Global analysis of Escherichia coli RNA degradosome function using DNA microarrays
Global analysis of Escherichia coli RNA degradosome function using DNA microarrays
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DOI：
10.1073/pnas.0308747101
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发表时间：
2004-03-02
影响因子：
11.1
通讯作者：
Lin-Chao, S
中科院分区：
文献类型：
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作者：
Bernstein, JA;Lin, PH;Lin-Chao, S
核糖核酸酶E是一种重要的内切核糖核酸酶，它通过其C-末端与多种蛋白质相互作用，形成一种称为RNA降解体的复合体。为了研究降解体作为RNA衰退机器的拟议角色，我们使用DNA微阵列在携带降解体成分RNase E、多核苷酸磷酸化酶、RHIB解旋酶和烯醇化酶突变的细菌中，全局评估了单基因分辨率下4,289个大肠杆菌mRNAs的稳态丰度和衰减率的变化。我们的结果表明，这四种蛋白质的功能都是正常的信使核糖核酸周转所必需的。我们鉴定了特定的转录本和功能上可区分的转录本类别，它们的半衰期和丰度受到多种降解体蛋白的一致影响，受到降解体成分突变的不同影响，或者不被降解体突变检测到改变。我们的结果认为，一些大肠杆菌mRNAs在体内的衰退取决于组装的降解体的作用，而另一些则是由不依赖于复合体的降解体蛋白作用的，这意味着存在以特定类别的mRNAs为靶点的结构特征或生化因素。
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, RhIB 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.