Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <named-content content-type="genus-species">Escherichia coli</named-content> K-12 Genome

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 sup...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Kaneyoshi Yamamoto, Yuki Yamanaka, Tomohiro Shimada, Paramita Sarkar, Myu Yoshida, Neerupma Bhardwaj, Hiroki Watanabe, Yuki Taira, Dipankar Chatterji, Akira Ishihama
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Escherichia coli RNA polymerase omega subunit prophage transcription regulation Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/3e098837f78245f792d00e7b28eebda3
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:3e098837f78245f792d00e7b28eebda3
record_format	dspace
spelling	oai:doaj.org-article:3e098837f78245f792d00e7b28eebda32021-12-02T19:45:30ZAltered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <named-content content-type="genus-species">Escherichia coli</named-content> K-12 Genome10.1128/mSystems.00172-172379-5077https://doaj.org/article/3e098837f78245f792d00e7b28eebda32018-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00172-17https://doaj.org/toc/2379-5077ABSTRACT 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 H-NS within prophages. Since all 10 prophages in E. coli K-12 carry only a small number of promoters, the altered occupancy of RpoZ-defective RNAP and of transcripts might represent transcription initiated from as-yet-unidentified host promoters. The genes that exhibited transcription enhanced by RpoZ-defective RNAP are located in the regions of low-level H-NS binding. By using phenotype microarray (PM) assay, alterations of some phenotypes were detected for the rpoZ-deleted mutant, indicating the involvement of RpoZ in regulation of some genes. Possible mechanisms of altered distribution of RNAP inside prophages are discussed. IMPORTANCE 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.Kaneyoshi YamamotoYuki YamanakaTomohiro ShimadaParamita SarkarMyu YoshidaNeerupma BhardwajHiroki WatanabeYuki TairaDipankar ChatterjiAkira IshihamaAmerican Society for MicrobiologyarticleEscherichia coliRNA polymeraseomega subunitprophagetranscription regulationMicrobiologyQR1-502ENmSystems, Vol 3, Iss 1 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Escherichia coli RNA polymerase omega subunit prophage transcription regulation Microbiology QR1-502
spellingShingle	Escherichia coli RNA polymerase omega subunit prophage transcription regulation Microbiology QR1-502 Kaneyoshi Yamamoto Yuki Yamanaka Tomohiro Shimada Paramita Sarkar Myu Yoshida Neerupma Bhardwaj Hiroki Watanabe Yuki Taira Dipankar Chatterji Akira Ishihama Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <named-content content-type="genus-species">Escherichia coli</named-content> K-12 Genome
description	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 H-NS within prophages. Since all 10 prophages in E. coli K-12 carry only a small number of promoters, the altered occupancy of RpoZ-defective RNAP and of transcripts might represent transcription initiated from as-yet-unidentified host promoters. The genes that exhibited transcription enhanced by RpoZ-defective RNAP are located in the regions of low-level H-NS binding. By using phenotype microarray (PM) assay, alterations of some phenotypes were detected for the rpoZ-deleted mutant, indicating the involvement of RpoZ in regulation of some genes. Possible mechanisms of altered distribution of RNAP inside prophages are discussed. IMPORTANCE 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.
format	article
author	Kaneyoshi Yamamoto Yuki Yamanaka Tomohiro Shimada Paramita Sarkar Myu Yoshida Neerupma Bhardwaj Hiroki Watanabe Yuki Taira Dipankar Chatterji Akira Ishihama
author_facet	Kaneyoshi Yamamoto Yuki Yamanaka Tomohiro Shimada Paramita Sarkar Myu Yoshida Neerupma Bhardwaj Hiroki Watanabe Yuki Taira Dipankar Chatterji Akira Ishihama
author_sort	Kaneyoshi Yamamoto
title	Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <named-content content-type="genus-species">Escherichia coli</named-content> K-12 Genome
title_short	Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <named-content content-type="genus-species">Escherichia coli</named-content> K-12 Genome
title_full	Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <named-content content-type="genus-species">Escherichia coli</named-content> K-12 Genome
title_fullStr	Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <named-content content-type="genus-species">Escherichia coli</named-content> K-12 Genome
title_full_unstemmed	Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <named-content content-type="genus-species">Escherichia coli</named-content> K-12 Genome
title_sort	altered distribution of rna polymerase lacking the omega subunit within the prophages along the <named-content content-type="genus-species">escherichia coli</named-content> k-12 genome
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/3e098837f78245f792d00e7b28eebda3
work_keys_str_mv	AT kaneyoshiyamamoto altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome AT yukiyamanaka altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome AT tomohiroshimada altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome AT paramitasarkar altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome AT myuyoshida altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome AT neerupmabhardwaj altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome AT hirokiwatanabe altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome AT yukitaira altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome AT dipankarchatterji altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome AT akiraishihama altereddistributionofrnapolymeraselackingtheomegasubunitwithintheprophagesalongthenamedcontentcontenttypegenusspeciesescherichiacolinamedcontentk12genome
_version_	1718376020161069056

Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <named-content content-type="genus-species">Escherichia coli</named-content> K-12 Genome

Ejemplares similares