TABLE 3.
Daptomycin stimulona
| Gene | Signal intensityb
|
Fold change | Gene functionc | Regulon (reference) | |
|---|---|---|---|---|---|
| +DAP | −DAP | ||||
| liaH | 78,930 | 59 | 1,336 | PspA homolog, cell membrane protection | LiaRS (35) |
| liaI | 78,935 | 61 | 1,294 | Putative membrane protein | LiaRS (35) |
| liaG | 37,639 | 133 | 283 | Putative membrane-anchored protein | LiaRS (35) |
| liaF | 50,616 | 341 | 149 | Negative regulator of LiaR | LiaRS (35) |
| liaS | 15,435 | 122 | 126 | TCS histidine kinase | LiaRS (35) |
| liaR | 3535 | 47 | 75 | TCS response regulator | LiaRS (35) |
| yhcY | 149 | 45 | 3.3 | TCS histidine kinase | LiaRS (35) |
| yhcZ | 631 | 289 | 2.2 | TCS response regulator | LiaRS (35) |
| yvrI | 2,754 | 4.8 | 574 | σ factor yvrI | YvrI (41) |
| yvrL | 1,390 | 2.6 | 535 | Negative regulator of yvrI | YvrI (41) |
| yqjL | 303 | 39 | 7.8 | Hydrolase; paraquat resistance | σMW (11) |
| ydaH | 306 | 49 | 6.2 | Uncharacterized membrane protein | σM (32) |
| ypbG | 211 | 58 | 3.6 | Marker for inhibition of cell wall biosynthesis | σM (32) |
| yebC | 155 | 43 | 3.6 | Hypothetical conserved | σM (17) |
| ywaC | 124 | 36 | 3.5 | ppGpp synthase | σM (48) |
| bcrC | 358 | 115 | 3.1 | Similar to bacteriocin transport permease | σM (9) |
| rodA | 150 | 56 | 2.7 | Cell division membrane protein | σM (17) |
| yhdL | 208 | 82 | 2.5 | ECF anti-σ factor | σM (17) |
| maf | 605 | 245 | 2.5 | Cell division and shape determination | σM (17) |
| murG | 386 | 163 | 2.4 | Peptidoglycan biosynthesis | σM (17) |
| murB | 710 | 353 | 2.0 | UDP-N-acetylenolpyruvoyl glucosamine reductase | σM (17) |
| sigM | 199 | 93 | 2.1 | ECF σ factor | σM (26) |
| yuaF | 707 | 148 | 4.8 | Hypothetical protein | σW (29) |
| yuaG | 329 | 168 | 2.0 | Flotillin-like protein | σW (29) |
| yxjI | 144 | 68 | 2.1 | Unknown | σW (10) |
| ywrE | 159 | 76 | 2.1 | Unknown | σW (10) |
| ydjP | 328 | 168 | 2.0 | Similar to chloroperoxidase | σW (10) |
| yoeB | 2,855 | 1,332 | 2.1 | Protection against autolysins | YycFG (51) |
| yfiC | 11,780 | 3,349 | 3.5 | Similar to ABC transporter (ATP-binding protein) | |
| fabHA | 1,203 | 521 | 2.3 | Fatty acid biosynthesis | |
| fabHB | 73 | 26 | 2.8 | Fatty acid biosynthesis | |
| yvcB | 1,214 | 45 | 27 | Unknown | |
| yvkN | 302 | 12 | 26 | Unknown | |
| yvzA | 424 | 42 | 10 | Unknown | |
| yvzC | 261 | 10 | 26 | Hypothetical protein | |
| yvpB | 257 | 19 | 14 | Hypothetical protein | |
| sdpI | 2,233 | 252 | 8.9 | Immunity protein for SdpC; signal transduction | SdpR (19) |
| ywdD | 163 | 31 | 5.3 | Hypothetical protein | |
| ywdE | 504 | 51 | 9.9 | Hypothetical protein | |
| ywfB | 299 | 38 | 7.9 | Similar to bacilysin biosynthesis protein | |
| yknU | 2,917 | 372 | 7.8 | Similar to ABC transporter (ATP-binding protein) | |
| hutM | 126 | 40 | 3.2 | Histidine permease | |
| ypeB | 469 | 151 | 3.1 | Sporulation protein | |
| yitI | 630 | 215 | 2.9 | Probable acetyltransferase | |
| rpmB | 892 | 1,631 | 0.5 | Ribosomal protein L28 | |
| degR | 115 | 216 | 0.5 | Activation of degradative enzymes (AprE, NprE, SacB) | |
| yisY | 138 | 264 | 0.5 | Similar to chloride peroxidase | |
| ydgK | 39 | 77 | 0.5 | Similar to bicyclomycin resistance protein | |
| yocH | 759 | 1,513 | 0.5 | Similar to cell wall-binding protein (autolysin) | YycFG (3, 51) |
| yxeQ | 60 | 119 | 0.5 | Putative MmgE/Prp family protein | |
| lmrB | 261 | 534 | 0.5 | Lincomycin resistance | |
| rpsT | 541 | 1,140 | 0.5 | Ribosomal protein S20 | |
| yxeM | 66 | 156 | 0.4 | Similar to amino acid ABC transporter (binding protein) | |
| ywhE | 386 | 926 | 0.4 | pbpG, penicillin-binding protein (sporulation) | |
Genes induced or repressed >2-fold are shown with their respective antibiotic-responsive regulator. Induced genes controlled by regulator(s) known to be responsive to antibiotic-elicited stress are shown together with genes of predicted function or those with unknown function that are strongly induced (>5-fold). Induced and repressed genes were filtered to remove those with low overall expression levels (combined signal intensity < 100). Altogether, daptomycin induced 83 genes at least twofold (234 genes, ≥1.5-fold) and repressed 25 genes at least twofold (181 genes, ≥1.5-fold) (NCBI GEO series accession no. GSE13900).
“+DAP” and “−DAP” correspond to average results of triplicates of the signal intensities of daptomycin-treated or untreated samples, respectively.
Functions were assigned based on the SubtiList database or BSORF entry.