EAGER: Tool development for proteomics and environmental metaproteomics
EAGER:蛋白质组学和环境宏蛋白质组学工具开发
基本信息
- 批准号:0938190
- 负责人:
- 金额:$ 8.76万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Standard Grant
- 财政年份:2009
- 资助国家:美国
- 起止时间:2009-08-01 至 2011-07-31
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
This EAGER project to Brian Palenik, UC San Diego, is for tools development to identify previously unknown, putative genes in metagenomic sequence data. Metagenomic sequences represent the full complement of microbial genomes in a community and are difficult to analyse because of their complexity. Even the genomes of cultured organisms are difficult to annotate as typically 50% of the genome sequence can contain unknown or novel genes. Proteomics uses mass spectrometry to analyze peptides derived from the proteolysis of samples. This analysis allows for the determination of the presence or absence of specific proteins in the original sample. In some forms, proteomics can use genomic databases as a starting point for peptide and protein identification. More recently, a form of "reverse proteomics" is being tested where mass spectrometry data are used to improve whole genome annotation by demonstrating the presence of proteins not predicted in the initial genome annotation. This technology is now beginning to show promise in the analysis of complex environmental samples, such as metaproteomic samples. This type of community-level analysis can lead to new information about not only the biodiversity but the functioning of ecosystems. However, the coupling of mass spectrometry and genome and metagenome data to analyze environmental samples still requires tool development. This development is best done when the metagenome and metaproteome sampling can be coordinated to optimize and test the tools. This PI is developing several tools for analyzing metaproteomes using metagenomics data obtained from the same site. The tools include computational procedures to discover new open reading frames and genes, methods to identify which species are present without DNA sequencing and an approach for analysing post-translational modifications in Synechococcus metagenomes. This aspect of the work is higher risk than the other aims but is important because this will allow them to evaluate which genes in the metagenome are active. This project represents a novel interdisciplinary collaboration between a marine microbiologist and a mass spectroscopist, and it is timely as it takes advantage of ongoing metagenome sequencing funded by another NSF proposal. If successful, these tools will allow for the identification of activated genes within communities. Further, new or novel genes will be identified in the metagenomes and the products of these novel genes will be identified. This research team will focus on marine cyanobacterial communities as the test metagenome. The PI has already sequenced the genomes of two Synechococcus (marine cyanobacteria) and he will use these as reference genomes for the metagenomic/metaproteomic analyses. Synechococcus assemblages in the ocean are not very diverse, therefore Synechococcus metagenomes are some of the best metagenomes for these tests because these populations can be enriched from seawater to produce a nearly pure samples for proteomic analysis. The PI is overseeing training of two post-docs as a result of this award.
加州大学圣地亚哥分校的Brian Palenik渴望的这个项目是为了开发工具,在元基因组序列数据中识别以前未知的推定基因。元基因组序列代表了一个群落中微生物基因组的完整补充,由于其复杂性,很难进行分析。即使是培养生物的基因组也很难注释,因为通常50%的基因组序列可能包含未知或新的基因。蛋白质组学使用质谱学来分析从样品的蛋白质分解中提取的多肽。这种分析可以确定原始样品中特定蛋白质的存在或不存在。在某些形式下,蛋白质组学可以使用基因组数据库作为鉴定多肽和蛋白质的起点。最近,一种形式的“反向蛋白质组学”正在测试中,通过证明初始基因组注释中没有预测到的蛋白质的存在,使用质谱学数据来改进整个基因组注释。这项技术现在开始在复杂环境样品的分析中显示出希望,例如偏蛋白质组样品。这种社区一级的分析不仅可以产生关于生物多样性的新信息,而且可以产生关于生态系统功能的新信息。然而,将质谱学与基因组和元基因组数据相结合来分析环境样品仍然需要开发工具。当可以协调元基因组和元蛋白质组采样以优化和测试工具时,这种开发是最好的。这个PI正在开发几个工具,用于使用从同一站点获得的元基因组数据来分析代谢蛋白质组。这些工具包括发现新的开放阅读框架和基因的计算程序,识别哪些物种存在而不进行DNA测序的方法,以及分析聚球藻后基因组翻译后修饰的方法。这方面的工作比其他目标风险更高,但也很重要,因为这将使他们能够评估元基因组中哪些基因是活跃的。这个项目代表了海洋微生物学家和质谱学家之间的一种新的跨学科合作,而且它是及时的,因为它利用了由另一项NSF提案资助的正在进行的元基因组测序。如果成功,这些工具将允许在社区内识别激活的基因。此外,将在元基因组中识别新的或新的基因,并将识别这些新基因的产物。这个研究小组将专注于海洋蓝藻群落作为测试元基因组。PI已经对两个聚球藻(海洋蓝藻)的基因组进行了测序,他将使用这些基因组作为元基因组/元蛋白质组分析的参考基因组。海洋中的聚球藻组合并不是非常多样化,因此聚球藻的Metagenome是这些测试的最佳元基因组之一,因为这些群体可以从海水中浓缩以产生用于蛋白质组分析的几乎纯的样本。作为这一奖项的结果,PI正在监督两名博士后的培训。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Brian Palenik其他文献
Immersed in situ microcosms: A tool for the assessment of pollution impact on phytoplankton
- DOI:
10.1016/j.jembe.2006.10.045 - 发表时间:
2007-03-05 - 期刊:
- 影响因子:
- 作者:
Denis de la Broise;Brian Palenik - 通讯作者:
Brian Palenik
Niche adaptation in ocean cyanobacteria
海洋蓝细菌的生态位适应
- DOI:
10.1038/24297 - 发表时间:
1998-11-19 - 期刊:
- 影响因子:48.500
- 作者:
Michael J. Ferris;Brian Palenik - 通讯作者:
Brian Palenik
Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b
- DOI:
10.1007/bf00245165 - 发表时间:
1992-02-01 - 期刊:
- 影响因子:2.600
- 作者:
Sallie W. Chisholm;Sheila L. Frankel;Ralf Goericke;Robert J. Olson;Brian Palenik;John B. Waterbury;Lisa West-Johnsrud;Erik R. Zettler - 通讯作者:
Erik R. Zettler
Brian Palenik的其他文献
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{{ truncateString('Brian Palenik', 18)}}的其他基金
IMAGINE: Adaptation of cyanobacterial light harvesting and metal homeostasis traits to environmental change.
想象一下:蓝藻光捕获和金属稳态特性对环境变化的适应。
- 批准号:
2029299 - 财政年份:2020
- 资助金额:
$ 8.76万 - 项目类别:
Standard Grant
Collaborative Research: Seasonal bloom dynamics: Synechococcus-grazer interactions as a model system
合作研究:季节性水华动态:聚球藻-食草动物相互作用作为模型系统
- 批准号:
1233085 - 财政年份:2012
- 资助金额:
$ 8.76万 - 项目类别:
Standard Grant
Collaborative Research: Constitutive and Inducible Predation Defenses in Cyanobacteria
合作研究:蓝藻的组成型和诱导型捕食防御
- 批准号:
1021421 - 财政年份:2010
- 资助金额:
$ 8.76万 - 项目类别:
Standard Grant
Copper Metabolism in Marine Synechococcus
海洋聚球藻中的铜代谢
- 批准号:
0817775 - 财政年份:2008
- 资助金额:
$ 8.76万 - 项目类别:
Continuing Grant
Collaborative Research: A Post-Genomic Approach to Synechococcus-grazer Interactions
合作研究:聚球藻-食草动物相互作用的后基因组方法
- 批准号:
0648175 - 财政年份:2007
- 资助金额:
$ 8.76万 - 项目类别:
Standard Grant
Coordinated Shotgun Metagenomic Sequencing and Proteomics: A Double-Barreled Approach to Cyanobacterial Community Analysis
协调鸟枪法宏基因组测序和蛋白质组学:蓝藻群落分析的双管方法
- 批准号:
0731771 - 财政年份:2007
- 资助金额:
$ 8.76万 - 项目类别:
Standard Grant
Microbial Genome Sequencing: Life at the Land/Ocean Margin: Genomic Analysis of a Coastal Cyanobacterium
微生物基因组测序:陆地/海洋边缘的生命:沿海蓝细菌的基因组分析
- 批准号:
0333162 - 财政年份:2003
- 资助金额:
$ 8.76万 - 项目类别:
Standard Grant
SGER: A multi-user, combined thermal cycler and microfluorimeter for studies of marine organisms
SGER:用于研究海洋生物的多用户组合热循环仪和微量荧光计
- 批准号:
0075927 - 财政年份:2000
- 资助金额:
$ 8.76万 - 项目类别:
Standard Grant
Molecular Probes for Nutrient Stress in Phytoplankton: Emiliania Huxleyi as a Model
浮游植物营养胁迫的分子探针:Emiliania Huxleyi 作为模型
- 批准号:
9818543 - 财政年份:1999
- 资助金额:
$ 8.76万 - 项目类别:
Standard Grant
Physiological Ecology of Marine Cyanobacterial Communities
海洋蓝藻群落的生理生态学
- 批准号:
9633111 - 财政年份:1996
- 资助金额:
$ 8.76万 - 项目类别:
Continuing Grant
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