Abstract
Streptomyces sp. N11-34 is a producer of bicyclic peptides named nyuzenamides A and B. We elucidated its taxonomic position and surveyed its nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters by whole genome analysis. Streptomyces sp. N11-34 showed 16S rRNA gene sequence similarities of 99.9% and 99.8% to Streptomyces hygroscopicus NBRC 13472T and Streptomyces demainii NRRL B-1478T, respectively. Although these members formed a clade in a phylogenetic tree based on 16S rRNA gene sequences, the clade split into two closely related subclades in multilocus sequence analysis (MLSA). One included Streptomyces sp. N11-34, S. demainii NRRL B-1478T, S. hygroscopicus NBRC 100766, S. hygroscopicus NBRC 16556 and S. hygroscopicus TP-A0867 and the other comprised S. hygroscopicus NBRC 13472T and S. hygroscopicus NBRC 12859. These phylogenetic relationships were supported by phylogenomic analysis. Although Streptomyces sp. N11-34 was classified to S. hygroscopicus at the species level based on MLSA evolutionary distances and DNA–DNA relatedness, these distances and relatedness of members between the two subclades were comparatively far (0.004–0.006) and low (75.4–76.4%), respectively. Streptomyces sp. N11-34 possessed six NRPS, seven PKS and four hybrid PKS/NRPS gene clusters in the genome. Among the seventeen, ten were identified to be biosynthetic gene clusters (BGCs) of nyuzenamide, echoside, coelichelin, geldanamycin, mediomycin, nigericin, azalomycin, spore pigment, alchivemycin and totopotensamide, whereas the remaining seven were orphan in our bioinformatic analysis. All seventeen are conserved in S. hygroscopicus NBRC 100766, S. hygroscopicus NBRC 16556 and S. hygroscopicus TP-A0867. In contrast, S. hygroscopicus NBRC 13472T and S. hygroscopicus NBRC 12859 lacked the BGCs of alchivemycin, totopotensamide, a nonribosomal peptide and a hybrid polyketide/nonribosomal peptide compound. This difference was in a good accordance with the abovementioned phylogenetic relationship. Based on phenotypic differences in addition to phylogenetic relationship, DNA–DNA relatedness and BGCs, strains of S. hygroscopicus should be reclassified to two subspecies: S. hygroscopicus subsp. hygroscopicus and a new subspecies, for which we proposed S. hygroscopicus subsp. sporocinereus subsp. nov. The type strain is NBRC 100766T (=ATCC 43692T = DSM 41460T = INMI 32T = JCM 9093T = NRRL B-16376T = VKM Ac-312T). S. demainii was classified in this subspecies.
Highlights
Based on phenotypic differences in addition to phylogenetic relationship, DNA–DNA relatedness and biosynthetic gene clusters (BGCs), strains of S. hygroscopicus should be reclassified to two subspecies: S. hygroscopicus subsp. hygroscopicus and a new subspecies, for which we proposed
Sim minimal polyketide synthase (PKS) module consists of an acyltransferase (AT) domain for selecting in acyl-CoAs, a ketosynthase (KS) domain for condensing the new building block w acyl intermediate from the previous module and an acyl carrier protein (ACP) dom carrying the growing polyketide chain
N11-34, as described in the Section 3.1, we examined whether the seventeen PKS and nonribosomal peptide synthetase (NRPS) gene clusters found in Streptomyces sp
Summary
Domain pounds seem tofrom be synthesized through pathway, biosynthetic gene for carrying polyketide chain.InIndividual modules are we responsible for the the tax (BGC). N11-34 and analyzed NRPS and PKS gene clusters to Optional domains may be present in each module, which methylate or epimerize incorpothe nyuzenamide-BGC reveal hidden produce other compounds rated amino acid residues inand nonribosomal peptidespotential or reduce to a keto group in polyketide quently, wewe classified sp.products. Streptomyces from sea water and bioactive found two compo pharmaceutical industries.nyuzenamides This speciesAonce four subspecies with valid novel compounds designated and Bincluded from the strain. As various bioactive secondary metabolites have been discovered from the members, it is expected as a source for searching novel bioactive compounds in pharmaceutical industries This species once included four subspecies with validly published names. We here propose a new subspecies of S. hygroscopicus
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