Gene expression changes during overexpression of bacterial small RNA, DicF. Escherichia coli str. K-12 substr. MG1655

Hundreds of small RNAs (sRNAs) have been identified in diverse bacterial species, and while the functions of most remain unknown, some regulate key processes, particularly stress responses. The sRNA DicF was identified over twenty-five years ago as an inhibitor of cell division, but since then has remained uncharacterized. DicF is 53 nucleotides and is encoded on a prophage (Qin) in the genomes of many Escherichia coli strains. Here, we performed RNA-Seq analyses of an E. coli strain with chromosomal deletion of dicF and overexpressing either empty plasmid or dicF from a plasmid. Systems analysis using computational methods identified additional mRNA targets of DicF: xylR and pykA mRNAs, encoding the xylose uptake and catabolism regulator and pyruvate kinase, respectively. We have further validated these target genes experimentally. Overall design: RNA-Seq analyses was performed on E. coli strains overexpressing either the vector control or the small RNA DicF.

目前已在多种细菌物种中鉴定出数百种小RNA（small RNAs, sRNAs），尽管绝大多数的功能仍未明确，但部分小RNA可调控关键生理过程，尤其是应激响应。小RNA DicF早在25年前就被鉴定为细胞分裂抑制剂，但此后一直未被深入表征。DicF全长53个核苷酸，由诸多大肠杆菌（Escherichia coli）菌株基因组中的前噬菌体（prophage）Qin所编码。本研究对一株染色体缺失dicF基因、且分别过表达空质粒载体或质粒编码dicF的大肠杆菌菌株开展了RNA测序（RNA-Seq）分析。通过计算方法进行系统分析后，本研究鉴定出DicF的额外信使RNA（mRNA）靶标：xylR与pykA mRNA，二者分别编码木糖摄取与分解代谢调控因子以及丙酮酸激酶。我们进一步通过实验手段验证了上述靶标基因。实验设计概述：本研究对分别过表达空载体对照或小RNA DicF的大肠杆菌菌株开展了RNA测序分析。