Supplementary Table S1. Primers Designed and Used in This Study

Supplementary Table S1. Primers designed and used in this study.

Gene ID / COG / Gene name / Gene description / Primer name / Primer sequence / Product size, bp
Exig0005 / COG0187 / gyrB / Type IIA topoisomerase (DNA gyrase/topo II topoisomerase IV) B subunit / or2561_1106F / TCATGATGGAGAATCCGACA / 393
or2561_1498R / TATGATACCGGGCTTTCTCG
Exig0006 / COG0188 / gyrA / Type IIA topoisomerase (DNA gyrase/topo II topoisomerase IV) A subunit / or2562_1292F / TGACTGGTCTCGAACGTGAG / 373
or2562_1664R / ATCGTATCATGCGTCGAACA
Exig0047 / COG1188 / Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) / or0249_1F / ATGGAATCAATCAAAGCAGGA / 303
or0249_301R / ACATCGATTCTTCGGAATTCACT
Exig0065 / COG4463 / ctsR / Transcriptional repressor of class III stress genes / or2392_69F / AATCAAACGCCAGGAAATTG / 364
or2392_432R / GACGGTTTGCATCAAATGAG
Exig0119 / COG0361 / infA / Translation initiation factor 1 (IF-1) / or2188_46F / TCGTGTTTGTGACCGATGAT / 301
or2188_346R / GTCCGCGAGTCAAGTCGTAT
Exig0136 / COG1595 / rpoE / DNA-directed RNA polymerase specialized sigma subunit sigma24 homolog / or0268_109F / CGTGTTTTACGGGATCGAAT / 327
or0268_435R / AAGCGGAATCCGGTATTTTT
Exig0137 / COG5662 / Predicted transmembrane transcriptional regulator (anti-sigma factor) / or0269_154F / CTTTCAGCACCCAAGCTTTC / 363
or0269_516R / TTTGCCGTCGACAGTCATTA
Exig0151 / COG1468 / RecB family exonuclease / or0281_132F / ACAGGCACTTCACCAAAAGG / 383
or0281_514R / TCGTAACCGTCGCTAAAACC
Exig0164 / COG1595 / rpoE / DNA-directed RNA polymerase specialized sigma subunit sigma24 homolog / or0293_148F / GTCGTCCAGGAAACGGTCTA / 380
or0293_527R / CGTGCTTCGACATAATCGAG
Exig0299 / COG3706 / pleD / Response regulator containing a CheY-like receiver domain and a GGDEF domain / or0461_550F / CTGCAGGAATTACGCAAACA / 376
or0461_925R / CAAAATGTTGATCGGCACAG
Exig0364 / COG0589 / uspA / Universal stress protein UspA and related nucleotide-binding protein / or1387_62F / CTTTTGAAAAAGCCGTCCAG / 342
or1387_403R / ATCGGGCAATGTTTTCAGAG
Exig0423 / COG0389 / dinP / Nucleotidyltransferase/DNA polymerase involved in DNA repair / or0938_104F / CGACGAAACTTGCTGTCGTA / 398
or0938_501R / CAGCTTTGCAATGACGTTGT
Exig0432 / COG0182 / Predicted translation initiation factor 2B subunit eIF-2B alpha/beta/delta family / or0976_51F / TTTGGATCAGACCCGTCTTC / 364
or0976_414R / GATTTGACGGGATGTTTTGG
Exig0471 / COG0484 / dnaJ / DnaJ-class molecular chaperone with C-terminal Zn finger domain / or2100_170F / ATGAAGAAAAACGGGCACAG / 381
or2100_550R / CATCTCCCGCAATTCCTTTA
Exig0534 / COG1764 / osmC / Predicted redox protein regulator of disulfide bond formation / or1729_45F / CAATGATGTCGGTCAAATCG / 384
or1729_428R / ACCGCCTCTAACGAAACCTT
Exig0664 / COG0219 / cspR / Predicted rRNA methylase (SpoU class) / or0720_105F / GCTTGGATTTTCAACGGATG / 360
or0720_464R / TTGGCATATCCTTGTTGTCG
Exig0683 / COG0389 / dinP / Nucleotidyltransferase/DNA polymerase involved in DNA repair / or0709_275F / TTCTTGAGGTCACGCCTCTT / 306
or0709_580R / ACGTCTGCTCCGTGACTTTT
Exig0730 / COG1074 / recB / ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) / or0897_1323F / ACGATTCCAACAAACCGAAG / 349
or0897_1671R / ATCACGGTATTCGCACTTCC
Exig0743 / COG1943 / Transposase and inactivated derivatives / or0882_64F / AAATACAGACGCAAAGTGATCG / 399
or0882_372R / GTGTCTGATGACGTCGCTTG
Exig0779 / COG1420 / hrcA / Transcriptional regulator of heat shock gene / or1979_537F / ACGGTTGAACCAAACGCTAC / 382
or1979_918R / GACGCCATCAACGGAATAAT
Exig0780 / COG0576 / grpE / Molecular chaperone GrpE (heat shock protein) / or1980_44F / CAACCGAGCAACAAACAGAA / 335
or1980_378R / TTCCACCAATTGACGTTTGA
Exig0781 / COG0443 / dnaK / Molecular chaperone / or1981_1050F / ATTGACAGGGGACGTCAAAG / 400
or1981_1449R / TTGGTCGATGTCTGCTTCAG
Exig0782 / COG0484 / dnaJ / DnaJ-class molecular chaperone with C-terminal Zn finger domain / or1982_51F / TGCCTCAGCAGCAGAGATTA / 375
or1982_425R / GTTCCGCAATCTTCTTCGAC
Exig0832 / COG0568 / rpoD / DNA-directed RNA polymerase sigma subunit (sigma70/sigma32) / or1523_439F / GGCATGCTGTTCCTTGATTT / 397
or1523_835R / CTGTCGCATCTTGGTCTTCA
Exig0900 / COG0231 / efp / Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) / or1097_78F / TAAATGGGAATCGCTCCTTG / 303
or1097_380R / TCCAGTTAATCGTTCGAGAGG
Exig0961 / COG0550 / topA / TopoisomeraseIA / or1852_1365F / GCTCGAGAAACAGACGGAAC / 386
or1852_1750R / GTGTTTTCGCATCCTGGACT
Exig1006 / COG0652 / ppiB / Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family / or1957_68F / ATGCACCGATCACAACAGAA / 342
or1957_409R / CAGCGCCTTGTTTCATTTTT
Exig1026 / COG0468 / recA / RecA/RadA recombinase / or2241_31F / GCATTGCGTCAGATTGAGAA / 391
or2241_421R / CGACGAGGATATCAACAGCA
Exig1113 / COG0675 / Transposase and inactivated derivatives / or0823_490F / TACTTCGTCTCCCTGCTCGT / 392
or0823_881R / AACTTGCGGTTCTTCTGCAT
Exig1163 / COG1943 / Transposase and inactivated derivatives / or1017_29F / CCACCGTTTCTCTGATCCAT / 357
or1017_385R / GTTGCTCGACATAACGCTTG
Exig1164 / COG0675 / Transposase and inactivated derivatives / or1018_143F / TGACGAGCAAGAATGTCCAG / 383
or1018_525R / CAGATCCACACCGAGAACCT
Exig1264 / COG2026 / relE / Cytotoxic translational repressor of toxin-antitoxin stability system, plasmid stabilization system / or1151_91F / CGGATCATCATGTCCTGGAT / 308
or1151_398R / CACGTTGCTCCTTTTCATCA
Exig1430 / COG2801 / Transposase and inactivated derivatives / or0173_283F / AGCGTACTTGCGAAGTGGAT / 392
or0173_674R / CGTGACCTCCTCTCGATCTC
Exig1514 / COG1983 / pspC / Putative stress-responsive transcriptional regulator protein / or0360_79F / CGTTCGCGAGAATCATGTAA / 309
or0360_387R / ACCACATGTCCAACTGCTCA
Exig1543 / COG1595 / rpoE / DNA-directed RNA polymerase specialized sigma subunit sigma24 homolog / or0376_107F / AGGAACAGGAAGCACTCGAA / 397
or0376_503R / TGTTGCCGCTGTAATTTTTG
Exig1585 / COG1825 / RplY / Ribosomal protein L25 (general stress protein Ctc) / or0313_108F / GGAAAGCACACCGATTTCAT / 352
or0313_459R / CGAATCTCCGATTGCAAGTT
Exig1589 / COG0187 / gyrB / Type IIA topoisomerase (DNA gyrase/topo II topoisomerase IV) B subunit / or0401_638F / AAGCGGACACGTTCCAATAC / 398
or0401_1035R / CGGTGAACCGAGTTTTGATT
Exig1590 / COG0188 / gyrA / Type IIA topoisomerase (DNA gyrase/topo II topoisomerase IV) A subunit / or0402_126F / GGTTCAACGCCGTATCTTGT / 383
or0402_508R / AACCGTTCATCAGCAGGTTC
Exig1683 / No COGs model hits / RNA polymerase ECF-type sigma factor / or0792_103F / TAATGAATCGGTTCGCGTTG / 301
or0792_403R / AACAAAGTGTTTACAGAGGGGATG
Exig1686 / COG1278 / cspC / Cold shock protein / 0793_44F / GGACTTCGGCCTGAATGTTA / 303
0793_346R / AGGCAACACACATGGAACAA
Exig1716 / COG1734 / dksA / DnaK suppressor protein / or0768_101F / CAGGGGAACTGTCGAGCTAC / 373
or0768_473R / TTTCCGAACTCACCGACTTT
Exig1777 / COG1199 / dinG / Rad3-related DNA helicase / or2541_48F / GATTAAATCCGGCGATGAGA / 387
or2541_434R / TGCGTCAACTGTAACGCTTC
Exig1826 / COG1674 / ftsK / DNA segregation ATPase FtsK/SpoIIIE and related protein / or2959_276F / TGACTTGCTGCTTGGTCAAC / 399
or2959_674R / TGTGTCTCTTTTGCCTGTGG
Exig1832 / COG1185 / pnp / Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) / or2894_768F / AGCCGTTCAAGTCGAAGAAA / 397
or2894_1164R / AGAGAACGGCGGGAAGTTAT
Exig1836 / COG0858 / rbfA / Ribosome-binding factor A / or1099_5F / GCGTACGTTCCAATCGTGTA / 326
or1099_330R / CAAGTTCCGGAGCAACTCAT
Exig1837 / COG0532 / infB / Translation initiation factor 2 (IF-2; GTPase) / or1098_1287F / TCCAATCGTTGTCGGTCATA / 389
or1098_1675R / CACCTGAGTGGACGATGTTG
Exig1838 / COG1358 / RPL8A / Ribosomal protein HS6-type (S12/L30/L7a) / or2515_57F / AACCGGCTGTGTTATTTTGG / 356
or2515_412R / GGGTGGTTCATCGAAAGTCA
Exig1840 / COG0195 / nusA / Transcription elongation factor / or1095_555F / AGTCGATCCGATGGTCAAAG / 398
or1095_952F / TTGCGAGTGACAATTGGAAG
Exig1843 / COG0442 / proS / Prolyl-tRNA synthetase / or1092_683F / ATTATGCCGCAAACTTGGAG / 370
or1092_1052R / AATGCCCGAACTGCATAATC
Exig1845 / COG0743 / dxr / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / or1090_717F / CCGAGAATCCATCATCCACT / 396
or1090_1112R / TCCGACTCCAAAATCTGGTC
Exig1848 / COG0233 / frr / Ribosome recycling factor / or1087_93F / TGCAAACGTCTCAATCCTTG / 364
or1087_456R / ATCGTCTTCCGTCAATACGC
Exig1888 / COG0550 / topA / TopoisomeraseIA / or2975_44F / TTGTCGAATCACCTGCAAAG / 313
or2975_356R / TTAAAGACAACCCGGCATTC
Exig1960 / COG1589 / ftsQ / Cell division septal protein / or2480_205F / GCGACATTTGATGTCACTGG / 373
or2480_577R / CTTTCGGCTCGATTTTAACG
Exig1991 / COG0415 / phrB / Deoxyribodipyrimidine photolyase / or2155_471F / TAAACCGTATCCGGTCAAGC / 395
or2155_865R / GTTCATTAACCGGCAGTCGT
Exig2062 / COG2826 / Tra8 / Transposase and inactivated derivatives IS30 family / or0411_539F / TCGAGCGAAAGAGTCGTTTT / 392
or0411_930R / GTGCAACACTTCTTCCGTGA
Exig2075 / COG1468 / recD / ATP-dependent exoDNAse (exonuclease V) alpha subunit - helicase superfamily I member / or2570_1576F / TCCGACCGTCGTTTTTATTC / 400
or2570_1975R / GATCCCAGTCACTCCGGTTA
Exig2096 / COG0809 / queA / S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) / or2969_198F / ACGCCTATTTGGTGTCAAGG / 397
or2969_594R / CTGAACCCCTTTATCCGTCA
Exig2098 / COG0632 / ruvA / Holliday junction resolvasome DNA-binding subunit / or2605_111F / GACCGGAGACGAACAGGTTA / 400
or2605_510R / TTTTTCGACTTCCCGTTCAC
Exig2147 / COG0544 / tig / FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) / or2606_399F / CGTCATCGGATCTGGAAACT / 325
or2606_723R / AGTCGCAGCTTCAACCAACT
Exig2194 / COG1484 / dnaC / DNA replication protein / or2014_500F / TCGGGAAAACGTATCTGCTC / 352
or2014_851R / AGACGCATGGCTTTCAGTTT
Exig2195 / COG3611 / dnaB / Replication initiation/membrane attachment protein / or2013_311F / ATCAAATCCGTGTCCCGTTA / 387
or2013_697R / GTTCTGCCATGAGTGCTTCA
Exig2223 / COG0589 / uspA / Universal stress protein UspA and related nucleotide-binding protein / or1904_42F / CGGATCAAAAGAGGCAGAAC / 398
or1904_439R / AAAGGCGGACGATTAAGACA
Exig2416 / COG0556 / uvrB / Helicase subunit of the DNA excision repair complex / or2116_1361F / AAATGTCGGAGGATTTGACG / 388
or2116_1748R / GGCGTGATACCGTGTTCTTT
Exig2427 / COG1544 / Ribosome-associated protein Y (PSrp-1) / or1322_175F / ATGCCAAACCTCTTGCTACG / 342
or1322_516R / GACGTTCGTGTTACCCGTTT
Exig2428 / COG1278 / cspC / Cold shock protein / or1321_40F / CTTGCTCTCGCAATCCAGTT / 345
or1321_384R / TGTTGCCTGTTGATATTAGCGTA
Exig2463 / COG2747 / flgM / Negative regulator of flagellin synthesis (anti-sigma28 factor) / or1298_8F / CCAAGCGATGCTTGATTCTT / 371
or1298_378R / CGAGTCGCCCCTATTGTCTA
Exig2532 / COG1595 / rpoE / DNA-directed RNA polymerase specialized sigma subunit sigma24 homolog / or1876_99F / TTCATTCGCTCATCGCTTTA / 393
or1876_491R / CTGGTTTTCACCGTTCCAAG
Exig2596 / COG3239 / desA / Fatty acid desaturase / or0611_471F / CGGACCACTCCTGTTGATTT / 398
or0611_868R / CCGTATGCGCTTTTTCTAGG
Exig2605 / COG0745 / ompR / Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain / or0605_152F / ATTTAATGCTGCCCGATACG / 378
or0605_529R / GCAATTCTTCCCGTTCAAAA
Exig2610 / COG0484 / dnaJ / DnaJ-class molecular chaperone with C-terminal Zn finger domain / or0600_211F / GGAATTGGTGGAAGTGCCTA / 357
or0600_567R / CGTCAACTCACCATCGAAGA
Exig2768 / COG0459 / groL / Chaperonin GroEL (HSP60 family) / or2629_1249F / TTCATTCACGTCACGAAAGC / 357
or2629_1605R / CATATCAGGCATTGCAGGTG
Exig2769 / COG0234 / groS / Co-chaperonin GroES (HSP10) / or2628_43F / AGGAGGATGTTTCGCATGTT / 320
or2628_362R / TGACTGAAATCCCCCTTTGA
Exig2794 / COG0675 / Transposase and inactivated derivatives / or1938_547F / GGAATTGACCTTGGTCTGGA / 324
or1938_870R / GATCGATTTGGCGATCGTAT
Exig2932 / COG0513 / srmB / Superfamily II DNA and RNA helicase / or2578_199F / GAGAGCAAAACGGTTCAAGC / 393
or2578_591R / ATACGTTTTCGCGAGTTGCT
Exig2939 / COG3666 / Transposase and inactivated derivatives / or1723_83F / CCGTTCATCATCTTGTCGAG / 384
or1723_466R / ATTTTCGCCAGACGAACGTA
Exig2952 / COG1764 / osmC / Predicted redox protein regulator of disulfide bond formation / or0842_54F / AAAGGTCGCCTCTGACGATA / 327
or0842_380R / GCTTTTGAATACGGGCAGAA
Exig2953 / COG1061 / SSL2 / DNA or RNA helicase of superfamily II / or1730_2694F / GTTGACCGGTTCTCAATCGT / 393
or1730_3086R / GGTTTTGATCCGTGACTGCT
Exig3031 / COG0745 / ompR / Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain / or0492_298F / TACGTCACGAAGCCATTCAG / 346
or0492_643R / TCGGGTTGTCTTCGACTTTT
Exig3033 / COG0305 / dnaB / Replicative DNA helicase / or0490_143F / AACGGATTTTCGAAACGATG / 366
or0490_508R / CATAGGCACTCGTCAGGACA
Exig3037 / COG0629 / ssb / Single-stranded DNA-binding protein / or0486_33F / AACTCGTGACCCTGAAATGC / 399
or0486_431R / GGCGAGGAAGAGTTGTTCTG
no hit / COG2963 / Transposase and inactivated derivatives / or0174_327F / GGCGTATTTGAGCGCTATTC / 392
or0174_718R / CCAAGCCGTTTAATCGTTGT
no hit / intergenic region / or0171_28F / GACGGTTCGGACCATTCC / 301
or0171_328R / GGCTGCCGATAATCGTTAAA