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Table 2 Genes containing RpoN-dependent promoters identified by the PromScan analysis and the transcriptome analysis.

From: Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

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  
  1. §Operon predictions in G. sulfurreducens are described in [18].
  2. Genes were discussed in the text and/or RpoN regulatory elements have been confirmed in their promoter regions by primer extension analyses
  3. *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.
  4. N.D.: Not detected.