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首页> 外文期刊>Applied Microbiology >Sequence-Based Analysis of Secondary-Metabolite Biosynthesis in Marine Actinobacteria
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Sequence-Based Analysis of Secondary-Metabolite Biosynthesis in Marine Actinobacteria

机译：海洋放线菌中次级代谢代谢物生物合成的基于序列的分析

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A diverse collection of 60 marine-sediment-derived Actinobacteria representing 52 operational taxonomic units was screened by PCR for genes associated with secondary-metabolite biosynthesis. Three primer sets were employed to specifically target adenylation domains associated with nonribosomal peptide synthetases (NRPSs) and ketosynthase (KS) domains associated with type I modular, iterative, hybrid, and enediyne polyketide synthases (PKSs). In total, two-thirds of the strains yielded a sequence-verified PCR product for at least one of these biosynthetic types. Genes associated with enediyne biosynthesis were detected in only two genera, while 88% of the ketosynthase sequences shared greatest homology with modular PKSs. Positive strains included representatives of families not traditionally associated with secondary-metabolite production, including the Corynebacteriaceae , Gordoniaceae, Intrasporangiaceae , and Micrococcaceae . In four of five cases where phylogenetic analyses of KS sequences revealed close evolutionary relationships to genes associated with experimentally characterized biosynthetic pathways, secondary-metabolite production was accurately predicted. Sequence clustering patterns were used to provide an estimate of PKS pathway diversity and to assess the biosynthetic richness of individual strains. The detection of highly similar KS sequences in distantly related strains provided evidence of horizontal gene transfer, while control experiments designed to amplify KS sequences from Salinispora arenicola strain CNS-205, for which a genome sequence is available, led to the detection of 70% of the targeted PKS pathways. The results provide a bioinformatic assessment of secondary-metabolite biosynthetic potential that can be applied in the absence of fully assembled pathways or genome sequences. The rapid identification of strains that possess the greatest potential to produce new secondary metabolites along with those that produce known compounds can be used to improve the process of natural-product discovery by providing a method to prioritize strains for fermentation studies and chemical analysis.
机译：通过PCR筛选了代表52个操作生物分类单元的60种海洋沉积物衍生的放线菌，收集了与次级代谢物生物合成相关的基因。使用三个引物组特异性靶向与非核糖体肽合成酶（NRPSs）和酮合酶（KS）域相关的与I型模块化，迭代，杂合和烯二炔聚酮合酶（PKS）相关的腺苷酸化域。总共，三分之二的菌株针对这些生物合成类型中的至少一种产生了经序列验证的PCR产物。仅在两个属中检测到与烯二炔生物合成相关的基因，而88％的酮合成酶序列与模块化PKS具有最大的同源性。阳性菌株包括传统上与次级代谢产物生产无关的家族的代表，包括棒状杆菌科，Gordoniaceae，孢子管内科和微球菌科。在KS序列的系统发育分析显示与与实验表征的生物合成途径相关的基因密切进化关系的五分之四的案例中，可以准确预测次级代谢产物的产生。序列聚类模式用于提供PKS途径多样性的估计并评估单个菌株的生物合成丰富度。在远距离相关菌株中检测到高度相似的KS序列提供了水平基因转移的证据，而设计用于扩增沙门氏菌CNS-205菌株的KS序列（其基因组序列可用）的对照实验导致检出了70％的靶向的PKS途径。结果提供了次级代谢物生物合成潜力的生物信息学评估，该评估可在没有完全组装的途径或基因组序列的情况下应用。快速鉴定具有最大潜力产生新的次生代谢产物的菌株以及产生已知化合物的菌株，可以通过提供一种将菌株优先进行发酵研究和化学分析的方法，来改善天然产物的发现过程。

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