Table 1.
Proteins commonly affected by the ftsH deletion in Newman and USA300.
| NM | USA | Gene | Product | Fold changes (ftsH/WT)a | ||
|---|---|---|---|---|---|---|
| Mass Spec | RNA-seq | |||||
| Up-regulated (17) | NM | USA | USA | |||
| 0197c | 0257 | lrgB | antiholin-like protein LrgB | 3.6 | 2.8 | 0.5 |
| 0252 | 0310 | hypothetical protein | 3.1 | 3.6 | - b | |
| 0474 | 0490 | hslO | Hsp33-like chaperonin | 7.7 | 6.9 | 7.2 |
| 0559 | 0579 | hypothetical protein | 3.7 | 2.1 | — | |
| 0676 | 0692 | saeQ | SaeS regulatory protein SaeQd | 1.6 | 4.8 | — |
| 0887 | 0918 | murG | diacylglycerol glucosyltransferase | 11.0 | 11.8 | — |
| 0952 | 0986 | cydA | cytochrome D ubiquinol oxidase, subunit I | 1.7 | 2.3 | — |
| 0981 | 1016 | cyoE | protoheme IX farnesyltransferase | 12.0 | 19.3 | — |
| 1147 | 1130 | ffh | signal recognition particle protein | 1.6 | 1.5 | — |
| 1371 | 1351 | hypothetical protein | 2.3 | 1.8 | — | |
| 1566 | 1619 | hemA | glutamyl-tRNA reductase | 38.2 | 56.4 | — |
| 1621 | 1674 | htrA | putative serine protease | 1.7 | 1.9 | — |
| 2261 | 2306 | hrtA | ATP-binding protein | 35 | 55.3 | 127.0 |
| 2262 | 2307 | hrtB | ABC transporter permease protein | 5.7 | 26.8 | 211.0 |
| 2529 | 2565 | clfB | clumping factor B precursor | 1.5 | 1.8 | 1.5 |
| 2602 | 2637 | conserved hypothetical protein | 5.0 | 5.3 | 14.2 | |
| 2606 | 2640 | putative transcriptional regulator | 117.4 | 130.7 | 365.9 | |
| Down-regulated (16) | ||||||
| 0136 | 0194 | ptsG | sucrose-specific PTS transporter IIBC | 0.4 | 0.6 | — |
| 0473 | 0489 | ftsH | ATP-dependent metalloprotease | 0.0 | 0.0 | 0.0 |
| 0885 | 0916 | hypothetical protein | 0.6 | 0.7 | — | |
| 0933 | 0966 | purE | phosphoribosylaminoimidazole carboxylase catalytic subunit | 0.5 | 0.5 | — |
| 0948 | 0982 | hypothetical protein | 0.6 | 0.6 | 1.4 | |
| 1162 | 1145 | xerC | tyrosine recombinase xerC | 0.4 | 0.6 | — |
| 1459 | 1516 | ATP-binding protein | 0.4 | 0.7 | — | |
| 1603 | 1655 | ald | alanine dehydrogenase | 0.5 | 0.6 | 1.6 |
| 1681 | 1731 | pckA | phosphoenolpyruvate carboxykinase | 0.6 | 0.6 | — |
| 1847 | 1890 | sspB | staphopain thiol proteinase | 0.2 | 0.6 | — |
| 1922 | 1970 | phage exonuclease | 0.5 | 0.7 | — | |
| 2093 | 2149 | lacG | 6-phospho-beta-galactosidase | 0.2 | 0.3 | — |
| 2096 | 2152 | lacD | tagatose 1,6-diphosphate aldolase | 0.1 | 0.4 | — |
| 2232 | 2278 | hutU | urocanate hydratase | 0.3 | 0.6 | — |
| 2509 | 2545 | betA | choline dehydrogenase | 0.5 | 0.4 | — |
| 2510 | 2546 | betB | glycine betaine aldehyde dehydrogenase | 0.5 | 0.6 | — |
| Differentially regulated (3) | ||||||
| 1242 | 1228 | thrB | Homoserine kinase | 0.4 | 2.1 | 0.5 |
| 1579 | 1632 | nrdR | Transcription regulator NrdR | 0.5 | 1.5 | — |
| 2523 | 2558 | nsaS/braS | Histidine kinase | 0.5 | 3.2 | — |
aListed are the results with p ≤ 0.05 by Student’s t-test (two-tailed, paired). Statistical analysis results can be found in S1-5Tables; b -, no significant change; cThe 11 putative FtsH substrate proteins were bold-faced; dThe four proteins whose degradation by FtsH was demonstrated in vitro (Fig. 4C) were underlined.