Collaborative Research: Metaproteomics: Linking Natural Microbial Community Structure and Function Via Protein identification

合作研究：宏蛋白质组学：通过蛋白质鉴定连接天然微生物群落结构和功能

• 批准号: 0537041
• 负责人: Feng Chen
• 金额: --
• 依托单位: University of Maryland Biotechnology Institute
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-10-01 至 2007-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0537041&HistoricalAwards=false
• 关键词: Collaborative; Research; Metaproteomics; Linking; Natural

Microbes are the most abundant organisms on the planet in terms of biomass, containing ~5,000 times the amount of carbon found in the entire human population. A single teaspoon of ocean water often contains over 1 million individual microbial cells. Given limited differences in size and shape, distinguishing one species from another under the microscope is difficult. Associating specific functions with individual cells or populations is even more challenging. Marine microbes drive biogeochemical cycles of carbon, nitrogen, oxygen and other elements that are critical to the function of the biosphere. Understanding relationships between microbial diversity, microbial metabolism and biogeochemistry is one of the great challenges facing microbial ecologists today. Metaproteomics is a new and untried approach to identify proteins present in microbial communities. Proteins are the engines that drive all chemical reactions in cells and can be used to identify specific microbes as each contains unique protein profiles. Thus, identifying proteins in microbial communities will provide information about what microbes are present in a given sample and what they are doing at the time of sampling. This research will apply metaproteomics to marine microbial communities to: 1) compare the protein expression patterns over geographic and temporal scales; 2) identify proteins of particular interest from specific samples; and 3) link specific microbial functions with individual microbial groups. Proteins extracted from microbial community samples will be resolved based on mass and charge to provide an image of the community protein profile. Similarities and differences between different samples will be quantified by comparing these images. Sequence information for specific proteins of interest will be gathered and used to identify both the protein and most probable microbial source of the protein. This project will provide the first in depth metaproteomic study of a dynamic and highly complex marine microbial assemblage. Metaproteomics is an alternative and complementary approach to metagenomics and environmental transcriptomics. Although many novel microorganisms have been detected in the ocean, the vast majority of marine microbes still cannot be grown in the laboratory. As a culture-independent approach, metaproteomics will address what proteins are actually expressed in microbial communities rather than the potential expression measurements provided by metagenomics and transcriptomics. This project will support two graduate students and provide both with highly interdisciplinary training spanning the fields of microbial diversity, biological oceanography, analytical chemistry, and bioinformatics.

就生物量而言，微生物是地球上最丰富的生物体，其碳含量是整个人类的5,000倍。一茶匙的海水通常含有超过100万个微生物细胞。由于大小和形状的差异有限，在显微镜下区分一个物种是困难的。将特定功能与单个细胞或群体相关联甚至更具挑战性。海洋微生物驱动着碳、氮、氧和其他对生物圈功能至关重要的元素的地球化学循环。了解微生物多样性、微生物代谢和生物地球化学之间的关系是当今微生物生态学家面临的重大挑战之一。元蛋白质组学是一种新的和未经尝试的方法来确定蛋白质存在于微生物群落。 蛋白质是驱动细胞中所有化学反应的引擎，可用于识别特定的微生物，因为每种微生物都含有独特的蛋白质谱。 因此，鉴定微生物群落中的蛋白质将提供关于给定样品中存在哪些微生物以及它们在采样时正在做什么的信息。 这项研究将把元蛋白质组学应用于海洋微生物群落：1）比较蛋白质在地理和时间尺度上的表达模式; 2）从特定样品中鉴定出特别感兴趣的蛋白质; 3）将特定的微生物功能与单个微生物群体联系起来。从微生物群落样品中提取的蛋白质将基于质量和电荷进行解析，以提供群落蛋白质谱的图像。 不同样本之间的相似性和差异将通过比较这些图像进行量化。将收集感兴趣的特定蛋白质的序列信息，并用于鉴定蛋白质和蛋白质的最可能的微生物来源。该项目将提供第一个深入的元蛋白质组学研究的动态和高度复杂的海洋微生物组合。 元蛋白质组学是元基因组学和环境转录组学的替代和补充方法。 尽管在海洋中发现了许多新的微生物，但绝大多数海洋微生物仍然无法在实验室中生长。 作为一种独立于培养的方法，元蛋白质组学将解决微生物群落中实际表达的蛋白质，而不是宏基因组学和转录组学提供的潜在表达测量。该项目将支持两名研究生，并提供跨微生物多样性，生物海洋学，分析化学和生物信息学领域的高度跨学科的培训。