Type II secretion

pulC                         no              no                no

pulD                         no              no                no




                                       125
pulE                       no         no   no

pulF                       no         no   no

pulG                       no         no   no

pulH                       no         no   no

pulI                       no         no   no

pulJ                       no         no   no

pulK                       no         no   no

pulL                       no         no   no

pulM                       no         no   no

pulN                       no         no   no

pulO                       no         no   no

Type III secretion

LcrD family proteins

lcrD (Y. enterocolitica)   no         no   no

invA (S. typhimurium)      no         no   no

mxiA (virH) (Shigella      no         no   no

sonnei)

sepA (E.coli)              no         no   no

hrcV (Erwinia              no         no   no

amylovora)

flhA (E.coli K-12)         no         no   no

Bordetella bpeI system

bscI                       no         no   no




                                126
bscJ                       no         no   no

bscK                       no         no   no

bscL                       no         no   no

bscN                       no         no   no

bscO                       no         no   no

Yersinia type III system

yscC                       no         no   no

yscD                       no         no   no

yscF                       no         no   no

yscG                       no         no   no

yscH                       no         no   no

yscI                       no         no   no

yscJ                       no         no   no

yscK                       no         no   no

yscL                       no         no   no

yscM                       no         no   no

yscN                       no         no   no

yscO                       no         no   no

Shigella type III system

ipaA                       no         no   no

ipaD                       no         no   no

ipaC                       no         no   no

ipaB                       no         no   no




                                127
Salmonella type III

system



leucine rich repeat        no         no   no

secreted by SPI-1

secreted effector protein no          no   no

secreted by SPI-2

secreted effector protein no          no   no

secreted by SPI-1

invG                       no         no   no

prgH                       no         no   no

prgK                       no         no   no

prgI                       no         no   no

prgJ                       no         no   no

E. coli type III system



sepZ                       no         no   no

Type IV secretion

Agrobacterium
tumefaciens vir system
virA                       no         no   no

sensor kinase

virB1                      no         no   no

type IV secretion system




                                128
apparatus lytic

transglycosylase

virB2                      no         no   no

prepropilin

virB3                      no         no   no

type IV secretion system

apparatus component

virB4                      no         no   no

type IV secretion sytem

apparatus ATPase

virB5                      no         no   no

type IV secretion system

apparatus component

virB6                      no         no   no

type IV secretion system

apparatus component

virB7                      no         no   no

type IV secretion system

apparatus outer

membrane lipoprotein

precursor

virB8                      no         no   no

type IV secretion system




                                129
 apparatus component

 virB9                       no                      no                    no

 type IV secretion system

 apparatus outer

 membrane protein

 virB10                      no                      no                    no

 type IV secretion

 apparatus inner

 membrane protein

 virB11                      no                      no                    no

 type IV secretion

 apparatus ATPase

*has autotransporter Hia-like and YadA-like domains at C-terminal



B. Pili

Gene                         H. somnus 129Pt          H. ducreyi 35000HP   H. influenzae Rd

Possible competence, pili,

secretion system genes in

H. somnus 129Pt

Competence

comA                         HS_1109                  HD0427               HI0439

competence protein A

comB                         HS_1110                  no                   HI0438




                                               130
competence protein B

comC                         HS_1111         HD0432   HI0437

competence protein C

comD                         no              no       HI0436

competence protein D

comE                         HS_1112         HD0434   HI0435

competence protein E

Type 4 pili

pilA                         HS_0250         HD1123   HI0299

pilin

pilB                         HS_1430         HD1124   HI0298

nucleotide binding protein

pilC                         HS_0457         HD1125   HI0297

inner membrane protein

pilD                         HS_0458         HD1126   HI0296

prepilin peptidase and

methylase

pilM                         no              no       no

domains in common with

cell division protein FtsA

and rod-shape-determining

protein MreB

pilN                         no              no       no




                                       131
cytoplasmic membrane

protein

pilO                          no         no   no

cytoplasmic membrane

protein

pilP                          no         no   no

possible lipoprotein

pilQ outer membrane           no         no   no

protein

secretin – pilus extrudes

through this

pilT                          no         no   no

motor required for motility

minor pilin-like proteins

pilE                          no         no   no

pilV                          no         no   no

pilW                          no         no   no

pilX                          no         no   no

fimT (not essential)          no         no   no

fimU                          no         no   no

H. influenzae type b pilus

hifA                          no         no   no

hifY3                         no         no   no




                                   132
hifY1                     no                      no                      no

hifY2                     no                      no                      no

hifB                      no                      no                      no

hifC                      no                      no                      no

hifD                      no                      no                      no

hifE                      no                      no                      no

E. coli type 1 pilus

fimA                      no                      HD0281                  no

                                                  38% aa identity

fimB                      no                      no                      no

fimH                      no                      no                      no

fimC                      no                      HD0284                  no

                                                  32% aa identity

fimD                      no                      HD0283                  no

                                                  28% aa identity




C. Adheins and outer membrane proteins

 Gene                          H. somnus 129Pt    H. ducreyi 35000HP H. influenzae Rd

 H. somnus autotransporters

 possible large adhesin        HS_0209            no                 no




                                            133
possible large adhesin    HS_0383         no                    no

possible large adhesin    HS_0478         no                    no

possible large adhesin    HS_0589         no                    no

possible large adhesin    HS_0602         no                    no

possible large adhesin    HS_0790         no                    no

possible large adhesin    HS_1058         no                    no

possible large adhesin    HS_1085         no                    no

possible large adhesin    HS_1154         no                    no

possible large adhesin    HS_1234         no                    no

Autotransporter adhesin   HS_1543         no                    no

possible large adhesin    HS_1616         no                    no

possible large adhesin    HS_1632         no                    HI1718

periplasmic zinc          HS_1256         HD0198                HI0119

transporter/adhesin B

precursor

                          no              HD0281                no

                                          major pilin protein

                                          precursor/adhesin B

                                          precursor

H. influenzae adhesins

hmw1A                     no              no                    no

HMW1




                                    134
hmw2A                         no              no       no

HMW2

hia                           no              no       no

hsf                           no              no       no

hap                           no              no       no

H. ducreyi autotransporters

dsrA                          HS_1543         HD0769   no




ncaA                          no              HD1920   no

Outer membrane proteins

oapA                          HS_1287         HD0651   HI0330

oapB                          no              HD0652   HI0331

P2                            no              HD1433   HI0139

                                              HD1435

P1                            HS_1548         HD1078   HI0401

P4                            no              HD1170   HI0693

P5                            HS_1035         HD0045   HI1164

                                              HD0046

P6                            HS_0263         HD1772   HI0381




                                        135
Table S12. Genes for iron transport and utilization

 Gene                                H. somnus 129Pt H. ducreyi 35000HP H. influenzae Rd

 TonB system

 tonB                                HS_0689          HD0327             HI0251



 exbD                                HS_0690          HD0328             HI0252

 exbB                                HS_0691          HD0329             HI0253

 Fe-S cluster metabolism

 cyaY                                HS_1712          HD0473             HI0727.1

                                     N-terminal                          N-terminal

 Fur

 fur                                 HS_1211          HD0367             HI0190

 ferric uptake regulation protein

 Heme biosynthesis

 gltX                                HS_0456          HD0320             HI0274

 glutamyl-tRNA synthetase

 hemA                                HS_0810          no                 no

 glutamyl-tRNA reductase

 hemB                                HS_0548          no                 no

 5-aminolevulinate dehydratase

 (porphobilinogen

 synthase)




                                               136
hemC                              HS_0044     no       no

hydroxymethylbilane synthase

(porphobilinogen deaminase)

hemD                              HS_0045     HD1742   no

uroporphyrinogen-III synthase



hemE                              HS_1540     no       no

uroporphyrinogen decarboxylase

hemF                              no          no       no

coproporphyrinogen III oxidase

hemG                              HS_1569     no       no

protoporphyrin flavoprotein

oxidase

hemH                              HS_1047     no       HI1160

ferrochelatase

hemL                              HS_1229     no       no

glutamate-1-semialdehyde

aminotransferase

hemM (lolB)                       HS_0998     HD1629   HI1607

outer membrane lipoprotein LolB

precursor

hemN                              HS_0472     HD1668   HI0463

coproporphyrinogen oxidase,




                                        137
oxygen-independent                                      HD0037

(coproporphyrinogen-III oxidase)                        this one may be a

                                                        paralog

hemR                                HS_0728             HD0388              HI0113

hemin receptor, outer membrane

protein

hemX                                HS_0046             HD1741              HI0603

uroporphyrin-III C-

methyltransferase

hemY                                HS_0047             HD1740              HI0602

porphyrin biosynthesis protein

cyoE                                no                  no                  no

protohaeme IX farnesyltransferase

cysG                                no                  no                  no

siroheme synthase

aroB                                HS_1114             HD0422              HI0208

3-dehydroquinate synthase

Transferrin binding proteins

tbpA                                HS_0097*            no                  HI0994

transferrin-binding protein A       C-terminal region

                                    HS_0098*            no

                                    central fragment

                                    HS_0102*            no




                                             138
                                 N-terminal region

tbpB                             HS_0448             no       HI0995

transferrin-binding protein B

tbpA                             HS_0449             no       HI0994

transferrin-binding protein A

tbpA                             HS_0582             no       HI0994

transferrin binding protein A



transferrin-binding protein,     no                  no       HI1217

putative

Iron-regulated proteins

iron-regulated outer membrane    HS_0069             no       no

protein

iron-regulated outer membrane    HS_1306             no       no

protein

Heme utilization proteins

heme utilization protein hugZ    HS_0722             HD0620   no

heme utilization protein         HS_0723             no       no

tdhA                             no                  HD0388   no

TonB-dependent heme receptor A

hxuC                             no                  no       HI0262

heme-hemopexin utilization

protein C




                                         139
hxuB                          no               no           HI0263

heme-hemopexin utilization

protein B

hxuA                          no               no           HI0264

heme-hemopexin utilization

protein A

Hemoglobin binding proteins

hgbB                          no               no           HI0635

                                                            20 CAAC repeats

hgbA                          HS_0721 N-       HD2025       HI0661

                              terminal         no repeats   20 CAAC repeats

                              HS_0720 C-                    near beginning of

                              terminal                      gene

                              no repeats



hgbB                          no               no           HI0712

                                                            36 CAAC repeats

                                                            near beginning of

                                                            gene

hemoglobin binding protein    no               no           HI1565

                                                            18 CAAC repeats

                                                            near beginning of

                                                            gene




                                         140
TonB-dependent receptor, putative no              no        HI1567



Iron transporters                15 total         9 total   17 total

Chelated iron ABC

yfeD                             HS_0325          HD1024    HI0359

yfeC                             HS_0326          HD1025    HI0360

yfeB                             HS_0327          HD1817    HI0361

yfeA                             HS_0328          HD1816    HI0362

Heme ABC

ccmA                             HS_0393          HD0786    HI1089

ccmB                             HS_0394          HD0787    HI1090

ccmC                             HS_0395          HD0789    HI1091

ccmD                             HS_0396          HD0790    HI1092

                                                  HD0215    HI0853

Fe3+ /Iron III ABC

afuC                             HS_0639          no        HI0126

afuB                             HS_0640          no        HI0129

afuA                             HS_0641          no        HI0131

afuA                             HS_0643          no        no



hitA/fbpA                        HS_0783          no        HI0097

hitB/fbpB                        HS_0782          no        HI0098

hitC/fbpC                        HS_0781          no        HI0099




                                            141
                                    no                no                   HI1470

                                    no                no                   HI1471

                                    no                no                   HI1472



* These fragments represent the H. somnus 129Pt counterpart of tbpA2 from H. somnus strain

649 and tbpA from H. ovis.




                                             142
Table S13. Genes involved in DNA uptake and transformation

  Gene                 H. somnus 129Pt    H. ducreyi 35000HP H. influenzae Rd

  comA (comEC)         HS_1109            HD0427              HI0439

  comB                 HS_1110            HD0432              HI0438

  comC                 HS_1111            no                  HI0437

  comD                 no                 no                  HI0436

  comE                 HS_1112            HD0434              HI0435

  comF                 HS_1490            HD0209              HI0434

  comG                 HS_1491            HD0378              HI0433

  comJ                 HS_1107            HD1760              HI0441

  comL                 HS_0366            HD0470              HI0177

  tpc                  no                 no                  no

  N. gonorrhoeae

  tfoX(sxy)            HS_1715            HD1985              HI0601

  crp                  HS_0139            HD0738              HI0957

  pilF2 involved in    HS_1197            HD0318              HI0366

  uptake but not

  binding of DNA

  pulJ involved in     HS_0278            HD0440              HI0937

  DNA binding

  and uptake --

  related to type II




                                           143
secretion system

pulG related to     HS_0264   HD0182   HI0938

type II secretion

system

pilA                HS_0250   HD1123   HI0299

pilB                HS_1430   HD1124   HI0298

pilC                HS_0457   HD1125   HI0297

pilD                HS_0458   HD1126   HI0296

pilE pilin          no        no       no




                              144
Table S14. Hemolysins and toxins

 Gene                             H. somnus 129Pt H. ducreyi 35000HP H. influenzae Rd

 Hemolysins

 possible hemolysin               HS_0237          HD1145             HI0301

 possible hemolysin               HS_0737          HD0800             HI1658

 bi-functional hemolysin (N-      HS_0842          no                 no

 terminal) and outer membrane

 protein A homolog (C-terminal)

 hhdB                             no               HD1326             no

 hhdA                             no               HD1327             no

 possible hemolysin               HS_1429          HD0770             HI0107

 hemolysin accessory protein      no               HD1155             no

 Cytotoxins

 cdtA                             no               HD0902             no

 cytolethal distending toxin A

 cdtB                             no               HD0903             no

 cytolethal distending toxin B

 cdtC                             no               HD0904             no

 cytolethal distending toxin C

 RTX toxins

 RTX toxins and related Ca2+-     no               no                 no

 binding proteins




                                             145
ZP_00132930

RTX toxins and related Ca2+-    no         no   no

binding proteins

ZP_00132933.2

AAG40310.1|AF314526_1           no         no   no

leukotoxin [Pasteurella

trehalosi]

CAC80494.1| pore-forming        no         no   no

RTX-Toxin; EHEC-hemolysin

[Escherichia coli]

CAA60041.1| EHEC-hlyC           no         no   no

[Escherichia coli]

P15377|RT2A_ACTPL RTX-II no                no   no

toxin determinant A (APX-IIA)

(Hemolysin IIA) (HLY-IIA)

(Cytolysin IIA) (CLY-IIA)




                                     146
Table S15. Restriction-modification system genes

 Gene         H.         Flanked by     Near DNA    H. ducreyi   H. influenzae Rd

              somnus     mobile         uptake      35000HP

              129Pt      element?       sequence?

 Type I

 hsdS         HS_0556 yes HS_0555       yes         no           no

 hsdR         HS_0559 see above         yes         no           HI1285

 hsdS         HS_0560 see above         yes         no           no

 hsdM         no         NA             NA          no           HI0215

                                                                 contains a

                                                                 frameshift

 hsdS         no         NA             NA          no           HI0216

 hsdR         no         NA             NA          no           HI0218

                                                                 contains

                                                                 frameshift

 hsdS         no         NA             NA          no           HI1286

 hsdM         no         NA             NA                       HI1287

 possible     no         NA             NA          HD0914       no

 type I

 methyltran

 sferase

 protein




                                              147
Type II

hindIIR       no   NA   NA         no       HI0512

hindIIM       no   NA   NA         no       HI0513

type II       no   NA   NA         no       HI1040

restriction

enzyme,

putative

hindVM        no   NA   NA         no       HI1041



hindIIIM      no   NA   NA         no       HI1392

hindIIIR      no   NA   NA         no       HI1393

Type III

type III      no   NA   NA         HD1690   no

restriction

-

modificati

on system

enzyme

type III      no   NA   NA         HD1691   no

restriction

-

modificati

on system




                             148
methyltran

sferase,

subunit

type III       no         NA          NA          HD1692   HI1056

restriction/                                      HD1693

modificati

on system

modificati

on

methylase

Other

possible       HS_1780 yes HS_0001    yes         HD0917   no

antirestrict              phage

ion                       integrase

enzyme

bcgIA          HS_0430 yes HS_0424    no          HD0293   no

                          phage

                          integrase

bcgIB          HS_0431 see above      no          HD0294   no

bcgIB          HS_0432 see above      no          no       no

               C-

               terminal

possible       HS_0010 yes HS_0001    yes         HD1795   HI0305




                                            149
endonucle

ase

involved

in

recombina

tion




            150
Table S16. Putative exopolysaccharide biosynthesis genes

 Gene                   H. somnus 129Pt     H. ducreyi 35000HP   H. influenzae Rd

 mrsA/glmM              HS_0730             HD0201               HI1463

 phosphoglucomutase/                                             HI1337

 phosphomannomutase

 (PGM)

 galU                   HS_1117             HD1431               HI0812

 UDP-glucose

 pyrophosphorylase

 (UGP)

 galE                   HS_0789             HD0829               HI0351

 UDP-glucose

 epimerase (UGE)

 pgi                    HS_0938             HD0418               HI1576

 Glucose-6-phosphate

 isomerase (PGI)

 manA                   HS_0605             HD0765               HI1710 N-terminal

 phosphomannose                                                  fragment

 isomerase (PMI)

 manB                   HS_1670             HD1507               HI0740

 phosphomannomutase

 (PMM)




                                             151
manB                 HS_1118   no    no

phosphomannomutase

(PMM)

manC                 no        no    no

GDP-D-mannose-

pyrophosphorylase

(GMP)




                               152

				
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