Isolation and characterization of putative Pseudobutyrivibrio ruminis promoters

Microbiology (Reading). 2007 Sep;153(Pt 9):3071-3080. doi: 10.1099/mic.0.2007/006502-0.

Abstract

Novel plasmids were constructed for the analysis of DNA fragments from the rumen bacterium Pseudobutyrivibrio ruminis. Five previously unidentified promoters were characterized using a novel primer extension method to identify transcription start sites. The genes downstream of these promoters were not identified, and their activity in expression of genomic traits in wild-type P. ruminis remains putative. Comparison with promoters from this and closely related species revealed a consensus sequence resembling the binding motif for the RNA polymerase sigma(70)-like factor complex. Consensus -35 and -10 sequences within these elements were TTGACA and ATAATATA respectively, interspaced by 15-16 bp. The consensus for the -10 element was extended by one nucleotide upstream and downstream of the standard hexamer (indicated in bold). Promoter strengths were measured by reverse transcription quantitative PCR and beta-glucuronidase assays. No correlation was found between the composition and context of elements within P. ruminis promoters, and promoter strength. However, a mutation within the -35 element of one promoter revealed that transcriptional strength and choice of transcription start site were sensitive to this single nucleotide change.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Butyrivibrio / chemistry
  • Butyrivibrio / genetics*
  • Butyrivibrio / growth & development
  • Butyrivibrio / metabolism
  • Consensus Sequence
  • DNA Primers
  • DNA-Binding Proteins / chemistry
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • Gene Library
  • Molecular Sequence Data
  • Promoter Regions, Genetic / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Rumen / microbiology*
  • Sequence Analysis, DNA
  • Sigma Factor

Substances

  • DNA Primers
  • DNA-Binding Proteins
  • Sigma Factor
  • RNA polymerase sigma 70
  • DNA-Directed RNA Polymerases

Associated data

  • GENBANK/DQ841994
  • GENBANK/DQ841995
  • GENBANK/DQ841996
  • GENBANK/DQ841997
  • GENBANK/DQ841998
  • GENBANK/DQ841999
  • GENBANK/DQ842000