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

尽管蛋白质是海洋中新有机氮的主要来源，但在破译大量可能的序列和降解副产物时，识别单个蛋白质和调节其保存的机制面临着分析和计算方面的挑战。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研究表明，海洋硅藻产生的一组蛋白质中，似乎只有一小部分能在降解过程中存活下来，而那些存活下来的蛋白质在很大程度上受到了物理和焓屏障的保护，免遭微生物的攻击。尽管这些发现有助于解释单个蛋白质的存活，但它们也产生了多个问题，如细菌是有机氮和碳的主要回收者，以及需要特定的方法来表征改性蛋白质产品。细菌在水柱和沉积系统的数量和多样性上都占主导地位，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，老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循环中的作用及其潜在贡献。通过将基于高质量精度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，他们希望鉴定出在有机物回收过程中最初合成的细菌蛋白质。本研究的目的有三个：(1)确定细菌蛋白对海洋有机物质的潜在贡献；(2)识别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）修饰是否代表了我们在海洋颗粒和沉积物分析中看到的保存但未识别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，并实现将结果和工具传播给广泛受众的目标。在更传统的角色中，该项目将扩大女性海洋蛋白质组学首席研究员的职业生涯，支持ODU的研究生和本科生，包括少数民族充实的机会，并为华盛顿大学的博士后提供培训。在更广泛的层面上，ODU PI参与了为当地学校的优秀学生提供暑期实习和充实计划的高中拓展计划。

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.