TABLE 3.
SigF regulon (P < 0.01) in M. smegmatis grown in LB-Tween batch cultures
| Gene category | Expression in ΔsigF strain | Locus | Gene product |
|---|---|---|---|
| SigF-regulated genes exclusive to | Decreaseda | MSMEG_0266 | Arginine decarboxylase |
| stationary phase (μ = 0.07 ± | MSMEG_0267 | Esterase | |
| 0.01 h−1) | MSMEG_0536 | Intracellular protease, PfpI family protein | |
| MSMEG_0600 | Dehydrogenase | ||
| MSMEG_0637 | Iron-sulfur binding oxidoreductase | ||
| MSMEG_0670 | FAD-dependent oxidoreductase | ||
| MSMEG_0671 | S-(Hydroxymethyl)glutathione dehydrogenase | ||
| MSMEG_0684 | Aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding | ||
| MSMEG_0963 | Hypothetical protein | ||
| MSMEG_1112 | Aconitate hydratase, putative | ||
| MSMEG_1315 | Small conductance mechanosensitive ion channel (MscS) family protein | ||
| MSMEG_1358 | Conserved hypothetical protein | ||
| MSMEG_1605 | Phosphate transport system regulatory protein PhoU | ||
| MSMEG_1766 | Conserved hypothetical protein | ||
| MSMEG_1767 | Conserved hypothetical protein | ||
| MSMEG_1768 | Conserved hypothetical protein | ||
| MSMEG_1769 | UsfY protein | ||
| MSMEG_1775 | Cytochrome P450 monooxygenase | ||
| MSMEG_1781 | Hypothetical protein | ||
| MSMEG_1783 | Hypothetical protein | ||
| MSMEG_1787 | RsbW protein | ||
| MSMEG_1792 | Conserved hypothetical protein | ||
| MSMEG_1794 | Dehydrogenase | ||
| MSMEG_1801 | Hypothetical protein | ||
| MSMEG_2160 | Hypothetical protein | ||
| MSMEG_2344 | Dehydrogenase | ||
| MSMEG_2345 | Lycopene cyclase | ||
| MSMEG_2346 | Phytoene synthase | ||
| MSMEG_2347 | Phytoene dehydrogenase | ||
| MSMEG_2376 | Conserved hypothetical protein | ||
| MSMEG_2913 | Hydrolase | ||
| MSMEG_2925 | Permease membrane component | ||
| MSMEG_2926 | Glycine betaine/carnitine/choline transport ATP binding protein OpuCA | ||
| MSMEG_3184 | Malto-oligosyltrehalose trehalohydrolase | ||
| MSMEG_3186 | Glycogen-debranching enzyme GlgX | ||
| MSMEG_3304 | Succinate semialdehyde dehydrogenase | ||
| MSMEG_3311 | Acyl carrier protein | ||
| MSMEG_3418 | Conserved hypothetical protein | ||
| MSMEG_3536 | Sugar transport protein | ||
| MSMEG_3541 | Cytochrome c biogenesis protein transmembrane region | ||
| MSMEG_3543 | Soluble secreted antigen MPT53 | ||
| MSMEG_3560 | Conserved hypothetical protein | ||
| MSMEG_3673 | 4-Alpha-glucanotransferase | ||
| MSMEG_4195 | Conserved hypothetical protein | ||
| MSMEG_4562 | Conserved hypothetical protein | ||
| MSMEG_4993 | Hypothetical protein | ||
| MSMEG_5342 | Conserved hypothetical protein | ||
| MSMEG_5343 | Conserved hypothetical protein | ||
| MSMEG_5400 | Dehydrogenase | ||
| MSMEG_5542 | Transcriptional regulator, HTH_3 family protein | ||
| MSMEG_5590 | Carboxylate-amine ligase Nfa27300 | ||
| MSMEG_5606 | Cytochrome bd-I oxidase subunit II | ||
| MSMEG_5616 | Glyoxalase/bleomycin resistance protein/dioxygenase | ||
| MSMEG_5721 | Acetyl coenzyme A acetyltransferase | ||
| MSMEG_5826 | Pyruvate decarboxylase | ||
| MSMEG_5936 | Conserved hypothetical protein | ||
| MSMEG_6210 | Conserved hypothetical protein | ||
| MSMEG_6213 | Manganese-containing catalase | ||
| MSMEG_6232 | Catalase KatA | ||
| MSMEG_6305 | Conserved hypothetical protein | ||
| MSMEG_6354 | Serine esterase, cutinase family protein | ||
| MSMEG_6355 | Hypothetical protein | ||
| MSMEG_6501 | Hypothetical protein | ||
| MSMEG_6541 | Anti-sigma factor antagonist | ||
| MSMEG_6542 | B12 binding domain protein | ||
| MSMEG_6612 | ATPase, MoxR family protein | ||
| MSMEG_6615 | hypothetical protein | ||
| MSMEG_6616 | S-(Hydroxymethyl)glutathione dehydrogenase | ||
| MSMEG_6663 | C5-O-methyltransferase | ||
| MSMEG_6727 | Amino acid permease-associated region | ||
| MSMEG_6728 | Conserved hypothetical protein | ||
| MSMEG_6751 | Hypothetical protein | ||
| MSMEG_6767 | Mycocerosic acid synthase | ||
| Increasedb | MSMEG_3297 | Transcriptional regulator, CadC | |
| MSMEG_5934 | Conserved hypothetical protein | ||
| SigF-regulated genes exclusive to | Decreased | MSMEG_2343 | Methylesterase |
| exponential phase (μ = | MSMEG_3254 | RDD family protein, putative | |
| 0.25 ± 0.02 h−1) | MSMEG_3443 | Hypothetical protein | |
| MSMEG_5078 | Glucose-1-phosphate adenylyltransferase | ||
| MSMEG_5117 | Proline dehydrogenase | ||
| MSMEG_5119 | 1-Pyrroline-5-carboxylate dehydrogenase | ||
| MSMEG_5188 | CAAX amino protease family protein | ||
| MSMEG_5189 | Oxidoreductase | ||
| MSMEG_5335 | Formamidase | ||
| MSMEG_5336 | Amidate substrates transporter protein | ||
| MSMEG_5337 | Putative regulatory protein, FmdB family | ||
| Increased | MSMEG_2751 | Hypothetical protein | |
| MSMEG_3298 | Response regulator receiver domain protein | ||
| MSMEG_3299 | Putative oxidoreductase | ||
| SigF-regulated genes in both | Decreased | MSMEG_0451 | Oxidoreductase, FAD linked |
| exponential and stationary | MSMEG_0672 | Conserved hypothetical protein | |
| phases | MSMEG_0685 | Oxidoreductase, molybdopterin-binding subunit | |
| MSMEG_0696 | Alanine-rich protein | ||
| MSMEG_0697 | Integral membrane protein | ||
| MSMEG_1076 | Conserved hypothetical protein | ||
| MSMEG_1097 | Glycosyl transferase, group 2 family protein | ||
| MSMEG_1558 | Conserved hypothetical protein | ||
| MSMEG_1758 | Hypothetical protein | ||
| MSMEG_1770 | Conserved hypothetical protein | ||
| MSMEG_1771 | Methylase, putative | ||
| MSMEG_1772 | Conserved hypothetical protein | ||
| MSMEG_1773 | Conserved hypothetical protein | ||
| MSMEG_1774 | Conserved hypothetical protein | ||
| MSMEG_1777 | UsfY protein | ||
| MSMEG_1782 | Oxidoreductase, short-chain dehydrogenase/reductase family | ||
| MSMEG_1788 | Conserved hypothetical protein | ||
| MSMEG_1789 | Conserved hypothetical protein | ||
| MSMEG_1790 | Conserved hypothetical protein | ||
| MSMEG_1802 | ChaB protein | ||
| MSMEG_1804 | RNA polymerase sigma-F factor | ||
| MSMEG_1950 | Conserved hypothetical protein | ||
| MSMEG_1951 | Conserved domain protein | ||
| MSMEG_2112 | Secreted protein | ||
| MSMEG_2115 | Conserved hypothetical protein | ||
| MSMEG_2337 | Isopentenyl-diphosphate delta-isomerase, type 2 | ||
| MSMEG_2415 | Hemerythrin HHE cation binding region | ||
| MSMEG_2830 | ISMsm4, transposase | ||
| MSMEG_2924 | Permease binding protein component | ||
| MSMEG_2927 | ABC transporter, permease protein OpuCB | ||
| MSMEG_2958 | Conserved hypothetical protein | ||
| MSMEG_3022 | Transglycosylase-associated protein | ||
| MSMEG_3185 | Putative maltooligosyl trehalose synthase | ||
| MSMEG_3255 | DoxX subfamily protein, putative | ||
| MSMEG_3419 | Hypothetical protein | ||
| MSMEG_3439 | Hypothetical protein | ||
| MSMEG_4618 | Isochorismatase family protein | ||
| MSMEG_5402 | Dehydrogenase DhgA | ||
| MSMEG_5543 | Hypothetical protein | ||
| MSMEG_5550 | Protein-glutamate methylesterase | ||
| MSMEG_5617 | Immunogenic protein MPT63 | ||
| MSMEG_5722 | Conserved hypothetical protein | ||
| MSMEG_5799 | Nucleoside-diphosphate-sugar epimerase | ||
| MSMEG_6211 | Hypothetical protein | ||
| MSMEG_6212 | Hemerythrin HHE cation binding domain subfamily protein | ||
| MSMEG_6467 | Starvation-induced DNA-protecting protein | ||
| MSMEG_6500 | Conserved hypothetical protein | ||
| MSMEG_6579 | Conserved hypothetical protein | ||
| MSMEG_6610 | Protein of unknown function DUF58, putative | ||
| MSMEG_6665 | Integral membrane protein | ||
| MSMEG_6819 | Conserved domain protein |
a
ΔsigF strain/wild-type ratio of <0.5.
b
ΔsigF strain/wild-type ratio of >2.