comparative analysis of regulatory elements between escherichia coli and klebsiella pneumoniae by genome-wide transcription start site profiling比较分析监管元素之间的大肠杆菌和肺炎克雷伯菌的全基因组转录启动网站分析.pdfVIP

Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome- Wide Transcription Start Site Profiling 1. 1. 1 1 1 Donghyuk Kim , Jay Sung-Joong Hong , Yu Qiu , Harish Nagarajan , Joo-Hyun Seo , Byung- 1¤ 2 1 Kwan Cho , Shih-Feng Tsai , Bernhard Ø. Palsson * 1 Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America, 2 Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan Abstract Genome-wide transcription start site (TSS) profiles of the enterobacteria Escherichia coli and Klebsiella pneumoniae were experimentally determined through modified 59 RACE followed by deep sequencing of intact primary mRNA. This identified 3,746 and 3,143 TSSs for E. coli and K. pneumoniae, respectively. Experimentally determined TSSs were then used to define promoter regions and 59 UTRs upstream of coding genes. Comparative analysis of these regulatory elements revealed the use of multiple TSSs, identical sequence motifs of promoter and Shine-Dalgarno sequence, reflecting conserved gene expression apparatuses between the two species. In both species, over 70% of primary transcripts were expressed from operons having orthologous genes during exponential growth. However, expressed orthologous genes in E. coli and K. pneumoniae showed a strikingly different organization of upstream regulatory regions with only 20% identical promoters with TSSs in both species. Over 40% of promoters had TSSs identified in only one species, despite conserved promoter sequences existing in the other spec