使用DNA微阵列以单基因分辨率对盐沼盐杆菌NRC-1中的mRNA衰变进行全局分析。

Global analysis of mRNA decay in Halobacterium salinarum NRC-1 at single-gene resolution using DNA microarrays.

作者信息

Hundt Sonja, Zaigler Alexander, Lange Christian, Soppa Jörg, Klug Gabriele

机构信息

Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.

出版信息

J Bacteriol. 2007 Oct;189(19):6936-44. doi: 10.1128/JB.00559-07. Epub 2007 Jul 20.

Abstract

RNA degradation is an important factor in the regulation of gene expression. It allows organisms to quickly respond to changing environmental conditions by adapting the expression of individual genes. The stability of individual mRNAs within an organism varies considerably, contributing to differential amounts of proteins expressed. In this study we used DNA microarrays to analyze mRNA degradation in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1 on a global level. We determined mRNA half-lives for 1,717 open reading frames, 620 of which are part of known or predicted operons. Under the tested conditions transcript stabilities ranged from 5 min to more than 18 min, with 79% of the evaluated mRNAs showing half-lives between 8 and 12 min. The overall mean half-life was 10 min, which is considerably longer than the ones found in the other prokaryotes investigated thus far. As previously observed in Escherichia coli and Saccharomyces cerevisiae, we could not detect a significant correlation between transcript length and transcript stability, but there was a relationship between gene function and transcript stability. Genes that are known or predicted to be transcribed in operons exhibited similar mRNA half-lives. These results provide initial insights into mRNA turnover in a euryarchaeon. Moreover, our model organism, H. salinarum NRC-1, is one of just two archaea sequenced to date that are missing the core subunits of the archaeal exosome. This complex orthologous to the RNA degrading exosome of eukarya is found in all other archaeal genomes sequenced thus far.

摘要

RNA降解是基因表达调控中的一个重要因素。它使生物体能够通过调整单个基因的表达来快速应对不断变化的环境条件。生物体中单个mRNA的稳定性差异很大,这导致了蛋白质表达量的差异。在本研究中,我们使用DNA微阵列在全球范围内分析了极端嗜盐广古菌盐沼盐杆菌NRC-1指数生长培养物中的mRNA降解情况。我们确定了1717个开放阅读框的mRNA半衰期,其中620个是已知或预测操纵子的一部分。在测试条件下,转录本稳定性范围从5分钟到超过18分钟,79%的评估mRNA半衰期在8到12分钟之间。总体平均半衰期为10分钟,这比迄今为止研究的其他原核生物中的半衰期长得多。正如之前在大肠杆菌和酿酒酵母中观察到的那样,我们没有检测到转录本长度与转录本稳定性之间的显著相关性,但基因功能与转录本稳定性之间存在关系。已知或预测在操纵子中被转录的基因表现出相似的mRNA半衰期。这些结果为广古菌中的mRNA周转提供了初步见解。此外,我们的模式生物盐沼盐杆菌NRC-1是迄今为止测序的仅有的两种缺少古菌外切体核心亚基的古菌之一。与真核生物的RNA降解外切体同源的这个复合体在迄今为止测序的所有其他古菌基因组中都有发现。

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