Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204, USA.
Chembiochem. 2013 May 27;14(8):955-62. doi: 10.1002/cbic.201300147. Epub 2013 May 3.
The use of genome sequences has become routine in guiding the discovery and identification of microbial natural products and their biosynthetic pathways. In silico prediction of molecular features, such as metabolic building blocks, physico-chemical properties or biological functions, from orphan gene clusters has opened up the characterization of many new chemo- and genotypes in genome mining approaches. Here, we guided our genome mining of two predicted enediyne pathways in Salinispora tropica CNB-440 by a DNA interference bioassay to isolate DNA-targeting enediyne polyketides. An organic extract of S. tropica showed DNA-interference activity that surprisingly was not abolished in genetic mutants of the targeted enediyne pathways, ST_pks1 and spo. Instead we showed that the product of the orphan type II polyketide synthase pathway, ST_pks2, is solely responsible for the DNA-interfering activity of the parent strain. Subsequent comparative metabolic profiling revealed the lomaiviticins, glycosylated diazofluorene polyketides, as the ST_pks2 products. This study marks the first report of the 59 open reading frame lomaiviticin gene cluster (lom) and supports the biochemical logic of their dimeric construction through a pathway related to the kinamycin monomer.
在指导微生物天然产物及其生物合成途径的发现和鉴定方面，基因组序列的使用已经成为常规手段。从孤儿基因簇中对代谢结构单元、物理化学性质或生物功能等分子特征进行计算机预测，为基因组挖掘方法中许多新的化学和基因型的特征提供了可能。在这里，我们通过 DNA 干扰生物测定指导了对盐单胞菌 CNB-440 中两种预测的烯二炔途径的基因组挖掘，以分离 DNA 靶向烯二炔聚酮化合物。盐单胞菌 CNB-440 的有机提取物表现出 DNA 干扰活性，令人惊讶的是，这种活性在靶向烯二炔途径的遗传突变体 ST_pks1 和 spo 中并没有被消除。相反，我们表明，孤儿型 II 聚酮合酶途径的产物 ST_pks2 是亲本菌株 DNA 干扰活性的唯一原因。随后的比较代谢分析显示，lomaviticin 是 ST_pks2 的产物，这是一种糖基化二氮杂芴聚酮化合物。这项研究首次报道了 59 个开放阅读框 lomaiviticin 基因簇（lom），并通过与 kinamycin 单体相关的途径支持了它们二聚体结构的生化逻辑。
