Evolution of the streptomycin and viomycin biosynthetic clusters and resistance genes

Abstract

The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. It was hypothesised that non-antibiotic producers that are niche competitors with producers will need to possess resistance to the antibiotic and will thus have acquired resistance genes. A detailed phylogenetic study, utilizing a novel multilocus sequence typing (MLST) scheme, was made of a collection of isolates and types strains with a Streptomyces griseus phenotype in addition to type strains from known producers of streptomycin and related compounds. strA and vph were found either within a biosynthetic gene cluster or independently. S. griseus strains possessing the streptomycin cluster formed part of a clonal complex and have been readily isolated from soil originating in every continent except Antarctica. Few copies of strA were detected in soil total community DNA, none of which were identical to the gene from the streptomycin cluster. All S. griseus strains possessing solely strA belonged to two clades and were closely related to streptomycin producers. The strA in the resistance-only strains is likely to have originated from the self-resistance gene of another aminoglycoside cluster and arrived in those S. griseus strains via horizontal gene transfer. S. griseus strains with only vph also formed two clades and were more distantly related to the producers than to one another. The high sequence divergence of the viomycin resistance genes also suggests that the vph homologue arrived in these two groups from another peptide antibiotic cluster via horizontal gene transfer. The expression of the strA gene was constitutive in resistance-only strains from both subgroups whereas streptomycin producers showed peak strA expression in late log phase which correlates with the switch on of streptomycin biosynthesis. One example of horizontal gene transfer of the streptomycin cluster was discovered, to a Streptomyces platensis strain, which contained a cluster with 84% sequence identity and almost identical gene structure and arrangement to that of the S. griseus cluster. Its expression pattern was also highly similar to that of S. griseus producers, but at a much lower level. Whilst there is evidence that antibiotics have diverse roles in nature, this work clearly supports the co-evolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources