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S1 Medium components used in the study
S1. Medium components used in the study
成分
Ingredient液体培养基
Selective liquid medium固体培养基
Selective agar mediumg∙L−1 胰蛋白酶粉 Trypsin powder 10 10 酵母提取物 Yeast extract 5 5 Na2HPO4 12.8 12.8 KH2PO4 3.1 3.1 NaCl 10.5 10.5 MgSO4 0.5 0.5 (NH4)SO4 1.0 1.0 Agar 0 5 
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S2 Sequencing and assembly statistics of transcriptome
S2. Sequencing and assembly statistics of transcriptome
Sample Raw reads Clean reads Q20(%) Q30(%) GC(%) Total mapped (%) Cu0-1 29180330 29110346 98.51 95.52 62.53 99.76 Cu0-2 37063354 36969330 98.43 95.31 63.66 99.75 Cu0-3 34666388 34591286 96.95 91.55 65.34 99.78 Cu0.8-1 39645592 39521954 98.31 95.02 64.12 99.69 Cu0.8-2 44228530 44097962 98.51 95.5 65 99.7 Cu0.8-3 30151082 30079424 96.53 90.58 65.75 99.76 Cu1.6-1 35272426 35172560 96.57 90.75 64.46 99.72 Cu1.6-2 35726940 35585524 98.42 95.3 62.72 99.6 Cu1.6-3 64765060 64554014 98.46 95.39 63.12 99.67
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S3 PCR and gene expression of strain Lysobacter soli RCu6 at a copper concentration of 1.6 mmol∙L−1
S3. PCR and gene expression of strain Lysobacter soli RCu6 at a copper concentration of 1.6 mmol∙L−1
ID GeneName Description RT-qPCR (GAPDH)
(Log2FoldChange)RT-qPCR(16S rRNA)
(Log2FoldChange)RNA-Seq 1.6 mmol∙L−1 Cu
(Log2FoldChange)1_1472 copZ Copper chaperone 6.45 7.45 6.53 1_2614 copA1 metal ABC transporter ATPase 7.57 6.01 5.93 1_585 1_585 TonB-dependent receptor 5.05 5.25 5.91 1_1922 hisD histidinol dehydrogenase 2.23 3.62 5.22 1_1445 copG copper amine oxidase 5.80 5.16 5.10 1_1921 hisG ATP phosphoribosyltransferase 2.27 3.28 4.90 1_1443 copM cytochrome C 6.63 5.39 4.38 1_2615 cueR helix_turn_helix, mercury resistance 4.54 4.38 4.11 1_2613 copB2 copper resistance protein CopB 4.19 4.13 3.54 1_1405 sufC cysteine desulfurase 1.11 1.75 2.44 1_1440 copL copper resistance protein L 1.49 0.93 2.33 1_3665 copB3 Cation transport ATPase −3.08 −3.84 −5.24
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S4 Primer sequences of PCR
S4. Primer sequences of PCR
ID GeneName Description Forward primer Reverse primer Ct value (mean±SEM) Cycling conditions Control Cd treatment 16S rRNA 16S rRNA 16S ribosomal RNA 5´-TAAAGCGTGCGTAGGTGGTT-3´ 5´-GCTACACCGGGAATTCCACA-3´ 5.31±0.82 3.62±0.62 95 ℃×3 min;
35 cycles of 95 ℃×5 s and 60 ℃×30 s1_1131 GAPDH glyceraldehyde 3-phosphate dehydrogenase 5´-ACCTTCGTCAAGCTCGTCAG-3´ 5´-CTTGACCATTTCCAGGCACTTG-3´ 20.25±0.26 21.06±0.21 1_1472 copZ Copper chaperone 5´-TTCCGCCATTCATCAGTTGG-3´ 5´-AGATGGGAATGAGGACTGCTG-3´ 26.30±0.09 17.16±0.41 1_2614 copA1 metal ABC transporter ATPase 5´-TCGATCTGGCGCTGCTATC-3´ 5´-TGCGGATTGTTTGCGTTCTG-3´ 27.08±0.80 20.32±0.36 1_585 1_585 TonB-dependent receptor 5´-ACGGAGATCGGCCTGAAATAC-3´ 5´-TGGTTCGGATCCACGACAAG-3´ 26.81±0.80 22.58±0.32 1_1922 hisD histidinol dehydrogenase 5´-CACGCGCGTGTTCAAGATC-3´ 5´-CAAATAGCTTGTCGCAACGC-3´ 29.35±0.02 27.38±0.36 1_1445 copG copper amine oxidase 5´-GGATTCCCAGTTGAGGTGCA-3´ 5´-ATCGCTTGATGTCTTGGGCA-3´ 24.42±0.52 18.25±0.71 1_1921 hisG ATP phosphoribosyltransferase 5´-AGCGGCTGGAAGAACTCAAG-3´ 5´-ATGCCAGCATTCCCTCCAC-3´ 28.15±0.11 24.78±0.15 1_1443 copM cytochrome C 5´-CCATGTGCTCAGGGTGTCAT-3´ 5´-CATCCCGCTGGCTTTTATGC-3´ 24.42±0.30 17.34±0.41 1_2615 cueR helix_turn_helix, mercury resistance 5´-AGATGATCCGGCACTACGAAAG-3´ 5´-ATCGTTGTAGAGGCGATACCC-3´ 26.37±0.46 21.47±0.81 1_2613 copB2 copper resistance protein CopB 5´-CCGTACAAGTTCGAAGTGAGC-3´ 5´-TCAGCAGCACCTCGTATTCG-3´ 27.63±0.39 22.95±0.52 1_1405 sufC cysteine desulfurase 5´-TTCGATGCAGTTCCTCAAGC-3´ 5´-ATCTCGTTGCGCTTCTTCTC-3´ 24.40±0.29 22.94±0.53 1_1440 copL copper resistance protein L 5´-CGATAGCGTCGGTGCAAATG-3´ 5´-GACTTGCAGCAGTCCGAATC-3´ 23.95±0.92 21.33±0.57 1_3665 copB3 Cation transport ATPase 5´-TTCTTCCGCTGGATCACCTTC-3´ 5´-AGTTCGCGCCACATACCTTC-3´ 23.81±0.19 25.97±0.65
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S5 KEGC pathways of Lysobacter soli RCu6 under 0.8 mol∙L−1 and 1.6 mmol∙L−1 copper stress
S5. KEGC pathways of Lysobacter soli RCu6 under 0.8 mol∙L−1 and 1.6 mmol∙L−1 copper stress
Pathway ko_ID Adjusted P-value 0.8 mmol∙L−1 1.6 mmol∙L−1 Histidine metabolism ko00340 0.043589899 1.43E-08 Biosynthesis of amino acids ko01230 0.000630418 9.20E-08 Oxidative phosphorylation ko00190 — 9.20E-08 Carbon metabolism ko01200 0.000884953 2.26E-07 Citrate cycle (TCA cycle) ko00020 0.000363644 1.97E-06 Sulfur metabolism ko00920 0.065463933 0.000491874 Cysteine and methionine metabolism ko00270 — 0.001270466
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S6 Top 20 genes up- and down-regulated Lysobacter soli RCu6 under 0.8 mmol∙L−1 copper stress
S6. Top 20 genes up- and down-regulated Lysobacter soli RCu6 under 0.8 mmol∙L−1 copper stress
GeneID Gene Name log2foldchange P adjust Description 上调 Up-regulation 1_1472 copZ 7.675076964 1.83E−21 Copper chaperone 1_2614 copA1 7.455185783 1.23E−17 Heavy metal translocating Ptype atpase 1_801 fabG 7.366897737 5.38E−46 3-oxoacyl-acyl-carrier protein reductase 1_1471 7.067571805 3.81E−49 1_493 6.373644471 1.12E−73 Hypothetical protein 1_2539 FhuE 6.324336872 1.12E−58 Outer-membrane receptor 1_492 6.276953969 6.96E−39 Hypothetical protein 1_1400 fiu 6.144871379 1.10E−69 Outer membrane receptor for monomeric catechols 1_2147 cadI 6.084754317 3.37E−57 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily 1_2615 cueR 5.601239524 2.12E−14 Mercury resistance 1_3670 5.577318167 8.06E−24 OmpA-like transmembrane domain 1_3189 5.570814038 8.67E−21 Transcriptional regulators 1_2146 arsC 5.415765231 3.9E−43 Low molecular weight phosphotyrosine protein phosphatase 1_2538 5.365573206 4.36E−20 Iron uptake protein 1_1268 hmuP 5.135847869 6.51E−46 Hemin transporter HemP 1_861 5.074778015 3.48E−39 Membrane protein 1_3190 5.024578865 8.97E−23 Major facilitator Superfamily 1_2148 arsR 5.010259594 2.17E−44 Transcriptional regulators 1_2537 4.982803387 1.48E−50 PepSY-associated TM region 1_1261 acr 4.929472784 1.57E−39 Receptor 下调 Down-regulation 1_143 −4.167340098 0.00000639 Outer membrane receptor proteins 1_144 −3.060548562 1.63E−08 1_295 cioA −2.925204479 0.000061 Oxidase, subunit 1_3656 −2.784229132 8.72E−11 1_294 cioB −2.454203691 0.0000211 Oxidase, subunit II 1_3029 bfrA −2.350918645 7.97E−17 Iron-storage protein 1_1163 mcpY −2.313617653 0.000000479 Chemotaxis protein 1_2038 −2.262798789 0.00000487 1_1453 hutC −2.207378236 1.16E−09 Histidine utilization repressor 1_558 UbiH −2.12548026 0.00122665 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases 1_990 bfr −2.115354484 0.000783762 Iron-storage protein 1_1451 hutG −2.080852698 0.00000541 Catalyzes the conversion of N-formimidoyl-L-glutamate to L-glutamate and formamide 1_2290 −2.025740343 0.001455256 Membrane 1_2411 −1.903030901 0.006273652 Peptidoglycan-synthase activator LpoB 1_1147 napC −1.866603504 0.00000268 NapC/NirT cytochrome c family, N-terminal region 1_2781 ccmC −1.860960722 0.0000452 Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes 1_1146 napB −1.834441837 1.51E−09 Nitrate reductase cytochrome c-type subunit (NapB) 1_2428 −1.826263193 0.00474395 1_2288 azu −1.8054881 0.00000128 Transfers electrons from cytochrome c551 to cytochrome oxidase 1_2448 −1.791074188 0.007179161
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S7 Top 20 genes up- and down-regulated Lysobacter soli RCu under 1.6 mmol∙L−1 copper stress
S7. Top 20 genes up- and down-regulated Lysobacter soli RCu under 1.6 mmol∙L−1 copper stress
GeneID GeneName log2foldchange P adjust Description 上调 Up-regulation 1_1268 hmuP 9.882450621 2.60E−216 Hemin uptake protein 1_2539 9.074391369 4.56E−236 Outer-membrane receptor 1_1400 receptor 8.806436154 2.56E−255 1_1271 8.305728287 1.46E−100 1_2538 7.935613754 7.74E−52 Iron uptake protein 1_1270 7.795459576 0 1_2537 7.302461505 1.48E−262 PepSY-associated TM region 1_1269 phuR 6.788855033 9.35E−153 Receptor/Outer membrane receptor proteins, mostly Fe transport 1_1472 copZ 6.526940235 2.79E−16 Copper chaperone 1_1399 6.460192541 3.95E−63 Fe(II)-dependent oxygenase 1_1397 6.353710257 1.16E−88 Periplasmic protein 1_1261 acr 6.30440876 1.66E−55 Receptor/Outer membrane receptor proteins, mostly Fe transport 1_1398 6.165375292 2.97E−105 Membrane protein 1_2614 copA1 5.931818409 0.00000423 Heavy metal translocating P-type atpase 1_585 5.913941737 1.18E−113 Outer membrane receptor proteins, mostly Fe transport 1_587 5.89776771 1.68E−24 1_1471 5.85747186 1.08E−33 1_1181 5.734917608 0.000887261 1_586 5.704836483 3.60E−14 1_1262 acr 5.695731978 7.91E−70 Outer membrane receptor proteins, mostly Fe transport 下调 Down-regulation 1_1160 −6.658092361 1.67E−35 1_558 trxB −6.595647368 4.75E−39 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases 1_2288 azu −6.52244835 1.00E−81 Transfers electrons from cytochrome c551 to cytochrome oxidase 1_1130 ompW −6.488693371 5.34E−47 Outer membrane protein W 1_3664 ccoH −6.38842668 1.02E−68 FixH 1_3606 −5.874420268 3.10E−78 Metallo-beta-lactamase superfamily 1_3654 hemN −5.800117762 4.41E−163 Belongs to the anaerobic coproporphyrinogen-III oxidase family 1_3663 ccoG −5.608401967 1.43E−44 IG-like fold at C-terminal of FixG, putative oxidoreductase 1_3662 −5.326328916 1.71E−40 Membrane protein 1_3661 ccoP −5.295985455 1.40E−127 C-type cytochrome. Part of the cbb3-type cytochrome c oxidase complex 1_1155 −5.257669075 6.79E−44 Chemotaxis protein 1_3665 copB −5.23865363 4.42E−28 COG2217 Cation transport ATPase 1_3660 ccoQ −5.07135429 0.00000302 Cbb3-type cytochrome oxidase component FixQ 1_3029 bfrA −5.018393542 1.52E−83 Iron-storage protein, whose ferroxidase center binds Fe(2 ) ions, oxidizes them by dioxygen to Fe(3 ), and participates in the subsequent Fe(3 ) oxide mineral core formation within the central cavity of the protein complex 1_144 −5.003019191 3.18E−22 1_1146 napB −4.973748875 1.86E−57 Nitrate reductase cytochrome c-type subunit (NapB) 1_3658 ccoN −4.938375904 5.25E−83 Belongs to the heme-copper respiratory oxidase family 1_1166 −4.793318148 1.29E−33 Fis family transcriptional regulator 1_1143 napF −4.789570534 2.72E−47 Ferredoxin-type protein NapF 1_3659 ccoO −4.768327804 2.47E−48 COG2993 Cbb3-type cytochrome oxidase, cytochrome c subunit
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S8 Expression of resistance-related genes of Lysobacter soli RCu6 under 0.8 mmol∙L−1 and 1.6 mmol∙L−1 copper stress
S8. Expression of resistance-related genes of Lysobacter soli RCu6 under 0.8 mmol∙L−1 and 1.6 mmol∙L−1 copper stress
GeneID Description GeneName 0.8 mmol∙L−1 1.6 mmol∙L−1 log2fold
changelog2fold change FDR Significant log2fold change FDR Significant Copper resistance-related genes 1 1_1440 Transcriptional regulator copL 1.47 1.89E−03 Yes 2.33 3.67E−11 Yes 9.88 2 1_1441 Multicopper copA2 4.11 1.53E−07 Yes 4.39 9.74E−10 Yes 3 1_1442 Copper resistance copB1 4.23 3.44E−12 Yes 4.89 1.07E−17 Yes 4 1_1443 Cytochrome C oxidase, cbb3-type, subunit III copM 3.71 4.08E−07 Yes 4.38 4.73E−11 Yes 5 1_1445 CopG family transcriptional regulator copG 4.36 1.16E−12 Yes 5.10 1.43E−19 Yes 6 1_1447 Heavy metal translocating P-type atpase copA1 3.74 3.25E−04 Yes 3.22 1.21E−03 Yes 7 1_1448 3.37 2.21E−06 Yes 3.49 1.21E−07 Yes 8 1_1449 3.89 8.79E−08 Yes 4.30 2.56E−10 Yes 9 1_1467 Belongs to the resistancenodulation-cell division (RND) (TC 2.A.6) family cusA 1.40 8.31E−03 Yes — — NO 10 1_1468 Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family cusB 1.27 4.33E−03 Yes — — NO 11 1_1469 Outer membrane efflux protein czcC 1.30 4.14E−06 Yes — — NO 0 12 1_1471 Transcriptional regulator, MerR family SoxR 7.07 3.81E−49 Yes 5.86 1.08E−33 Yes 13 1_1472 Copper chaperone copZ 7.68 1.83E−21 Yes 6.53 2.79E−16 Yes 14 1_2288 Azurin azu −1.81 1.28E−06 Yes −6.52 1.00E−81 Yes 15 1_2611 Regulatory protein copL 1.45 2.74E−06 Yes 1.60 1.88E−09 Yes 16 1_2612 Multicopper copA2 3.34 4.75E−05 Yes 3.04 1.47E−04 Yes 17 1_2613 Copper resistance protein B precursor (CopB) copB1 3.83 1.11E−06 Yes 3.54 6.35E−06 Yes −6.66 18 1_2614 Heavy metal translocating P-type atpase CopA1 7.46 1.23E−17 Yes 5.93 4.23E−06 Yes 19 1_2615 helix_turn_helix, mercury resistance cueR 5.60 2.12E−14 Yes 4.11 2.72E−08 Yes 20 1_3371 Transcriptional regulatory protein copR — — NO −1.91 2.00E−20 Yes 21 1_3665 Cation transport ATPase copB2 −1.35 2.98E−02 NO −5.24 4.42E−28 Yes 22 1_114 Outer membrane efflux protein czcC 4.29 2.12E−10 Yes 3.75 2.08E−10 Yes 23 1_115 Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family czcB 3.78 1.76E−18 Yes 2.62 7.59E−10 Yes 24 1_116 Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family czcA 3.99 4.04E−26 Yes 3.24 2.79E−17 Yes 25 1_2347 Transporter czcD 1.27 9.76E−03 Yes 0.99 8.11E−03 NO 26 1_713 Cytochrome c oxidase subunit II coxB — — — 1.76 1.50E−05 Yes 27 1_2571 Cytochrome o ubiquinol oxidase subunit II cyoA — — — 1.16 6.33E−03 Yes Iron-sulfur clusters 1 1_105 4Fe-4S dicluster domain HybA — — −0.94 6.35E−07 Yes 2 1_1026 NADH dehydrogenase rutE 1.33 7.31E−04 Yes 1.29 2.89E−06 Yes 3 1_1386 Sulfite reductase cysI — — −1.88 2.86E−07 Yes 4 1_1403 Cysteine desulfurase / selenocysteine lyase sufS 1.30 6.46E−05 Yes 1.67 1.73E−09 Yes 5 1_1404 Fe-S cluster assembly protein SufD sufD 1.23 9.91E−04 Yes 1.61 1.11E−10 Yes 6 1_1405 Fe-S cluster assembly ATP-binding protein sufC 1.86 1.59E−07 Yes 2.44 7.06E−18 Yes 7 1_1406 Fe-S cluster assembly protein SufB sufB 1.36 2.57E−05 Yes 2.16 9.02E−16 Yes 8 1_1516 Rieske Fe-S protein qcrA — — −1.20 4.13E−08 Yes 10 1_1672 (2Fe-2S)-binding protein — — −0.86 1.75E−03 Yes 11 1_2061 Fe-S cluster assembly protein iscA 1.22 3.61E−03 Yes 1.20 2.58E−06 Yes 12 1_2081 Succinate dehydrogenase sdhD, frdD −0.78 2.56E−02 NO −0.82 7.00E−05 Yes 13 1_2082 Fumarate reductase sdhA, frdA — — −0.97 1.11E−04 Yes 14 1_2083 Fumarate reductase sdhA, frdA — — −0.63 5.52E−03 Yes 15 1_2084 Succinate dehydrogenase sdhB, frdB — — −0.69 1.85E−03 Yes 17 1_2154 Fe-S-cluster oxidoreductase 1.05 1.14E−04 Yes 18 1_2204 Fe/S biogenesis protein NfuA nfuA — — −0.75 9.40E−04 Yes 19 1_2472 Rieske [2Fe-2S] domain yhfW — — 1.37 3.47E−03 Yes 20 1_2833 NADH-quinone oxidoreductase subunit N nuoN — — −0.76 4.57E−03 Yes 21 1_2836 NADH-quinone oxidoreductase subunit K nuoK 1.37 3.47E−03 Yes −1.46 2.13E−05 Yes 22 1_2839 NADH-quinone oxidoreductase subunit N nuoN — — −0.92 9.92E−04 Yes 24 1_3654 Fe-S oxidoreductases hemN, hemZ −1.42 3.54E−11 Yes −5.80 4.41E−163 Yes 25 1_3663 (Fe-S)-binding protein NapH −1.45 2.44E−05 Yes −5.61 1.43E−44 Yes Ion ion binding/iron coordination entity transport 1 1_559 Energy transducer TonB tonB — — −1.69 5.89E−05 Yes 2 1_1160 Interacts with outer membrane receptor proteins — — −6.66 1.67E−35 Yes 3 1_1269 Receptor phuR 3.31 1.66E−20 Yes 6.79 9.35E−153 Yes 4 1_2539 Outer-membrane receptor 6.32 1.12E−58 Yes 9.07 4.56E−236 Yes 5 1_2780 Heme ABC transporter permease — — −0.89 6.33E−03 Yes 6 1_2781 Heme ABC transporter permease ccmC −1.86 4.52E−05 −2.28 3.67E−08 Yes 7 1_2783 Cytochrome C biogenesis protein ccmF −1.38 4.83E−04 −1.94 9.54E−09 Yes 8 1_585 Outer membrane receptor proteins, mostly Fe transport cirA 4.22 2.02E−30 Yes 5.91 1.18E−113 Yes 9 1_588 Iron-regulated membrane protein PiuB 3.19 1.33E−12 Yes 5.15 4.71E−70 Yes 10 1_990 Iron-storage protein bfr −2.12 7.84E−04 Yes −2.38 1.79E−05 Yes 11 1_1399 Fe(II)-dependent oxygenase piuC 3.87 8.93E−36 Yes 6.46 3.95E−63 Yes 12 1_1950 Fe2 transport system protein A feoA 1.49 6.27E−03 Yes 3.94 1.83E−28 Yes 13 1_1951 Ferrous iron transport protein B feoB 2.29 7.95E−15 Yes 3.64 1.20E−58 Yes 14 1_3029 Iron-storage protein bfrA −2.35 7.97E−17 Yes −5.02 1.52E−83 Yes Oxidation-reduction process 1 1_16 Mannitol 2-dehydrogenase uxuB — — NO 1.39 9.13E−03 Yes 2 1_106 PFAM DMSO reductase anchor subunit dmsC −0.91 2.46E−04 Yes −1.37 2.59E−08 Yes 3 1_118 Twin-arginine translocation pathway signal protein iorB — — NO −1.09 4.89E−04 Yes 4 1_187 Alcohol dehydrogenase fdh — — NO 1.33 1.97E−03 Yes 5 1_193 Stearoyl-CoA 9-desaturase desC — — NO 2.11 8.89E−08 Yes 6 1_194 Amine oxidase, flavin-containing — — NO 2.07 4.90E−09 Yes 7 1_204 Aldehyde dehydrogenase fdhA — — NO 1.18 6.56E−03 Yes 8 1_279 Pyridine nucleotide-disulfide oxidoreductase ndh — — NO −0.70 1.28E−03 Yes 9 1_294 Ubiquinol oxidase subunit II cioB −2.45 2.11E−05 Yes −2.48 4.54E−06 Yes 10 1_295 Cytochrome D ubiquinol oxidase subunit I cioA −2.93 6.10E−05 Yes −2.90 1.23E−05 Yes 11 1_299 Coproporphyrinogen III oxidase hemF — — NO −0.62 1.50E−03 Yes 12 1_558 Ubiquinone biosynthesis hydroxylase trxB −2.13 1.23E−03 Yes −6.60 4.75E−39 Yes 13 1_575 Putative hydroxylase — — NO −0.95 1.58E−05 Yes 14 1_637 Aminotransferase desA 0.84 2.10E−03 Yes 0.85 6.56E−04 Yes 15 1_655 3-beta hydroxysteroid dehydrogenase cdh1 — — NO −0.99 3.05E−05 Yes 16 1_713 Ccytochrome B5 ctaC — — NO 1.76 1.50E−05 Yes 17 1_717 MFS transporter ctaE — — NO 1.08 8.54E−05 Yes 18 1_772 S-(hydroxymethyl)glutathione dehydrogenase adhC — — NO 1.09 2.36E−08 Yes 19 1_798 Pyruvate dehydrogenase aceE — — NO 0.73 8.78E−04 Yes 20 1_1026 Nitroreductase rutE 1.33 7.31E−04 Yes 1.29 2.89E−06 Yes 21 1_1049 Ketol-acid reductoisomerase ilvC 1.50 2.49E−04 Yes 0.84 3.47E−03 Yes 22 1_1109 Type II citrate synthase gltA — — NO 1.22 9.43E−03 Yes 23 1_1137 Ribonucleoside-diphosphate reductase nrdA 1.65 8.78E−13 Yes 1.01 3.37E−05 Yes 24 1_1145 Nitrate reductase napA −1.45 2.71E−04 Yes −4.42 2.12E−27 Yes 25 1_1289 2OG-Fe(II) oxygenase superfamily — — NO 1.10 5.05E−05 Yes 26 1_1385 Phosphoadenosine phosphosulfate reductase cysH — — NO −1.81 5.66E−06 Yes 27 1_1386 Sulfite reductase cysI — — NO −1.88 2.86E−07 Yes 28 1_1394 Sulfite reductase subunit alpha cysJ 1.84 7.52E−07 Yes 4.08 1.61E−57 Yes 29 1_1399 Fe(II)-dependent oxygenase piuC 3.87 8.93E−36 Yes 6.46 3.95E−63 Yes 30 1_1441 Copper oxidase copA2 4.11 1.53E−07 Yes 4.39 9.74E−10 Yes 31 1_1447 Heavy metal translocating P-type atpase copA1 3.74 3.25E−04 Yes 3.22 1.21E−03 Yes 32 1_1456 Oxidoreductase FAD-binding domain 1.25 1.09E−02 NO 1.68 1.96E−05 Yes 33 1_1516 Ubiquinol-cytochrome C reductase petA — — NO −1.20 4.13E−08 Yes 34 1_1672 (2Fe-2S)-binding protein — — NO −0.86 1.75E−03 Yes 35 1_1728 Glycine dehydrogenase gcvP 0.71 4.02E−03 Yes 0.81 2.18E−03 Yes 36 1_1922 Histidinol dehydrogenase hisD — — NO 5.22 1.40E−37 Yes 37 1_1988 Glucose-fructose oxidoreductase iolG — — NO 1.17 4.67E−03 Yes 38 1_2082 Fumarate reductase sdhA — — NO −0.97 1.11E−04 Yes 39 1_2083 Fumarate reductase sdhA — — NO −0.63 5.52E−03 Yes 40 1_2084 Succinate dehydrogenase sdhB — — NO −0.69 1.85E−03 Yes 41 1_2133 Sulfoxide reductase catalytic subunit YedY msrP — — NO 1.90 1.18E−11 Yes 42 1_2141 FMN-dependent NADH-azoreductase azoR 2.35 7.88E−13 Yes 3.71 9.31E−65 Yes 43 1_2256 2-methylisocitrate dehydratase acnB 1.44 5.97E−06 Yes 3.26 8.88E−36 Yes 44 1_2300 Aldo/keto reductase brachysporum — — NO 2.29 2.51E−17 Yes 45 1_2304 Alcohol dehydrogenase qor, CRYZ 3.10 2.97E−12 Yes 2.67 1.16E−16 Yes 46 1_2351 Xanthine dehydrogenase yagR −0.92 8.88E−03 Yes −1.75 1.60E−13 Yes 47 1_2352 Molybdopterin dehydrogenase FAD-binding yagS — — NO −1.23 4.04E−03 Yes 48 1_2472 FAD-dependent oxidoreductase yhfW — — NO 1.37 3.47E−03 Yes 49 1_2500 NADH dehydrogenase — — NO 2.11 6.74E−04 Yes 50 1_2532 Carboxymuconolactone decarboxylase lpxK — — NO 1.54 5.85E−03 Yes 51 1_2571 Cytochrome O ubiquinol oxidase cyoA — — NO 1.16 6.33E−03 Yes 52 1_2612 Copper oxidase copA2 3.34 4.75E−05 Yes 3.04 1.47E−04 Yes 53 1_2642 3-hydroxyacyl-CoA dehydrogenase fadB 0.63 3.17E−02 NO −1.66 9.44E−09 Yes 54 1_2689 Glutathione peroxidase gpo — — NO 0.66 3.64E−03 Yes 55 1_2788 Cysteine dioxygenase — — NO −2.00 1.21E−07 Yes 56 1_2833 NADH:ubiquinone oxidoreductase subunit N nuoN — — NO −0.76 4.57E−03 Yes 57 1_2835 NADH:ubiquinone oxidoreductase subunit L nuoL — — NO −1.12 1.57E−03 Yes 58 1_2836 NADH-quinone oxidoreductase subunit K nuoK −1.37 1.13E−02 NO −1.46 2.13E−05 Yes 59 1_2839 NADH:ubiquinone oxidoreductase subunit H nuoH — — NO −0.92 9.92E−04 Yes 60 1_2840 NADH dehydrogenase nuoG −0.66 7.77E−03 Yes −1.13 8.27E−08 Yes 61 1_2941 Vi polysaccharide biosynthesis protein VipA/TviB wbpO — — NO 1.94 8.65E−03 Yes 62 1_2950 Catalase/hydroperoxidase HPI(I) katG 4.07 7.96E−25 Yes 2.24 3.03E−11 Yes 63 1_3066 Oxidoreductase namA 1.39 4.09E−03 Yes 1.17 8.33E−07 Yes 64 1_3152 Amino acid dehydrogenase dadA — — NO −0.80 7.87E−03 Yes 65 1_3233 Malate dehydrogenase mdh 0.95 2.01E−03 Yes 0.95 6.66E−05 Yes 66 1_3290 Glutamyl-tRNA reductase hemA −1.03 5.94E−05 Yes −1.35 1.16E−11 Yes 67 1_3317 Pyridine nucleotide transhydrogenase subunit beta pntB — — NO 1.10 2.12E−03 Yes 68 1_3332 Alkyl hydroperoxide reductase subunit C ahpC 3.08 7.63E−37 Yes 1.49 4.51E−14 Yes 69 1_3333 Alkyl hydroperoxide reductase ahpF 3.44 4.35E−10 Yes 0.78 3.39E−04 Yes 70 1_3501 Riboflavin biosynthesis protein RibD ribD — — NO −1.15 8.08E−05 Yes 71 1_3612 Homogentisate 1,2-dioxygenase hmgA — — NO −1.11 3.51E−04 Yes 72 1_3644 tRNA-dihydrouridine synthase A dusA — — NO −0.63 3.02E−03 Yes 73 1_3654 Coproporphyrinogen III oxidase hemN −1.42 3.54E−11 Yes −5.80 4.41E−163 Yes 74 1_3658 Cbb3-type cytochrome c oxidase subunit I ccoN −1.10 1.51E−04 Yes −4.94 5.25E−83 Yes histidine metabolic 1 1_1451 Catalyzes the conversion of N-formimidoyl-L-glutamate to L-glutamate and formamide hutG −2.08 5.41E−06 Yes −2.03 1.00E−07 Yes 2 1_1452 Histidine ammonia-lyase hutH −1.50 4.37E−04 Yes −1.71 5.95E−05 Yes 3 1_1453 Histidine utilization repressor hutC −2.21 1.16E−09 Yes −1.44 4.84E−03 Yes 4 1_1921 ATP phosphoribosyltransferase hisG — — 4.90 1.34E−22 Yes 5 1_1922 Histidinol dehydrogenase hisD — — 5.22 1.40E−37 Yes 6 1_1923 Histidinol-phosphate aminotransferase hisC — — 5.23 1.34E−50 Yes 7 1_1924 Imidazoleglycerol-phosphate dehydratase hisB — — 5.55 7.17E−74 Yes 8 1_1925 Imidazole glycerol phosphate synthase hisH — — 5.45 7.90E−111 Yes 9 1_1926 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase hisA — — 5.03 4.99E−52 Yes 10 1_1927 Imidazole glycerol phosphate synthase hisF — — 5.36 1.93E−53 Yes 11 1_1928 Phosphoribosyl-ATP pyrophosphatase hisI — — 5.21 6.97E−54 Yes Sulfur metabolism 1 1_193 Stearoyl-CoA 9-desaturase desC 2.11 8.89E−08 Yes 2 1_1149 Cysteine synthase cysK 0.79 3.56E−02 0.83 1.13E−02 NO 3 1_1385 Phosphoadenosine phosphosulfate reductase cysH 3.13 4.07E−09 Yes 4 1_1386 Sulfite reductase cysI 1.78 1.40E−05 Yes 5 1_1394 Sulfite reductase, alpha subunit (Flavoprotein) cysJ 1.84 7.52E−07 Yes −1.81 5.66E−06 Yes 6 1_1314 Homoserine acetyltransferase metX −1.88 2.86E−07 Yes 7 1_1315 Cystathionine gamma-synthase metB 4.08 1.61E−57 Yes Oxidative phosphorylation 1_279 Pyridine nucleotide-disulfide oxidoreductase ndh 1_479 Cytochrome ccoP 1_1516 Ubiquinol-cytochrome C reductase petA 1_1824 CYTH domain protein cyaA 1_2081 Succinate dehydrogenase sdhD, frdD 1_2082 Fumarate reductase sdhA, frdA 1_2083 Fumarate reductase sdhA, frdA 1_2084 Succinate dehydrogenase sdhB, frdB 1_2571 Cytochrome O ubiquinol oxidase cyoA 1_2836 NADH-quinone oxidoreductase subunit K nuoK 1_2839 NADH:ubiquinone oxidoreductase subunit H nuoH 1_2840 NADH dehydrogenase nuoG 1_3658 Cbb3-type cytochrome c oxidase subunit I ccoN 1_3659 Peptidase S41 ccoO 1_3661 Cytochrome C oxidase subunit III ccoP
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