Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality
Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality
复制标题
DOI：
10.1073/pnas.1714381115
复制
发表时间：
2017-12-26
影响因子：
11.1
通讯作者：
Jensen, Paul R.
中科院分区：
文献类型：
--
作者：
Amos, Gregory C. A.;Awakawa, Takayoshi;Jensen, Paul R.
细菌天然产物仍然是新药的重要来源。DNA测序表明，大多数天然产物生物合成基因簇（BGC）保持在细菌基因组中尚未连接到它们编码的生物合成的小分子。努力发现这些孤儿BGC的产物正在推动基因组挖掘技术的发展，该技术基于许多在正常实验室培养期间转录沉默的前提。在这里，我们采用比较转录组学评估BGC的表达四个密切相关的菌株属于属盐孢属海洋细菌。结果显示，略多于一半的BGC的表达水平应有助于产物检测。通过比较不同菌株中相似基因簇的表达谱，我们确定了其失活似乎与簇沉默有关的调控基因。表达和沉默的BGC之间的这些细微差异的意义不能被先验地预测，只能通过比较转录组学来揭示。沉默簇在大量基因组序列可用的菌株中的保守性的证据表明，它们可能处于与表达形式不同的调节控制下，或者沉默可能代表基因簇进化的未被充分认识的机制。耦合基因表达和代谢组学数据建立了salinipostins及其相关BGC之间的生物信息学联系，而遗传操作建立了这一系列化合物的遗传基础，这是以前未知的太平洋盐孢菌。
Bacterial natural products remain an important source of new medicines. DNA sequencing has revealed that a majority of natural product biosynthetic gene clusters (BGCs) maintained in bacterial genomes have yet to be linked to the small molecules whose biosynthesis they encode. Efforts to discover the products of these orphan BGCs are driving the development of genome mining techniques based on the premise that many are transcriptionally silent during normal laboratory cultivation. Here, we employ comparative transcriptomics to assess BGC expression among four closely related strains of marine bacteria belonging to the genus Salinispora. The results reveal that slightly more than half of the BGCs are expressed at levels that should facilitate product detection. By comparing the expression profiles of similar gene clusters in different strains, we identified regulatory genes whose inactivation appears linked to cluster silencing. The significance of these subtle differences between expressed and silent BGCs could not have been predicted a priori and was only revealed by comparative transcriptomics. Evidence for the conservation of silent clusters among a larger number of strains for which genome sequences are available suggests they may be under different regulatory control from the expressed forms or that silencing may represent an underappreciated mechanism of gene cluster evolution. Coupling gene expression and metabolomics data established a bioinformatic link between the salinipostins and their associated BGC, while genetic manipulation established the genetic basis for this series of compounds, which were previously unknown from Salinispora pacifica.