Molecular mechanisms of adaptation in waterborne microbes

水生微生物适应的分子机制

• 批准号: RGPIN-2016-03839
• 负责人: Dong, Tao
• 金额: $ 2.62万
• 依托单位: University of Calgary
• 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=649447
• 关键词: Molecular; mechanisms; adaptation; waterborne; microbes

The long-term objective of my research program is to understand the molecular adaptation mechanisms of bacteria in the environment. I will use Escherichia coli as a model in my study because (i) E. coli K-12 is the best studied model bacterium; (ii) E. coli natural isolates can be found in various sources; (iii) my lab has all the required genetic tools for mutant construction and gene expression.*** Not only are the genomes of natural E. coli strains highly divergent but also they differ phenotypically in stress adaption and antibiotic resistance. Little is known about the functions of a vast number of genes in environmental strains. I hypothesize that these environmental genes code for important functions for cells to adapt to specific host or environmental conditions. A uniqe environment is municipal wastewater at the treatment facility that collects the individual gut microbiomes, as well as antibiotics and other pharmaceutical drugs, from the city residents. During treatment process, microbes are challenged with stress conditions including osmotic shock, oxidative stress, and UV exposure. Those hostile conditions conceivably pose a strong selection for genes that may encode specific enzymes or regulators to alleviate stress/antibiotic toxicity. *** My specific objectives are: (1) to identify E. coli isolates with enhanced stress and antibiotic resistance; (2) to characterize genes required for resistance to stress and antibiotics using genome sequencing and functional genomics approaches. My lab has established a large E. coli collection (>4000 isolates) isolated from the Calgary Wastewater Treatment Plants. Using this E. coli collection, we will screen for isolates that are highly resistant to stress conditions and antibiotic resistance. We hypothesize that these selected isolates have acquired adaptation specific genes encoding specific enzymes or regulatory factors to alleviate the stress and antibiotic exposure. We will use whole genome sequencing and transposon mutagenesis to identify genes required for the adaptation. We will also use biochemical assays including affinity-pull down, co-immunoprecipitation, and chromatin-immunoprecipitation to characterize the gene functions and underlying mechanisms of adaptation. *** This study will provide important mechanistic insights regarding the adaption strategy of microbes in municipal wastewater, one of the most complex environments. **

我的研究计划的长期目标是了解细菌在环境中的分子适应机制。在我的研究中，我将使用大肠杆菌作为模型，因为(I)大肠杆菌K-12是研究得最好的模型细菌；（ii）大肠杆菌天然分离株可在各种来源找到；（iii）我的实验室拥有突变体构建和基因表达所需的所有遗传工具。***天然大肠杆菌菌株不仅基因组高度分化，而且它们在逆境适应和抗生素耐药性方面也存在表型差异。我们对环境菌株中大量基因的功能知之甚少。我假设这些环境基因为细胞适应特定宿主或环境条件的重要功能编码。一个独特的环境是城市污水处理设施，收集个人肠道微生物群，以及抗生素和其他药物，从城市居民。在处理过程中，微生物受到胁迫条件的挑战，包括渗透休克、氧化应激和紫外线暴露。可以想象，这些恶劣的环境可能会对基因产生强烈的选择，这些基因可能编码特定的酶或调节因子，以减轻压力/抗生素毒性。***我的具体目标是：(1)鉴定具有增强应激和抗生素耐药性的大肠杆菌分离株；(2)利用基因组测序和功能基因组学方法鉴定抗应激和抗抗生素所需的基因。我的实验室建立了一个从卡尔加里废水处理厂分离的大型大肠杆菌收集（bbbb4000株）。利用这些大肠杆菌收集，我们将筛选对应激条件和抗生素耐药性具有高度抗性的分离株。我们假设这些被选择的分离株已经获得了适应性的特定基因，编码特定的酶或调节因子，以减轻压力和抗生素暴露。我们将使用全基因组测序和转座子诱变来鉴定适应所需的基因。我们还将使用包括亲和拉下、共免疫沉淀和染色质免疫沉淀在内的生化分析来表征基因功能和潜在的适应机制。***本研究将为微生物在城市污水这一最复杂的环境之一中的适应策略提供重要的机制见解。**