Streptomyces avermitilis NBRC 14893^T has complestatin and oxazolomycin analog biosynthetic gene clusters, which do not exist in the reported genome sequence of S. avermitilis MA-4680^T

Abstract

The complete genome sequence of Streptomyces avermitilis ATCC 31267^T, known as an avermectin producer, was reported in 2001 (Omura et al., 2001), and is now published as that of S. avermitilis MA-4680^T in GenBank/EMBL/DDBJ (Ikeda et al., 2003). In our PCR-based nonribosomal peptide synthetase (NRPS) gene analysis for actinomycetes, NRPS genes that are not present in the S. avermitilis complete genome sequence were unexpectedly amplified from S. avermitilis NBRC 14893^T. To investigate the reason of this unexpected result, we sequenced the whole genome of S. avermitilis NBRC 14893^T using Genome Sequencer FLX and Illumina HiSeq1000. Consequently, the genome size was estimated at approximately 10 Mb, and 92 contig/scaffold sequences were obtained. Some of the sequences were not present in the published S. avermitilis genome sequence. Approximately 40 kb of NRPS gene cluster and 65 kb NRPS/polyketide synthase hybrid gene cluster, previously unreported in S. avermitilis, were discovered in the NBRC 14893^T-specific genome sequences. Bioinformatic analyses suggested that the two gene clusters were likely involved in the synthesis of demethylcomplestatin and a novel oxazolomycin analog, respectively. According to strain transfer histories among culture collections, the original type strain S. avermitilis MA-4680^T had been deposited to Agricultural Research Service Culture Collection (NRRL), and the NRRL strain had been subsequently deposited to KCC Culture Collection of Actinomycetes, Kaken Pharmaceutical Co., Ltd. (KCC) and American Type Culture Collection (ATCC). NBRC 14893^T is derived from the KCC strain, while the complete genome-elucidated strain is from ATCC 31267^T. It is hard to imagine that pure culture stocks acquire additional DNA coding large biosynthetic gene clusters. Furthermore, plasmid loss and dynamic genome reconstitution frequently occur in the genus Streptomyces. Therefore, the deletion of the two gene clusters we discovered here had probably occurred after the type strain of S. avermitilis was transferred from NRRL to ATCC.