title: Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria.
abstract: Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with earlier evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in clustered regularly interspaced short palindromic repeat sequences suggest that S. arenicola may possess a higher level of phage immunity, whereas a highly duplicated family of polymorphic membrane proteins provides evidence for a new mechanism of marine adaptation in Gram-positive bacteria.
authors.affiliation: Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Penn
authors.forename: Caroline
authors.initials: C
authors.lastname: Jenkins
authors.forename: Markus
authors.initials: M
authors.lastname: Nett
authors.forename: Daniel W
authors.initials: DW
authors.lastname: Udwary
authors.forename: Erin A
authors.initials: EA
authors.lastname: Gontang
authors.forename: Ryan P
authors.initials: RP
authors.lastname: McGlinchey
authors.forename: Brian
authors.initials: B
authors.lastname: Foster
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Sheila
authors.initials: S
authors.lastname: Podell
authors.forename: Eric E
authors.initials: EE
authors.lastname: Allen
authors.forename: Bradley S
authors.initials: BS
authors.lastname: Moore
authors.forename: Paul R
authors.initials: PR
authors.lastname: Jensen
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D000220:Adaptation, Biological; D000222:Adaptation, Physiological; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008969:Molecular Sequence Data; D012623:Seawater / Q000382:microbiology; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D004269:DNA, Bacterial