Functional characterization of genetic networks involved in marine chitin degradation by Vibrio species

弧菌物种海洋几丁质降解涉及的遗传网络的功能表征

• 批准号: RGPIN-2019-05807
• 负责人: Thomas, Nikhil
• 金额: $ 2.33万
• 依托单位: Dalhousie University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2019
• 资助国家: 加拿大
• 起止时间: 2019-01-01 至 2020-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=684281
• 关键词: Functional; characterization; genetic; networks; involved

Carbon mobilization in oceans and other marine environments is a biogeochemical activity that significantly impacts many of Earth's ecosystems. Marine bacterial Vibrio species are central to carbon mobilization by naturally degrading the second most abundant carbon biopolymer on earth, chitin. My NSERC proposal is focused on understanding the genetic regulatory circuits and cell biology of Vibrio sp. My previous NSERC grant on Vibrio genetics allowed us to identify ExsA and HlyU proteins as genetic regulators involved in cell surface structures and secretion systems. We now propose to investigate genome-wide aspects of chitin metabolism by Vibrio sp. to better understand the role of Vibrios in ocean chitin and carbon cycling.******Researchers have identified a set of genes that contribute to chitin utilization by Vibrio species, however, aspects of carbon assimilation, modifying enzymes, signalling pathways, and genetic regulatory factors remain obscure. Detailed knowledge of how Vibrio bacteria metabolize chitin is incomplete. We believe that genetic approaches to address this knowledge gap will provide an understanding of how chitin and carbon are mobilized by these microbes in ocean and marine environments.******The main goal of this research proposal is to discover genome-wide regulatory mechanisms involved in Vibrio chitin utilization. Innovative genomic and metabolomic approaches, alongside mass spectrometry technology, will be used to study chitin degradation by the marine microbe Vibrio parahaemolyticus. Our research proposal consists of 4 main objectives: ***Objective 1: To create a high-density transposon insertion library of V. parahaemolyticus mutants that will be screened on a colloidal chitin growth medium as the only carbon source to conditionally select against mutants with chitin utilization defects. ***Objective 2: To identify V. parahaemolyticus genes, and other genetic regulatory elements (e.g. non-coding RNAs or genetic loci) that contribute to chitin utilization using a population-based Tn-seq approach combined with next generation sequencing (NGS) and bioinformatics.***Objective 3: To functionally characterize V. parahaemolyticus chitin degradation gene regulatory networks using metabolomics and quantitative enzymatic reporter assays.***Objective 4: In collaboration with the CFIA, we will investigate genetic diversities linked to chitin metabolism within newly isolated environmental Vibrio sp. from oyster farms and Canadian coastal waters.******We will gain genome-wide knowledge relating to chitinase enzymes, polysaccharide transport, signalling pathways, and unknown regulatory mechanisms such as non-coding RNAs and post-translational modifications. This research program aligns with Dalhousie's Strategic Initiatives in i) Oceans Research, and ii) Genomics Applications. The project will support HQP development and training in the omic' research sector which is rapidly expanding and requires a specialized bioinformatic skill set.*****

海洋和其他海洋环境中的碳动员是一种生物地球化学活动，可显着影响地球许多生态系统。 海洋细菌纤维种类是通过自然降解地球上第二大碳生物聚合物壳蛋白的碳动员至关重要的。 我的Nserc提议的重点是了解颤音的遗传调节回路和细胞生物学。 我以前对颤音遗传学的NSERC赠款使我们能够将EXSA和Hlyu蛋白识别为参与细胞表面结构和分泌系统的遗传调节剂。 现在，我们建议通过vibrio sp。研究几丁质代谢的全基因组方面。为了更好地了解颤音在海洋几丁质和碳循环中的作用。详细了解颤音细菌如何代谢几丁质是不完整的。 我们认为，解决这一知识差距的遗传方法将对这些研究建议的主要目标是如何通过海洋和海洋环境中的这些微生物动员几根和碳动员。 创新的基因组和代谢组方法以及质谱技术以及质谱技术将用于研究海洋微生物弧菌旁溶血症的差差降解。 我们的研究建议由4个主要目标组成：***目标1：创建一个高密度的转座子插入库库，副溶血杆菌突变体的插座库将在胶体壳蛋白生长培养基上进行筛选，作为唯一有条件地选择具有金属蛋白利用率的突变体的唯一有条件选择的碳源。 ***目标2：确定副溶血基因的基因以及其他遗传调节元素（例如非编码RNA或遗传基因座），使用基于人群的TN-SEQ方法结合了下一代测序（NGS）和生物信息的下一代序列3：parahaaaaaahaaahaa v. parahaaaa v. v. v. parahaaaa v. ***目标4：与CFIA合作，使用代谢组学和定量酶促报告基因分析的网络，我们将研究与新隔离的环境颤音中与几丁质代谢相关的遗传多样性。从牡蛎农场和加拿大沿海水域。 该研究计划与Dalhousie在i）海洋研究中的战略举措相吻合，ii）基因组学应用程序。该项目将支持OMIC研究领域的HQP开发和培训，该领域正在迅速扩展，需要专门的生物信息学技能。*****