TABLE 4.
Significantly down-regulated genes at pH 5 in S. aureus COL biofilm-associated (A) and planktonic cells (B) (p < 0.05).
| Function | Gene name | Gene number (in S. aureus COL) | Gene annotation | log2 fold-change | p-Value |
| (A) | |||||
| Transcription regulators | – | SACOL0420 | ref | NP_388770.1 Predicted transcriptional regulator | −3.57 | 0.0035 |
| bglG | SACOL0228 | pir| G97906 Transcription antiterminator BgIG family BgIG | −3.42 | 0.0057 | |
| hutR | SACOL2325 | ref | NP_52065S.l Probable transcription regulator transcription regulator protein | −3.40 | 0.0059 | |
| – | SACOL2517 | ref | NP_665411.1 Putative transcriptional activator regulator protein | −3.19 | 0.0031 | |
| rpoB | SACOL0588 | sp| P47768| RPOB_STAAU DNA-directed RNA polymerase beta chain | −3.17 | 0.0087 | |
| agrD | SACOL2024 | gb | AAF72185-11AF255950J. AgrD signal peptide precursor | −3.17 | 0.0116 | |
| airR | SACOL1905 | ref | NP_714049.1 Two-component response regulator transcriptional regulator protein | −3.11 | 0.0028 | |
| dps | SACOL2131 | ref | NP_45980S.l| Stress response DNA-binding protein; starvation induced resistance to H202 | −3.05 | 0.0107 | |
| Biofilm formation | mapW | SACOL0985 | emb | CAB51807.1 Cell surface protein Map-W | −3.40 | 0.0023 |
| epiG | SACOL1871 | dbj | 8AB95623.11 Epidermin immunity protein F | −3.26 | 0.0036 | |
| Antigen - Toxin - Virulence | Ssl11 | SACOL0478 | pir| C89808Exotoxinl5 | −3.49 | 0.0006 |
| Ssl1 | SACOL0468 | pir| G89806Exotoxin6 | −3.37 | 0.0018 | |
| General functions [transporters, DNA-RNA, general] | infB | SACOL1285 | emb | CAD55362.1 Probable translational initiation factor; putative translation initiation factor lF-2(fragment) | −4.05 | 0.0365 |
| ftsK | SACOL1295 | ref | NP_459936.1 Cell division protein, required for cell division and chromosome partitioning | −3.41 | 0.0022 | |
| lytM | SACOL0243 | pir| F89789 Cell division and morphogenesis-related protein | −3.37 | 0.0051 | |
| tufA | SACOL0594 | pir| T44381 Translation elongation factorTu (EF-Tu) TufA | −3.11 | 0.0167 | |
| mob | SACOLRS00015 | gb| AAA93296.1 Mobilization (Mob):recombination (Pre) protein | −2.37 | 0.0272 | |
| ebsS | SACOL1522 | gb | AAC441352 Cell surface elastin binding protein | −3.19 | 0.0085 | |
| (B) | |||||
| Transcription regulators | hfq | SACOL1324 | sp | P255211 HFQ_ECOLI Hfq protein (Host factor-! protein) (HF-I) (HF-1) | −3.53 | 0.0024 |
| sarA | SACOL0672 | gb | AAM74164.11 AF515775_2 Staphylococcal accessory regulator variant | −3.39 | 0.0308 | |
| Biofilm formation | scc | SACOL1169 | ref | NP_374275.11 Hypothetical protein, similartofibrinogen-binding protein | −3.47 | 0.0163 |
| mapW | SACOL0985 | emb | CAB51S07.1 Cell surface protein Map-W | −3.43 | 0.0019 | |
| Antigen - Toxin - Virulence | Ssl14 | SACOU1S0 | ref | NP_374284.l| Hypothetical protein, similarto exotoxin 3 | −3.49 | 0.0139 |
| isaB | SACOL2660 | pir| F90071 Immunodominant antigen B | −3.27 | 0.0066 | |
| General functions [transporters, DNA-RNA, general] | maoC | SACOL0032 | ref | NP_280923.1 Monoamine oxidase regulatory-like; MaoCl | −3.49 | 0.0097 |
| parC | SACOL1390 | ref | NP_758033.1 DNA topoisomerase IV subunit A | −3.44 | 0.0050 | |
| metN2 | SACOL0504 | pir | G71363 Probable amino acid ABC transporter, ATP-binding protein (abc) | −3.44 | 0.0066 | |
| mntC | SACOL0683 | ref | NP_720653.1 Putative ABC transporter, metal binding lipoprotein; surface adhesin precursor; lipoprotein receptor Lral | −3.42 | 0.0027 | |
| prsA | SACOL1897 | sp | Q92H911 PLP_RICCN Parvulin-like PPIase precursor (Peptidyl-prolyl cis-trans isomerase Pip) | −3.23 | 0.0093 | |
| – | not found | ref | NP_437451.1 Conserved putative membrane protein, possibly a permease | −3.05 | 0.0129 |
The genes have been ranked according to their log2 fold change (pH5/pH7) value in each functional category.