Table 1. Genes differentially expressed in the ΔspdC mutant compared to the parental HG001 strain.
| SpdC-activated genes | |||
| Id(a) | Gene name/function | Fold change(b) | Also regulated by(c) |
| Virulence | |||
| 00069* | spa | -59.69 | VraSR, WalKR |
| 02709* | hlgC | -5.53 | SaeSR, WalKR |
| 02710* | hlgB | -4.97 | ArlSR, GraSR, SaeSR, WalKR |
| 00545* | sdrD | -4.19 | ArlSR, GraSR, AirSR |
| 02169* | chp | -2.86 | SaeSR, GraSR, WalKR |
| 01939* | splC | -2.16 | BraSR, SaeSR, WalKR |
| 01941* | splB | -2.49 | ArlSR, SaeSR, WalKR |
| 02171* | sak | -2.03 | SaeSR |
| 01112* | formyl peptide receptor-like 1 inhibitory prot. | -2.23 | SaeSR, WalKR |
| 01110* | fibrinogen-binding prot. | -2.04 | SaeSR, WalKR |
| Regulators | |||
| 00070* | sarS | -2.55 | WalKR, GraSR, BraSR |
| 00961 | comK | -2.12 | |
| 01879 | rot | -2.03 | ArlSR, GraSR, |
| ABC transporters | |||
| 02820 | ABC transporter ATP binding prot. | -5.94 | VraSR,GraSR, BraSR |
| 02821 | ABC transporter permease | -5.27 | ArlSR, GraSR, BraSR |
| 01389 | PstS phosphate ABC transporter | -3.39 | |
| Amino acid metabolism | |||
| 01452 | alanine dehydrogenase | -4.29 | ArlSR, SaeSR, GraSR, BraSR, |
| 01451* | threonine dehydratase | -5.32 | ArlSR, SaeSR, GraSR, BraSR, WalKR |
| 01450 | putative AA permease | -4.42 | |
| Carbohydrate metabolism | |||
| 00051 | 1-phosphatidylinositol phosphodiesterase | -3.27 | |
| 00187 | formate acetyl transferase | -2.92 | SaeSR |
| 00188* | pyruvate formate-lyase 1 activating enzyme | -3.04 | SaeSR, WalKR |
| 00608 | alcohol dehydrogenase | -2.75 | SaeSR |
| 00113 | bifunctional acetaldehyde-CoA/alcohol dehydrogenase | -2.72 | BraSR, GraSR |
| 02830* | D-lactate dehydrogenase | -2.20 | GraSR, WalKR |
| 02922 | L-lactate dehydrogenase | -2.11 | BraSR |
| Other | |||
| 01448 | putative transporter/multidrug resistance prot. | -3.31 | ArlSR, GraSR, SaeSR |
| 02108 | FtnA ferritin | -2.21 | SaeSR, GraSR |
| 02862* | clpC | -2.15 | WalKR |
| 02127 | staphopain thiol protease | -2.05 | |
| 00625 | monovalent cation/H+ antiporter subunit A | -2.02 | |
| 02941 | anaerobic ribonucleoside-triphosphate reductase activating prot. (nrdG) | -2.08 | |
| HP without homology | |||
| 02781 | -2.85 | GraSR | |
| 00966 | -2.82 | ||
| 00203 | -2.61 | BraSR | |
| 01123 | -2.52 | ||
| 02782 | -2.51 | ||
| 00094* | -2.31 | WalKR, BraSR | |
| 02294 | -2.20 | ||
| 02973 | -2.17 | ||
| 02842 | -2.14 | GraSR, WalKR | |
| 01798 | -2.10 | BraSR | |
| SpdC-repressed genes | |||
| Id(a) | Gene name/function | Fold change(b) | Also regulated by(c) |
| Cell wall metabolism | |||
| 02333* | sceD | 10.80 | GraSR, WalKR |
| 02576* | ssaA | 5.64 | GraSR, WalKR, SaeSR |
| 00248* | lytM | 3.81 | WalKR |
| 00994* | atlA | 2.21 | GraSR, WalKR |
| ABC transporters | |||
| 02430 | ABC transporter substrate-binding prot. | 2.69 | GraSR |
| 02153 | ABC-2 transporter family prot. | 2.20 | |
| 02154 | ABC transporter ATP-binding prot. | 2.19 | |
| 02152 | ABC transporter ATP-binding prot. | 2.13 | |
| Φ12 phage proteins | |||
| 01535 | HP | 4.00 | |
| 01573 | HP | 3.02 | |
| 01538 | phage terminase large subunit | 2.93 | |
| 01536 | scaffolding protease | 2.66 | |
| 01515 | peptidoglycan hydrolase | 2.66 | |
| 01516 | holin prot. | 2.63 | |
| 01530 | HP | 2.60 | |
| 01532 | SLT orf 110-like prot. | 2.50 | |
| 01570 | PVL orf 37-like prot. | 2.43 | |
| 01566 | phi APSE P51-like prot. | 2.43 | |
| 01531 | SLT orf 123-like prot. | 2.42 | |
| 01519 | SLT orf 129-like prot. | 2.37 | |
| 01520 | SLT orf 488-like prot. | 2.33 | |
| 01571 | SLT orf 71-like prot. | 2.28 | |
| 01533 | HP | 2.17 | |
| 01527 | HP | 2.13 | |
| 01529 | major tail prot. | 2.03 | |
| Φ13 phage proteins | |||
| 02234 | repressor-like prot. | 4.83 | |
| 02233 | phi PVL orf 32-like prot. | 3.77 | |
| 02221 | HP | 3.19 | |
| 02220 | phi ETA orf 18-like prot. | 2.71 | |
| 02228 | HP | 2.61 | |
| 02211 | phi PVL orf 50-like prot. | 2.58 | |
| 02225 | HP | 2.26 | |
| 02219 | phi ETA orf 20-like prot. | 2.21 | |
| 02216 | phage DnaC-like prot. | 2.20 | |
| 02223 | phi PVL orf 39-like prot. | 2.06 | |
| 02222 | HP | 2.05 | |
| Nucleotide metabolism | |||
| 01172* | PyrE orotate phosphoribosyltransferase | 8.02 | SaeSR, WalKR |
| 01171* | orotidine 5'-phosphate decarboxylase | 7.99 | SaeSR, WalKR |
| 01170* | CarB carbamoyl phosphate synthase large subunit | 7.04 | SaeSR, WalKR, BraSR |
| 01166* | pyrB | 3.53 | SaeSR, WalKR |
| 01017 | purH | 2.19 | GraSR, SaeSR |
| 02558 | UreA urease subunit gamma | 2.14 | ArlSR, GraSR , SaeSR |
| 01016 | phosphoribosylglycinamide formyltransferase | 2.12 | GraSR, SaeSR |
| 01018 | phosphoribosylamine—glycine ligase | 2.07 | GraSR, SaeSR |
| 01015 | phosphoribosylaminoimidazole synthetase | 2.00 | GraSR, SaeSR |
| Nitrogen metabolism | |||
| 02685 | nitrite reductase transcriptional regulator NirR | 2.48 | BraSR |
| 02684 | assimilatory nitrite reductase [NAD(P)H] large subunit | 2.03 | VraSR |
| 02681 | nitrate reductase subunit alpha | 2.03 | BraSR |
| Amino acid metabolism | |||
| 01367 | anthranilate synthase component II | 2.49 | |
| Capsular biosynthesis | |||
| 00116 | Cap5C | 2.40 | |
| 00117 | Cap5D | 2.37 | BraSR, ArlSR |
| 00122 | Cap5I | 2.32 | BraSR, GraSR |
| 00114 | Cap5A | 2.28 | ArlSR |
| 00115 | Cap5B | 2.28 | |
| 00128 | Cap5O | 2.19 | |
| 00120 | Cap5G | 2.17 | BraSR |
| 00121 | Cap5H | 2.13 | BraSR, GraSR |
| 00123 | Cap5J | 2.12 | GraSR |
| 00125 | Cap5L | 2.09 | BraSR |
| 00126 | Cap5M | 2.03 | |
| HP without homology | |||
| 01173 | 3.70 | SaeRS | |
| 01583 | 2.75 | BraSR, SaeSR | |
| 01084 | 2.71 | ||
| 01584 | 2.54 | ||
| 02863 | 2.06 | ||
*: Genes also regulated by the WalKR system
(a): Id indicates the S. aureus NCTC 8325 genome sequence SAOUHSC _ annotation.
(b): Fold change was determined as the ratio of the signal values between the ΔsdpC strain and the parental strain. Negative values indicate the gene is less expressed in the ΔspdC mutant strain and positive values that it is more highly expressed in the mutant strain. Only fold changes >2 with a P value <0.05 for the three biological replicates were considered.
(c): SpdC-regulated genes identified by RNA-Seq data analysis were compared with publicly available transcriptome analyses of S. aureus TCS mutants (http://www.satmdorg/) and TCSs with which SpdC was shown to interact are listed. Names in bold indicate positive regulation by the TCS in question as opposed to negative regulation.