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

我将开发一个跨学科的研究计划，以确定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提供从事分子生物学，生物化学和有机化学等领域的机会。 通过了解细菌用于合成复杂分子的机制，科学家可以应用相同的方法来设计细菌，使其产生新的和潜在有用的分子。这对通过发酵大规模制造复杂分子具有深远的影响，发酵代表了全化学合成的成本效益和环境负责的替代方案。 该计划的主要焦点是一种名为假交替单胞菌的细菌，该细菌已显示出作为有趣生物分子来源的希望，但迄今为止尚未得到充分研究。从长远来看，该计划将扩大到包括其他显示生物合成潜力的海洋变形菌。将使用基因组到分子的方法来鉴定潜在的非规范生物合成途径，然后将其捕获并在宿主细菌中表达，以允许分子发现和生物合成酶的研究。 最初，我们将集中在识别潜在的有趣的途径，通过分析细菌基因组序列使用一个过程称为“基因组挖掘”。一项名为“转化相关的纯化”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和选择性地捕获DNA的靶区域，促进随后的表达和遗传操作实验。这种方法最近已经被世界上为数不多的实验室应用于捕获和研究天然产物的生物合成基因，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，在加拿大科学界也是全新的。 在采用该技术捕获途径之后，它们将在宿主细菌中异源表达，并且产物分子将被鉴定。利用遗传学和酶学的方法，生物合成基因和相应的酶将被探测。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显着工作。 HQP在此计划中接受培训，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将开发全球网络，将最大限度地提高他们的能力，以促进加拿大科学界，无论是在学术界和工业界。

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.