Table 1.
Genes activated by RemA.a
| Gene | Fold | Annotation | Gene | Fold | Annotation |
|---|---|---|---|---|---|
| (Biofilm genes)b | (Miscellaneous cont.) | ||||
| epsA | 136.5 | EPS synthesis, length regulator? | cgeA | 10.5 | Spore coat protein |
| epsB | 87.3 | EPS synthesis, tyrosine kinase? | cgeB | 4.3 | Maturation of the spore coat |
| epsC | 123.3 | EPS synthesis, epimerase | cotG | 9.8 | Spore coat protein |
| epsD | 120.1 | EPS synthesis, glycosyltransferase | cotJC | 4.2 | Spore coat protein |
| epsE | 136.3 | EPS synthesis and flagellar clutch | glgA | 3.6 | Glycogen synthase |
| epsF | 136.4 | EPS synthesis, glycosyltransferase | glgB | 3.5 | 1,4-a-glucan branching enzyme |
| epsG | 142.3 | EPS synthesis, unknown | glgP | 3.6 | Glycogen phosphorylase |
| epsN | 4.8 | EPS synthesis, aminotransferase | sacT | 3.6 | Transcriptional antiterminator |
| epsO | 6.9 | EPS synthesis, pyruvyltransferase | sigL | 3.9 | Sigma factor L |
| tapA | 116.3 | TasA anchoring protein | sodF | 4.6 | Superoxide dismutase |
| sipW | 145.7 | TapA/TasA signal peptidase | spoVR | 3.6 | Involved in spore cortex synthesis |
| tasA | 112.5 | Extracellular amyloid fibre | spoVID | 4.0 | Assembly of spore coat |
| slrR | 35.4 | Regulator motility/autolysin genes | sqhC | 3.3 | Squalene-hopene synthase |
| bslA | 4.2 | Extracellular matrix protein | ycdA | 7.5 | Unknown |
| (Osmoprotection) | ycsF | 3.6 | Similar to lactam utilization protein | ||
| opuAA | 54.1 | Glycine betaine ABC transporter | ycsG | 3.4 | Similar to amino acid transporter |
| opuAB | 44.4 | Glycine betaine ABC transporter | yfjB | 7.2 | Unknown |
| opuAC | 43.7 | Glycine betaine ABC transporter | yfjC | 6.3 | Unknown |
| opuBA | 16.0 | Choline ABC transporter | yfjD | 6.5 | Unknown |
| opuBB | 15.4 | Choline ABC transporter | yfjE | 4.2 | Unknown |
| opuBC | 11.0 | Choline ABC transporter | ykoL | 7.5 | Unknown |
| opuBD | 12.8 | Choline ABC transporter | ykzB | 7.9 | Unknown |
| opuCA | 11.3 | Glycine betaine/choline transporter | yobB | 5.3 | Unknown |
| opuCB | 9.9 | Glycine betaine/choline transporter | yozY | 5.0 | Unknown |
| opuCC | 4.3 | Glycine betaine/choline transporter | yqfZ | 4.7 | Unknown |
| opuCD | 5.6 | Glycine betaine/choline transporter | yrbD | 9.9 | Putative alanine transporter |
| (Nitrogen metabolism) | ysnE | 3.4 | Similar to acetyltransferase | ||
| ansZ | 12.0 | Asparaginase | yueB | 4.6 | Surface receptor for phage SPP1 |
| bpr | 7.6 | Bacillopeptidase F | yueC | 4.4 | Unknown |
| frlM | 5.2 | Amino sugar permease | yuiA | 16.3 | Unknown |
| frlN | 5.1 | Amino sugar permease | yuiB | 10.9 | Unknown |
| ispA | 7.4 | Intracellular protease | yukB | 5.2 | Unknown |
| nasB | 9.7 | Nitrate reductase (electron transfer) | yukC | 4.6 | Unknown |
| nasC | 10.2 | Nitrate reductase (catalytic subunit) | yukD | 5.3 | Putative bacteriocin |
| nasD | 7.5 | Assimilatory nitrate reductase | yukE | 3.7 | Unknown |
| nasE | 6.3 | Assimilatory nitrate reductase | yvbF | 4.6 | Unknown |
| nasA | 14.0 | Nitrate transporter | yvcB | 3.7 | Unknown |
| nrgA | 5.6 | Ammonium transporter | ywhK | 4.0 | Unknown |
| nrgB | 6.6 | Nitrogen regulated PII protein | ywqH | 4.6 | Unknown |
| pnbA | 7.8 | Para-nitrobenzyl esterase | ywqI | 4.3 | Unknown |
| pucA | 7.8 | Xanthine dehydrogenase | ywqJ | 4.4 | Putative toxin |
| pucB | 11.6 | Xanthine dehydrogenase | ywqK | 4.1 | Unknown |
| pucC | 11.3 | Xanthine dehydrogenase | ywqL | 3.5 | Endonuclease V |
| pucD | 7.5 | Xanthine dehydrogenase | ywrD | 8.6 | Unknown |
| pucE | 8.3 | Xanthine dehydrogenase | ywrK | 5.4 | Similar to arsenic exporter |
| pucI | 6.3 | Allantoin permease | ywzE | 9.5 | Unknown |
| pucJ | 4.3 | Uric acid permease | ywzF | 8.6 | Unknown |
| pucK | 5.2 | Uric acid permease | yxiB | 5.4 | Unknown |
| pucL | 7.2 | Uricase | yxiC | 6.6 | Unknown |
| ureA | 9.9 | Urease | yxiD | 4.6 | Toxin |
| ureB | 9.7 | Urease | yyzB | 5.1 | Unknown |
| ureC | 7.0 | Urease | |||
| vpr | 3.1 | Extracellular protease |
a.
Microarray expression values of strain DS207 (sinR epsH) divided by microarray array expression values of strain DS9771 (remA sinR epsH).
b.
Genes epsH through epsM in the eps operon failed to show a threefold change in expression presumably due to the integration of thetetracycline resistance gene inserted into the epsH gene (epsH::tet).
Genes assigned to functional categories in bold. (σD) indicates genes previously identified as being expressed under the control of σD (Serizawa et al., 2004; Kearns and Losick, 2005).