Table st01_ XLSX - mBio

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Table st01_ XLSX - mBio Powered By Docstoc
					Table S1 - Genes negatively selected during growth in the presence of tobramycin.

                                                                                                                          Previous Study4             This study
                                                                           Pre-Growth Growth -Tob Growth +Tob Selection                     Mutants Mutants
                                                                              1      2    1      2    1      2       3                                                 6
Locus      Gene    Function                                 Length (bp)   Hits Reads Hits Reads Hits Reads     Ratio      ID'd      MIC     Available tested       MIC
PA0392             conserved hypothetical                       594         5      644 5      1374 0         0    0        no                   1         2†       0.25
PA4077             transcriptional regulator                    207         3     1572 3      1230 0         0    0        no                   0         1†       0.25
PA5199     amgS    two-component sensor                        1320        18      764 20      663 0         0    0        yes     0.125        4
PA5366     pstB    phosphate transport                          834         8     1748 8       761 0         0    0        yes      0.25       21
PA3649     mucP    conserved hypothetical                      1353         8      521 6       171 0         0    0        yes      0.5         3
PA2656             two-component sensor                        1338        18     1364 18     1339 2         4  0.00       no                  13        11†        0.5
PA5200     amgR    two-component response regulator             744         9      752 12      396 1         2  0.00       yes     0.063        6
PA0016     trkA    potassium uptake                            1374        16     1089 16      823 2         5  0.01       yes      0.25       12
PA4941     hflC    protease subunit                             870        11     3128 11     2475 4        26  0.01       no                   3          2        0.5
PA4315     mvaT    transcriptional regulator                    375         8     8331 7      5465 3        59  0.01       no                   7          3        0.5
PA2737             conserved hypothetical                       258         4     1232 4      1545 1        18  0.01       no                   1         2†        0.5
PA4942     hflK    protease subunit                            1203        14     2436 16     2104 2        30  0.01       yes      0.25        4
PA0011             lipopolysaccharide biosynthesis              888         7     2074 7      1093 1        21  0.02       no                   6          4        0.5
PA5054     hslU    heat shock protein                          1344        20     1712 21     1997 2        50  0.03       no                   5          2        0.5
PA5053     hslV    heat shock protein                           534         5     1279 5      1180 2        33  0.03       yes       0.5        4
PA2491             oxidoreductase                              1020         6      225 6       169 2         7  0.04       no                   0
PA3014     faoA    fatty-acid oxidation                        2148        23     1465 27     1227 5        56  0.05       no                  18          5        0.25
PA4398             two-component sensor                        2097        19      862 19      633 2        30  0.05       yes      0.25        6
PA5071             conserved hypothetical                       708         8      613 7       308 2        15  0.05       no                   0
PA5528             hypothetical                                 855        12     2363 13     2839 4       161  0.06       yes     0.125        8
PA2658             hypothetical                                 315         3     2226 3      3137 1       178  0.06       no                   4          2        0.5
PA3735     thrC    threonine synthesis                         1410         6      586 6       534 1        31  0.06       no                   0         1†        0.5
PA5429     aspA    aspartate ammonia-lyase                     1425        19     2144 21     2246 7       154  0.07       no                  12         5†        0.5
PA5130             conserved hypothetical                       420        13     3571 12     2658 2       189  0.07       no                   2          1        0.5
PA3210     trkH    potassium uptake                            1455        27     2542 25     1691 6       128  0.08       yes       0.5        3
PA1805     ppiD    peptidyl-prolyl isomerase                   1866        29     3920 29     4583 12      397  0.09       no                  21          5        0.25
PA3657     map     methionine aminopeptidase                    786         9     2512 9      2279 4       233  0.10       no                   3          2          1
PA0762     algU    sigma factor                                 582         8     1442 8       731 2        75  0.10       no                   0         1†         0.5
PA3016             hypothetical                                 435         9     1630 8       840 1        87  0.10       yes     0.125        2
PA5133             conserved hypothetical                      1287        17     1982 17     1804 7       214  0.12       no                  11          4        0.5
PA0013             conserved hypothetical                       654         5     1510 5      1816 3       216  0.12       no                   1
PA5344             transcriptional regulator                    933        14     1710 13      470 3        58  0.12       no                  12          2         0.5
PA0667             conserved hypothetical                      1344        33     4088 28     3249 17      412  0.13       no                  10          2         0.5
PA4223             ABC transporter component                   1713        19      638 19      790 10      106  0.13       no                   3          3        0.25
PA2666             coenzyme (queuosine) metabolism              357         2      843 3       814 3       113  0.14       no                   0
PA1800     tig     trigger factor                              1311        21     2165 22     1420 6       208  0.15       no                   2          1        0.5
PA5428             transcriptional regulator                    909        19     1189 21     2289 8       337  0.15       no                  16          4        0.5
PA4387             conserved hypothetical                       468         6     2145 6      2893 5       434  0.15       no                   4          1        0.5
PA2876     pyrF    pyrimidine transport and metabolism          699         7     1497 9      1046 6       163  0.16       no                   0
PA4960             phosphoserine phosphatase                   1290        15      916 17      507 2        80  0.16       no                   2          2        0.25
PA0374     ftsE    cell division                                672         8     4583 8      4366 4       705  0.16       no                   5          3       0.125‡
PA3013     foaB    fatty-acid oxidation                        1176        29     3632 32     2925 14      485  0.17       yes      0.25       11
PA5471             hypothetical                                1140         8      655 8       755 4       129  0.17       yes      0.25        3
PA0502             biotin biosynthesis                          723         9     1131 9       627 3       108  0.17       no                   1          1        0.25
PA3194     edd     carbohydrate metabolism                     1827        10      253 11      161 5        29  0.18       no                   9          1       0.125
PA3485             hypothetical                                 438         5     1306 5      1272 4       227  0.18       no                   1          1         1
PA2991     sth     pyridine nucleotide transhydrogenase        1395        17      772 16      351 12       63  0.18       no                   0
PA1775     cmpX    cytoplasmic membrane protein                 825        13     1670 11      747 7       134  0.18       no                  10          3        0.25
PA5261     algR    alginate biosynthesis regulation             747        19     6800 20     8084 18     1509  0.19       no                   6          2          1
PA0966     ruvA    Holliday junction DNA helicase               606         6      829 5       516 3        98  0.19       no                   3          1          1
PA5256     dsbH    disulfide bond formation protein             492         9     2788 11     3781 8       722  0.19       no                   4          3         0.5
PA0014             hypothetical                                 273         4     1201 4      1607 4       317  0.20       no                   1          1         0.5
PA4404             hypothetical                                 924        15     1583 15     3569 11      710  0.20       no                   7          2         0.5
PA0592     ksgA    rRNA dimethyltransferase                     807        16     2406 18     1924 7       384  0.20       yes       0.5        4
PA0375     ftsX    cell division                               1008        33     5593 33     4577 17      917  0.20       yes       0.5       14
PA4427     sspB    stringent starvation protein                 408         3      772 4      1172 3       236  0.20       no                   6
PA3050     pyrD    dihydroorotate dehydrogenase                1029         5      332 8       185 2        38  0.21       no                   5          1        0.5
PA5368     pstC    phosphate transport                         2034        17     1411 18      483 13      101  0.21       yes      0.5        46
PA0427     oprM    multidrug efflux                            1458        15     1877 15     1427 6       298  0.21       yes      0.25       40
PA4222             ABC transporter component                   1725        16      551 18      333 6        74  0.22       no                   2          2        0.25
PA2812             ABC transporter component                    933        13     1422 15     1356 11      304  0.22       no                   2          2          1
PA4426             conserved hypothetical                       579         5     1085 5      1086 4       260  0.24       no                   3          1         0.5
PA0967     ruvB    Holliday junction DNA helicase              1059         7      581 7       226 4        56  0.25       no                   1
PA4698             hypothetical                                 330         2      882 4      1652 2       406  0.25       no                   2
PA0662     argC    amino acid metabolism                       1035        25     3235 26     3596 22      902  0.25       no                   9          2        0.5
PA5493     polA    DNA polymerase I                            2742        32      906 32      545 8       139  0.25       yes       0.5       20




b221d9de-81f5-4492-9483-c795c6bf3bb1.xlsx                                           Page 1 of 2
                                                                                                                                             Previous Study4             This study
                                                                                              Pre-Growth Growth -Tob Growth +Tob Selection                     Mutants Mutants
                                                                                                 1      2    1      2    1      2                                                          6
Locus          Gene  Function                                                 Length (bp)    Hits Reads Hits Reads Hits Reads     Ratio3     ID'd      MIC     Available tested       MIC
PA4768         smpB  regulation of translational fidelity                         480          8     3606 9      1677 7       428  0.26       no                   0
PA3824         queA  tRNA and rRNA base modification                             1044         18     1731 19     2222 14      569  0.26       no                   4         2         0.5
PA5369         pstS  phosphate transport                                          972         10     1037 9       631 3       164  0.26       no                  33         3        0.25‡
PA3823         tgt   queuine tRNA-ribosyltransferase                             1119         23     3619 22     2823 14      736  0.26       yes       0.5       12
PA0411         pilJ  twitching motility                                          2049         22     2884 23     3431 19      897  0.26       no                  21         2         0.5
PA4422               conserved hypothetical                                       849         10     1180 10     1026 7       271  0.26       yes       0.5        9
PA4410         ddlB  peptidoglycan biosynthesis                                   960          9      893 9       918 4       250  0.27       no                   1         1          1
PA5351         rubA1 energy production and conversion                             168          3     2237 3      3150 3       909  0.29       no                   1         1         0.5
PA0332               hypothetical                                                 468          5      961 6      1959 5       569  0.29       no                   4
PA5227               conserved hypothetical                                       315          3     1787 3      1975 3       575  0.29       no                   1         2         0.5
PA4329         pykA pyruvate kinase II                                           1452         15     1156 17     1656 15      482  0.29       no                   8
PA3086               hypothetical                                                 861         14     3265 15     2580 14      756  0.29       no                   7
PA2018         mexY multidrug efflux                                             3138         45     3025 46     2761 40      811  0.29       yes      0.25       12
PA3903         prfC  peptide chain release factor 3                              1584         19     2603 19     2668 18      786  0.29       no                   2
PA0408         pilG  twitching motility                                           408          8     4424 8      4370 7      1293  0.30       no                   0
PA3169               methionine metabolism                                       1077         13     2128 14     3069 13      912  0.30       no                   8
PA5285               hypothetical                                                 318          4     1293 4      1559 4       466  0.30       no                   5         4        0.25
PA2604               conserved hypothetical                                       669          8     2736 9      2162 8       649  0.30       no                   9         3        0.25
PA1183         dctA  C4-dicarboxylate transport protein                          1311          6     1041 9      1461 5       440  0.30       no                  13
PA2811               ABC transporter component                                    780          7      733 8       622 5       189  0.30       no                   0
PA5367         pstA  phosphate transport                                         1677         12     1022 13      604 6       185  0.31       yes       0.5       58
PA5175         cysQ  3,5-bisphosphate nucleotidase                                822         11     1056 11      996 10      309  0.31       no                   4         4         0.5
PA5331         pyrE  pyrimidine ribonucleotide biosynthesis                       642         12     1509 12     1669 5       524  0.31       no                   1
PA3857         pcs   glycerophospholipid metabolism                               717         12     3512 12     4131 11     1306  0.32       no                  11
PA2627               conserved hypothetical                                       621          8     1221 8      2758 6       874  0.32       no                   1
PA0413         chpA chemotaxis signal transduction                               7419         94     2014 98     1997 60      671  0.34       no                  30         2          1
PA5194               hypothetical                                                 804         11     1815 12     1862 9       631  0.34       no                   5         2          1
PA5551               hypothetical                                                 510          8     3212 8      3138 8      1066  0.34       no                   2         2          1
PA0664               hypothetical                                                 423         14     4338 14     7031 10     2447  0.35       no                   5         2         0.5
PA5241         ppx   exopolyphosphatase                                          1521         25     1693 25     1520 14      538  0.35       no                   1         1          1
PA0298         spuB glutamine synthetase                                         1359         14     1155 12      704 5       252  0.36       no                   7         1         0.5
PA5479         gltP  proton-glutamate symporter                                  1335         19     2532 19     2652 13      952  0.36       yes       0.5       18
PA2840               ATP-dependent RNA helicase                                  1704         16      871 14      876 13      317  0.36       no                   3
PA5475               hypothetical                                                 561          6     1299 6      2115 5       765  0.36       no                   7         2         0.5
PA0424         mexR multidrug resistance operon repressor MexR                    444          7     3081 9      2454 7       902  0.37       no                   3         2         0.5
PA4316         sbcB  exodeoxyribonuclease I                                      1443         14      907 14     1081 11      400  0.37       no                   9
PA2019         mexX multidrug efflux                                             1191         20     2403 21     2488 18      930  0.37       yes      0.25        1
PA3733               hypothetical                                                1230          5      270 6      1028 5       386  0.37       no                   2
PA2806               conserved hypothetical                                       831         11     3858 11     1601 11      601  0.38       no                   4
PA0663               hypothetical                                                 720         18     5330 18     5165 16     1943  0.38       no                   5         2         0.5
PA3237               hypothetical                                                 222          2      336 3      1540 2       581  0.38       no                   2
PA0047               hypothetical                                                 510          4     1009 5       959 4       363  0.38       no                   4         2         1
PA0858               conserved hypothetical                                       939         16     3172 18     3802 16     1439  0.38       no                  13
PA5406               hypothetical                                                 333          2     1086 4      1200 2       465  0.39       no                   2         2         0.5
PA4823               hypothetical                                                 210          3     5668 3      5413 3      2102  0.39       no                   0
PA3018               hypothetical                                                 687          7     2376 6      2059 6       804  0.39       no                   2
PA1996         ppiC1 peptidyl-prolyl isomerase                                    279          2      368 3      2118 2       829  0.39       no                   2
PA0934         relA  stringent response signaling                                2244         34     1972 34     1730 27      678  0.39       no                   9
PA4050         pgpA phospholipid biosynthesis                                     516          6     1931 7      1214 4       483  0.40       no                   4         3        0.125
PA2495         oprN multidrug efflux                                             1419         10     1123 10     1606 9       639  0.40       no                  10
PA0108         coIII cytochrome c oxidase                                         888         10     2543 11     3033 8      1213  0.40       no                   4         2         0.5

Notes:
1
    Number of insertion locations detected.
2
    Total normalized reads averaged from two technical replicates.
3
    Ratio = (reads after growth with tobramycin) / (reads after growth without tobramycin)
4
    Lee et al. 2009. PNAS 34(106):14570-14575
5
    Number of insertion mutants available in the defined library.
†
    Includes one deletion mutant.
6
    Bold = identity of mutant whose MIC is reported was confirmed by re-sequencing.
‡
    phenotype may be due to expression of hybrid proteins.




b221d9de-81f5-4492-9483-c795c6bf3bb1.xlsx                                                            Page 2 of 2

				
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