Genome mining of marine bacteria to uncover and interrogate secondary metabolite biosynthetic pathways

海洋细菌的基因组挖掘揭示和探究次生代谢物生物合成途径

• 批准号: RGPIN-2015-06078
• 负责人: Ross, Avena
• 金额: $ 2.33万
• 依托单位: Queen's University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2018
• 资助国家: 加拿大
• 起止时间: 2018-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=663702
• 关键词: Genome; mining; marine; bacteria; uncover

I will develop an interdisciplinary research program to identify bioactive compounds from marine bacterial sources and understand the fundamental mechanisms by which they are biosynthesized. This program will provide HQP with the opportunity to engage in several fields including molecular biology, biochemistry, and organic chemistry.***By learning about the mechanisms that bacteria use to synthesise complex molecules, scientists can apply the same approaches to engineer bacteria to make new and potentially useful molecules. This has far reaching impacts on large-scale manufacture of complex molecules by fermentation that represents a cost effective and environmentally responsible alternative to total chemical synthesis. ***The primary focus of this program is a genus of bacteria called Pseudoalteromonas that has shown promise as a source of interesting biomolecules but is under-investigated to date. In the long term this program will expand to encompass other marine proteobacteria that display biosynthetic potential. A genome-to-molecule approach will be used to identify potentially non-canonical biosynthetic pathways that will then be captured and expressed in a host bacterium to allow molecule discovery and investigation of the biosynthetic enzymes.***Initially we will focus on the identification of potentially interesting pathways by analysis of bacterial genome sequences using a process called "Genome Mining". A groundbreaking technology called Transformation-Associated Recombination will be used to capture pathways of interest. This highly innovative technique enables specific and selective capture of target regions of DNA facilitating subsequent expression and genetic manipulation experiments. This approach has very recently been applied to the capture and study of natural product biosynthetic genes by a very small number of laboratories worldwide, including that of my postdoctoral supervisor, Dr. Moore at UCSD. The use of this technique will be critical to the program, and also completely novel in the Canadian scientific community.****After this technique is employed to capture the pathways, they will be heterologously expressed in a host bacterium and product molecules will be identified. Using genetic and enzymology approaches, the biosynthetic genes and corresponding enzymes will then be probed. This technique will allow us to uncover novel biosynthetic processes, prepare novel molecules and better understand the remarkable workings of biosynthetic enzymes. ***HQP trained within this program will develop strong communication and leadership skills to complement critical thinking and subject expertise. Through research collaborations, research exchanges and conference attendance, HQP will develop global networks that will maximise their capacity to contribute to the Canadian scientific community, both in academia and industry.**

我将开发一个跨学科研究计划，以识别来自海洋细菌来源的生物活性化合物，并了解它们生物合成的基本机制。该计划将为 HQP 提供参与分子生物学、生物化学和有机化学等多个领域的机会。***通过了解细菌合成复杂分子的机制，科学家可以应用相同的方法来改造细菌，以制造新的和潜在有用的分子。这对通过发酵大规模生产复杂分子产生了深远的影响，发酵是一种具有成本效益且对环境负责的全化学合成替代方案。 ***该计划的主要焦点是一种称为假交替单胞菌的细菌，它已显示出作为有趣生物分子来源的前景，但迄今为止尚未得到充分研究。从长远来看，该计划将扩展到包括其他具有生物合成潜力的海洋变形菌。 基因组到分子的方法将用于识别潜在的非规范生物合成途径，然后在宿主细菌中捕获并表达这些途径，以允许分子发现和生物合成酶的研究。***最初，我们将通过使用称为“基因组挖掘”的过程分析细菌基因组序列来专注于识别潜在有趣的途径。 一种名为“转化相关重组”的突破性技术将用于捕获感兴趣的途径。这种高度创新的技术能够特异性、选择性地捕获 DNA 的目标区域，从而促进后续的表达和基因操作实验。这种方法最近已被全球极少数实验室应用于天然产物生物合成基因的捕获和研究，其中包括我的博士后导师、加州大学圣地亚哥分校的摩尔博士。这项技术的使用对该计划至关重要，并且在加拿大科学界也是完全新颖的。****采用该技术捕获途径后，它们将在宿主细菌中异源表达，并鉴定产物分子。然后将使用遗传和酶学方法来探测生物合成基因和相应的酶。这项技术将使我们能够发现新的生物合成过程，制备新的分子并更好地了解生物合成酶的非凡作用。 ***在此计划中接受培训的 HQP 将培养强大的沟通和领导技能，以补充批判性思维和学科专业知识。通过研究合作、研究交流和出席会议，HQP 将发展全球网络，最大限度地发挥其能力，为加拿大学术界和工业界的科学界做出贡献。 **