Komaki Hisayuki, Igarashi Yasuhiro, Tamura Tomohiko
Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba 292-0818, Japan.
Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan.
Microorganisms. 2022 Feb 2;10(2):349. doi: 10.3390/microorganisms10020349.
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. sp. N11-34 showed 16S rRNA gene sequence similarities of 99.9% and 99.8% to NBRC 13472 and NRRL B-1478, 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 sp. N11-34, NRRL B-1478, NBRC 100766, NBRC 16556 and TP-A0867 and the other comprised NBRC 13472 and NBRC 12859. These phylogenetic relationships were supported by phylogenomic analysis. Although sp. N11-34 was classified to 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. 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 NBRC 100766, NBRC 16556 and TP-A0867. In contrast, NBRC 13472 and 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 should be reclassified to two subspecies: subsp. and a new subspecies, for which we proposed subsp. subsp. nov. The type strain is NBRC 100766 (=ATCC 43692 = DSM 41460 = INMI 32 = JCM 9093 = NRRL B-16376 = VKM Ac-312). was classified in this subspecies.
菌株N11 - 34是双环肽纽泽酰胺A和B的产生菌。我们通过全基因组分析阐明了它的分类地位，并对其非核糖体肽合成酶（NRPS）和聚酮合酶（PKS）基因簇进行了研究。菌株N11 - 34的16S rRNA基因序列与NBRC 13472和NRRL B - 1478的相似性分别为99.9%和99.8%。尽管这些成员在基于16S rRNA基因序列的系统发育树中形成了一个分支，但在多位点序列分析（MLSA）中，该分支分裂为两个密切相关的亚分支。一个亚分支包括菌株N11 - 34、NRRL B - 1478、NBRC 100766、NBRC 16556和TP - A0867，另一个亚分支由NBRC 13472和NBRC 12859组成。这些系统发育关系得到了系统基因组分析的支持。尽管根据MLSA进化距离和DNA - DNA相关性，菌株N11 - 34在物种水平上被分类，但两个亚分支成员之间的这些距离和相关性相对较远（0.004 - 0.006）和较低（75.4 - 76.4%）。菌株N11 - 34在基因组中拥有六个NRPS、七个PKS和四个杂交PKS/NRPS基因簇。在这十七个基因簇中，有十个被鉴定为纽泽酰胺、回声菌素、天蓝色菌素、格尔德霉素、间霉素、尼日利亚菌素、氮霉素、孢子色素、阿奇霉素和托托波坦酰胺的生物合成基因簇（BGCs），而其余七个在我们的生物信息学分析中是未知的。所有十七个基因簇在NBRC
