Table 2.
Selected R. pomeroyi DSS-3 genes responding uniquely to a C-, N-, P-, or S-limited regime.
| Locus tag | Product (gene name, if available) | Fold-change ratioa |
Response strategy |
|||
|---|---|---|---|---|---|---|
| Probe 1 | Probe 2 | Scavenging | Quota Change | Gate-keeping | ||
| C-LIMITED | ||||||
| SPO0107 | ATP-dependent DNA helicase (recQ) | 1.0 | 6.3 | • | ||
| SPO0149 | Chromosomal replication initiation protein (dnaA) | 16.5 | 1.2 | • | ||
| SPO0171 | Flagellar biosynthetic protein | 1.3 | 6.7 | • | ||
| SPO0183 | H+-transporting two-sector ATPase, flagellum-specific | 6.3 | 1.0 | • | ||
| SPO0590 | LacI family transcriptional regulator (carbon catabolite repression domain-containing) | 14.5 | – | • | ||
| SPO0970 | Aquaporin Z (apqZ) | 3.1 | 1.3 | • | ||
| SPO1132 | Glycine betaine/proline ABC transporter, ATP-binding protein | 3.1 | 3.0 | • | ||
| SPO1156 | Imidazole glycerol phosphate synthase subunit (hisF) | 3.0 | 3.5 | • | ||
| SPO1463 | TRAP dicarboxylate transporter, DctM subunit | 8.3 | – | • | ||
| SPO1645 | Oligopeptide/dipeptide ABC transporter, permease protein | 4.6 | – | • | ||
| SPO1807 | DNA polymerase III epsilon subunit family exonuclease | 3.7 | 1.0 | • | ||
| SPO2370 | Sodium:alanine symporter family protein | 3.4 | – | • | ||
| SPO3291 | Branched-chain amino acid ABC transporter, periplasmic binding protein, putative | 5.5 | 4.0 | • | ||
| SPO3461 | Flagellar protein FlgJ, putative | 8.5 | – | • | ||
| SPO3783 | Sugar ABC transporter, ATP-binding protein | 8.0 | – | • | ||
| SPOA0097 | Branched-chain amino acid ABC transporter, permease protein | 3.6 | 1.4 | • | ||
| SPOA0160 | TRAP dicarboxylate transporter, DctM subunit | 8.7 | – | • | ||
| SPOA0299 | Branched-chain amino acid ABC transporter, permease protein | 0.9 | 3.7 | • | ||
| SPO0416 | Rod-shaped determining protein (mreD) | 0.3 | – | • | ||
| SPO1293 | Phasin (phaP) | 0.1 | 0.1 | • | ||
| SPO1756 | Polysaccharide biosynthesis/export protein | 0.3 | 0.7 | • | ||
| N-LIMITED | ||||||
| SPO0860 | Xylose repressor, putative | 3.2 | 3.2 | • | ||
| SPO1707 | Urea transporter, ATP-binding protein (urtE) | 3.8 | 3.0 | • | ||
| SPOA0447 | Urea transporter, ATP-binding protein (urtD) | 5.5 | – | • | ||
| SPO1708 | Urea transporter, permease protein (urtC) | 11.6 | – | • | ||
| SPO2087 | Nitrogen regulation protein (ntrC) | 1.1 | 4.3 | • | ||
| SPO2294 | Nitrogen regulatory protein PII (glnB-1) | 9.0 | 6.6 | • | ||
| SPO2295 | Glutamine synthetase, type I (glnA) | 4.7 | 5.1 | • | ||
| SPO2364 | Amino acid ABC transporter, periplasmic binding protein | 1.3 | 4.1 | • | ||
| SPO3723 | Ammonium transporter (amt-2) | 28.0 | – | • | ||
| SPO3724 | Nitrogen regulatory protein PII (glnB-2) | 124.3 | 39.1 | • | ||
| SPOA0300 | Branched-chain amino acid ABC transporter, periplasmic binding protein | 6.6 | – | • | ||
| SPO0862 | Xylose ABC transporter, permease protein (xylH) | 0.3 | 0.3 | • | ||
| SPO1079 | Lysine exporter, putative | 0.1 | 2.0 | • | ||
| SPO1743 | Glutamate dehydrogenase | 0.2 | 0.2 | • | ||
| SPO3156 | l-threonine aldolase, low-specificity, putative | 1.3 | 0.3 | |||
| SPO3712 | Aspartate-semialdehyde dehydrogenase (asd) | 0.2 | 0.3 | • | ||
| SPO3720 | Aromatic amino acid aminotransferase (tyrB) | 0.3 | 0.9 | • | ||
| SPOA0011 | S-adenosylmethionine synthetase (metK) | 0.2 | 0.4 | • | ||
| SPOA0057 | Glycine cleavage system T protein (gcvT) | 0.2 | 0.3 | • | ||
| SPOA0215 | Nitric oxide reductase Q protein (norQ) | 2.2 | 0.1 | • | ||
| SPOA0220 | Cytochrome cd1 nitrite reductase (nirS) | 0.2 | – | • | ||
| P-LIMITED | ||||||
| SPO0147 | Enoyl-CoA hydratase | 4.3 | 3.0 | • | ||
| SPO0304 | Lipoprotein, putative | 7.0 | 5.4 | • | ||
| SPO0468 | Alkylphosphonate utilization protein (phnG) | 5.2 | – | • | ||
| SPO0472 | Phosphonate C-P lyase system protein (phnK) | 10.9 | – | • | ||
| SPO0781 | Phosphonate ABC transporter, periplasmic phosphonate-binding (phnD) | 103.5 | – | • | ||
| SPO1860 | Alkaline phosphatase (phoX) | 7.4 | – | • | ||
| SPO1948 | Phosphate ABC transporter, periplasmic binding protein (pstS) | 47.9 | – | • | ||
| SPO1949 | Phosphate ABC transporter, permease protein (pstC) | 4.7 | – | • | ||
| SPO1951 | Phosphate transporter ATP-binding protein (pstB) | 7.4 | – | • | ||
| SPO1953 | Phosphate regulon transcriptional regulatory protein (phoB) | 10.7 | 26.1 | • | ||
| SPOA0294 | Phosphatidylethanolamine N-methyltransferase (pmtA) | 3.6 | 1.2 | • | ||
| S-LIMITED | ||||||
| SPO1256 | Polyphosphate kinase 2 (ppk2) | 5.0 | 4.0 | |||
| SPO1409 | RNA polymerase factor sigma-32 (rpoH-2) | 12.5 | – | |||
| SPO2596 | 5-amino-levulinate synthase (hemA-1) | 1.8 | 4.6 | |||
| SPO2632 | Uroporphyrinogen-III C-methyltransferase (cobA-1) | 3.4 | 5.9 | |||
| SPO2634 | Sulfite reductase, putative | 5.7 | 5.3 | |||
| SPO3383 | Thiol-specific antioxidant protein | 4.9 | 4.5 | |||
| SPO3527 | Universal stress protein family protein | 3.7 | 5.3 | |||
| SPO3532 | Coproporphyrinogen III oxidase (hemN) | 7.3 | – | |||
| SPO0371 | Autoinducer-binding transcriptional regulator (luxR-1) | 0.0 | 0.2 | |||
| SPO1679 | DNA-binding response regulator (ctrA) | 0.2 | 0.2 | |||
The enriched genes included here (unshaded rows) represent 36% of all enriched genes (Table A4 in Appendix); the depleted genes (gray-shaded rows) represent 27% of all depleted genes (Table A5 in Appendix).
aCalculated as the median value for limitation-to-excess pairwise comparisons.
Black dots indicate response strategy assignment.