大肠杆菌Small RNA EsrE的转录调控

【背景】大肠杆菌中Small RNA EsrE调控琥珀酸脱氢酶的表达并影响细胞生长,对其调控机制的探究有利于加深EsrE对细胞生长影响的认识。【目的】探究大肠杆菌Small RNA EsrE的转录调控机制。【方法】通过双质粒报告系统筛选转录调控因子,并通过凝胶迁移实验(electrophoretic mobilityshiftassay,EMSA)和qRT-PCR研究方法验证转录调控因子。【结果】双质粒报告系统证明RNA聚合酶亚基σ~(32) (RpoH)上调P_(esrE),β-羟酰-ACP脱水酶(FabZ)下调PesrE。EMSA结果和体内实验显示RpoH结合P_(esrE)片段,FabZ不结合P_(esrE)片段。【结论】RpoH直接结合启动子序列参与调控,FabZ以其他方式间接参与Small RNA EsrE的转录调控。     

Identifying Hfq-binding small RNA targets in Escherichia coli

The Hfq-binding small RNAs (sRNAs) have recently drawn much attention as regulators of translation in Escherichia coli. We attempt to identify the targets of this class of sRNAs in genome scale and gain further insight into the complexity of translational regulation induced by Hfq-binding sRNAs. Using a new alignment algorithm, most known negatively regulated targets of Hfq-binding sRNAs were identified. The results also show several interesting aspects of the regulatory function of Hfq-binding sRNAs.     

The correlation between architecture and mRNA abundance in the genetic regulatory network of Escherichia coli

Background  

Two aspects of genetic regulatory networks are the static architecture that describes the overall connectivity between the genes and the dynamics that describes the sequence of genes active at any one time as deduced from mRNA abundances. The nature of the relationship between these two aspects of these networks is a fundamental question. To address it, we have used the static architecture of the connectivity of the regulatory proteins of Escherichia coli to analyse their relationship to the abundance of the mRNAs encoding these proteins. In this we build on previous work which uses Boolean network models, but impose biological constraints that cannot be deduced from the mRNA abundances alone.     

Key players in regulatory RNA realm of bacteria

Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network.     

Conservation analysis of small RNA genes in Escherichia coli

MOTIVATION: Small RNA (sRNA) genes in Escherichia coli have been in focus recently, as 44 out of 55 experimentally confirmed sRNA genes have been precisely located in the genome. The object of this study is to analyze quantitatively the conservation of these sRNA genes and compare it with the conservation of protein-encoding genes, function-unknown regions and tRNA genes. RESULTS: The results show that within an evolutionary distance of 0.26, both sRNA genes and protein-encoding genes display a similar tendency in their degrees of conservation at the nucleotide level. In addition, the conservation of sRNA genes is much stronger than function-unknown regions, but much weaker than tRNA genes. Based on the conservation of studied sRNA genes, we also give clues to estimate the total number of sRNA genes in E.coli. SUPPLEMENTARY INFORMATION: Supplementary information is available at http://www.bioinfo.org.cn/SM/sRNAconservation.htm