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.

Figure 1

Linear alignment of the S. tropica and S. arenicola genomes starting with the origins of replication. (a) Positional orthologs (core) flanked by islands (E, F), heat-mapped HGT genes (D, G), rearranged orthologs (C, H), species-specific genes (B, I), secondary metabolite genes (green), MGEs (pink) with prophage (P) and AICES (E) indicated (A, J). For genomic islands, predicted (lower case) and isolated (uppercase with structures) secondary metabolites are given (not shown are six non-island secondary metabolic gene clusters of unknown function). Shared positional (blue) and rearranged (red) secondary metabolite clusters are indicated. *Previously isolated from other bacteria. (b) Expanded view of SA pks5 revealing gene and modular architecture. (c) Neighbor-joining phylogenetic tree of KS domains from SA pks5 revealing gene and modular duplication events (erythromycin root, % bootstrap values from 1000 re-samplings).

Figure 2

S. tropica prophage and S. arenicola CRISPRs. Four of 8 SA CRISPRs (1, 5, 7, 8) have spacers (color coded) that share 100% sequence identity with genes (Stro numbers and annotation given) in ST prophage 1 (Table S2, inverted for visual purposes). Other CRISPRs are colored purple. SA CRISPRs 2-3 and 5-6 share the same direct repeats and may have at one time been a single allele. CRISPR associated (CAS) genes (red) and genes interrupting CRISPRs (black) are indicated. None of the spacer sequences possessed 100% identity to prophage in the NCBI non-redundant sequence database, the SDSU Center for Universal Microbial Sequencing database, or the CAMERA metagenomic database.

Figure 3

Composition, evolutionary history, and function of island genes in S. tropica (ST) and S. arenicola (SA). (a) 3040 genes comprising 21 genomic islands were analyzed for positional orthology (ie., the gene is part of the shared “core” genome), re-arranged orthology (ie., the gene is present in the other genome but not in the same position or island), and species-specificity (gene totals presented in wedges). (b) The ST and SA species-specific island genes were analyzed for evidence of parology, xenology, and HGT. Pseudogenes and the number of genes with no evidence for any of these processes were also identified. (c) Functional annotation of the species-specific island genes. (d) Distribution of species-specific island genes that have no evidence for HGT or parology among 27 Actinobacterial genomes.