Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the Escherichia coli K-12 Genome

Author:

Yamamoto Kaneyoshi12,Yamanaka Yuki2,Shimada Tomohiro23,Sarkar Paramita14,Yoshida Myu1,Bhardwaj Neerupma4,Watanabe Hiroki1,Taira Yuki1,Chatterji Dipankar4,Ishihama Akira2

Affiliation:

1. Department of Frontier Bioscience, Hosei University, Tokyo, Japan

2. Micro-Nano Technology Research Center, Hosei University, Tokyo, Japan

3. Meiji University, School of Agriculture, Kawasaki, Kanagawa, Japan

4. Indian Institute of Science, Molecular Biophysics Unit, Bangalore, India

Abstract

The 91-amino-acid-residue small-subunit omega (the rpoZ gene product) of Escherichia coli RNA polymerase plays a structural role in the formation of RNA polymerase (RNAP) as a chaperone in folding the largest subunit (β′, of 1,407 residues in length), but except for binding of the stringent signal ppGpp, little is known of its role in the control of RNAP function. After analysis of genomewide distribution of wild-type and RpoZ-defective RNAP by the ChIP-chip method, we found alteration of the RpoZ-defective RNAP inside open reading frames, in particular, of the genes within prophages. For a set of the genes that exhibited altered occupancy of the RpoZ-defective RNAP, transcription was found to be altered as observed by qRT-PCR assay. All the observations here described indicate the involvement of RpoZ in recognition of some of the prophage genes. This study advances understanding of not only the regulatory role of omega subunit in the functions of RNAP but also the regulatory interplay between prophages and the host E. coli for adjustment of cellular physiology to a variety of environments in nature.

Funder

JSPS Indo-Japan Bilateral Joint Research

MEXT Cooperative Research Program of Network Joint Research for Materials and Devices

MEXT-Supported Program for Strategic Research Foundation at Private Universities

Publisher

American Society for Microbiology

Subject

Computer Science Applications,Genetics,Molecular Biology,Modeling and Simulation,Ecology, Evolution, Behavior and Systematics,Biochemistry,Physiology,Microbiology

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