Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information

Gene. 2006 Dec 15;384:73-95. doi: 10.1016/j.gene.2006.06.025. Epub 2006 Jul 20.

Abstract

RpoS, the sigma S subunit of RNA polymerase, is vital during the growth and survival of Geobacter sulfurreducens under conditions typically encountered in its native subsurface environments. We investigated the conservation of sites that may be important for RpoS function in G. sulfurreducens. We also employed sequence information and expression microarray data to predict G. sulfurreducens genome sites that may be related to RpoS regulation. Hierarchical clustering identified three clusters of significantly downregulated genes in the rpoS deletion mutant. The search for conserved overrepresented motifs in co-regulated operons identified likely -35 and -10 promoter elements upstream of a number of functionally important G. sulfurreducens operons that were downregulated in the rpoS deletion mutant. Putative -35/-10 promoter elements were also identified in the G. sulfurreducens genome using sequence similarity searches to matrices of -35/-10 promoter elements found in G. sulfurreducens and in Escherichia coli. Due to a sufficient degree of sequence similarity between -35/-10 promoter elements for RpoS, RpoD, and other sigma factors, both the sequence similarity searches and the search for conserved overrepresented motifs using microarray data may identify promoter elements for both RpoS and other sigma factors.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics*
  • Base Sequence
  • Citrates / metabolism
  • Computational Biology
  • Conserved Sequence
  • DNA-Directed RNA Polymerases / chemistry
  • DNA-Directed RNA Polymerases / genetics*
  • Escherichia coli
  • Escherichia coli Proteins
  • Gene Deletion
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial*
  • Genes, Bacterial
  • Genome, Bacterial
  • Geobacter / genetics*
  • Geobacter / growth & development
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis
  • Operon / genetics*
  • Promoter Regions, Genetic
  • Sigma Factor / chemistry
  • Sigma Factor / genetics*
  • Transcription, Genetic

Substances

  • Bacterial Proteins
  • Citrates
  • Escherichia coli Proteins
  • Sigma Factor
  • sigma factor KatF protein, Bacteria
  • RNA polymerase sigma 70
  • DNA-Directed RNA Polymerases