Bernstein Jonathan A, Lin Pei-Hsun, Cohen Stanley N, Lin-Chao Sue
Department of Genetics, Stanford University, Stanford, CA 94305, USA.
Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2758-63. doi: 10.1073/pnas.0308747101. Epub 2004 Feb 23.
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.
核糖核酸酶E是大肠杆菌中一种必需的内切核糖核酸酶，它通过其C末端区域与多种其他蛋白质相互作用，形成一种称为RNA降解体的复合物。为了研究降解体作为RNA衰变机器的假定作用，我们使用DNA微阵列在单基因分辨率下全面评估了4289种大肠杆菌mRNA在稳态丰度和衰变方面的变化，这些大肠杆菌携带降解体成分核糖核酸酶E、多核苷酸磷酸化酶、RhlB解旋酶和烯醇酶的突变。我们的结果表明，这四种蛋白质的功能对于正常的mRNA周转都是必需的。我们鉴定出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差异影响，或者未被降解体突变检测到改变。我们的结果表明，体内一些大肠杆菌mRNA的衰变取决于组装好的降解体的作用，而其他一些mRNA则受到独立于复合物发挥作用的降解体蛋白的作用，这意味着存在一些结构特征或生化因子，它们将特定类别的mRNA靶向由降解体进行衰变。
