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G3 (Bethesda). 2018 May 31;8(6):2079-2089. doi: 10.1534/g3.118.200265.

Regulation of Global Transcription in Escherichia coli by Rsd and 6S RNA.

Author information

1
National Centre for Biological Sciences, and avlal@stanford.edu aswin@ncbs.res.in.
2
Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India.

Abstract

In Escherichia coli, the sigma factor σ70 directs RNA polymerase to transcribe growth-related genes, while σ38 directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to σ70, and the non-coding 6S RNA which binds to the RNA polymerase-σ70 holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial. Here we use RNA-Seq in five phases of growth to elucidate their function on a genome-wide scale. We show that Rsd and 6S RNA facilitate σ38 activity throughout bacterial growth, while 6S RNA also regulates widely different genes depending upon growth phase. We discover novel interactions between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. Finally, we present a mathematical model of transcription which highlights the crosstalk between Rsd and 6S RNA as a crucial factor in controlling sigma factor competition and global gene expression.

KEYWORDS:

6S RNA; RNA polymerase; Rsd; gene regulation; sigma factors

PMID:
29686109
PMCID:
PMC5982834
DOI:
10.1534/g3.118.200265
[Indexed for MEDLINE]
Free PMC Article

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