Table S2.Distribution of ChIP-seq peaks in the promoter regions of LuxR-regulated genes.

Chromo-some
Numbera / Locus / Predicted Function / Gene Strandb / Gene Start / Gene Stop / Peak Positionsc / LuxR Fold-Regulationd
chr1 / VIBHAR_00046 / transcriptional regulator AphA / + / 47235 / 47840 / 46973, 47026, 47146 / -2.91
chr1 / VIBHAR_00050 / transcriptional repressor protein MetJ / + / 52900 / 53220 / 52722 / -2.86
chr1 / VIBHAR_00081 / nuclease / - / 81056 / 84004 / 84191, 84233 / -3.17
chr1 / VIBHAR_00130 / lysyl-tRNAsynthetase / - / 127536 / 128507 / 128721, 128677 / -2.32
chr1 / VIBHAR_00176 / diguanylatecyclase / + / 178950 / 180014 / 178920 / -4.92
chr1 / VIBHAR_00284 / hypothetical protein / - / 275121 / 275345 / 275503, 275418 / -2.15
chr1 / VIBHAR_00298 / signal transduction protein / - / 285590 / 286813 / 286844 / -2.74
chr1 / VIBHAR_00305 / sensory transduction protein kinase / - / 292334 / 294820 / 294994, 295033, 294887 / 2.39
chr1 / VIBHAR_00530 / hypothetical protein / + / 510792 / 511391 / 510674, 510621 / -2.33
chr1 / VIBHAR_00710 / hypothetical protein / + / 702536 / 702883 / 702412 / -2.12
chr1 / VIBHAR_00795 / malate dehydrogenase / + / 779619 / 780554 / 779357, 779476 / 2.08
chr1 / VIBHAR_00834 / PTS system, mannitol-specific II ABC component / - / 823458 / 825410 / 825632, 825592, 825543, 825473 / 8.80
chr1 / VIBHAR_00936 / ribonuclease activity regulator protein RraA / + / 940687 / 941169 / 940568 / 2.28
chr1 / VIBHAR_01133 / hypothetical protein / + / 1148640 / 1149914 / 1148580, 1148620 / -2.39
chr1 / VIBHAR_01191 / hypothetical protein / - / 1207019 / 1208584 / 1208619 / -3.88
chr1 / VIBHAR_01256 / bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor UshA / + / 1264459 / 1266120 / 1264255, 1264302 / -4.66
chr1 / VIBHAR_01274 / hypothetical protein / + / 1285975 / 1286571 / 1285800, 1285896 / -17.63
chr1 / VIBHAR_01297 / flagellar hook-associated protein FlgK / + / 1302912 / 1304825 / 1302900 / -2.27
chr1 / VIBHAR_01320 / hypothetical protein / - / 1328742 / 1329692 / 1329696, 1329750 / -2.25
chr1 / VIBHAR_01371 / hypothetical protein / - / 1384904 / 1385749 / 1385803, 1385913, 1385847 / -2.18
chr1 / VIBHAR_01398 / hypothetical protein / + / 1411351 / 1412571 / 1411218, 1411289 / 2.57
chr1 / VIBHAR_01438 / hypothetical protein / - / 1456789 / 1457379 / 1457409, 1457599 / -3.63
chr1 / VIBHAR_01614 / quinolinatesynthetase / + / 1623312 / 1624373 / 1623173, 1623222 / -2.36
chr1 / VIBHAR_01749 / hypothetical protein / - / 1755165 / 1756283 / 1756342, 1756400 / 93.38
chr1 / VIBHAR_01762 / hypothetical protein / - / 1769778 / 1771922 / 1772019, 1771971, 1772091, 1772179 / -2.52
chr1 / VIBHAR_02041 / hypothetical protein / + / 2035335 / 2035673 / 2035333 / 7.46
chr1 / VIBHAR_02100 / histidine decarboxylase / - / 2098096 / 2099256 / 2099419, 2099476, 2099272 / 3.25
chr1 / VIBHAR_02240 / hypothetical protein / + / 2240749 / 2241717 / 2240615, 2240528 / -3.18
chr1 / VIBHAR_02274 / ferredoxin / + / 2273281 / 2274942 / 2273000, 2273160, 2273218 / -2.49
chr1 / VIBHAR_02431 / sensor kinase CitA / - / 2445700 / 2447325 / 2447420, 2447354 / -2.41
chr1 / VIBHAR_02472 / hypothetical protein / + / 2488989 / 2490461 / 2488831, 2488875, 2488933 / 36.50
chr1 / VIBHAR_02542 / hypothetical protein / - / 2565897 / 2567108 / 2567220, 2567180, 2567112 / -3.06
chr1 / VIBHAR_02566 / hypothetical protein / - / 2589152 / 2589520 / 2589593 / 2.22
chr1 / VIBHAR_02610 / transcriptional regulator / + / 2626151 / 2626522 / 2626104, 2626146 / -18.16
chr1 / VIBHAR_02617 / hypothetical protein / + / 2630465 / 2631412 / 2630381, 2630418 / -45.41
chr1 / VIBHAR_02629 / hypothetical protein / + / 2644196 / 2645116 / 2644152 / -2.67
chr1 / VIBHAR_02665 / bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor UshA / + / 2685410 / 2687146 / 2685328, 2685287, 2685390 / -7.10
chr1 / VIBHAR_02702 / histidine kinase / - / 2725857 / 2727227 / 2727282, 2727232 / -3.02
chr1 / VIBHAR_02754 / hypothetical protein / + / 2777598 / 2778308 / 2777476, 2777534 / -32.50
chr1 / VIBHAR_02920 / hypothetical protein / + / 2941785 / 2943344 / 2941571, 2941640 / -2.98
chr1 / VIBHAR_02986 / hypothetical protein / + / 3008870 / 3010003 / 3008606, 3008695, 3008758 / -2.69
chr1 / VIBHAR_02988 / hypothetical protein / + / 3012833 / 3013222 / 3012544 / -2.51
chr1 / VIBHAR_03063 / glutamate decarboxylase / + / 3086216 / 3087610 / 3086164 / 2.69
chr1 / VIBHAR_03117 / hypothetical protein / - / 3143129 / 3143593 / 3143732, 3143824, 3143681 / -4.88
chr1 / VIBHAR_03197 / hypothetical protein / - / 3222655 / 3223968 / 3223989 / -4.46
chr1 / VIBHAR_03244 / hypothetical protein / - / 3271353 / 3271838 / 3271914, 3271958, 3272136, 3272070 / -3.33
chr1 / VIBHAR_03248 / hypothetical protein / - / 3273532 / 3275100 / 3275214, 3275368, 3275154 / -2.39
chr1 / VIBHAR_03263 / hypothetical protein / + / 3290053 / 3290181 / 3289930 *, 3289800 / -10.23
chr1 / VIBHAR_03265 / hypothetical protein / + / 3290174 / 3291385 / 3290081, 3289930 *, 3290131 / -8.10
chr1 / VIBHAR_03387 / hypothetical protein / + / 3422187 / 3424226 / 3422000 / -2.62
chr1 / VIBHAR_03458 / hypothetical protein / - / 3511316 / 3511846 / 3512019 *, 3512070 *, 3511953 * / -2.42
chr1 / VIBHAR_03459 / transcriptional regulator LuxR / + / 3512168 / 3512785 / 3512019 *, 3512070 *, 3511953 * / 33.88
chr1 / VIBHAR_03493 / hypothetical protein / - / 3549146 / 3549787 / 3549884, 3549829 / -2.82
chr1 / VIBHAR_03494 / hypothetical protein / + / 3550362 / 3551489 / 3550266, 3550219 / -2.47
chr1 / VIBHAR_03544 / hypothetical protein / - / 3596896 / 3597147 / 3597232, 3597164 / -2.09
chr1 / VIBHAR_03571 / endonuclease I / + / 3620740 / 3621435 / 3620690, 3620635 / -3.46
chr1 / VIBHAR_03619 / hypothetical protein / - / 3652241 / 3653491 / 3653564, 3653513 / -2.58
chr1 / VIBHAR_03625 / hypothetical protein / - / 3658621 / 3658926 / 3659139 * / 11.29
chr1 / VIBHAR_03626 / hypothetical protein / + / 3659175 / 3660458 / 3659139 * / 15.32
chr2 / VIBHAR_04790 / integrase / + / 53646 / 54470 / 53364, 53413 / -2.54
chr2 / VIBHAR_04807 / hypothetical protein / - / 68189 / 69142 / 69213, 69174, 69352 * / -4.77
chr2 / VIBHAR_04809 / hypothetical protein / + / 69545 / 71338 / 69352 *, 69458 / 7.12
chr2 / VIBHAR_04815 / permease / - / 77053 / 78348 / 78530 / 2.24
chr2 / VIBHAR_04846 / small RNA Qrr2 / + / 111193 / 111301 / 111032, 111095 / -8.77
chr2 / VIBHAR_04850 / 4-alpha-glucanotransferase MalQ / + / 117545 / 119725 / 117543, 117481 / 3.22
chr2 / VIBHAR_04871 / lipolytic enzyme / - / 138130 / 139386 / 139387, 139458 / -3.20
chr2 / VIBHAR_04901 / hypothetical protein / - / 170225 / 170902 / 171127, 170994, 171068, 171181 / -4.15
chr2 / VIBHAR_04989 / hypothetical protein / - / 244692 / 245165 / 245215 / -6.84
chr2 / VIBHAR_05020 / hypothetical protein / - / 272076 / 272408 / 272599 * / 74.93
chr2 / VIBHAR_05021 / hypothetical protein / + / 272864 / 272968 / 272599 * / 5.48
chr2 / VIBHAR_05086 / carbonic anhydrase / + / 319778 / 320503 / 319613, 319561, 319699 / 2.30
chr2 / VIBHAR_05100 / hypothetical protein / - / 338596 / 339342 / 339513, 339599 / -2.67
chr2 / VIBHAR_05169 / azurin / - / 423613 / 424065 / 424355 / 2.25
chr2 / VIBHAR_05185 / hypothetical protein / + / 442351 / 443193 / 442181, 442238 / -4.68
chr2 / VIBHAR_05222 / thioesterase / - / 476447 / 476926 / 476950 / -6.54
chr2 / VIBHAR_05291 / hypothetical protein / - / 530106 / 530498 / 530756, 530613 / -7.39
chr2 / VIBHAR_05364 / putative threonine efflux protein / - / 593572 / 594192 / 594224 / -11.61
chr2 / VIBHAR_05400 / hypothetical protein / + / 623560 / 624282 / 623428, 623508 / 2.06
chr2 / VIBHAR_05730 / sensory transduction protein kinase / - / 932281 / 933462 / 933506, 933582 / -2.06
chr2 / VIBHAR_05807 / isopenicillin N synthase / - / 996591 / 997430 / 997550 *, 997525 * / -3.70
chr2 / VIBHAR_05809 / hypothetical protein / + / 997653 / 998249 / 997550 *, 997525 *, 997395 / -4.66
chr2 / VIBHAR_05843 / transcriptional regulator / - / 1027026 / 1027937 / 1028106, 1028066, 1028143 / -2.65
chr2 / VIBHAR_05881 / phytase / + / 1077542 / 1078906 / 1077479, 1077527 / -22.32
chr2 / VIBHAR_05968 / glycine cleavage system protein T2 / - / 1157566 / 1158696 / 1158871 *, 1158815, 1158950 * / 3.05
chr2 / VIBHAR_05969 / hypothetical protein / - / 1158697 / 1158840 / 1158871 *, 1158950 * / 2.72
chr2 / VIBHAR_06007 / iron-dicitrate transporter substrate-binding subunit FecB / + / 1193131 / 1194027 / 1193041 / -3.09
chr2 / VIBHAR_06094 / acyl-CoA desaturase / + / 1257434 / 1258558 / 1257352, 1257318 / -2.69
chr2 / VIBHAR_06128 / hypothetical protein / - / 1291893 / 1310528 / 1310632, 1310548 / -2.32
chr2 / VIBHAR_06137 / hypothetical protein / - / 1316334 / 1317014 / 1317099, 1317020 / -4.22
chr2 / VIBHAR_06139 / hypothetical protein / - / 1317873 / 1318610 / 1318875 / -2.53
chr2 / VIBHAR_06140 / hypothetical protein / - / 1318769 / 1318987 / 1319032, 1319248 / -33.47
chr2 / VIBHAR_06146 / D-ribose pyranase / - / 1324838 / 1325257 / 1325333, 1325408 / -2.31
chr2 / VIBHAR_06161 / C-5 sterol desaturase / - / 1336407 / 1337222 / 1337299, 1337374, 1337231 / 2.24
chr2 / VIBHAR_06238 / 3,4-dihydroxy-2-butanone 4-phosphate synthase / - / 1419098 / 1419790 / 1420000, 1420049 / 109.14
chr2 / VIBHAR_06244 / fatty acid reductase LuxC / - / 1424774 / 1426207 / 1426489, 1426384 / 203.30
chr2 / VIBHAR_06253 / sensory transduction protein kinase / + / 1430960 / 1433251 / 1430888, 1430770, 1430717, 1430805 / -2.86
chr2 / VIBHAR_06362 / oxidoreductase / - / 1530116 / 1534354 / 1534616 *, 1534571 * / -2.46
chr2 / VIBHAR_06363 / hypothetical protein / + / 1534658 / 1535107 / 1534616 *, 1534571 * / -19.19
chr2 / VIBHAR_06466 / hypothetical protein / - / 1624226 / 1625368 / 1625499 / 21.41
chr2 / VIBHAR_06479 / hypothetical protein / + / 1635239 / 1635673 / 1635099 / -3.99
chr2 / VIBHAR_06515 / L-asparaginase II AnsB / + / 1669995 / 1671011 / 1669712 / -2.79
chr2 / VIBHAR_06578 / hypothetical protein / - / 1725906 / 1726418 / 1726440 / 2.69
chr2 / VIBHAR_06697 / small RNA Qrr4 / - / 1833376 / 1833484 / 1833626, 1833561, 1833698 / -11.86
chr2 / VIBHAR_06837 / peptidase / - / 1948023 / 1949447 / 1949723 * / 3.75
chr2 / VIBHAR_06838 / phosphomethylpyrimidine kinase / + / 1949984 / 1950871 / 1949796, 1949723 * / -3.17
chr2 / VIBHAR_06860 / hypothetical protein / + / 1969575 / 1970366 / 1969387, 1969313 / 31.45
chr2 / VIBHAR_06861 / lactoylglutathionelyase / + / 1970462 / 1970740 / 1970400 / 34.24
chr2 / VIBHAR_06862 / hypothetical protein / + / 1970740 / 1971942 / 1970511 / 18.60
chr2 / VIBHAR_06888 / hypothetical protein / - / 1989683 / 1990102 / 1990399, 1990261 / 10.56
chr2 / VIBHAR_06914 / prolyloligopeptidase / + / 2011111 / 2013078 / 2010999, 2010861 / 2.87
chr2 / VIBHAR_06923 / hypothetical protein / - / 2019698 / 2019817 / 2020010, 2019933, 2019870 / -2.48
chr2 / VIBHAR_06936 / hypothetical protein / - / 2031297 / 2032319 / 2032341, 2032391 / -12.49
chr2 / VIBHAR_06994 / hypothetical protein / + / 2077287 / 2077895 / 2077204, 2077167 / -10.48
chr2 / VIBHAR_07107 / hypothetical protein / - / 2177956 / 2178123 / 2178124 / -2.54
plasmid / VIBHAR_p08271 / hypothetical protein / + / 83694 / 83912 / 83497, 83667, 83602 / -2.60

a. V. harveyi chromosome number: 1, CP000789; 2, CP000790; and plasmid, CP000791.

b. Orientation of gene (+ or -).

c. Predicted center position of LuxR binding peaks determined by CSDeconv analysis of ChIP-seq data. LuxR binding peaks that lie within 300bp upstream of the start codon of a LuxR-regulated gene are listed. Nine regions contain LuxR binding peaks that are associated with two divergently transcribed genes; denoted by asterisks.

d. Fold-change in transcript levels of LuxR-regulated genes (5).