Genome Analysis In Plant Pathogenic Streptomyces

Abstract

The soil bacteria Streptomyces have been extensively studied because of the variety of secondary metabolites that they produce, and their ability to degrade recalcitrant polymers in the environment. Streptomyces are mainly soil saprophytes, however, a relatively small number of species are pathogenic and cause lesions on potato and other root and tuber crops. All plant pathogenic Streptomyces species produce a phytotoxin, thaxtomin, which is required for pathogenicity. Additionally, these pathogens possess virulence genes that vary across species. Comparative genomic analysis of 11 Streptomyces spp. demonstrated that this genus possesses a surprisingly small core genome; this common set of orthologues encode biological processes that define a streptomycete. Among these are transcriptional regulators and proteins associated with morphological differentiation. Comparisons between the genomes of saprophytic and pathogenic species identified the portion of the accessory genome that is associated with pathogenesis, the patho-genome, including novel transcriptional regulators and secreted proteins with putative virulence functions. Phylogenetic analysis of 11 species of Streptomyces, carried out using a subset of genes in the core genome resulted in only partial resolution of the evolutionary relationship of the genus. This analysis suggested that the plant pathogens S. scabies and ipomoeae have a common evolutionary history, while S. turgidiscabies is a newly evolved pathogen. The poor resolution of the phylogenetic relationships among these species resulted from extensive recombination within the core genome, affecting even informational genes. Our results suggest that homologous recombination is an important evolutionary force in the genus Streptomyces. Analysis of the Streptomyces turgidiscabies genome revealed a large genomic island, PAISt, containing authentic and putative virulence genes and organization typical of an integrative conjugative element (ICE). PAISt contained genes expected to be involved in the integration and mobilization of the ICE. Based on bioinformatic and experimental analysis, the recombinase responsible for the integration of PAISt into the chromosome of Streptomyces spp. appears to represent a novel member of the tyrosine recombinase family.