Table 1.
Genes differentially expressed in strain 13 after growth in the presence of homocysteine or cystine.
| Gene name (synonym) | Function/similarity | Transcriptome analysis | qRT-PCR | ||
|---|---|---|---|---|---|
| Homocysteine/cysteine | p-value | Homocysteine/cysteine | |||
| T-boxCys controlled genes | |||||
| cpe1321 (cysE) | Serine acetyl-transferase | 7.91 | 0.0001 | ||
| cpe1322 (cysK) | OAS-thiol-lyase | 6.86 | 0.0002 | 120 | |
| cpe0967 | Na+-H+/Amino acid symporter | 15.53 | 6.6E-06 | ||
| cpe0947 | Na+-H+/Amino acid symporter | 7.01 | 0.0002 | ||
| S-box controlled genes | |||||
| cpe2177 (metK) | SAM-synthase | 2.7 | 0.015 | 14 | |
| cpe2317 | probable Na+-H+ antiporter | 1.4 | 0.01 | ||
| Iron sulfur clusters | |||||
| cpe1786 | Rrf2-type regulator | 3.41 | 0.0001 | 14 | |
| cpe1785 (iscS) | Cysteine desulfurase | 3.36 | 0.00027 | ||
| cpe1784 (iscU) | Iron sulfur cluster assembly | 6.73 | 0.00008 | ||
| cpe1783 (trmU) | Methylaminomethyl-2-Thiouridylate- | 3.5 | < 1E-05 | ||
| methyltransferase | |||||
| cpe1469 | IscS-like protein | 2.5 | 0.0009 | 8 | |
| cpe0664 | HesB-like protein | 3.83 | 1.5E-05 | 11 | |
| Functions associated to redox | |||||
| cpe2511 (fer) | Ferredoxin [3Fe-4S] | 3.2 | < 1E-05 | ||
| cpe777 (rubR1) | Rubredoxin | 1.8 | 0.001 | ||
| cpe0780 (rubR2) | Rubredoxin | 2.4 | < 1E-05 | 4.3 | |
| cpe0778 | Probable flavohemoprotein | 1.62 | 0.005 | ||
| cpe1331 (rubY) | Rubrerythrine | 1.64 | 0.01 | ||
| cpe2447 (fer) | Ferredoxin 2[2Fe-2S] | 0.52 | 0.01 | ||
| cpe0782 | Alkyl hydrogen peroxide reductase | 0.49 | < 1E-05 | ||
| cpe2537 | cytochrome c-type biogenesis protein | 0.41 | < 1E-05 | ||
| cpe2538 | Unknown | 0.25 | 3.5E-05 | ||
| Carbon metabolism | |||||
| cpe2308 | Mannose-1-phosphate | 3.5 | 2.3E-05 | ||
| guanylyltransferase | |||||
| cpe0103 (ldh) | Lactate dehydrogenase | 2.73 | 0.004 | 15 | |
| Transporters, membrane or exported proteins | |||||
| cpe2151 | Mercure-copper binding protein | 5.1 | < 1E-05 | ||
| cpe1371 | Na+-dependent symporter | 3.3 | 0.009 | 5 | |
| cpe0049 | Membrane protein | 3.02 | < 1E-05 | ||
| cpe2456 | Membrane protein | 2.84 | 1E-05 | ||
| cpe0554 | Protein with signal sequence | 2.74 | 0.0002 | ||
| cpe0383 | Holin-like protein | 2.6 | 0.004 | ||
| cpe2595 | Na+/H+ antiporter | 0.34 | < 1E-05 | ||
| Virulence | |||||
| cpe0163 | Perfringolysin O | 0.3 | 0.02 | 0.16 | |
| cpe1523 (nagL) | Hyaluronidase | 1.82 | 9.5E-05 | 2.3 | |
| Proteins of unknown function | |||||
| cpe1078 | Unknown (73 aa) | 10.8 | < 1E-05 | ||
| cpe1079 | Unknown | 7.77 | 3E-05 | ||
| cpe1385 | Unknown | 4.2 | 6E-05 | ||
| cpe1386 | Unknown (85aa) | 8.73 | < 1E-05 | ||
| cpe1387 | Unknown (71aa) | 6.4 | 5E-06 | ||
| cpe1388 | Unknown | 5.94 | 5E-05 | ||
| cpe0651 | Unknown | 4.8 | < 1E-05 | ||
| cpe0015 | Unknown | 4.7 | 2E-05 | ||
| cpe0114 | Unknown (74 aa) | 4.49 | 1.33E-05 | ||
| cpe0113 | Unknown (75 aa) | 3.98 | 6E-05 | ||
| cpe0264 | Unknown (98 aa) | 3.94 | 0.001 | ||
| cpe2619 | Unknown (63 aa) | 3.88 | < 1E-05 | ||
| cpe0067 | Unknown | 3.6 | 1E-05 | ||
| cpe0102 | Unknown (90 aa) | 3.52 | 0.01 | ||
| cpe1472 | Unknown | 3.36 | 0.00735 | ||
| cpe2037 | Unknown (89 aa) | 3.16 | 0.0006 | ||
| cpe0363 | Unknown (118 aa) | 3.11 | 0.002 | ||
The results presented are representative of 8 differential hybridizations using RNA preparations obtained from 4 independent cultures. aa means amino acids.