Ju Kou-San, Gao Jiangtao, Doroghazi James R, Wang Kwo-Kwang A, Thibodeaux Christopher J, Li Steven, Metzger Emily, Fudala John, Su Joleen, Zhang Jun Kai, Lee Jaeheon, Cioni Joel P, Evans Bradley S, Hirota Ryuichi, Labeda David P, van der Donk Wilfred A, Metcalf William W
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801;
Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801; Department of Microbiology, University of Illinois, Urbana, IL 61801;
Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):12175-80. doi: 10.1073/pnas.1500873112. Epub 2015 Aug 31.
Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed "genome mining" as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities. Genome sequencing identified a diverse collection of phosphonate biosynthetic gene clusters within 278 strains. These clusters were classified into 64 distinct groups, of which 55 are likely to direct the synthesis of unknown compounds. Characterization of strains within five of these groups resulted in the discovery of a new archetypical pathway for phosphonate biosynthesis, the first (to our knowledge) dedicated pathway for H-phosphinates, and 11 previously undescribed phosphonic acid natural products. Among these compounds are argolaphos, a broad-spectrum antibacterial phosphonopeptide composed of aminomethylphosphonate in peptide linkage to a rare amino acid N(5)-hydroxyarginine; valinophos, an N-acetyl l-Val ester of 2,3-dihydroxypropylphosphonate; and phosphonocystoximate, an unusual thiohydroximate-containing molecule representing a new chemotype of sulfur-containing phosphonate natural products. Analysis of the genome sequences from the remaining strains suggests that the majority of the phosphonate biosynthetic repertoire of Actinobacteria has been captured at the gene level. This dereplicated strain collection now provides a reservoir of numerous, as yet undiscovered, phosphonate natural products.
尽管天然产物一直是人类药物的特别丰富来源，但基于活性的筛选导致已知分子的重新发现率非常高。基于微生物基因组中大量的天然产物生物合成基因，许多人提出“基因组挖掘”作为发现工作的替代方法；然而，这一想法尚未在大规模实验中得到验证。在这里，我们通过筛选超过10000株放线菌，以寻找合成膦酸的遗传潜力，来证明大规模、高通量基因组挖掘的可行性，膦酸是一类具有多样且有用生物活性的天然产物。基因组测序在278个菌株中鉴定出了各种各样的膦酸酯生物合成基因簇。这些簇被分为64个不同的组，其中55个可能指导未知化合物的合成。对其中五个组内菌株的表征导致发现了一种新的膦酸酯生物合成原型途径，这是（据我们所知）第一个专门用于次膦酸酯的途径，以及11种以前未描述的膦酸天然产物。在这些化合物中，有阿戈拉磷，一种广谱抗菌膦肽，由氨基甲基膦酸酯与稀有氨基酸N(5)-羟基精氨酸以肽键相连；缬氨磷，2,3-二羟基丙基膦酸酯的N-乙酰-L-缬氨酸酯；以及膦基胱氨酸肟，一种不寻常的含硫代肟的分子，代表了含硫膦酸酯天然产物的一种新化学类型。对其余菌株基因组序列的分析表明，放线菌的大多数膦酸酯生物合成库已在基因水平上被捕获。这个经过去重复处理的菌株库现在提供了大量尚未发现的膦酸酯天然产物的储存库。
