Table S10.- Downregulated genes in the ron1-1 microarray encoding chloroplast-targeted proteins
Fold change in
ron1-1
AGI code microarray
At4g08790 0.87
At2g37920 0.82
At5g14320 0.79
At4g02770 0.78
At5g08415 0.77
At4g26900 0.77
At1g62780 0.76
At5g48730 0.75
At1g23360 0.75
At2g43630 0.75
At3g24430 0.74
At1g75350 0.73
At5g19750 0.73
At5g27390 0.71
At3g28460 0.70
At1g59990 0.70
At2g39080 0.69
At4g17260 0.69
At2g42220 0.68
At2g17972 0.67
At1g67280 0.67
At1g32550 0.66
At5g64580 0.65
At3g60210 0.65
At5g08610 0.65
At3g52150 0.65
At1g03475 0.64
At1g10910 0.64
At5g16710 0.64
At4g30825 0.63
At5g05480 0.63
At3g03710 0.63
At5g07900 0.63
At2g24060 0.62
At2g48120 0.62
At1g70070 0.62
At3g26900 0.61
At4g33350 0.61
At3g54090 0.60
At5g51100 0.59
At3g04260 0.59
At4g24750 0.59
At5g58250 0.59
At3g24506 0.58
At2g44760 0.58
At3g52155 0.58
At2g24120 0.58
At3g24590 0.57
At5g04900 0.56
At4g20120 0.56
At5g66090 0.56
At2g34640 0.55
At1g31410 0.55
At1g74640 0.54
At3g20930 0.53
At2g04530 0.53
At1g31160 0.53
At3g17170 0.51
At5g66470 0.51
At1g51110 0.51
At4g10750 0.51
At5g10160 0.50
At1g10522 0.49
At3g20440 0.49
At3g59980 0.49
At5g24490 0.49
At5g04360 0.48
At5g64816 0.48
At1g22590 0.47
At3g05800 0.47
At3g14900 0.47
At2g02740 0.46
At2g31840 0.46
At3g09580 0.45
At3g28760 0.45
At1g70820 0.45
At5g10390 0.44
At5g58260 0.43
At2g36390 0.43
At5g26570 0.42
At1g67660 0.42
At1g54570 0.41
At3g04550 0.41
At1g24610 0.40
At5g64860 0.38
At3g56330 0.37
At1g10760 0.36
At1g05385 0.36
At1g66520 0.35
At2g47840 0.34
At2g30930 0.33
At5g15530 0.30
At3g26740 0.29
At1g04620 0.27
At5g06690 0.14
At4g04330 0.11
Bold highlighted genes contain the "evening element" in their promoter.
Downregulated genes in the ron1-1 microarray encoding chloroplast-targeted proteins
Description
nitrilase, putative
EMB1513__EMB1513 (EMBRYO DEFECTIVE 1513); copper ion transmembrane transporter
30S ribosomal protein S13, chloroplast (CS13)
PSAD-1__PSAD-1 (photosystem I subunit D-1)
lipoic acid synthase family protein
AT-HF_HISHF_HISN4__AT-HF (ARABIDOPSIS THALIANA HISF PROTEIN)
similar to hypothetical protein [Vitis vinifera] (GB:CAN83165.1)
pentatricopeptide (PPR) repeat-containing protein
UbiE/COQ5 methyltransferase family protein
similar to glycine-rich protein [Arabidopsis thaliana] (TAIR:AT3G59640.2); similar to glycine-rich protein [Arabidopsis
HCF101__HCF101 (HIGH-CHLOROPHYLL-FLUORESCENCE 101); ATP binding
EMB2184__EMB2184 (EMBRYO DEFECTIVE 2184); structural constituent of ribosome
peroxisomal membrane 22 kDa family protein
expressed protein
similar to hypothetical protein [Vitis vinifera] (GB:CAN74970.1); contains InterPro domain Protein of unknown function
DEAD/DEAH box helicase, putative (RH22)
binding / catalytic
L-lactate dehydrogenase, putative
rhodanese-like domain-containing protein
similar to unnamed protein product [Vitis vinifera] (GB:CAO48225.1)
lactoylglutathione lyase, putative / glyoxalase I, putative
ferredoxin family protein
AAA-type ATPase family protein
chloroplast chaperonin 10, putative
DEAD box RNA helicase (RH26)
RNA recognition motif (RRM)-containing protein
ATCPO-I_HEMF1_LIN2__LIN2 (LESION INITIATION 2); coproporphyrinogen oxidase
similar to PTAC2 (PLASTID TRANSCRIPTIONALLY ACTIVE2) [Arabidopsis thaliana] (TAIR:AT1G74850.1); similar
DHAR3__DHAR3 (DEHYDROASCORBATE REDUCTASE 1); glutathione dehydrogenase (ascorbate)
pentatricopeptide (PPR) repeat-containing protein
similar to unknown protein [Arabidopsis thaliana] (TAIR:AT3G14920.1); similar to hypothetical protein [Vitis vinifera]
RIF10__RIF10 (RESISTANT TO INHIBITION WITH FSM 10); 3'-5'-exoribonuclease/ RNA binding / nucleic acid
mitochondrial transcription termination factor family protein / mTERF family protein
translation initiation factor 3 (IF-3) family protein
PAC__PAC (PALE CRESS)
PDE317_EMB25_ISE2__EMB25 (EMBRYO DEFECTIVE 25); ATP-dependent helicase/ RNA helicase
shikimate kinase family protein
chloroplast inner membrane import protein Tic22, putative
pfkB-type carbohydrate kinase family protein
FSD2__FSD2 (FE SUPEROXIDE DISMUTASE 2); iron superoxide dismutase
PTAC3__PTAC3 (PLASTID TRANSCRIPTIONALLY ACTIVE3); DNA binding
similar to rhodanese-like domain-containing protein [Arabidopsis thaliana] (TAIR:AT3G08920.1); similar to unnamed
similar to hypothetical protein [Vitis vinifera] (GB:CAN75840.1); contains domain PD020337 (PD020337)
similar to unknown protein [Arabidopsis thaliana] (TAIR:AT2G17240.1); similar to unknown [Populus trichocarpa]
similar to unnamed protein product [Vitis vinifera] (GB:CAO70515.1)
similar to hypothetical protein OsJ_027559 [Oryza sativa (japonica cultivar-group)] (GB:EAZ44076.1); contains
PDE319_SCA3__PDE319/SCA3 (SCABRA 3); DNA binding / DNA-directed RNA polymerase
signal peptidase I family protein
short-chain dehydrogenase/reductase (SDR) family protein
ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase-related
similar to unnamed protein product [Vitis vinifera] (GB:CAO23263.1); contains domain Adenine nucleotide alpha
PTAC12__PTAC12 (PLASTID TRANSCRIPTIONALLY ACTIVE12)
putrescine-binding periplasmic protein-related
similar to unnamed protein product [Vitis vinifera] (GB:CAO64553.1); contains domain SSF53474 (SSF53474);
RNA recognition motif (RRM)-containing protein
CPZ__CPZ
zinc-binding protein, putative / protein kinase C inhibitor, putative
RFC3__RFC3 (REGULATOR OF FATTY-ACID COMPOSITION 3); structural constituent of ribosome
GTP binding / RNA binding
plastid-lipid associated protein PAP / fibrillin family protein
HpcH/HpaI aldolase family protein
beta-hydroxyacyl-ACP dehydratase, putative
similar to unnamed protein product [Vitis vinifera] (GB:CAO40945.1)
BE1_EMB2729__BE1/EMB2729 (BRANCHING ENZYME 1); alpha-amylase
tRNA-binding region domain-containing protein
30S ribosomal protein, putative
ATPU1__ATLDA/ATPU1 (PULLULANASE 1); alpha-amylase/ limit dextrinase
Identical to Uncharacterized protein At5g64816 precursor [Arabidopsis Thaliana] (GB:Q8L8Q8;GB:Q9LV96); similar
AGL87__AGL87
transcription factor
similar to unnamed protein product [Vitis vinifera] (GB:CAO39402.1); contains domain PTHR12839 (PTHR12839)
ATWHY3_PTAC11__ATWHY3/PTAC11 (A. THALIANA WHIRLY 3)
similar to unknown protein [Arabidopsis thaliana] (TAIR:AT4G28590.1); similar to hypothetical protein [Vitis vinifera]
amine oxidase family protein
similar to unnamed protein product [Vitis vinifera] (GB:CAO14940.1); contains InterPro domain 3-dehydroquinate
phosphoglucomutase, putative / glucose phosphomutase, putative
histone H3
Encodes subunit NDH-N of NAD(P)H:plastoquinone dehydrogenase complex (Ndh complex) present in the thylakoid
BE3_SBE2.1__SBE2.1 (STARCH BRANCHING ENZYME 2.1); 1,4-alpha-glucan branching enzyme
ATGWD3_PWD_ATGWD3_OK1__PWD (PHOSPHOGLUCAN WATER DIKINASE)
DNA binding / magnesium ion binding / nuclease
esterase/lipase/thioesterase family protein
similar to unknown protein [Arabidopsis thaliana] (TAIR:AT5G28500.1); similar to unnamed protein product [Vitis
SET domain-containing protein
DPE1__DPE1 (DISPROPORTIONATING ENZYME); 4-alpha-glucanotransferase
N2,N2-dimethylguanosine tRNA methyltransferase family protein
SEX1_GWD_SOP__SEX1 (STARCH EXCESS 1)
photosystem II 11 kDa protein-related
PDE194__PDE194 (PIGMENT DEFECTIVE 194); formyltetrahydrofolate deformylase/ hydroxymethyl-, formyl- and
tic20 protein-related
similar to unknown protein [Arabidopsis thaliana] (TAIR:AT1G06540.1)
BCCP2_CAC1-B_BCCP2__BCCP2 (biotin carboxyl carrier protein 2); biotin binding
CCL__CCL (CCR-LIKE)
coenzyme F420 hydrogenase family / dehydrogenase, beta subunit family
(THIOREDOXIN-LIKE 5); thiol-disulfide exchange intermediate
similar to unnamed protein product [Vitis vinifera] (GB:CAO69665.1)
hted genes contain the "evening element" in their promoter.
255118_at
266091_at
250190_at
255457_at
246005_at
253921_at
262693_at
248669_at
263044_at
260586_at
257168_at
261119_at
245937_at
257903_at
263679_at
266192_at 266193_at
245324_at
267635_at
265819_at
264970_at
256468_at
247235_at
251425_at
250529_at
252032_at
264820_at
260465_at
246454_at
253589_at
250784_at
259344_at
250554_at
266575_at
262316_at
264748_at
258281_at
253381_at
251935_at
248493_at
258573_at
254117_at
247862_at
258135_at
266874_at
252039_at
265991_at
258128_at
250812_at
247139_at
266957_at
256483_at
260232_at
256805_at
263864_at
263701_at
257891_at
247098_at
245744_at 245745_at
254937_at
250470_at
263209_at
257667_at
251442_at
249742_at
245712_at
247258_at
261942_at
258742_at
257207_at
267474_at
263488_at
258708_at
256585_at
262309_at
250434_at
247816_at
263912_at
246829_at
245188_at
264186_at
258800_at
265021_at
247216_at
251730_at
262784_at
261388_at
256361_at
266463_at
267209_at
246565_at
257832_at
264597_at
250649_at
255331_at
nitrilase,
putative
EMB1513__
EMB1513
30S
ribosomal
PSAD-
1__PSAD-1
lipoic acid
synthase
AT-
HF_HISHF_
similar to
hypothetical
protein [Vitis
vinifera]
(GB:CAN83165.
1)
pentatricopeptide
(PPR) repeat-
containing
protein
UbiE/COQ5
methyltransferas
e family protein
similar to glycine-
rich protein
[Arabidopsis
thaliana]
(TAIR:AT3G596
40.2); similar to
glycine-rich
protein
[Arabidopsis
thaliana]
(TAIR:AT3G596
40.1); similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO46269.
1)
HCF101__HCF1
01 (HIGH-
CHLOROPHYLL-
FLUORESCENC
E 101); ATP
binding
EMB2184__EMB
2184 (EMBRYO
DEFECTIVE
2184); structural
constituent of
ribosome
peroxisomal
membrane 22
kDa family
protein
similar to
hypothetical
protein [Vitis
vinifera]
(GB:CAN74970.
1); contains
InterPro domain
Protein of
unknown
function
methylase
putative
(InterPro:IPR016
065)
DEAD/DEAH
box helicase,
putative (RH22)
binding / catalytic
L-lactate
dehydrogenase,
putative
rhodanese-like
domain-
containing
protein
similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO48225.
1)
lactoylglutathion
e lyase, putative
/ glyoxalase I,
putative
ferredoxin family
protein
AAA-type
ATPase family
protein
chloroplast
chaperonin 10,
putative
DEAD box RNA
helicase (RH26)
RNA recognition
motif (RRM)-
containing
protein
ATCPO-
I_HEMF1_LIN2_
_LIN2 (LESION
INITIATION 2);
coproporphyrino
gen oxidase
similar to PTAC2
(PLASTID
TRANSCRIPTIO
NALLY
ACTIVE2)
[Arabidopsis
thaliana]
(TAIR:AT1G748
50.1); similar to
hypothetical
protein
OsI_002384
[Oryza sativa
(indica cultivar-
group)]
(GB:EAY74537.1
); similar to
putative PPR
protein [Oryza
sativa (japonica
cultivar-group)]
(GB:BAD87953.
1); similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO24702.
1); contains
InterPro domain
Pentatricopeptid
e repeat
(InterPro:IPR002
885)
DHAR3__DHAR
3
(DEHYDROASC
ORBATE
REDUCTASE 1);
glutathione
dehydrogenase
(ascorbate)
pentatricopeptide
(PPR) repeat-
containing
protein
similar to
unknown protein
[Arabidopsis
thaliana]
(TAIR:AT3G149
20.1); similar to
hypothetical
protein [Vitis
vinifera]
(GB:CAN73340.
1)
RIF10__RIF10
(RESISTANT TO
INHIBITION
WITH FSM 10);
3'-5'-
exoribonuclease/
RNA binding /
nucleic acid
binding
mitochondrial
transcription
termination
factor family
protein / mTERF
family protein
translation
initiation factor 3
(IF-3) family
protein
PAC__PAC
(PALE CRESS)
PDE317_EMB25
_ISE2__EMB25
(EMBRYO
DEFECTIVE 25);
ATP-dependent
helicase/ RNA
helicase
shikimate kinase
family protein
chloroplast inner
membrane
import protein
Tic22, putative
pfkB-type
carbohydrate
kinase family
protein
FSD2__FSD2
(FE
SUPEROXIDE
DISMUTASE 2);
iron superoxide
dismutase
PTAC3__PTAC3
(PLASTID
TRANSCRIPTIO
NALLY
ACTIVE3); DNA
binding
similar to
rhodanese-like
domain-
containing
protein
[Arabidopsis
thaliana]
(TAIR:AT3G089
20.1); similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO64218.
1); contains
InterPro domain
Rhodanese-like
(InterPro:IPR001
763)
similar to
hypothetical
protein [Vitis
vinifera]
(GB:CAN75840.
1); contains
domain
PD020337
(PD020337)
similar to
unknown protein
[Arabidopsis
thaliana]
(TAIR:AT2G172
40.1); similar to
unknown
[Populus
trichocarpa]
(GB:ABK93895.1
)
similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO70515.
1)
similar to
hypothetical
protein
OsJ_027559
[Oryza sativa
(japonica cultivar-
group)]
(GB:EAZ44076.1
); contains
InterPro domain
Phosphoglycerat
e mutase
(InterPro:IPR013
078)
PDE319_SCA3_
_PDE319/SCA3
(SCABRA 3);
DNA binding /
DNA-directed
RNA polymerase
signal peptidase
I family protein
short-chain
dehydrogenase/r
eductase (SDR)
family protein
similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO23263.
1); contains
domain Adenine
nucleotide alpha
hydrolases-like
(SSF52402)
PTAC12__PTAC
12 (PLASTID
TRANSCRIPTIO
NALLY
ACTIVE12)
putrescine-
binding
periplasmic
protein-related
similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO64553.
1); contains
domain
SSF53474
(SSF53474);
contains domain
G3DSA:3.40.50.
1820
(G3DSA:3.40.50.
1820)
RNA recognition
motif (RRM)-
containing
protein
CPZ__CPZ
zinc-binding
protein, putative /
protein kinase C
inhibitor, putative
RFC3__RFC3
(REGULATOR
OF FATTY-ACID
COMPOSITION
3); structural
constituent of
ribosome
GTP binding /
RNA binding
plastid-lipid
associated
protein PAP /
fibrillin family
protein
HpcH/HpaI
aldolase family
protein
beta-hydroxyacyl-
ACP
dehydratase,
putative
similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO40945.
1)
BE1_EMB2729_
_BE1/EMB2729
(BRANCHING
ENZYME 1);
alpha-amylase
tRNA-binding
region domain-
containing
protein
30S ribosomal
protein, putative
ATPU1__ATLDA
/ATPU1
(PULLULANASE
1); alpha-
amylase/ limit
dextrinase
Identical to
Uncharacterized
protein
At5g64816
precursor
[Arabidopsis
Thaliana]
(GB:Q8L8Q8;GB
:Q9LV96);
similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO22147.
1)
AGL87__AGL87
transcription
factor
similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO39402.
1); contains
domain
PTHR12839
(PTHR12839)
ATWHY3_PTAC
11__ATWHY3/P
TAC11 (A.
THALIANA
WHIRLY 3)
similar to
unknown protein
[Arabidopsis
thaliana]
(TAIR:AT4G285
90.1); similar to
hypothetical
protein [Vitis
vinifera]
(GB:CAN75809.
1); contains
InterPro domain
Thioredoxin-like
fold
(InterPro:IPR012
336)
amine oxidase
family protein
similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO14940.
1); contains
InterPro domain
3-
dehydroquinate
synthase,
prokaryotic-type
(InterPro:IPR002
812)
phosphoglucomu
tase, putative /
glucose
phosphomutase,
putative
histone H3
Encodes subunit
NDH-N of
NAD(P)H:plastoq
uinone
dehydrogenase
complex (Ndh
complex) present
in the thylakoid
membrane of
chloroplasts.
This subunit is
thought to be
required for Ndh
complex
assembly.
BE3_SBE2.1__S
BE2.1 (STARCH
BRANCHING
ENZYME 2.1);
1,4-alpha-glucan
branching
enzyme
ATGWD3_PWD
_ATGWD3_OK1
__PWD
(PHOSPHOGLU
CAN WATER
DIKINASE)
DNA binding /
magnesium ion
binding /
nuclease
esterase/lipase/t
hioesterase
family protein
similar to
unknown protein
[Arabidopsis
thaliana]
(TAIR:AT5G285
00.1); similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO65032.
1)
SET domain-
containing
protein
DPE1__DPE1
(DISPROPORTI
ONATING
ENZYME); 4-
alpha-
glucanotransfera
se
N2,N2-
dimethylguanosi
ne tRNA
methyltransferas
e family protein
SEX1_GWD_SO
P__SEX1
(STARCH
EXCESS 1)
photosystem II
11 kDa protein-
related
PDE194__PDE1
94 (PIGMENT
DEFECTIVE
194);
formyltetrahydrof
olate
deformylase/
hydroxymethyl-,
formyl- and
related
transferase
tic20 protein-
related
similar to
unknown protein
[Arabidopsis
thaliana]
(TAIR:AT1G065
40.1)
BCCP2_CAC1-
B_BCCP2__BC
CP2 (biotin
carboxyl carrier
protein 2); biotin
binding
CCL__CCL
(CCR-LIKE)
coenzyme F420
hydrogenase
family /
dehydrogenase,
beta subunit
family
(THIOREDOXIN-
LIKE 5); thiol-
disulfide
exchange
intermediate
similar to
unnamed protein
product [Vitis
vinifera]
(GB:CAO69665.
1)