Genome plasticity and systems evolution in Streptomyces

Abstract

BackgroundStreptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation.ResultsWe present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication.ConclusionsOur results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A better understanding of the LSE gene families will, on the other hand, bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes, such as the production of novel antibiotics, pathogenesis, and adaptive response to environmental challenges.

Streptomyces coelicolor Encodes a Urate-Responsive Transcriptional Regulator with Homology to PecS from Plant Pathogens

“…The presence of multiple UrtR homologs is consistent with the frequent gene duplication and horizontal gene transfer events that have been inferred to occur in Streptomyces spp. (30). Neither TamR nor PecS homologs are ubiquitously present in Streptomyces species.…”

Recent advances in the biotechnological production of microbial poly(ɛ-l-lysine) and understanding of its biosynthetic mechanism

“…Among the five bacteria, four of them are S. albulus, and their genomes exhibit high similarity with each other. As reported, Streptomyces have some of the large genomes within the range of 8.7 to 11.9 Mb and GC contents within the range from 69 to 76 % (Harrison and Studholme 2014;Zhou et al 2012). It shows that the ɛ-PL-producing strains possess the basic features of Streptomyces.…”

Metabolomics-Based Chemotaxonomic Classification of Streptomyces spp. and Its Correlation with Antibacterial Activity

“…Streptomyces is a group of gram-positive filamentous bacteria that grow in soil and decaying vegetation. It is the largest genus of Actinobacteria and includes over 500 species [61]. Streptomycetes have historically been examined for their ability to biologically control plant disease and animal pathogens [22,23,41].…”