Collaborative Research: Proteins as functional biomarkers: integrating organic characterization with proteomics to track routes for carbon and nitrogen recycling and preservation

合作研究：蛋白质作为功能生物标志物：将有机表征与蛋白质组学相结合，以追踪碳和氮的回收和保存路径

• 批准号: 1636045
• 负责人: Rodger Harvey
• 金额: $ 39.21万
• 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: 2016
• 资助国家: 美国
• 起止时间: 2016-10-01 至 2020-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1636045&HistoricalAwards=false
• 关键词: Collaborative; Research; Proteins; functional; biomarkers

Proteins are a major contributor to organic carbon and nitrogen in the ocean and their amino acid building blocks comprise a major fraction of the total nitrogen identified in coastal and oceanic waters and sediments. Over the last decade, tandem mass spectrometry methods developed for the analysis of peptides and protein reconstruction together with informatics developments have re-assembled the amino acid signatures and unlocked the information inherent in the proteins they represent. This interdisciplinary research team has the combined expertise in marine organic biogeochemistry, proteomics, and bioinformatics to help determine the fate of individual proteins during degradation and likely mechanisms for their preservation. This research aims to identify and quantify the proteins responsible for chemical transformations of organic matter in the ocean, thereby exposing how microbial communities control and contribute to the carbon and nitrogen cycle and to organic matter preservation. This project has the potential to trigger a fundamental change in how we view, analyze, and model microbial degradation processes. Recent findings from microbial ecologists show that bacteria with broad responses to various nutrients (i.e. the generalists) can fine-tune the gene expression of various proteins as a reflection of substrate availability; the proponents of this project have observed a suite of bacterial proteins present during organic matter recycling and that this protein expression changes as degradation proceeds. These observations hint that bacterial proteins have potential as organic biomarkers to reflect the taxonomic distribution of the functioning catalysts in degradation processes. The investigators propose to build on these results to investigate the potential for organic matter preservation to be linked to proteomic expression of the microbial community that drive carbon and nitrogen cycling. The project objectives are: 1) to address the relationship between marine organic matter composition and protein expression by the bacterial community (metaproteome) which act as catalysts for degradation; 2) to detail protein expression in the context of detailed organic matter characterization and 3) to distinguish how proteins present in oceanic sediments derived from different kingdoms of life (e.g. eukaryotic or bacterial) reflect the complex process of organic matter preservation. The overall goal is to capture proteins as critical markers of both presence and process in marine systems. The investigators will link the rapid advances in protein identification to track bacterial proteins to act as "functional biomarkers" and indicators of carbon and nitrogen utilization. The project would provide multiple opportunities for interdisciplinary student training in marine geochemistry and proteomics, and address the goal of disseminating results and tools to a broad audience. In the more traditional role, the project will expand the career for a female research faculty member in marine proteomics and support both graduate and undergraduate student research at each participating institution. On the broader community level, both Harvey and Nunn are also heavily involved in high school outreach programs.

蛋白质是海洋中有机碳和氮的主要贡献者，其氨基酸组成部分构成沿海和海洋沃茨和沉积物中确定的总氮的主要部分。在过去的十年中，串联质谱法开发的肽和蛋白质重建的分析与信息学的发展已经重新组装的氨基酸的签名和解锁的信息，它们所代表的蛋白质中固有的。这个跨学科的研究团队拥有海洋有机生物化学，蛋白质组学和生物信息学的综合专业知识，以帮助确定单个蛋白质在降解过程中的命运及其保存的可能机制。这项研究旨在确定和量化负责海洋中有机物化学转化的蛋白质，从而揭示微生物群落如何控制和促进碳和氮循环以及有机物的保存。该项目有可能引发我们如何看待，分析和模拟微生物降解过程的根本性变化。微生物生态学家最近的研究结果表明，对各种营养素具有广泛反应的细菌（即通才）可以微调各种蛋白质的基因表达，以反映底物的可用性;该项目的支持者观察到有机物回收过程中存在一系列细菌蛋白质，并且这种蛋白质表达随着降解的进行而变化。这些观察结果表明，细菌蛋白质有潜力作为有机生物标志物，以反映在降解过程中的功能催化剂的分类分布。研究人员建议在这些结果的基础上，研究有机物保存与驱动碳和氮循环的微生物群落的蛋白质组表达相关的潜力。该项目的目标是：1）探讨海洋有机物组成与细菌群落蛋白质表达之间的关系（元蛋白质组），其充当降解的催化剂; 2）在详细的有机质表征的背景下详细描述蛋白质表达; 3）区分海洋沉积物中存在的蛋白质如何来自不同的生命王国（例如真核生物或细菌）反映了有机物保存的复杂过程。总体目标是捕获蛋白质作为海洋系统中存在和过程的关键标志物。研究人员将把蛋白质鉴定的快速进展与跟踪细菌蛋白质联系起来，以作为“功能性生物标志物”和碳氮利用的指标。该项目将提供多种机会，对学生进行海洋地球化学和蛋白质组学方面的跨学科培训，并实现向广大受众传播成果和工具的目标。在更传统的角色中，该项目将扩大海洋蛋白质组学女性研究人员的职业生涯，并支持每个参与机构的研究生和本科生研究。在更广泛的社区层面上，哈维和纳恩也积极参与高中外展计划。

项目成果

Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi

异养海洋细菌 Ruegeria pomeroyi 的生长期蛋白质组学

• DOI: 10.1038/s41597-019-0308-y
• 发表时间: 2019
• 期刊: Scientific Data
• 影响因子: 9.8
• 作者: Krayushkina, Dasha;Timmins-Schiffman, Emma;Faux, Jessica;May, Damon H.;Riffle, Michael;Harvey, H. Rodger;Nunn, Brook L.
• 通讯作者: Nunn, Brook L.

Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes

• DOI: 10.1038/s41396-019-0503-z
• 发表时间: 2020-01-01
• 期刊: ISME JOURNAL
• 影响因子: 11
• 作者: Mikan, Molly P.;Harvey, H. Rodger;Nunn, Brook L.
• 通讯作者: Nunn, Brook L.