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. 2022 Oct 27;10(6):e03191-22. doi: 10.1128/spectrum.03191-22

TABLE 2.

Fold change of expression of selected genesa

Gene Locus tagb Annotation Fold change under growth condition:
WH WD WDH K KH KD KDH
Oxidative stress genes
 katG 20080 Catalase-peroxidase 2.120c 0.703 0.936 NA NA NA NA
 soxR 04980 Redox-sensitive transcriptional activator 0.614 0.909 0.620 0.630 0.452 0.497 0.233d
 soxS 04985 Regulatory protein 0.935 3.218d 2.699d 0.855 0.949 1.394 2.021d
 sodB 11860 Fe-Mn family superoxide dismutase 0.992 0.567 0.227d 0.686 0.769 0.451c 0.154d
 oxyR 10675 H2O2-inducible genes activator 1.029 0.588 1.013 2.596d 2.153d 0.862 1.212
 lexA 10920 SOS response genes repressor 0.851 0.391c 0.297d 2.871c 1.791 0.330d 0.203d
 GPx 18990 Glutathione peroxidase 1.072 1.655 1.786c 3.228d 19.504d 1.722c 2.167d
 recA 10320 Recombinase 0.701 0.595 0.357d 2.320 2.113 0.436c 0.162d
 mutT 00305 8-oxo-dGTP diphosphatase 1.202 1.225 1.087 1.544 1.528d 1.323 1.061
 ruvB 15785 Holliday junction DNA helicase 1.054 1.085 1.567d 2.136d 1.873d 1.223 1.620d
 ruvA 15790 Holliday junction DNA helicase 1.063 0.965 1.488d 2.147d 2.156d 1.223 1.697d
 ruvC 15795 Crossover junction endodeoxyribonuclease 1.412 1.460 3.448d 2.637c 5.608d 2.808d 4.431d
 uvrA 11250 Excinuclease ABC subunit A 0.922 1.218 0.839 1.823 1.814d 0.825 0.511d
 uvrB 02750 Excinuclease ABC subunit B 1.033 1.324 1.110 1.280 1.430d 0.951 0.883
 uvrD 05950 Excinuclease ABC subunit C 0.760 0.672 0.590d 1.362 1.093 0.528d 0.386d
 sufD 10235 Fe-S cluster assembly protein 1.069 0.548 0.422d 1.554 1.494 0.446d 0.427d
 sufC 10240 Fe-S cluster assembly ATPase 1.317 1.179 0.890 2.150d 3.068d 0.987 0.744
 sufB 10265 Fe-S cluster assembly protein 0.950 1.033 0.836 2.093 3.431d 0.971 0.415d
Demethylation pathway genes
 dmdA 09710 DMSP demethylase 1.347 2.309d 2.100d 1.277 1.066 2.406d 1.847d
 dmdB1 10375 MMPA-CoA ligase 1.027 1.070 0.712 1.154 0.876 0.726 0.346d
 dmdB2 03420 MMPA-CoA ligase 1.147 1.195 1.277 1.583c 0.867 1.234 1.421d
 dmdC1 19300 MMPA-CoA dehydrogenase 0.910 3.422d 2.849d 1.180 1.819 3.719d 2.084d
 dmdC2 01515 MMPA-CoA dehydrogenase 1.487 2.605 1.601 3.223 1.038 1.418 0.475
 dmdC3 14785 MMPA-CoA dehydrogenase 1.114 3.957d 2.449c 2.127 0.967 2.099 0.734
 dmdD 19305 MTA-CoA hydratase 1.476 4.966d 2.217d 1.038 2.012 3.535d 1.720
Cleavage pathway genes
 dddP 11655 DMSP lyase 0.744 1.004 1.069 0.700 0.709c 1.006 1.081
 dddQ 22175 DMSP lyase 1.098 1.079 1.586c 0.911 0.828 1.257 1.874d
 dddW 02290 DMSP lyase 2.169 4.304d 14.979d 1.943 8.304d 12.113d 20.800d
 acuI 09715 NADPH-dependent acryloyl-CoA reductase 1.114 1.693 1.356 1.010 1.248 1.474 1.420
Other DMSP pathway genes
 acuH 00755 Enoyl-CoA hydratase 1.021 0.991 0.539 0.747 1.063 0.692 0.261d
 mtoX 21180 MeSH oxidase 1.004 39.371d 13.000d 1.091 1.021 15.110d 4.171d
 adlH 00490 Aldehyde dehydrogenase 1.364 1.077 1.082 1.092 0.855 0.827 1.042
 prpE 14880 Propionyl-CoA synthetase 1.974 1.101 0.736 1.546 0.861 0.843 0.543d
Sulfate reduction genes
 cysJI 13360 Sulfite reductase 1.538 0.029d 0.056d 1.132 2.018 0.046d 0.088d
 cysH 13365 Phosophoadenylyl-sulfate reductase 1.290 0.030d 0.079d 0.987 1.227 0.054d 0.094d
 SAT 04535 Bifunctional sulfate adenylyltransferase/adenylylsulfate kinase 2.084 0.535 0.506 1.516 2.424 0.603 0.442
Sulfur oxidation sox enzyme system
 soxV 04990 Sulfur oxidation V protein 1.310 5.607d 21.655d 1.046 7.365d 14.899d 31.372d
 soxW 04995 Thioredoxin 0.662 0.849 0.585c 0.901 0.450d 0.483d 0.310d
 soxX 05000 l-cysteine S-thiosulfotransferase 0.710 1.890c 1.347 1.055 0.369d 0.474d 0.398d
 soxY 05005 Sulfur oxidation Y protein 0.550 1.068 0.666 0.770 0.262d 0.325d 0.326d
 soxZ 05010 Sulfur oxidation Z protein 0.620 0.999 0.462c 0.704 0.216d 0.171d 0.073d
 soxA 05015 l-cysteine S-thiosulfotransferase 0.645 1.088 0.651 0.828 0.303d 0.344d 0.284d
 soxB 05020 S-sulfosulfanyl-l-cysteine sulfohydrolase 0.682 2.754d 2.302d 0.845 0.409d 1.029 1.387
 soxC 05025 Sulfur oxidation molybdopterin C protein 0.695 10.367d 10.058d 0.960 1.536 3.637d 5.234d
 soxD 05030 S-disulfanyl-l-cysteine oxidoreductase 0.759 5.763d 5.591d 0.926 1.104 2.239d 3.523d
 soxE 05035 Diheme cytochrome c 0.984 1.516 1.186 0.705 0.447d 0.692 0.829
 soxF 05040 Sulfide-cytochrome c reductase 0.500d 0.733 0.638c 0.598 0.352d 0.319d 0.364d
Quinone-reducing molybdenum sulfite dehydrogenase SoeABC
 soeC 17005 Sulfite dehydrogenase subunit C 1.456 1.805 6.018d 0.981 2.885d 4.516d 8.861d
 soeB 17010 Sulfite dehydrogenase subunit B 0.856 1.208 1.664c 1.118 1.245 1.423 2.160d
 soeA 17015 Sulfite dehydrogenase subunit A 1.067 1.205 3.568d 1.633 4.533d 3.150d 5.716d
Methionine and cysteine metabolism genes
 metY 07295 O-acetyl-l-homoserine sulfhydrylase 1.379 0.879 0.456d 0.834 0.706 0.578d 0.317d
 metZ 06880 O-succinyl-l-homoserine sulfhydrylase 1.385 0.704 1.019 0.929 2.006 1.098 1.499
 megL 21430 Methionine gamma-lyase 1.235 4.841c 38.284d 1.242 14.694d 27.219d 58.386d
 MTR 09575 5-methyltetrahydrofolate-homocysteine methyltransferase 0.736 0.515c 0.336d 1.086 0.560d 0.368d 0.203d
 cysQ 00195 3′(2′),5′-bisphosphate nucleotidase 1.228 1.330 0.947 0.746 1.265 1.236 0.628
 cysK 11395 Cysteine synthase A 1.211 0.367d 0.193d 0.929 1.392 0.184d 0.104d
 cysE 11400 Serine O-acetyltransferase 0.960 0.773 0.410d 0.947 0.704 0.426d 0.166d
Other gene
 dddD 08640 DMSP lyase DddD-like gene 0.911 1.105 2.480d 1.000 1.390 2.958d 4.846d
a

Abbreviations for growth conditions are defined in Fig. 2. Each comparison was made to the wild type with no additions or W transcriptome. Conditions in parentheses are controls for each comparison. NA, could not be compared due to the gene deletion.

b

All locus tags have the prefix SPO_RS.

c

Adjusted P value, <0.1.

d

Adjusted P value, <0.05.