Global analysis of Escherichia coli RNA degradosome function

Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

摘要：核糖核酸酶E（RNase E）是大肠杆菌（Escherichia coli）必需的内切核糖核酸酶，其通过C端区域与多种其他蛋白质相互作用，形成名为RNA降解体（RNA degradosome）的复合物。为探究RNA降解体作为RNA降解机器的已提出功能，我们采用DNA微阵列（DNA microarray）技术，以单基因分辨率对携带RNA降解体组分（核糖核酸酶E、多核苷酸磷酸化酶、RhlB解旋酶及烯醇化酶）突变的大肠杆菌中4289个大肠杆菌mRNA的稳态丰度与降解变化进行了全局分析。研究结果表明，这四种蛋白质的功能均为维持正常mRNA周转所必需。我们鉴定出了特定转录本及功能可区分的转录本类别，其半衰期与丰度或同时受多种降解体蛋白质的协同影响、或因降解体组分突变产生差异化变化、或未因降解体突变出现可检测到的变化。本研究结果表明，部分大肠杆菌体内mRNA的降解依赖组装完成的降解体的作用，而另一些则由独立于该复合物发挥功能的降解体蛋白质介导发挥作用，这提示存在能够将特定类别mRNA靶向交由降解体降解的结构特征或生化因子。本超系列由下述子系列构成。请参阅各独立系列。