Table 1.
Genes of Staphylococcus xylosus discussed in this study differentially expressed over time in meat in the presence of nitrate and nitrite.
| Functional category and family | Gene ID | Gene name | Protein | Mean ratio of expression | |
|---|---|---|---|---|---|
| 24 h | 72 h | ||||
| P: INORGANIC ION TRANSPORT AND METABOLISM | |||||
| Iron | SXYL_02116 | sstA | Iron compound ABC transporter, permease protein SstA | 2.8 | 3.3 |
| SXYL_02115 | sstB | Iron compound ABC transporter, permease protein SstB | 3.1 | 5.3 | |
| SXYL_02114 | sstC | Iron compound ABC transporter, ATP-binding protein SstC | 2.5 | 3.9 | |
| SXYL_02113 | sstD | Lipoprotein SstD | 2.5 | 3.8 | |
| SXYL_02202 | fhuB | ABC-type cobalamin Fe3+-siderophores transport system permease component | 2.6 | 1.8 | |
| SXYL_02203 | fhuC | ABC-type cobalamin Fe3+-siderophores transport system ATPase component | 2.7 | ||
| SXYL_02201 | fhuG | ABC-type cobalamin/Fe3+-siderophores transport systems, permease components | 2.2 | 1.8 | |
| SXYL_00667 | fhuD1 | Iron(3+)-hydroxamate-binding protein | 2.3 | 1.8 | |
| SXYL_02681 | fhuD2 | Iron(3+)-hydroxamate-binding protein | 2.0 | 1.8 | |
| SXYL_00748 | sfaA | Transporter SfaA | 1.9 | 1.6 | |
| SXYL_00749 | sfaB | Siderophore biosynthesis protein, IucA/IucC family | 1.7 | 1.4 | |
| SXYL_00750 | sfaC | amino acid racemase | 1.5 | 1.3 | |
| SXYL_00747 | sfaD | Siderophore biosynthesis protein, IucA/IucC family | 2.4 | 2.0 | |
| SXYL_00751 | htsA | Iron compound ABC transporter, iron compound-binding protein | 3.1 | 2.5 | |
| SXYL_00752 | htsB | Iron compound ABC transporter, permease protein | 1.7 | 2.0 | |
| SXYL_00753 | htsC | Iron compound ABC transporter, permease protein | 1.7 | 1.9 | |
| SXYL_00755 | isdG | Heme-degrading monooxygenase | 2.0 | ||
| SXYL_00944 | ftnA | Ferritin | 1.6 | ||
| Manganese | SXYL_01831 | mntH | Divalent metal cation transporter MntH | 1.5 | 2.3 |
| Magnesium | SXYL_01923 | mgtE | Divalent cation transporter MgtE | 0.7 | |
| O: POST-TRANSLATIONAL MODIFICATION, PROTEIN TURNOVER, CHAPERONES | |||||
| Antioxidant defenses | SXYL_02505 | katA | Catalase A | 0.3 | 0.6 |
| SXYL_01551 | katB | Catalase B | 2.3 | ||
| SXYL_02533 | katC | Catalase C | 2.3 | ||
| SXYL_02534 | ahpC | Alkyl hydroperoxide reductase subunit C | 2.0 | ||
| SXYL_02083 | trxB | Thioredoxin reductase | 1.6 | ||
| SXYL_00973 | bcp | Bacterioferritin comigratory protein | 2.0 | ||
| SXYL_01572 | bsaA | Glutathione peroxidase | 2.2 | ||
| SXYL_00570 | Ferredoxin–NADP reductase | 2.4 | 1.9 | ||
| SXYL_00895 | Nitroreductase family protein | 1.8 | |||
| SXYL_02021 | Nitroreductase family protein | 2.1 | |||
| SXYL_00410 | Putative NAD(P)H nitroreductase | 1.9 | |||
| SXYL_01517 | msrA1 | Peptide methionine sulfoxide reductase MsrA 1 | 1.5 | ||
| Chaperones | SXYL_00898 | groS | 10 kDa chaperonin | 2.0 | |
| SXYL_02418 | hslO | 33 kDa chaperonin | 1.9 | ||
| SXYL_02396 | clpC | ATP-dependent Clp protease ATP-binding subunit ClpC | 2.1 | ||
| G: CARBOHYDRATE TRANSPORT AND METABOLISM | |||||
| SXYL_02255 | Phosphotransferase system (PTS) maltose-specific enzyme IICB component | 2.3 | |||
| SXYL_00253 | PTS system, glucose-specific IIBC component | 0.5 | |||
| SXYL_00278 | PTS system, fructose-specific IIABC components | 3.4 | |||
| SXYL_00626 | PTS system arbutin-like IIBC component | 1.5 | |||
| SXYL_01351 | malA | Alpha-D-1,4-glucosidase | 1.9 | ||
| SXYL_01960 | pgi | Glucose-6-phosphate isomerase | 2.2 | ||
| SXYL_00426 | fbp | Fructose-1,6-bisphosphatase | 1.8 | ||
| SXYL_00039 | iolJ | Fructose-bisphosphate aldolase, class II | 1.9 | ||
| SXYL_00221 | fda | Fructose-bisphosphate aldolase class 1 | 2.5 | ||
| SXYL_01518 | rbsB | Ribose ABC transporter substrate-binding protein | 2.2 | ||
| SXYL_01519 | rbsC | Ribose ABC transporter permease | 2.3 | ||
| SXYL_01521 | rbsD | D-ribose pyranase | 2.1 | ||
| SXYL_00125 | araA | L-arabinose isomerase | 0.4 | ||
| SXYL_00124 | araD | L-ribulose-5-phosphate 4-epimerase | 0.4 | ||
| SXYL_00126 | araT | Arabinose-proton symporter | 0.6 | ||
| SXYL_00607 | araB1 | Ribulokinase | 2.0 | ||
| SXYL_02331 | araB2 | Ribulokinase | 0.5 | ||
| E: AMINO ACID TRANSPORT AND METABOLISM | |||||
| Valine, leucine, isoleucine | SXYL_02474 | brnQ1 | Branched-chain amino acid transport system II carrier protein | 0.3 | 0.5 |
| SXYL_00871 | leuA | 2-isopropylmalate synthase | 0.2 | 0.2 | |
| SXYL_00870 | leuB | 3-isopropylmalate dehydrogenase | 0.2 | 0.2 | |
| SXYL_00869 | leuC | 3-isopropylmalate dehydratase large subunit | 0.2 | 0.2 | |
| SXYL_00868 | leuD | 3-isopropylmalate dehydratase small subunit | 0.2 | 0.3 | |
| SXYL_00867 | ilvA | L-threonine dehydratase biosynthetic IlvA | 0.3 | 0.3 | |
| SXYL_00874 | ilvB | Acetolactate synthase | 0.3 | 0.2 | |
| SXYL_00872 | ilvC | Ketol-acid reductoisomerase | 0.2 | 0.2 | |
| SXYL_00875 | ilvD1 | Dihydroxy-acid dehydratase | 0.3 | 0.2 | |
| Glycine, serine, threonine | SXYL_01317 | gcvT | Aminomethyltransferase | 3.5 | |
| SXYL_01318 | gcvPA | Probable glycine dehydrogenase [decarboxylating] subunit 1 | 3.6 | ||
| SXYL_01319 | gcvPB | Probable glycine dehydrogenase [decarboxylating] subunit 2 | 3.0 | ||
| SXYL_02528 | sdaAA1 | L-serine dehydratase, iron-sulfur-dependent, alpha subunit | 0.6 | ||
| SXYL_02529 | sdaAB1 | L-serine dehydratase subunit beta | 0.5 | ||
| Methionine | SXYL_00012 | Homoserine O-acetyltransferase | 0.5 | ||
| Tryptophan, phenylalanine, tyrosine | SXYL_01497 | trpA | Tryptophan synthase alpha chain | 0.6 | 0.5 |
| SXYL_01498 | trpB | Tryptophan synthase beta chain | 0.4 | ||
| SXYL_01500 | trpC | Indole-3-glycerol phosphate synthase | 0.6 | 0.4 | |
| SXYL_01501 | trpD | Anthranilate phosphoribosyltransferase | 0.5 | 0.4 | |
| SXYL_01502 | trpG | Anthranilate synthase component II | 0.5 | 0.4 | |
| SXYL_01503 | trpE | Anthranilate synthase component I | 0.5 | 0.4 | |
| SXYL_01128 | DAHP synthetase-chorismate mutase | 0.5 | |||
| SXYL_01513 | tyrA | Prephenate dehydrogenase | 3.1 | ||
| SXYL_00922 | pheA | Prephenate dehydratase | 0.6 | ||
| SXYL_02022 | aroD | 3-dehydroquinate dehydratase | 1.7 | ||
| SXYL_01261 | aroE | Shikimate dehydrogenase | 0.6 | ||
| SXYL_01316 | aroK | Shikimate kinase | 0.5 | ||
| Urea, arginine, aspartate | SXYL_00296 | ureA | Urease gamma subunit | 3.1 | |
| SXYL_00294 | ureC | Urease subunit alpha | 3.3 | ||
| SXYL_00290 | ureD | Urease accessory protein UreD | 3.0 | ||
| SXYL_00291 | ureG | Urease accessory protein UreG | 3.0 | ||
| SXYL_00293 | ureE | Urease accessory protein ureE | 2.6 | ||
| SXYL_00292 | ureF | Urease accessory protein UreF | 2.7 | ||
| SXYL_00238 | rocD1 | Ornithine aminotransferase 1 | 0.6 | ||
| SXYL_00241 | argB | Acetylglutamate kinase | 0.6 | ||
| SXYL_00239 | argC | N-acetyl-gamma-glutamyl-phosphate reductase | 0.6 | ||
| SXYL_02450 | Arginine/lysine/ornithine decarboxylase | 0.7 | |||
| SXYL_01961 | argG | Argininosuccinate synthase | 1.6 | ||
| SXYL_01373 | asnA | L-asparaginase | 1.9 | ||
| Peptidase | SXYL_01980 | ampA | Cytosol aminopeptidase | 1.9 | |
| SXYL_01931 | Oligoendopeptidase F | 1.7 | |||
| SXYL_01348 | Peptidase T-like protein | 1.6 | |||
| SXYL_00377 | dapE | Probable succinyl-diaminopimelate desuccinylase | 2.3 | ||
| Glycine, betaine, carnitine, choline | SXYL_00488 | opuCA | Glycine betaine/carnitine/choline ABC transporter | 0.3 | |
| SXYL_00489 | opuCB | ABC-type proline glycine betaine transport system permease component | 0.3 | ||
| SXYL_00490 | opuCC | Glycine betaine/carnitine/choline ABC transporter opuCC | 0.3 | 1.8 | |
| SXYL_00491 | opuCD | ABC-type proline glycine betaine transport system permease component | 0.3 | 2.0 | |
| SXYL_01535 | opuD1 | Glycine betaine transporter | 0.5 | 0.5 | |
| C: ENERGY PRODUCTION AND CONVERSION | |||||
| SXYL_00830 | atpD | ATP synthase subunit beta | 0.7 | ||
| NA(+)/H(+) antiporter | SXYL_01976 | mnhG1 | Na(+)/H(+) antiporter subunit G1 | 1.4 | |
| SXYL_02226 | mnhA2 | Putative antiporter subunit A2 | 0.6 | 1.3 | |
| SXYL_02223 | mnhD2 | Putative antiporter subunit D2 | 0.5 | ||
| SXYL_02222 | mnhE2 | Putative antiporter subunit E2 | 0.5 | ||
| SXYL_02221 | mnhF2 | Putative antiporter subunit F2 | 0.5 | ||
| SXYL_02220 | mnhG2 | Putative antiporter subunit G2 | 0.6 | ||
| SXYL_00623 | Putative Na(+)/H(+) antiporter | 0.5 | 0.3 | ||
| SXYL_00425 | Na(+)/H(+) exchanger | 0.6 | |||
| SXYL_00363 | nhaC | Na(+)/H(+) antiporter NhaC | 2.0 | 2.2 | |
| M: CELL WALL/MEMBRANE BIOGENESIS | |||||
| SXYL_01990 | dltA | D-alanine—poly(phosphoribitol) ligase subunit 1 | 0.3 | 0.7 | |
| SXYL_01989 | dltB | D-alanyl transfer protein DltB | 0.3 | 0.7 | |
| SXYL_01988 | dltC | D-alanine—poly(phosphoribitol) ligase subunit 2 | 0.2 | ||
| SXYL_01987 | dltD | D-alanyl-lipoteichoic acid biosynthesis protein DltD | 0.2 | 0.7 | |
| F: NUCLEOTIDE TRANSPORT AND METABOLISM | |||||
| SXYL_02117 | nrdF | Ribonucleoside-diphosphate reductase beta chain | 1.7 | 3.7 | |
| SXYL_02119 | nrdI | Protein NrdI | 1.6 | 3.1 | |
| SXYL_00150 | nrdG | Anaerobic ribonucleotide reductase activating protein | 0.3 | ||
| H: COENZYME TRANSPORT AND METABOLISM | |||||
| SXYL_02415 | folB | Dihydroneopterin aldolase | 1.7 | 1.3 | |
| SXYL_01872 | folD | Bifunctional protein FolD | 2.4 | 1.4 | |
| SXYL_02414 | folK | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase | 1.4 | ||
| SXYL_02416 | folP | Dihydropteroate synthase | 1.7 | ||
| L: REPLICATION, RECOMBINATION AND REPAIR | |||||
| SXYL_01397 | nth | Endonuclease III | 1.4 | ||
| SXYL_01796 | uvrC | UvrABC system protein C | 1.8 | 1.4 | |
| K: TRANSCRIPTION, REGULATORS | |||||
| SXYL_00975 | perR | Peroxide-responsive repressor PerR | 2.0 | ||
| SXYL_00784 | czrA | Zinc and cobalt transport repressor CzrA | 2.1 | ||
| SXYL_01275 | hrcA | Heat-inducible transcription repressor HrcA | 0.7 | ||
| SXYL_01250 | greA | Transcription elongation factor GreA | 0.5 | ||
| SXYL_01657 | fapR | Transcription factor FapR | 0.6 | 0.7 | |
| SXYL_01129 | ccpA | Catabolite control protein A | 1.8 | ||