Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria

FEMS Microbiol Lett. 2001 Dec 18;205(2):315-22. doi: 10.1111/j.1574-6968.2001.tb10966.x.


The comparative approach to the recognition of transcription regulatory sites is based on the assumption that as long as a regulator is conserved in several genomes, one can expect that sets of co-regulated genes (regulons) and regulatory sites for the regulator in these genomes are conserved as well. We used this approach to analyze the ribose (RbsR), arabinose (AraC), and xylose (XylR) regulons of gamma Proteobacteria for which (almost) completely sequenced genomes were available. Candidate binding sites for RbsR and AraC were detected. The improved XylR site consensus was proposed. Potential new members of the xylose regulons were found in the Escherichia coli, Salmonella typhi, and Klebsiella pneumoniae genomes. The function of these new xylose-regulated operons is likely to be the utilization of oligosaccharides containing xylose. Finally, candidate cAMP receptor-protein sites were identified in the regulatory regions of the majority of RbsR-, AraC-, and XylR-regulated operons.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • AraC Transcription Factor
  • Bacterial Proteins*
  • Binding Sites
  • Computers
  • Cyclic AMP Receptor Protein / genetics
  • DNA-Binding Proteins / genetics
  • Escherichia coli Proteins*
  • Gammaproteobacteria / genetics*
  • Gammaproteobacteria / metabolism
  • Genes, Bacterial*
  • Operon
  • Pentoses / metabolism*
  • Regulon
  • Repressor Proteins / genetics
  • Transcription Factors / genetics
  • Transcription, Genetic


  • AraC Transcription Factor
  • AraC protein, E coli
  • Bacterial Proteins
  • Cyclic AMP Receptor Protein
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Pentoses
  • RbsR protein, E coli
  • Repressor Proteins
  • Transcription Factors
  • XylR protein, Pseudomonas