Global analysis of mRNA decay and abundance in Escherichia coli

Abstract: Much of the information available about factors that affect mRNA decay in Escherichia coli, and by inference in other bacteria, has been gleaned from study of less than 25 of the approximately 4,300 predicted E. coli messages. To investigate these factors more broadly, we examined the half-lives and steady-state abundance of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. An rRNA-based strategy for normalization of microarray data was developed to permit quantitation of mRNA decay after transcriptional arrest by rifampicin. We found that globally, mRNA half-lives were similar in nutrient-rich media and defined media in which the generation time was approximately tripled. A wide range of stabilities was observed for individual mRNAs of E. coli, although approximately 80% of all mRNAs had half-lives between 3 and 8 min. Genes having biologically related metabolic functions were commonly observed to have similar stabilities. Whereas the half-lives of a limited number of mRNAs correlated positively with their abundance, we found that overall, increased mRNA stability is not predictive of increased abundance. Neither the density of putative sites of cleavage by RNase E, which is believed to initiate mRNA decay in E. coli, nor the free energy of folding of 5' or 3' untranslated region sequences was predictive of mRNA half-life. Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability. This SuperSeries is composed of the SubSeries listed below. Overall design: Refer to individual Series

摘要：目前关于大肠杆菌（Escherichia coli）以及由此推断其他细菌中影响mRNA降解的因素的相关信息，大多来自对约4300个预测的大肠杆菌mRNA转录本中不足25个的研究。为更全面地探究这些影响因素，我们采用双色荧光DNA微阵列（two-color fluorescent DNA microarrays）技术，以单基因分辨率检测了已知及预测的大肠杆菌mRNA的半衰期与稳态丰度。我们开发了基于核糖体RNA（rRNA）的微阵列数据标准化策略，以实现在利福平（rifampicin）阻断转录后对mRNA降解的定量分析。研究发现，在营养丰富培养基与倍增时间约为其三倍的限定培养基中，mRNA的整体半衰期水平相似。大肠杆菌的单个mRNA稳定性存在广泛差异，但约80%的mRNA半衰期介于3至8分钟之间。具有生物学相关代谢功能的基因，其mRNA通常具有相近的稳定性。尽管少量mRNA的半衰期与其丰度呈正相关，但整体而言，mRNA稳定性的提升并不能预测其丰度的升高。被认为可启动大肠杆菌mRNA降解的核糖核酸酶E（RNase E）的潜在切割位点密度，以及5'或3'非翻译区（untranslated region, UTR）序列的折叠自由能，均无法用于预测mRNA半衰期。本研究结果揭示了全局层面上此前未被发现的mRNA降解特征，同时也表明，基于单个基因转录本研究得出的降解相关普遍性结论，其适用范围可能有限。本超级数据集（SuperSeries）由以下所列的子数据集（SubSeries）组成。整体设计：详见各子数据集。