TABLE 2.
Significantly upregulated 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 | cymR | SACOL16S1 | ref | NP_464509.1 Weakly similar to two-component response regulator | 3.25 | 0.0316 |
| Biofilm formation | mapW | SACOL09S5 | ref | NP_374103.l| Hypothetical protein, similar to cell surface protein Map-W | 3.23 | 0.0149 |
| efb | SACOL1168 | pir| DS9852 Fibrinogen-binding protein A, clumping factor | 3.21 | 0.0048 | |
| vwb | SACOL0857 | ref | NP_645583.1 Truncated secreted von Willebrand factor-binding protein VWbp | 3.16 | 0.0182 | |
| Cell wall-Surface | capC | SACOL26S5 | pir| C89776 Capsular polysaccharide synthesis enzyme CapSC | 3.28 | 0.0092 |
| pgcA | SACOL2501 | ref | NP_109754.1 Two functions are possible, phosphomannomutase orphosphoglucomutase | 3.20 | 0.0032 | |
| ebsB | SACOL1471 | ref| NP_374547-l| Hypothetical protein, similarto cell wall enzyme EbsB | 3.12 | 0.0223 | |
| General functions [transporters, DNA-RNA, general] | yozE- like | SACOL2556 | NP_375655.1 hypothetical protein | 3.28 | 0.0127 |
| - | SACOL0366 | ref | NP_646219-lTerminase small subunit | 3.21 | 0.0029 | |
| metN1 | SACOL0504 | pir| A!0131Methionine import ATP-binding protein MetNl | 3.20 | 0.0028 | |
| hsdM | SACOL0476 | dbj | BAB41620.1/probale type I site-specific deoxyribonuclease Lldl chain hsdM | 3.20 | 0.0030 | |
| (B) | |||||
| Transcription regulators | bglG | SACOL0228 | pir| G97906 Transcription antiterminator BglG family BglG | 3.25 | 0.0028 |
| waIR | SACOL0019 | ref | NP_519473-1 Probable two-component response regulator transcription regulator protein | 3.22 | 0.0050 | |
| rpoB | SACOL05S8 | sp| P4776S RPOB_STAAU DNA-directed RNA polymerase beta chain | 3.21 | 0.0010 | |
| – | SACOL0420 | ref| NP_388770.1 Predicted transcriptional regulator | 3.20 | 0.0356 | |
| mgrA | SACOL0746 | gb | AAK62673.1 Transcriptional regulator MgrA | 3.19 | 0.0008 | |
| Cell wall-Surface | tarS | SACOL0243 | ref| NP_346205-lGlycosyl transferase, family 2:glycosyl transferase family 8 | 3.28 | 0.0014 |
| capB | SACOL0137 | ref | NP_370674.1 Capsular polysaccharide synthesis enzyme Cap5B | 3.14 | 0.0046 | |
| copC | SACOL0138 | pir | C89776 Capsular polysaccharide synthesis enzyme Cap8C | 3.07 | 0.0235 | |
| Drug resistance | femA | SACOL1410 | gb | AAC69631.1 Factor essential for methicillin resistance FemA | 4.12 | 0.0354 |
| pis | SACOL0050 | sp | P80544 MRSP_STAAU Methicillin-resistant surface protein precursor | 3.10 | 0.0026 | |
| General functions [transporters, DNA-RNA, general] | – | not found | ref | NP_656125-lMS_channel, Mechanosensitive ion channel | 3.50 | 0.0005 |
| recF | SACOL0004 | sp | Q9RVE01 RECF_DEIRA DNA replication and repair protein RecF | 3.34 | 0.0058 | |
| mdtB | SACOL2430 | ref | NP_502776.1 Predicted CDS, ABC transporter with ABC transporter transmembrane region family member | 3.20 | 0.0113 | |
| sasA | SACOL2676 | gb | AAL5S470.11 AF459093_1 Serine-threonine rich antigen | 3.17 | 0.0055 | |
| hchA | SACOL0597 | dbj | BAA15794.1 H-NS-repressed protein, 30K | 2.99 | 0.0074 | |
| hup | SACOL1513 | sp | P091681 OGT_ECOLI DNA-binding protein HU | 2.74 | 0.0154 |
The genes have been ranked according to their log2 fold change (pH5/pH7) value in each functional category.