Table 1.
Genes expressed differentially in strain 1457ΔlytSR compared to the wild-type strain
| ORF | Gene name | Description or predicted function | Expression ratio (Mutant/WT) |
|---|---|---|---|
| Amino acid biosynthesis | |||
| SERP0034 | metE | 5-methyltetrahydropteroyltriglutamate homocysteine methyltransferase | 2.096 |
| SERP0108 | gltB | glutamate synthase large subunit | 2.405 |
| SERP0548 | argH | argininosuccinate lyase | 5.03 |
| SERP1103 | aroK | shikimate kinase | 2.274 |
| SERP1668 | ilvC | ketol-acid reductoisomerase | 2.087 |
| SERP1669 | leuA | 2-isopropylmalate synthase | 2.344 |
| SERP1670 | leuB | 3-isopropylmalate dehydrogenase | 2.229 |
| SERP1671 | leuC | 3-isopropylmalate dehydratase small subunit | 11.45 |
| SERP2301 | hisF | imidazoleglycerol phosphate synthase, cyclase subunit | 5.429 |
| Amino acid transport | |||
| SERP0392 | di-tripeptide transporter, putative | 3.362 | |
| SERP0571 | oppC | oligopeptide transport system permease protein OppC | 12.38 |
| SERP0950 | peptide ABC transporter, ATP-binding protein, putative | 3.383 | |
| SERP1440 | putP | proline permease | 2.124 |
| SERP1935 | gltS | sodium:glutamate symporter | 3.267 |
| Inorganic ion transport and metabolism | |||
| SERP0284 | Na+/H+ antiporter, MnhD component, putative | 3.294 | |
| SERP0287 | Na+/H+ antiporter, MnhG component, putative | 2.576 | |
| SERP0660 | cobalt transport family protein | 2.718 | |
| SERP1777 | iron compound ABC transporter, iron | 2.383 | |
| SERP1859 | modC | molybdenum transport ATP-binding protein | 3.294 |
| SERP2428 | arsA | arsenical pump-driving ATPase | 3.274 |
| Protein synthesis | |||
| SERP0721 | pheS | Phe-tRNA synthetase alpha chain | 2.036 |
| SERP1809 | infA | translation initiation factor IF-1 | 0.5 |
| SERP1812 | rplO | ribosomal protein L15 | 0.482 |
| SERP1813 | rpmD | ribosomal protein L30 | 0.333 |
| SERP1814 | rpsE | 30 S ribosomal protein S5 | 0.37 |
| SERP1815 | rplR | 50 S ribosomal protein L18 | 0.323 |
| SERP1816 | rplF | 50 S ribosomal protein L6 | 0.332 |
| SERP1817 | rpsH | 30 S ribosomal protein S8 | 0.357 |
| SERP1818 | rpsN-2 | 30 S ribosomal protein S14 | 0.306 |
| SERP1819 | rplE | 50 S ribosomal protein L5 | 0.324 |
| SERP1821 | rplN | 50 S ribosomal protein L14 | 0.346 |
| SERP1820 | rplX | 50 S ribosomal protein L24 | 0.356 |
| SERP1822 | rpsQ | 30 S ribosomal protein S17 | 0.344 |
| SERP1823 | rpmC | 50 S ribosomal protein L29 | 0.332 |
| SERP1824 | rplP | 50 S ribosomal protein L16 | 0.438 |
| SERP1825 | rpsC | 30 S ribosomal protein S3 | 0.345 |
| SERP1826 | rplV | 50 S ribosomal protein L22 | 0.374 |
| SERP1827 | rpsS | 30 S ribosomal protein S19 | 0.385 |
| SERP1828 | rplB | 50 S ribosomal protein L2 | 0.421 |
| SERP1829 | rplW | 50 S ribosomal protein L23 | 0.424 |
| Nucleotide metabolism | |||
| SERP0070 | guaA | bifunctional GMP synthase/glutamine amidotransferase protein | 2.546 |
| SERP0651 | purC | phosphoribosylaminoimidazole-succinocarboxamide synthase | 2.036 |
| SERP0654 | purL | phosphoribosylformylglycinamidine synthetase | 2.341 |
| SERP0655 | purF | phosphoribosylpyrophosphate amidotransferase | 2.164 |
| SERP0656 | purM | phosphoribosylformylglycinamidine cyclo-ligase | 2.369 |
| SERP0657 | purN | IMP cyclohydrolase | 2.111 |
| SERP1003 | thyA-1 | thymidylate synthase | 2.014 |
| SERP1810 | adk | adenylate kinase | 0.444 |
| Energy metabolism | |||
| SE0102-12228 | carbamate kinase, putative | 0.259 | |
| SE0104-12228 | transcription regulator Crp/Fnr family protein | 0.343 | |
| SE0106-12228 | arcA | arginine deiminase | 0.301 |
| SERP0672 | cydA | cytochrome d ubiquinol oxidase subunit II-like protein | 13.85 |
| SERP1985 | narJ | nitrate reductase delta chain | 0.441 |
| SERP1986 | narH | nitrate reductase beta chain | 0.327 |
| SERP1987 | narG | nitrate reductase alpha chain | 0.324 |
| SERP1990 | nirB | nitrite reductase nitrite reductase | 0.354 |
| SERP2168 | mqo-2 | malate:quinone oxidoreductase | 0.317 |
| SERP2169 | hypothetical protein | 0.0165 | |
| SERP2261 | manA-2 | mannose-6-phosphate isomerase | 0.479 |
| SERP2312 | mqo-3 | malate:quinone oxidoreductase | 0.451 |
| SERP2352 | arcC | putative carbamate kinase | 0.427 |
| DNA replication, recombination and repair | |||
| SERP0558 | ISSep1-like transposase | 4.66 | |
| SERP0599 | site-specific recombinase, resolvase family | 2.352 | |
| SERP0892 | IS1272, transposase | 2.774 | |
| SERP0909 | lexA | SOS regulatory LexA protein | 2.227 |
| SERP1023 | DNA replication protein DnaD, putative | 2.049 | |
| SERP2474 | hsdR | type I restriction-modification system, R subunit | 46.79 |
| Transcriptional regulator | |||
| SERP0635 | transcriptional regulator, MarR family | 3.216 | |
| SERP1879 | transcriptional regulator, AraC family | 21.2 | |
* The entire list of differentially expressed genes can be found on the National Center for Biotechnology Information Gene Expression Omnibus (GEO, available at http://www.ncbi.nlm.nih.gov/geo/ and is accessible through GEO Series accession number GSE20652