Abstract
Many Streptomyces strains are known to produce valinomycin (VLM) antibiotic and the VLM biosynthetic gene cluster (vlm) has been characterized in two independent isolates. Here we report the phylogenetic relationships of these strains using both parsimony and likelihood methods, and discuss whether the vlm gene cluster shows evidence of horizontal transmission common in natural product biosynthetic genes. Eight Streptomyces strains from around the world were obtained and sequenced for three regions of the two large nonribosomal peptide synthetase genes (vlm1 and vlm2) involved in VLM biosynthesis. The DNA sequences representing the vlm gene cluster are highly conserved among all eight environmental strains. The geographic distribution pattern of these strains and the strict congruence between the trees of the two vlm genes and the housekeeping genes, 16S rDNA and trpB, suggest vertical transmission of the vlm gene cluster in Streptomyces with no evidence of horizontal gene transfer. We also explored the relationship of the sequence of vlm genes to that of the cereulide biosynthetic genes (ces) found in Bacillus cereus and found them highly divergent from each other at DNA level (genetic distance values≥95.6%). It is possible that the vlm gene cluster and the ces gene cluster may share a relatively distant common ancestor but these two gene clusters have since evolved independently.
Highlights
Microbial natural products mediate a wide range of biological and biochemical interactions both among microbes and between microbes and higher organisms [1,2]
A classic example of horizontal gene transfer (HGT) is the transmission of nonribosomal peptide synthetase (NRPS) genes responsible for the production of b-lactam antibiotics, from bacteria to bacteria and from bacteria to fungi [5,6]
Strong similarity is indicated by the ability to amplify all three regions of the vlm genes from all taxa by PCR using primers based on the sequences of reference strain S. tsusimaensis (Fig. 1b)
Summary
Microbial natural products mediate a wide range of biological and biochemical interactions both among microbes and between microbes and higher organisms [1,2]. Information embedded in natural product biosynthetic genes and gene clusters includes biochemical codes for the production of diverse chemical molecules by enzyme catalysts, and evolutionary and ecological clues about the origin, transmission and distribution of the genetic determinants of natural product biosynthesis. HGT origins are typically identified by criteria including incongruence between phylogenetic trees constructed with genes involved in primary metabolism [i.e. housekeeping genes such as 16S rDNA, trpB (encoding tryptophan synthetase b-subunit), rpoC1 (encoding RNA polymerase b-chain)] and the genes in question, atypical sequence composition, the presence or absence of genes in closely related genera, and the flanking of genes by insertion elements such as transposons [4]. Two recent surveys of polyketide synthase genes revealed the independent evolution of bacterial speciation and natural product biosynthetic genes, supporting the theory of HGT [7,8]. [10] identified independent evolution traces of those genes within each genus, disfavoring an origin by HGT Analysis of the conserved cyanopeptolin biosynthetic genes from three genera of cyanobacteria by Rounge at al. [10] identified independent evolution traces of those genes within each genus, disfavoring an origin by HGT
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