Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora

Abstract

Significance Microbial natural products are a major source of new drug leads, yet discovery efforts are constrained by the lack of information describing the diversity and distributions of the associated biosynthetic pathways among bacteria. Using the marine actinomycete genus Salinispora as a model, we analyzed genome sequence data from 75 closely related strains. The results provide evidence for high levels of pathway diversity, with most being acquired relatively recently in the evolution of the genus. The distributions and evolutionary histories of these pathways provide insight into the mechanisms that generate new chemical diversity and the strategies used by bacteria to maximize their population-level capacity to produce diverse secondary metabolites.

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea

“…Given the wide geographical range from which the four Moorea strains were obtained, spanning some 16,000 km and existing in two distinct oceans, one could expect that they might show considerable sequence divergence. However, a precedent set from the genus Salinispora indicates that genomic conservation is in some cases observed for geographically divergent species (20). The four genomes investigated here were found to be remarkably similar with a very high average nucleotide identity (minimum of 94.6%), consistent with previously reported 16S rRNA gene identities of more than 99% (7).…”

Pictet–Spengler reaction-based biosynthetic machinery in fungi

“…This is why natural products remain a common stimulating force both for synthetic and material chemistry (8)(9)(10), and for pharmaceutical and agrochemical industries (6,7,39). Concerning the microbial generation of natural products, the long-time evolution has enabled microbes to organize the biosynthetic machineries in an ingenious way so that they can produce the organic molecular diversity as case-dependent responses to various outside events such as symbiosis (40), gene transfer (41), and host invasion (42). To get more structurally unprecedented small molecules, it is urgently necessary to activate the silent or less-active biosynthetic pathways in the producing organisms.…”

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

“…These bacteria are well known for secondary metabolite production (41), and their mycelial growth form creates the potential for the formation of large networks (42) that have yet to be spatially characterized. Antibiotic production in actinomycetes has been linked to nutrient sensing and morphological differentiation (43), and their biosynthetic potential is much larger than laboratory observations suggest (44,45). While the natural cues that trigger the production of most secondary metabolites remain unknown, many of these compounds are potent antibiotics and thus have the potential to affect members of the community with which they interact.…”

“…It is comprised of three named species, Salinispora arenicola, Salinispora tropica, and Salinispora pacifica (46,47), which are well delineated despite sharing 99% 16S rRNA gene sequence identity (48). Notably, these bacteria are a rich source of secondary metabolites (49), which have proven to be key phenotypic (50) and genotypic (45) features that differentiate the species. Secondary metabolism also distinguishes the competitive strategies employed by S. arenicola and S. tropica; in particular, the production of rifamycin antibiotics by S. arenicola contributes to its broad inhibitory capacity compared to that of the faster-growing S. tropica (18).…”

“…Secondary metabolism also distinguishes the competitive strategies employed by S. arenicola and S. tropica; in particular, the production of rifamycin antibiotics by S. arenicola contributes to its broad inhibitory capacity compared to that of the faster-growing S. tropica (18). With ϳ10% of the genome of S. arenicola devoted to secondary metabolism (45,51) and the potent bioactivity of its natural products, this species was an obvious choice to explore the effects of secondary metabolites on the sediment microbial community.…”