A comprehensive genetic characterization of bacterial motility.
A comprehensive genetic characterization of bacterial motility.
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DOI：
10.1371/journal.pgen.0030154
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发表时间：
2007-09
期刊：
影响因子：
4.5
通讯作者：
Tavazoie, Saeed
中科院分区：
文献类型：
--
作者：
Girgis, Hany S.;Liu, Yirchung;Ryu, William S.;Tavazoie, Saeed
我们开发了一个强大的实验框架，它将竞争选择和基于微阵列的基因足迹法相结合，以全面揭示细菌行为的遗传基础。将这种方法应用于大肠杆菌的运动性，鉴定出了95%已知的鞭毛和趋化性基因，并揭示了三十多个新的基因座，这些基因座在不同程度上且通过不同机制影响运动性。为了探究这些基因发挥作用的网络环境，我们开发了一种方法，通过对双突变体表型的综合分析来揭示全基因组的上位性相互作用。这使我们能够将新基因置于信号传导和调控网络的环境中，包括Rcs磷酸传递途径和环二鸟苷酸第二信使系统。这个统一的框架能够对整个微生物圈的复杂行为进行灵敏且全面的遗传特性分析。
细菌在无数极端环境中茁壮成长，伴随着奇特的新陈代谢和复杂的行为。然而，我们对细菌的现代分子层面的理解来自于对少数模式生物（如大肠杆菌和枯草芽孢杆菌）中有限范围的表型的研究。随着数以千计的细菌基因组被测序，现在迫切需要能够快速且全面地揭示整个微生物圈表型遗传基础的方法。为此，我们开发了一个全基因组实验框架，它能够量化基因组中每个基因对感兴趣表型的贡献程度，并揭示调控网络和信号通路中基因的组织方式。我们在此表明，将这种方法应用于大肠杆菌的游动和表面运动性，在几周的时间尺度内基本上揭示了鞭毛介导的趋化性的所有先前已知的组成部分。值得注意的是，我们还鉴定出了另外三十多个新的基因座，它们通过不同机制影响一种被认为已完全了解的行为。这个框架的速度、简便性和广泛适用性应该会极大地加速对大量未被研究的细菌行为的全面分析。
We have developed a powerful experimental framework that combines competitive selection and microarray-based genetic footprinting to comprehensively reveal the genetic basis of bacterial behaviors. Application of this method to Escherichia coli motility identifies 95% of the known flagellar and chemotaxis genes, and reveals three dozen novel loci that, to varying degrees and through diverse mechanisms, affect motility. To probe the network context in which these genes function, we developed a method that uncovers genome-wide epistatic interactions through comprehensive analyses of double-mutant phenotypes. This allows us to place the novel genes within the context of signaling and regulatory networks, including the Rcs phosphorelay pathway and the cyclic di-GMP second-messenger system. This unifying framework enables sensitive and comprehensive genetic characterization of complex behaviors across the microbial biosphere. Bacteria thrive in a limitless range of extreme environments, accompanied by exotic metabolisms and sophisticated behaviors. However, our modern molecular understanding of bacteria comes from studies of a limited range of phenotypes in a handful of model organisms such as E. coli and Bacillus subtilis. With the availability of thousands of sequenced bacterial genomes, there is now an urgent need for methods that rapidly and comprehensively reveal the genetic basis of phenotypes across the microbial biosphere. To this end, we have developed a genome-wide experimental framework that quantifies the degree to which every gene in the genome contributes to a phenotype of interest, and reveals the organization of genes within regulatory networks and signaling pathways. We show here that the application of this methodology to E. coli swimming and surface motility reveals essentially all the previously known components of flagellar-mediated chemotaxis on the time scale of weeks. Remarkably, we also identify three dozen additional novel loci that operate through diverse mechanisms to affect a behavior that was assumed to be completely characterized. The speed, ease, and broad applicability of this framework should greatly accelerate the global analysis of a wide range of uncharacterized bacterial behaviors.
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影响因子：
64.8
作者：
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通讯作者：
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DOI：
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发表时间：
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影响因子：
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作者：
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影响因子：
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作者：
Ebel, W;Vaughn, GJ;Trempy, JE
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