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，它们的氨基酸组成部分构成了沿海和海洋水域和沉积物中发现的总氮的主要部分。在过去的十年中，用于多肽分析和蛋白质重建的串联质谱方法与信息学的发展一起重新组装了氨基酸特征并解锁了它们所代表的蛋白质的固有信息。这个跨学科的研究团队结合了海洋有机生物地球化学、蛋白质组学和生物信息学的专业知识，以帮助确定降解过程中单个蛋白质的命运及其可能的保存机制。本研究旨在鉴定和量化海洋中负责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。这个项目有可能引发我们如何看待、分析和模拟微生物降解过程的根本变化。微生物生态学家的最新发现表明，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，作为底物可用性的反映；该项目的支持者已经观察到在有机物循环过程中存在一套细菌蛋白质，并且这种蛋白质的表达随着降解的进行而变化。这些观察结果提示细菌蛋白有潜力作为有机生物标志物来反映降解过程中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学表达之间的联系。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)在详细的有机物表征背景下详细描述蛋白质表达；3)区分来自不同生命王国（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联系起来，作为“功能性生物标志物”和碳氮利用的指标。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的研究。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.