Genome-guided Discovery of Bacteriocins

基因组数据的爆炸性增长和创新生物信息学工具的发展使天然产物研究发生了革命性的变化。这项提议旨在通过利用生物信息学的最新进展来利用大量的微生物基因组数据来搜索细菌素。细菌素是细菌为杀死其他细菌而产生的抗菌肽。它们主要作为天然防腐剂或抗菌剂用于食品和畜牧业。最近，它们在调节肠道微生物区系中的作用揭示了它们在促进人类健康方面的重要性。它们也被认为是传统抗菌剂的有前途的替代品或附加物。因此，我的计划是非常及时和重要的，因为抗菌素耐药性的日益普遍要求加大努力，为食品、农业和卫生部门发现新的抗菌化合物。该研究计划的主要目标是通过基因组挖掘来识别和表征新的细菌素，特别是头到尾的环化细菌素和无先导细菌素。从头到尾环化细菌素是环状多肽，其环化性质赋予多肽显着的稳定性。无先导细菌素是独一无二的，因为与其他细菌素类不同，它们不需要任何结构修饰就能发挥活性，这简化了它们的生物生产。搜索最初将针对这两个细菌素类，但从长远来看，我们将扩大到包括其他未被研究的细菌素类。该计划的积极成果将建立优先考虑目标细菌素的创新方法，最大限度地增加成功发现分子的可能性，这些方法将有助于未来对其他未被探索的细菌素类别的研究。短期(5年)目标包括详细的细菌素的电子计算机鉴定和分析，以及新肽的纯化和表征。我们将研究目标多肽的结构性质和生物活性，并研究它们的作用模式。这项工作将提供所需的基础知识，以指导实施将特征性多肽用作生物保鲜剂和/或治疗剂。此外，结构-活性研究将指导未来的生物工程努力设计具有所需性质的化合物。该课程涉及跨学科领域(即生物化学、分析化学、分子生物学、微生物学和生物信息学)，使学生接触到现代天然产品实验室中使用的各种工具。我的学生发展了强大的沟通、领导和科研技能，为他们提供了可转让的技能，并为未来在生物技术行业或学术界的职业生涯做好了特殊准备，使他们成为加拿大科学界的高生产率成员。

The explosion of genomic data and development of innovative bioinformatics tools have revolutionized natural product research. This proposal aims to leverage the vast amount of microbial genomic data by taking advantage of recent advances in bioinformatics to search for bacteriocins. Bacteriocins are antimicrobial peptides produced by bacteria to kill other bacteria. They are mainly used in food and animal industries as natural preservatives or antimicrobial agents. Recently, their role in regulating gut microbiota revealed their importance in promoting human health. They are also considered as promising alternatives or adjuncts to traditional antimicrobials. Thus, my program is very timely and important, as the increasing prevalence of antimicrobial resistance has called for increased efforts to discover novel antimicrobial compounds for the food, agriculture, and health sectors. The main objective of this research program is to identify and characterize new bacteriocins through genome mining, specifically head-to-tail cyclized and leaderless bacteriocins. Head-to-tail cyclized bacteriocins are circular peptides and their cyclic nature confers remarkable peptide stability. Leaderless bacteriocins are unique because unlike other bacteriocin classes, they do not require any structural modifications to be active, which simplifies their bioproduction. The search will initially be directed towards these 2 bacteriocin classes, but in the longer term, we will expand to encompass other under-investigated classes. Positive outcomes of this program will establish innovative ways of prioritizing target bacteriocins that maximize the probability of successful molecule discovery, approaches that will be useful for future investigations of other underexplored bacteriocin classes. Short-term (5-yr) objectives include detailed in silico identification and analysis of putative bacteriocins, and purification and characterization of novel peptides. We will study the structural properties and bioactivities of target peptides, and investigate their modes of action. This work will provide the foundational knowledge required to direct implementation of the use of the characterized peptides as biopreservatives and/or as therapeutic agents. Moreover, the structure-activity studies will guide future bioengineering efforts to design compounds with desired properties. This program involves interdisciplinary fields (i.e., biochemistry, analytical chemistry, molecular biology, microbiology, and bioinformatics), exposing students to various tools employed in a modern natural products laboratory. My students develop strong communication, leadership, and scientific research skills, providing them with transferable skills and exceptional preparation for a future career in biotechnological industries or in academia, and making them highly productive members of the Canadian scientific community.