Collaborative Research: Linking geochemistry and proteomics to reveal the impact of bacteria on protein cycling in the ocean

合作研究：将地球化学和蛋白质组学联系起来，揭示细菌对海洋蛋白质循环的影响

• 批准号: 1233589
• 负责人: Rodger Harvey
• 金额: $ 34.9万
• 依托单位: Old Dominion University Research Foundation
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-10-01 至 2016-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1233589&HistoricalAwards=false
• 关键词: Collaborative; Research; Linking; geochemistry; proteomics

Although proteins represent the primary source of new organic nitrogen in the ocean, the identification of individual proteins and mechanisms modulating their preservation has faced analytical and computational challenges in deciphering the vast suite of possible sequences and degradation by-products. Recent efforts to link geochemical cycling, biomedical proteomics and bioinformatics has demonstrated that only a small subset of the suite of proteins produced by marine diatoms appear to survive the degradation process, and those that do are largely protected by physical and enthalpic barriers to microbial attack. Although these discoveries help to explain the survival of individual proteins, they also generate multiple questions regarding bacteria as the dominant recyclers of organic nitrogen and carbon and needs for specific approaches to characterize modified protein products. Bacteria dominate the water column and sedimentary systems in both numbers and diversity, yet their relative contribution to the preserved proteomic pool appears low. In this project, researchers at Old Dominion Universityand the University of Washington will join forces to decipher the bacterial role in protein recycling and their potential contribution. By integrating high mass accuracy tandem mass spectrometry-based proteomics with stable isotope-based geochemical analysis, they hope to identify those bacterial proteins initially synthesized during organic matter recycling. Three research objectives drive this investigation: (1) to determine the potential contribution of bacteria proteins to marine organic matter; (2) to identify those protein(s) synthesized by heterotrophic marine bacteria during initial stages of organic matter degradation; (3) to determine if glycan (carbohydrate) modifications represent an important component of preserved, yet unidentified, peptides seen in our analysis of oceanic particles and sediments. Broader Impacts: This project will provide multiple opportunities for interdisciplinary student training in marine chemistry and proteomics as well as address the goal of disseminating results and tools to a broad audience. In the more traditional role, this project will expand the career for a female principal investigator in marine proteomics, support both graduate and undergraduate students at ODU which include opportunities for minority enrichment and provide training for a postdoctoral fellow at UW. On the broader level, the ODU PI participates in high school outreach programs for high achieving students in the local school which provides for summer internships and enrichment programs.

尽管蛋白质是海洋中新有机氮的主要来源，但单个蛋白质的识别和调节其保存的机制在破译大量可能的序列和降解副产物方面面临着分析和计算的挑战。 最近将地球化学循环、生物医学蛋白质组学和生物信息学联系起来的努力表明，海洋硅藻产生的蛋白质组中只有一小部分似乎能够在降解过程中幸存下来，而那些幸存下来的蛋白质在很大程度上受到针对微生物攻击的物理和热阻屏障的保护。尽管这些发现有助于解释单个蛋白质的生存，但它们也产生了多个问题，即细菌作为有机氮和碳的主要回收者，以及需要特定的方法来表征修饰的蛋白质产品。细菌在数量和多样性上主导着水柱和沉积系统，但它们对保存的蛋白质组库的相对贡献似乎很低。在这个项目中，奥道明大学和华盛顿大学的研究人员将联手破译细菌在蛋白质回收中的作用及其潜在贡献。通过将基于高质量串联质谱的蛋白质组学与基于稳定同位素的地球化学分析相结合，他们希望能够识别那些在有机物回收过程中最初合成的细菌蛋白质。三个研究目标推动了这项研究：（1）确定细菌蛋白对海洋有机物的潜在贡献； (2) 鉴定异养海洋细菌在有机物降解初始阶段合成的蛋白质； (3) 确定聚糖（碳水化合物）修饰是否代表我们在分析海洋颗粒和沉积物时发现的保存但未鉴定的肽的重要组成部分。更广泛的影响：该项目将为海洋化学和蛋白质组学的跨学科学生培训提供多种机会，并实现向广大受众传播结果和工具的目标。在更传统的角色中，该项目将扩大海洋蛋白质组学女性首席研究员的职业生涯，支持 ODU 的研究生和本科生，其中包括丰富少数民族的机会，并为华盛顿大学的博士后研究员提供培训。在更广泛的层面上，ODU PI 参与当地学校为成绩优异的学生提供的高中外展计划，该计划提供暑期实习和强化计划。