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

基本信息

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

项目摘要

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，为分析肽和蛋白质重建而开发的串联质谱方法以及信息学的发展已经重新组装了氨基酸特征并解锁了它们所代表的蛋白质固有的信息。这个跨学科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方面的综合专业知识，有助于确定单个蛋白质在降解过程中的命运及其可能的保存机制。这项研究旨在识别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保存。该项目有可能引发我们看待、分析和建模微生物降解过程的方式发生根本性变化。微生物生态学家的最新发现表明，对各种营养物质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，并且这种蛋白质的表达随着降解的进行而变化。这些观察结果表明，细菌蛋白有潜力作为有机生物标志物，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表达之间的联系。该项目的目标是： 1) 解决海洋有机物组成与作为降解催化剂的细菌群落（宏蛋白质组）蛋白质表达之间的关系； 2）在详细的有机物表征的背景下详细描述蛋白质表达，3）区分来自不同生命界（例如真核或细菌）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联系起来，以追踪细菌蛋白质作为“功能性生物标志物”以及碳和氮利用率的指标。该项目将为海洋地球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，哈维和纳恩也积极参与高中外展项目。

项目成果

期刊论文数量（4）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

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：
2019-12
期刊：
Scientific Data
影响因子：
9.8
作者：
Krayushkina, Dasha;Timmins;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

宏蛋白质组学揭示，北冰洋西部微生物组中有机物的快速扰动优先考虑功能重组而不是分类学

DOI：
10.1038/s41396-019-0503-z
发表时间：
2019-09
期刊：
The ISME Journal
影响因子：
0
作者：
Mikan, Molly P.;Harvey, H. Rodger;Timmins;Riffle, Michael;May, Damon H.;Salter, Ian;Noble, William S.;Nunn, Brook L.
通讯作者：
Nunn, Brook L.

MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data

MetaGOmics：一种基于网络的工具，用于对宏蛋白质组数据进行以肽为中心的功能和分类分析

DOI：
10.3390/proteomes6010002
发表时间：
2018-03
期刊：
Proteomes
影响因子：
3.3
作者：
Riffle, Michael;May, Damon;Timmins;Mikan, Molly;Jaschob, Daniel;Noble, William;Nunn, Brook
通讯作者：
Nunn, Brook

MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides

对一系列稀释的细菌：浮游植物进行 MS 分析，以改进低丰度细菌肽的检测