title: Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales.
abstract: BACKGROUND
  In the rhizobia, a group of symbiotic Gram-negative soil bacteria, RpoN (sigma54, sigmaN, NtrA) is best known as the sigma factor enabling transcription of the nitrogen fixation genes. Recent reports, however, demonstrate the involvement of RpoN in other symbiotic functions, although no large-scale effort has yet been undertaken to unravel the RpoN-regulon in rhizobia. We screened two complete rhizobial genomes (Mesorhizobium loti, Sinorhizobium meliloti) and four symbiotic regions (Rhizobium etli, Rhizobium sp. NGR234, Bradyrhizobium japonicum, M. loti) for the presence of the highly conserved RpoN-binding sites. A comparison was also made with two closely related non-symbiotic members of the Rhizobiales (Agrobacterium tumefaciens, Brucella melitensis).
  
  
  RESULTS
  A highly specific weight-matrix-based screening method was applied to predict members of the RpoN-regulon, which were stored in a highly annotated and manually curated dataset. Possible enhancer-binding proteins (EBPs) controlling the expression of RpoN-dependent genes were predicted with a profile hidden Markov model.
  
  
  CONCLUSIONS
  The methodology used to predict RpoN-binding sites proved highly effective as nearly all known RpoN-controlled genes were identified. In addition, many new RpoN-dependent functions were found. The dependency of several of these diverse functions on RpoN seems species-specific. Around 30% of the identified genes are hypothetical. Rhizobia appear to have recruited RpoN for symbiotic processes, whereas the role of RpoN in A. tumefaciens and B. melitensis remains largely to be elucidated. All species screened possess at least one uncharacterized EBP as well as the usual ones. Lastly, RpoN could significantly broaden its working range by direct interfering with the binding of regulatory proteins to the promoter DNA.
authors.affiliation: Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium.
authors.forename: Bruno
authors.initials: B
authors.lastname: Dombrecht
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
authors.forename: Jos
authors.initials: J
authors.lastname: Vanderleyden
authors.forename: Jan
authors.initials: J
authors.lastname: Michiels
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D005798:Genes, Bacterial; D008390:Markov Chains; D011237:Predictive Value of Tests; D011401:Promoter Regions, Genetic / Q000235:genetics; D051877:RNA Polymerase Sigma 54; D018085:Regulon / Q000235:genetics*; D012230:Rhizobiaceae / Q000235:genetics*; D012808:Sigma Factor / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics; D013559:Symbiosis / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D012808:Sigma Factor; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54