Project 4: Application of Comparative Genomics, Transcriptomics, & Proteomics Opt

项目4：比较基因组学、转录组学的应用，

• 批准号: 7439213
• 负责人: LISA ALVAREZ-COHEN
• 金额: $ 42.79万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7439213
• 关键词: Address; Advanced Development; Bacteria; Bioremediations; Chemicals; Communities; Complex; Condition; Data; Drug Metabolic Detoxication; Ethylene; Exposure to; Funding; Gene Expression; Gene Expression Profile; Genes; Genome; Genomics; Goals; Growth; Health; Human; In Situ; Kinetics; Laboratories; Length; Location; Mass Spectrum Analysis; Measures; Metabolic; Metabolic Pathway; Metabolism; Methodology; Microbe; Modeling; Molecular; Nitrogen; Numbers; Nutrient; Nutritional; Organism; Oxidation-Reduction; Pathway interactions; Physiological; Polymerase Chain Reaction; Process; Production; Proteins; Proteomics; Rate; Regulator Genes; Research; Role; Sampling; Signal Transduction; Site; Solvents; Stimulus; Surface; Technology; Testing; Time; Toxic effect; Trichloroethylene; Trypsin; Vitamin B 12; Work; base; cold temperature; comparative; dechlorination; dehalogenation; electron donor; exposed human population; gene interaction; improved; insight; microbial; microbial community; pollutant; protein expression; research study; response; superfund site; tool; transcriptomics

This proposal will apply advanced molecular tools to understand and optimize the microbial detoxification of common Superfund pollutants, perchloroethene (PCE) and trichloroethene (TCE), which pose a significant threat to human and ecological health. By studying the fundamental processes responsible for anaerobic microbial degradation of PCE and TCE, this work will promote improved situ bioremediation processes. Previous NIEHS-funded research sought to identify and understand the microbes within complex communities responsible for dechlorination. This work takes the next logical step by focusing on the only genus of bacteria, Dehalococcoides, known to completely reduce PCE and TCE to ethene. Whole-genome microarrays, proteomic analyses, and quantitative PCR will be used to characterize the genomic differences between a variety of Dehalococcoides strains and to evaluate gene expression and proteomic changes caused by reductive dechlorination of a variety of substrates, growth in simple and complex microbial communities, and other physiological perturbations. Genomic and transcriptomic comparison of Dehalococcoides strains with different degradation abilities will identify the pathways responsible for specific and general metabolism as well as reveal the evolutionary relationship between the various isolated strains. Transcriptomic comparison of Dehalococcoides strains in pure and mixed cultures will identify pathways involved in inter-species interactions, reveal the nutritional needs and metabolic roles of Dehalococcoides in consortia, and address the limitation in bioremediation applications presented by the poor growth of isolated Dehalococcoides strains. Data from strain identification, gene.expression, and protein production will be complied into kinetic models that can be used to predict rates of reductive dechlorination by poorly characterized microbial communities. This research will meet the SBRP goal of limiting the human exposure and toxicity of chemicals commonly found at Superfund sites by advancing the development of in situ bioremediation of PCE and TCE, a technology that destroys contaminants in their subsurface location without extraction to the surface, avoiding potential human and ecological exposure.

该提案将应用先进的分子工具来理解和优化微生物 超级基金常见污染物全氯乙烯 (PCE) 和三氯乙烯 (TCE) 的解毒， 对人类和生态健康构成重大威胁。通过研究基本过程 负责四氯乙烯和三氯乙烯的厌氧微生物降解，这项工作将促进原位改善 生物修复过程。之前 NIEHS 资助的研究旨在识别和理解 复杂群落中负责脱氯的微生物。这项工作采取了下一个合乎逻辑的步骤 通过关注唯一的细菌属 Dehalococcoides，已知可以将 PCE 和 TCE 完全降低至 乙烯。全基因组微阵列、蛋白质组分析和定量 PCR 将用于表征 多种 Dehalococcoides 菌株之间的基因组差异并评估基因表达 以及由多种底物的还原脱氯引起的蛋白质组变化，在简单和 复杂的微生物群落和其他生理扰动。基因组和转录组 比较具有不同降解能力的 Dehalococcoides 菌株将确定途径 负责特定和一般代谢，并揭示各物质之间的进化关系 各种分离菌株。纯培养物和混合培养物中 Dehalococcoides 菌株的转录组比较 将确定涉及物种间相互作用的途径，揭示营养需求和代谢作用 联盟中的 Dehalococcoides 的研究，并解决了由 Dehalococcoides 提出的生物修复应用的限制 分离的 Dehalococcoides 菌株生长不良。来自菌株鉴定、基因表达和 蛋白质生产将被编译成动力学模型，可用于预测还原率 由特征不明确的微生物群落进行脱氯。这项研究将实现 SBRP 的目标 通过推进超级基金站点中常见化学品的人类接触和毒性 四氯乙烯和三氯乙烯的原位生物修复技术的发展，一种破坏其污染物的技术 位于地下，无需提取到地表，避免潜在的人类和生态暴露。