New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor

BMC Microbiol. 2003 Feb 6;3:3. doi: 10.1186/1471-2180-3-3. Epub 2003 Feb 6.

Abstract

Background: Streptomyces coelicolor has long been considered a remarkable bacterium with a complex life-cycle, ubiquitous environmental distribution, linear chromosomes and plasmids, and a huge range of pharmaceutically useful secondary metabolites. Completion of the genome sequence demonstrated that this diversity carried through to the genetic level, with over 7000 genes identified. We sought to expand our understanding of this organism at the molecular level through identification and annotation of novel protein domains. Protein domains are the evolutionary conserved units from which proteins are formed.

Results: Two automated methods were employed to rapidly generate an optimised set of targets, which were subsequently analysed manually. A final set of 37 domains or structural repeats, represented 204 times in the genome, was developed. Using these families enabled us to correlate items of information from many different resources. Several immediately enhance our understanding both of S. coelicolor and also general bacterial molecular mechanisms, including cell wall biosynthesis regulation and streptomycete telomere maintenance.

Discussion: Delineation of protein domain families enables detailed analysis of protein function, as well as identification of likely regions or residues of particular interest. Hence this kind of prior approach can increase the rate of discovery in the laboratory. Furthermore we demonstrate that using this type of in silico method it is possible to fairly rapidly generate new biological information from previously uncorrelated data.

MeSH terms

  • Amino Acid Motifs
  • Automation / methods
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / classification*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / physiology
  • Cell Wall / metabolism
  • Conserved Sequence
  • Genome, Bacterial
  • Protein Structure, Tertiary
  • Streptomyces / genetics*
  • Streptomyces / metabolism
  • Streptomyces / physiology
  • Telomere / physiology

Substances

  • Bacterial Proteins