Lidamycin is an antitumor and antibacterial antibiotic synthesized by microorganisms of the species Streptomyces globisporus (strains C-1027 and TFH56). The aim of the work was to identify streptomycetes whose genomes contain probable clusters of lidamycin biosynthetic genes (LDM-cluster). The objects of the study were the nucleotide sequences of streptomycetes deposited in online databases (Nucleotide Collection, Whole-Genome Shotgun Contigs) on the server of the National Center for Biotechnology Information. The primary structures of the DNA were analyzed using the Basic Local Alignment Search Tool. The sequence of the LDM-cluster from S. globisporus C-1027 was used as a query for the computational analysis of nucleotide sequences. The online databases contain information about the primary structures of hundreds of thousands of chromosomes and plasmids of streptomycetes that are сomlete (Nucleotide Collection) or partially (Whole-Genome Shotgun Contigs) defined. In total, 78 streptomycetes were identified in both databases whose genomes contained complete LDM-clusters. The majority of streptomycetes in the set (65.4 %) belong to the species S. globisporus. As is known, LDM clusters are located on the plasmids SGLP1 (strain C-1027) and pTFHSG1 (strain TFH56). Six plasmids (complete genome) were found in the Nucleotide Collection database. The sequences of the identified plasmids and SGLP1 are not identical — only fragments with a molecular size of 104.5 kbp in their sequences are similar. The identified plasmids were found in the shape of molecules as both linear (CP108547, CP109060, pTFHSG1, CP109147, CP108593) and circular (pG-2-2). By molecular size, all 6 plasmids can be classified as large plasmids. Plasmids CP108593 and pG-2-2 differ in their sequence both from the structures of other plasmids and from the structures of the identified streptomycet contigs. Additionally, 72 streptomycetes whose genomes contained complete LDM clusters were discovered in the Whole-Genome Shotgun Contigs database. However, complete plasmid sequences were identified only in the sequences of several contigs. The complete sequence of plasmid pTFHSG1 was found in the contigs of S. badius SF7B6 (LWMP01000002, 134520 bp), S. badius SP6C4 (LWMQ01000002, 140513 bp), S. griseus S4-7 (JYBE02000002, 141125 bp) strains. The presence of complete LDM cluster sequences in the genomes of 78 streptomycetes was established, as represented in databases on the NCBI server. Six plasmids containing LDM clusters in their structures were identified.
Keywords: Streptomyces, lidamycin, LDM-cluster, plasmid, nucleotide sequence, computerized analysis, identity, query coverage
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