Table 2.
Genes containing RpoN-dependent promoters identified by the PromScan analysis and the transcriptome analysis.
| Operons§ | Genes | Annotations | Fold changes* | PromScan score |
|---|---|---|---|---|
| Amino acid biosynthesis and Nitrogen assimilation | ||||
| Glutamine synthase (GS) | GSU1835 (glnA)† | glutamine synthetase (GS) | +1.39 | 80 |
| GSU1836 (glnB)† | nitrogen regulatory protein PII | +1.77 | ||
| Glutamate synthase (GOGAT) | GSU1235 | hypothetical protein | N. D. | 88 |
| GSU1236 | hypothetical protein | N. D. | ||
| GSU1237 | pyridine nucleotide-disulphide oxidoreductase family protein | -1.44 | ||
| GSU1238 | iron-sulfur cluster-binding protein | N. D. | ||
| GSU1239 (gltB)† | glutamate synthase-related protein (GOGAT) | N. D. | ||
| Nitrogen assimilation | GSU2802 | NAD(+) – dinitrogen-reductase ADP-D-ribosyltransferase | N. D. | 86 |
| GSU2803 | dinitrogenase iron-molybdenum cofactor family protein | -1.21 | ||
| GSU2804 | ferredoxin family protein | -1.24 | ||
| GSU2805 (nifX) | nitrogenase molybdenum-iron cofactor biosynthesis protein NifX | -1.27 | ||
| GSU2806 (nifEN)† | nitrogenase molybdenum-iron cofactor biosynthesis protein NifEN | -1.34 | ||
| Appendages and Motility | ||||
| Flagella biogenesis | GSU3050 (flgA) | flagella basal body P-ring formation protein FlgA | -1.34 | 93 |
| GSU3051 (flgG) | flagellar basal-body rod protein FlgG | N. D. | ||
| GSU3052 (flgG) | flagellar basal-body rod protein FlgG | -1.19 | ||
| GSU3053 (fliA)† | RNA polymerase sigma factor for flagellar Operon/gene/gene | -1.50 | ||
| GSU3054 | ParA family protein | -1.21 | ||
| GSU3055 (flhF) | flagellar biosynthetic protein FlhF | -1.34 | ||
| GSU3056 (flhA) | flagellar biosynthetic protein FlhA | -1.42 | ||
| Flagella basal body | GSU0407 (flgB) | Flagellar basal-body rod protein FlgB | -1.38 | 92 |
| GSU0408 (flgC) | Flagellar basal-body rod protein FlgC | -1.31 | ||
| Flagella biogenesis | GSU0420 (fliL)† | flagellar protein FliL | -1.47 | 86 |
| GSU0421 (fliM) | flagellar motor switch protein FliM | -1.35 | ||
| GSU0422 (fliN) | flagellar motor switch protein FliN | -1.93 | ||
| GSU0423 (fliP) | flagellar biosynthetic protein FliP | N. D. | ||
| GSU0424 (fliQ) | flagellar biosynthetic protein FliQ | -1.32 | ||
| GSU0425 (fliR) | flagellar biosynthesis protein FliR | -1.72 | ||
| GSU0426 (flhB) | flagellar biosynthetic protein FlhB | -1.11 | ||
| Flagella biogenesis | GSU3040 | hypothetical protein | N. D. | 86 |
| GSU3041 | carbon storage regulator | -1.04 | ||
| GSU3042 (flgL) | flagellar hook-associated protein FlgL | -1.05 | ||
| GSU3043 (flgK) | flagellar hook-associated protein FlgK | -1.05 | ||
| GSU3044 | hypothetical protein | -1.21 | ||
| GSU3045 (flgM) | negative regulator of flagellin synthesis FlgM | -1.13 | ||
| GSU3046 (flgJ)† | flagellar protein FlgJ-like protein | -1.41 | ||
| Metabolisms | ||||
| Formate dehydrogenase | GSU0777(fdnG)† | formate dehydrogenase, major subunit, selenocysteine-containing | N. D. | 90 |
| GSU0778 | formate dehydrogenase, iron-sulfur subunit | N. D. | ||
| GSU0779 | formate dehydrogenase, b-type cytochrome subunit | -1.19 | ||
| GSU0780 | formate dehydrogenase accessory protein FdhD | N. D. | ||
| GSU0781 | twin-arginine translocation protein, TatA/E family | -1.41 | ||
| Solute transporter | ||||
| Fumarate/succinate exchanger | GSU2750 | hypothetical protein | +1.30 | 83 |
| GSU2751 (dcuB)† | C4-dicarboxylate transporter (DcuB) | +1.63 | ||
§Operon predictions in G. sulfurreducens are described in [18].
†Genes were discussed in the text and/or RpoN regulatory elements have been confirmed in their promoter regions by primer extension analyses
*Not all genes listed in the table matched the criteria for ≥ 1.25 fold-change cutoffs by the gene expression microarray analysis as described in Methods, but these genes are listed because one or more genes from the same operon matched the cutoff criteria.
N.D.: Not detected.