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

MSystems
Kaneyoshi YamamotoAkira Ishihama

Abstract

The RNA polymerase (RNAP) of Escherichia coli K-12 is a complex enzyme consisting of the core enzyme with the subunit structure α2ββ'ω and one of the σ subunits with promoter recognition properties. The smallest subunit, omega (the rpoZ gene product), participates in subunit assembly by supporting the folding of the largest subunit, β', but its functional role remains unsolved except for its involvement in ppGpp binding and stringent response. As an initial approach for elucidation of its functional role, we performed in this study ChIP-chip (chromatin immunoprecipitation with microarray technology) analysis of wild-type and rpoZ-defective mutant strains. The altered distribution of RpoZ-defective RNAP was identified mostly within open reading frames, in particular, of the genes inside prophages. For the genes that exhibited increased or decreased distribution of RpoZ-defective RNAP, the level of transcripts increased or decreased, respectively, as detected by reverse transcription-quantitative PCR (qRT-PCR). In parallel, we analyzed, using genomic SELEX (systemic evolution of ligands by exponential enrichment), the distribution of constitutive promoters that are recognized by RNAP RpoD holoenzyme alone and of general silencer ...Continue Reading

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Citations

Mar 13, 2018·Nucleic Acids Research·Tomohiro ShimadaAkira Ishihama
May 10, 2018·Journal of Industrial Microbiology & Biotechnology·Jason FontanaJames M Carothers
Nov 27, 2020·Biomolecules·Unnatiben Rajeshbhai PatelDipankar Chatterji
Sep 14, 2020·Molecular Microbiology·Juha KurkelaTaina Tyystjärvi
Jul 6, 2021·Frontiers in Microbiology·Tomohiro ShimadaAkira Ishihama

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Methods Mentioned

BETA
in vitro transcription
cross-linking studies
ChIP-chip
immunoprecipitation
PCR
phosphotransferase
SELEX
environmental stresses
transcription factor
electrophoresis

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