Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.
Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.
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DOI：
10.1371/journal.pgen.1004120
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发表时间：
2014-02
期刊：
影响因子：
4.5
通讯作者：
Emili A
中科院分区：
文献类型：
--
作者：
Babu M;Arnold R;Bundalovic-Torma C;Gagarinova A;Wong KS;Kumar A;Stewart G;Samanfar B;Aoki H;Wagih O;Vlasblom J;Phanse S;Lad K;Yeou Hsiung Yu A;Graham C;Jin K;Brown E;Golshani A;Kim P;Moreno-Hagelsieb G;Greenblatt J;Houry WA;Parkinson J;Emili A
大肠杆菌中的大规模蛋白质组学分析已经记录了多蛋白复合物的组成和物理关系，但没有记录它们在生物途径和过程中的功能组织。相反，遗传相互作用（GI）筛选可以提供对个体基因和高阶关联的生物学作用的见解。结合这两种方法的信息应该阐明复合物和途径在系统水平上如何在功能上相交。然而，由于缺乏相关的GI数据，这种综合分析受到了阻碍。在这里，我们提出了一个系统的，公正的，定量的合成基因阵列筛选E。描述了60多万个双基因突变体组合之间的遗传依赖性和功能串扰。将这种上位性信息与来自先前蛋白质组学数据和基于基因组背景的方法的推定功能模块相结合，揭示了意想不到的关联，包括铁硫和核糖体完整性的生物发生所需的新组件，以及分子伴侣和蛋白酶之间的相互作用。我们发现，γ-变形菌中共同保守的功能相关基因比具有不同进化模式的基因更有可能具有相关的GI谱。总的来说，在蛋白质复合物的背景下检查细菌GI为更深入地了解核心微生物系统的机制提供了途径。已经在酵母中进行了全基因组遗传相互作用（GI）筛选，但尚未报道针对细菌的类似大规模研究。在这里，我们使用了E。大肠杆菌合成基因阵列（eSGA）技术，我们的小组开发的定量地图地理标志，以揭示上位依赖性和功能的串扰之间的60万个双基因突变组合。通过将这种上位性信息与我们小组早期基于蛋白质组学和基因组背景（GC）的方法的努力所获得的功能模块相结合，我们确定了几个意想不到的通路水平依赖性，蛋白质复合物之间的功能联系，以及未表征的细菌基因产物的生物学作用。作为研究的一部分，我们从GI筛选中获得的两个途径预测得到了实验验证，我们证实了这些新组分在铁硫生物合成和核糖体完整性中的作用。我们还外推了E. coli中的233个远亲的缺乏GI信息的γ-变形菌物种，并确定了共同保守的基因和功能模块的细菌致病的重要。总的来说，这项研究描述了革兰氏阴性细菌中GI的第一个基因组规模的图谱，并通过与先前衍生的蛋白质-蛋白质和基于GC的相互作用网络的综合分析，提出了一些新的见解，这些见解对细菌途径的结构无法单独通过任何一个网络进行识别。
Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems. Genome-wide genetic interaction (GI) screens have been performed in yeast, but no analogous large-scale studies have yet been reported for bacteria. Here, we have used E. coli synthetic genetic array (eSGA) technology developed by our group to quantitatively map GIs to reveal epistatic dependencies and functional cross-talk among ∼600,000 digenic mutant combinations. By combining this epistasis information with functional modules derived by our group's earlier efforts from proteomic and genomic context (GC)-based methods, we identify several unexpected pathway-level dependencies, functional links between protein complexes, and biological roles of uncharacterized bacterial gene products. As part of the study, two of our pathway predictions from GI screens were validated experimentally, where we confirmed the role of these new components in iron-sulphur biogenesis and ribosome integrity. We also extrapolated the epistatic connectivity diagram of E. coli to 233 distantly related γ-proteobacterial species lacking GI information, and identified co-conserved genes and functional modules important for bacterial pathogenesis. Overall, this study describes the first genome-scale map of GIs in gram-negative bacterium, and through integrative analysis with previously derived protein-protein and GC-based interaction networks presents a number of novel insights into the architecture of bacterial pathways that could not have been discerned through either network alone.
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DOI：
10.1016/j.bbamcr.2011.06.007
发表时间：
2012-01
期刊：
Biochimica et biophysica acta
影响因子：
--
作者：
Baker TA;Sauer RT
通讯作者：
Sauer RT
影响因子：
48
作者：
Butland, Gareth;Babu, Mohan;Emili, Andrew
通讯作者：
Emili, Andrew
影响因子：
7
作者：
Campillos, M;von Mering, C;Bork, P
通讯作者：
Bork, P
影响因子：
64.8
作者：
Babu, Mohan;Vlasblom, James;Greenblatt, Jack F.
通讯作者：
Greenblatt, Jack F.
影响因子：
3.2
作者：
CLARK, RL;NEIDHARDT, FC
通讯作者：
NEIDHARDT, FC