New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor

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.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.Streptomyces coelicolor is a representative of a group of high G+C Gram positive bacteria whose successful adaptation to their niche is demonstrated by their almost ubiquitous presence in soil. This is largely accounted for by their broad metabolic capacity allowing them to cope with the many variables in their environment. They are able to utilise a wide range of food sources including the debris from plants, insects and fungi. Streptomycetes are also famed for their production of a range of secondary metabolites including antibiotics and other chemotherapeutic compounds.Unusually for bacteria, streptomycetes exhibit complex multicellular development, with branching, filamentous mycelia giving rise to aerial hyphae which in turn bear long chains of reproductive spores. These three developmental stages also display differential 'tissue-specific' gene expression.Also unusual is the size and structure of streptomycete chromosomes. Streptomyces coelicolor has a linear chromosome which at 8,667,507 base pairs is the largest complete bact