Table 2.
Selected NaOCl-sensitive proteins with >10% increased thiol-oxidations under NaOCl stress in M. smegmatis as revealed using the OxICAT method.
| Locus tag | Gene name | Protein function | Cys (a, b) | Buried/Exposed (d) | OxICAT Wild type | OxICAT ΔmshC | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| % Diff NaOCl/Co (e) | % ox Co (f) | % ox NaOCl (f) | % Diff NaOCl/Co (e) | % ox Co (f) | % ox NaOCl (f) | |||||
| Detoxification and adaptation to atypical environments | ||||||||||
| MSMEG_0127 | adhE1 | Alcohol DH, zinc-containing | 48* | B | 32,0 | 13,5 | 45,5 | 13,8 | 19,5 | 33,3 |
| MSMEG_0217 | adhB | Alcohol DH, zinc-containing | 105* | B | 39,1 | 20,1 | 64,8 | |||
| MSMEG_5866 | adhB2 | Alcohol DH, zinc-containing | 106* | B | 35,7 | 20,9 | 55,2 | 16,9 | 28,8 | 45,7 |
| MSMEG_4340 | adhE2 | Alcohol DH, zinc-containing | 107* | B | 33,1 | 23,8 | 54,2 | 15,3 | 34,8 | 50,0 |
| 145 | B | 34,6 | 18,0 | 43,8 | 18,5 | 28,7 | 47,2 | |||
| MSMEG_1138 | MSMEG_1138 | Alcohol DH, zinc-containing | 113* | B | 26,0 | 16,5 | 43,8 | |||
| MSMEG_4400 | MSMEG_4400 | Alcohol DH, zinc-containing | 65 | B | 27,8 | 6,4 | 34,1 | |||
| MSMEG_1977 | MSMEG_1977 | Alcohol DH, zinc-containing | 39* | B | 22,8 | 14,5 | 30,0 | 11,9 | 12,6 | 27,5 |
| MSMEG_0595 | MSMEG_0595 | Fe-S oxidoreductase | 142* | B | 13,9 | 12,4 | 23,4 | 7,6 | 30,2 | 37,8 |
| MSMEG_0690 | MSMEG_0690 | Fe-S oxidoreductase | 637* | B | 11,5 | 22,7 | 38,8 | 8,2 | 38,5 | 45,2 |
| MSMEG_0768 | MSMEG_0768 | Rhodanese domain protein | 83* | B | 42,6 | 17,2 | 55,5 | 23,0 | 30,5 | 53,8 |
| MSMEG_6425 | MSMEG_6425 | Rhodanese-domain protein | 66* | B | 14,0 | 7,1 | 20,9 | 7,8 | 13,1 | 22,7 |
| MSMEG_1416 | MSMEG_1416 | Pyridine nucleotide-disulfide oxidoreductase | 159 | B | 11,4 | 12,0 | 20,3 | 12,5 | 14,3 | 26,7 |
| MSMEG_1566 | MSMEG_1566 | Oxidoreductase | 122 | B | 14,2 | 15,1 | 24,9 | |||
| MSMEG_2263 | hybC | Cytochrome-c3 hydrogenase | 58 | B | 29,3 | 21,7 | 49,7 | 3,8 | 30,7 | 37,9 |
| MSMEG_2297 | nrdH | Glutaredoxin | 11* | B | 14,2 | 45,7 | 56,1 | 15,0 | 57,7 | 69,2 |
| MSMEG_2421 | osmC | OsmC family protein | 48* | B | 26,2 | 13,1 | 38,4 | 4,9 | 23,2 | 29,2 |
| 116* (MSH) | B | 10,5 | 12,7 | 22,8 | 13,0 | 18,3 | 32,3 | |||
| MSMEG_2784 | msrB2 | Methionine sulfoxide reductase | 51* | B | 14,2 | 27,0 | 37,7 | 2,2 | 36,3 | 38,5 |
| MSMEG_3479 | tpx | Thiol peroxidase | 60* (MSH;Cys) | B | 11,6 | 29,1 | 39,9 | 8,9 | 37,8 | 48,0 |
| MSMEG_4085 | MSMEG_4085 | Nitrilotriacetate monooxygenase | 336 | B | 31,2 | 14,3 | 32,2 | |||
| MSMEG_4309 | ptpA | LMW protein-tyrosine-phosphatase | 10* | B | 22,2 | 11,2 | 30,6 | |||
| 58 | E | 41,1 | 47,7 | 79,9 | 10,2 | 17,3 | 31,5 | |||
| Transcription and Transcriptional regulators | ||||||||||
| MSMEG_0219 | MSMEG_0219 | RNA polymerase sigma factor | 271 | B | 17,5 | 10,3 | 28,9 | 5,7 | 16,8 | 26,8 |
| MSMEG_1367 | rpoB | RNA polymerase beta SU | 674 | B | 20,3 | 25,3 | 45,6 | 15,3 | 44,3 | 59,6 |
| MSMEG_1368 | rpoC | RNA polymerase beta’ SU | 48* | B | 19,6 | 14,3 | 29,5 | |||
| MSMEG_1515 | MSMEG_1515 | Two-component sensor histidine kinase | 5 | E | 35,6 | 13,1 | 48,5 | 13,2 | 39,2 | 58,3 |
| MSMEG_1831 | whiB2 | Transcriptional regulator WhiB2 | 67* | B | 12,6 | 20,0 | 31,7 | |||
| 99* | B | 10,5 | 33,6 | 44,9 | ||||||
| MSMEG_1874 | mtrA | Two-component response regulator MtrA | 68* | B | 10,1 | 2,1 | 11,1 | |||
| MSMEG_1915 | rshA | Anti-sigma-factor for SigmaH (RshA) | 76* | B | 38,2 | 15,8 | 53,2 | |||
| MSMEG_5071 | rseA | Anti-sigma-factor for SigmaE (RseA) | 67* | B | 37,5 | 41,8 | 63,4 | −3,4 | 49,1 | 45,7 |
| MSMEG_2743 | nrdR | Transcriptional repressor NrdR | 71* | B | 24,9 | 7,0 | 30,9 | |||
| MSMEG_4471 | MSMEG_4471 | MarR-family transcriptional regulator | 58 | B | 42,3 | 12,3 | 54,0 | 34,6 | 25,8 | 61,1 |
| MSMEG_4487 | furB | Ferric uptake regulator FurB | 124* | B | 17,4 | 30,2 | 42,6 | 10,9 | 35,4 | 47,2 |
| MSMEG_5768 | MSMEG_5768 | TetR family transcriptional regulator | 61 | E | 22,7 | 12,5 | 22,7 | |||
| Protein biosynthesis and quality control | ||||||||||
| MSMEG_1339 | rpmG | 50 S ribosomal protein L33-1 | 15* | B | 23,9 | 30,5 | 53,4 | |||
| MSMEG_1468 | rpsN | 30 S ribosomal protein S14 type Z | 27* | B | 19,6 | 41,5 | 60,1 | 13,0 | 32,5 | 45,5 |
| MSMEG_1520 | rpmJ | 50 S ribosomal protein L36 | 27* | B | 33,5 | 21,7 | 43,6 | 13,5 | 22,4 | 35,9 |
| MSMEG_1521 | rpsM | 30 S ribosomal protein S13 | 86* (MSH;Cys) | B | 21,8 | 10,4 | 32,9 | 20,2 | 14,7 | 34,4 |
| MSMEG_1579 | rimI | Alanine acetyltransferase | 55 | B | 38,4 | 9,7 | 51,0 | |||
| MSMEG_1878 | MSMEG_1878 | 30 S ribosomal protein S30 | 83 | E | 40,4 | 46,7 | 84,6 | 22,7 | 59,7 | 82,6 |
| MSMEG_2400 | rpmB | 50 S ribosomal protein L28 | 5* | B | 35,7 | 40,3 | 74,5 | 26,5 | 41,8 | 70,4 |
| 52 | B | 36,8 | 42,7 | 76,9 | 24,8 | 48,3 | 74,2 | |||
| MSMEG_4951 | rpmE | 50 S ribosomal protein L31 | 16* | B | 20,2 | 22,2 | 39,6 | 14,5 | 22,4 | 32,9 |
| MSMEG_6895 | rpsR2 | 30 S ribosomal protein S18-2 | 20* | B | 24,6 | 73,6 | 84,8 | 8,9 | 76,0 | 84,9 |
| 57* (MSH;Cys) | B | 10,7 | 11,4 | 21,2 | 7,3 | 15,2 | 23,4 | |||
| MSMEG_0839 | lon1 | ATP-dependent protease | 72 (MSH) | B | 25,7 | 11,1 | 38,5 | |||
| Glycolysis/Gluconeogenesis and TCA cycle | ||||||||||
| MSMEG_0935 | gpmA | 2,3-bisphosphoglycerate-mutase | 149 | E | 20,0 | 7,3 | 27,9 | 9,9 | 13,6 | 22,0 |
| MSMEG_0970 | MSMEG_0970 | Phosphoglycerate mutase | 146 | B | 10,6 | 13,4 | 21,5 | |||
| MSMEG_1547 | pduC | Glycerol dehydratase large SU | 156 | B | 12,2 | 20,6 | 31,0 | 8,3 | 37,5 | 46,5 |
| 168 | B | 11,1 | 19,3 | 31,6 | 4,9 | 32,6 | 37,6 | |||
| 342* | B | 15,4 | 7,9 | 20,6 | 12,4 | 21,4 | 33,1 | |||
| Selected NaOCl-sensitive proteins with >10% increased thiol-oxidations under NaOCl stress in M. smegmatis | ||||||||||
| MSMEG_3227 | pyk2 | Pyruvate kinase | 9* | B | 10,6 | 10,1 | 20,6 | 8,7 | 21,2 | 30,4 |
| MSMEG_5239 | glpX | Fructose-1,6-bisphosphatase | 205 | B | 12,5 | 13,7 | 23,9 | |||
| MSMEG_6759 | glpK3 | Glycerol kinase | 294 (MSH) | B | 10,7 | 8,9 | 16,8 | 9,9 | 19,9 | 29,8 |
| MSMEG_0911 | aceA | Isocitrate lyase | 191 | B | 11,3 | 8,5 | 20,8 | 11,0 | 22,3 | 33,7 |
| 268 (MSH) | B | 11,4 | 12,7 | 20,3 | 12,8 | 24,8 | 37,6 | |||
| MSMEG_1670 | sdhA2 | Succinate DH | 385 | B | 15,5 | 31,0 | 35,1 | |||
| MSMEG_3640 | glcB | Malate synthase G | 612* | B | 12,8 | 9,7 | 20,9 | |||
| MSMEG_4645 | orB | a-OG ferredoxin oxidoreductase, beta SU | 59* | B | 10,1 | 9,4 | 20,9 | |||
| MSMEG_5676 | citA | Citrate (Si) synthase | 143* (MSH;Cys) | E | 14,2 | 4,8 | 19,0 | 7,5 | 13,0 | 20,5 |
| Metabolism of Fatty acid and phospholipids | ||||||||||
| MSMEG_0913 | umaA | Methoxy mycolic acid synthase 1 | 76* (MSH) | B | 10,5 | 9,1 | 17,6 | |||
| MSMEG_1340 | MSMEG_1340 | (3 R)-hydroxyacyl-ACP dehydratase SU HadA | 105 | B | 15,5 | 4,7 | 19,7 | 16,9 | 12,7 | 29,6 |
| MSMEG_1342 | MSMEG_1342 | (3 R)-hydroxyacyl-ACP dehydratase SU HadC | 127 | B | 14,0 | 8,7 | 22,0 | 2,8 | 24,5 | 39,7 |
| MSMEG_1553 | eutB | Ethanolamine ammonia-lyase | 36 | B | 10,6 | 6,1 | 16,0 | 6,5 | 15,0 | 20,1 |
| MSMEG_1554 | eutC | Ethanolamine ammonia-lyase light chain | 204* | B | 11,7 | 15,7 | 26,4 | |||
| MSMEG_1807 | accA3 | Acetyl-/propionyl-CoA carboxylase alpha chain | 236* | B | 13,4 | 12,6 | 26,0 | 22,8 | 25,7 | 45,7 |
| MSMEG_1813 | accD5 | Methylmalonyl-CoA carboxyltransferase | 356 (MSH;Cys) | B | 11,5 | 17,2 | 26,4 | 10,7 | 30,9 | 41,6 |
| MSMEG_2207 | MSMEG_2207 | Beta-ketothiolase | 9 | B | 12,9 | 11,0 | 26,2 | −2,9 | 39,4 | 36,9 |
| MSMEG_4116 | MSMEG_4116 | 3-hydroxyacyl-CoA DH | 148 | B | 18,8 | 12,9 | 34,4 | |||
| MSMEG_4327 | kasA | 3-oxoacyl-(Acyl-carrier-protein) synthase 1 | 171* | B | 28,0 | 15,4 | 50,0 | |||
| MSMEG_4328 | kasB2 | 3-oxoacyl-(Acyl-carrier-protein) synthase 1 | 227 | B | 26,0 | 11,7 | 36,0 | 12,2 | 21,6 | 34,9 |
| MSMEG_4329 | accD6 | Acetyl/propionyl-CoA carboxylase (Beta SU) | 191 | B | 19,5 | 14,2 | 32,7 | 14,6 | 28,2 | 38,4 |
| 213 | E | 15,7 | 13,8 | 27,1 | ||||||
| 294 (MSH) | B | 13,0 | 9,6 | 20,3 | ||||||
| MSMEG_4920 | MSMEG_4920 | Acetyl-CoA acetyltransferase | 107* | B | 43,0 | 0,6 | 43,3 | |||
| 398* | B | 32,2 | 5,4 | 38,1 | ||||||
| MSMEG_5199 | MSMEG_5199 | Acetyl-CoA acetyltransferase | 55 | B | 11,8 | 4,5 | 12,2 | |||
| MSMEG_5273 | fadA3 | Acetyl-CoA acetyltransferase | 90* | B | 20,0 | 8,7 | 28,0 | |||
| 390* | B | 20,8 | 9,0 | 21,8 | ||||||
| MSMEG_5291 | MSMEG_5291 | Acyl-CoA synthase | 16 | B | 17,1 | 4,5 | 22,5 | 20,2 | 12,0 | 32,2 |
| 359 | B | 17,7 | 7,2 | 22,8 | 8,1 | 16,3 | 30,1 | |||
| Metabolism of nucleotides | ||||||||||
| MSMEG_1602 | guaB | Inosine-5′-monophosphate DH | 325* (MSH) | B | 19,3 | 5,5 | 24,1 | 22,0 | 11,1 | 30,4 |
| MSMEG_3634 | guaB2 | Inosine-5′-monophosphate DH | 302* (MSH) | B | 33,4 | 8,2 | 44,6 | 8,4 | 18,2 | 29,2 |
| 321 | B | 15,5 | 12,6 | 32,0 | 7,8 | 12,5 | 20,5 | |||
| Metabolism of cofactors | ||||||||||
| MSMEG_0789 | thiE | Thiamine-P synthase | 20 | B | 24,1 | 5,1 | 28,2 | 18,0 | 19,5 | 37,9 |
| MSMEG_0791 | thiO | Glycine oxidase | 32 | B | 44,3 | 1,2 | 42,5 | 26,1 | 9,5 | 36,3 |
| MSMEG_0793 | thiG | Thiazole synthase | 75* (MSH) | B | 10,3 | 9,1 | 17,6 | |||
| MSMEG_2671 | folA | Dihydrofolate reductase | 106 | B | 47,5 | 10,5 | 49,8 | 38,6 | 14,9 | 51,9 |
| MSMEG_3067 | ribD | Riboflavin biosynthesis protein RibD | 78* | B | 47,4 | 8,5 | 56,4 | |||
| MSMEG_3072 | ribAB | Riboflavin biosynthesis protein RibBA | 264* | B | 19,3 | 52,3 | 65,2 | 7,3 | 61,7 | 69,1 |
| MSMEG_3126 | MSMEG_3126 | Nitrogen fixation protein NifU | 38* | B | 18,1 | 22,4 | 38,9 | 7,3 | 32,8 | 41,7 |
| MSMEG_4272 | yfhF2 | HesB/YadR/YfhF family protein | 47* (MSH) | B | 11,0 | 19,5 | 28,3 | 3,8 | 29,2 | 36,9 |
| MSMEG_4827 | MSMEG_4827 | Acyl-CoA DH | 44 (MSH) | E | 32,5 | 35,4 | 66,7 | |||
| MSMEG_5698 | moaA | Cyclic pyranopterin monoP synthase | 50* | B | 24,3 | 33,2 | 54,4 | 3,7 | 42,3 | 44,0 |
| 305* | B | 19,0 | 24,0 | 44,6 | ||||||
Selected NaOCl-sensitive proteins with >10% increased thiol-oxidations in response to NaOCl stress in M. smegmatis as revealed using the OxICAT method. The M. smegmatis wild type and mshC mutant were harvested before (control) and 30 min after exposure to 1 and 0.5 mM NaOCl, respectively. Reduced and reversibly oxidized Cys residues were labelled with light and heavy ICAT, respectively, using OxICAT. Quantification of % thiol-oxidations was performed using MaxQuant software. The table includes MSMEG accessions, protein names, functions, surface accessabilities and % oxidation of Cys residues under control and NaOCl. (a) Conserved Cys are bold. (b) S-mycothiolated or S-cysteinylated Cys are marked with (+MSH) and (+Cys). (d) Relative surface accessibility (RSA) for buried (B) or exposed (E) Cys residues. (e) The % thiol-oxidation of each identified Cys peptide was calculated using MaxQuant. Based on the % thiol-oxidation of each Cys under control and NaOCl stress conditions, the % oxidation increase (% Diff NaOCl/co) was calculated under NaOCl-treatment and (f) average values are shown from at least three independent biological replicates. Selected NaOCl-sensitive peptides with >10% increased thiol-oxidation under NaOCl stress are shown here as a subset of the complete Tables S3–S4.