Taxonomic Positions of a Nyuzenamide-Producer and Its Closely Related Strains

Hisayuki Komaki; Yasuhiro Igarashi; Tomohiko Tamura

doi:10.3390/microorganisms10020349

Taxonomic Positions of a Nyuzenamide-Producer and Its Closely Related Strains

Microorganisms. 2022 Feb 2;10(2):349. doi: 10.3390/microorganisms10020349.

Authors

Hisayuki Komaki¹, Yasuhiro Igarashi², Tomohiko Tamura¹

Affiliations

¹ Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba 292-0818, Japan.
² Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan.

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 13472^T and Streptomyces demainii NRRL B-1478^T, 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-1478^T, S. hygroscopicus NBRC 100766, S. hygroscopicus NBRC 16556 and S. hygroscopicus TP-A0867 and the other comprised S. hygroscopicus NBRC 13472^T 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 13472^T 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 100766^T (=ATCC 43692^T = DSM 41460^T = INMI 32^T = JCM 9093^T = NRRL B-16376^T = VKM Ac-312^T). S. demainii was classified in this subspecies.

Keywords: PKS; Streptomyces; biosynthetic gene; classification; nonribosomal peptide; subspecies.