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

蛋白质是海洋中有机碳和氮的主要贡献者，它们的氨基酸构成块构成沿海和海洋水域和沉积物中确定的总氮的主要部分。在过去的十年里，串联质谱学方法发展起来用于多肽和蛋白质重建的分析，以及信息学的发展，重新组装了氨基酸特征并解锁了它们所代表的蛋白质中固有的信息。这个跨学科的研究团队拥有海洋有机生物地球化学、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和可能的保存机制。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、氮循环和有机物保存。这个项目有可能从根本上改变我们看待、分析和模拟微生物降解过程的方式。微生物生态学家最近的发现表明，对各种营养物质有广泛反应的细菌(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了有机质循环过程中存在的一系列细菌蛋白质，并且这种蛋白质的表达随着降解的进行而变化。这些观察表明，细菌蛋白有可能作为有机生物标记物来反映降解过程中起作用的催化剂的分类分布。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有关的可能性。该项目的目标是：1)研究作为降解催化剂的细菌群落(元蛋白质组)的海洋有机物组成与蛋白质表达之间的关系；2)在详细的有机质特征描述的背景下详细说明蛋白质的表达；3)区分来自不同生物界(例如真核生物或细菌)的海洋沉积物中存在的蛋白质如何反映有机物保存的复杂过程。总的目标是捕获蛋白质，作为海洋系统中存在和过程的关键标记。研究人员将把蛋白质鉴定的快速进展与追踪细菌蛋白质作为“功能生物标记物”和碳、氮利用指标联系起来。该项目将为海洋地球化学和蛋白质组学方面的跨学科学生培训提供多种机会，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教员的职业生涯，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，哈维和努恩也都积极参与了高中外展项目。

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.