Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea.
Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
BMC Genomics. 2020 Feb 3;21(1):118. doi: 10.1186/s12864-020-6468-5.
Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment.
A high quality draft genome (7.8 Mb) of S. yeochonensis CN732 was obtained with a G + C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites.
This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.
嗜酸性放线菌属的成员可以成为新型次生代谢产物和生物聚合物降解酶的良好来源。在这项研究中，采用基于基因组的方法研究了中性耐酸链霉菌 S. yeochonensis CN732，这是一种具有代表性的嗜酸性放线菌，以检查其生物合成和酶潜力，以及是否存在适应酸性环境的任何遗传工具。
获得了 S. yeochonensis CN732 的高质量草图基因组（7.8 Mb），G+C 含量为 73.53%，包含 6549 个蛋白质编码基因。计算机分析预测存在多个生物合成基因簇（BGCs），这些 BGCs 与抗微生物、抗癌或抗寄生虫化合物的 BGCs 相似。然而，大多数情况下与已知 BGCs 的低相似性表明，来自预测基因簇的代谢产物具有新颖性。通过高效液相色谱-质谱联用分析也证实了各种新型代谢产物的产生。通过与相关链霉菌物种的比较基因组分析，可以鉴定出菌株 CN732 特有的基因和中性耐酸物种特有的基因，这表明在嗜酸物种中丰富了代谢多种环境的基因。此外，还存在针对碳水化合物活性酶（CAZyme）的菌株特异性基因以及许多其他单体，这表明菌株 CN732 的遗传组成具有独特性。本研究还观察到 BGCs 中存在半胱氨酸转肽酶（sortases），这表明它们在次生代谢产物生物合成中的潜在作用。
本研究使用基于基因组的方法强调了嗜酸链霉菌 S. yeochonensis 的生物活性潜力，包括次生代谢产物的产生和生物降解潜力。比较基因组分析揭示了 CN732 特有的基因和嗜酸物种中的基因，这可以为微生物在酸性环境中的适应提供一些见解。
