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Ribosome Profiling Reveals Genome-wide Cellular Translational Regulation upon Heat Stress in Escherichia coli.

Authors
  • Zhang, Yanqing1
  • Xiao, Zhengtao2
  • Zou, Qin2
  • Fang, Jianhuo2
  • Wang, Qifan1
  • Yang, Xuerui3
  • Gao, Ning4
  • 1 MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. , (China)
  • 2 MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China. , (China)
  • 3 MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China. Electronic address: [email protected] , (China)
  • 4 MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China. Electronic address: [email protected] , (China)
Type
Published Article
Journal
Genomics, proteomics & bioinformatics
Publication Date
Oct 01, 2017
Volume
15
Issue
5
Pages
324–330
Identifiers
DOI: 10.1016/j.gpb.2017.04.005
PMID: 29031842
Source
Medline
Keywords
License
Unknown

Abstract

Heat shock response is a classical stress-induced regulatory system in bacteria, characterized by extensive transcriptional reprogramming. To compare the impact of heat stress on the transcriptome and translatome in Escherichia coli, we conducted ribosome profiling in parallel with RNA-Seq to investigate the alterations in transcription and translation efficiency when E. coli cells were exposed to a mild heat stress (from 30 °C to 45 °C). While general changes in ribosome footprints correlate with the changes of mRNA transcripts upon heat stress, a number of genes show differential changes at the transcription and translation levels. Translation efficiency of a few genes that are related to environment stimulus response is up-regulated, and in contrast, some genes functioning in mRNA translation and amino acid biosynthesis are down-regulated at the translation level in response to heat stress. Moreover, our ribosome occupancy data suggest that in general ribosomes accumulate remarkably in the starting regions of ORFs upon heat stress. This study provides additional insights into bacterial gene expression in response to heat stress, and suggests the presence of stress-induced but yet-to-be characterized cellular regulatory mechanisms of gene expression at translation level.

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