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Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ(54) (RpoN) regulon of Salmonella Typhimurium LT2
BACKGROUND: Sigma54, or RpoN, is an alternative σ factor found widely in eubacteria. A significant complication in analysis of the global σ(54) regulon in a bacterium is that the σ(54) RNA polymerase holoenzyme requires interaction with an active bacterial enhancer-binding protein (bEBP) to initiate...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844500/ https://www.ncbi.nlm.nih.gov/pubmed/24007446 http://dx.doi.org/10.1186/1471-2164-14-602 |
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author | Samuels, David J Frye, Jonathan G Porwollik, Steffen McClelland, Michael Mrázek, Jan Hoover, Timothy R Karls, Anna C |
author_facet | Samuels, David J Frye, Jonathan G Porwollik, Steffen McClelland, Michael Mrázek, Jan Hoover, Timothy R Karls, Anna C |
author_sort | Samuels, David J |
collection | PubMed |
description | BACKGROUND: Sigma54, or RpoN, is an alternative σ factor found widely in eubacteria. A significant complication in analysis of the global σ(54) regulon in a bacterium is that the σ(54) RNA polymerase holoenzyme requires interaction with an active bacterial enhancer-binding protein (bEBP) to initiate transcription at a σ(54)-dependent promoter. Many bacteria possess multiple bEBPs, which are activated by diverse environmental stimuli. In this work, we assess the ability of a promiscuous, constitutively-active bEBP—the AAA+ ATPase domain of DctD from Sinorhizobium meliloti—to activate transcription from all σ(54)-dependent promoters for the characterization of the σ(54) regulon of Salmonella Typhimurium LT2. RESULTS: The AAA+ ATPase domain of DctD was able to drive transcription from nearly all previously characterized or predicted σ(54)-dependent promoters in Salmonella under a single condition. These promoters are controlled by a variety of native activators and, under the condition tested, are not transcribed in the absence of the DctD AAA+ ATPase domain. We also identified a novel σ(54)-dependent promoter upstream of STM2939, a homolog of the cas1 component of a CRISPR system. ChIP-chip analysis revealed at least 70 σ(54) binding sites in the chromosome, of which 58% are located within coding sequences. Promoter-lacZ fusions with selected intragenic σ(54) binding sites suggest that many of these sites are capable of functioning as σ(54)-dependent promoters. CONCLUSION: Since the DctD AAA+ ATPase domain proved effective in activating transcription from the diverse σ(54)-dependent promoters of the S. Typhimurium LT2 σ(54) regulon under a single growth condition, this approach is likely to be valuable for examining σ(54) regulons in other bacterial species. The S. Typhimurium σ(54) regulon included a high number of intragenic σ(54) binding sites/promoters, suggesting that σ(54) may have multiple regulatory roles beyond the initiation of transcription at the start of an operon. |
format | Online Article Text |
id | pubmed-3844500 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-38445002013-12-02 Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ(54) (RpoN) regulon of Salmonella Typhimurium LT2 Samuels, David J Frye, Jonathan G Porwollik, Steffen McClelland, Michael Mrázek, Jan Hoover, Timothy R Karls, Anna C BMC Genomics Research Article BACKGROUND: Sigma54, or RpoN, is an alternative σ factor found widely in eubacteria. A significant complication in analysis of the global σ(54) regulon in a bacterium is that the σ(54) RNA polymerase holoenzyme requires interaction with an active bacterial enhancer-binding protein (bEBP) to initiate transcription at a σ(54)-dependent promoter. Many bacteria possess multiple bEBPs, which are activated by diverse environmental stimuli. In this work, we assess the ability of a promiscuous, constitutively-active bEBP—the AAA+ ATPase domain of DctD from Sinorhizobium meliloti—to activate transcription from all σ(54)-dependent promoters for the characterization of the σ(54) regulon of Salmonella Typhimurium LT2. RESULTS: The AAA+ ATPase domain of DctD was able to drive transcription from nearly all previously characterized or predicted σ(54)-dependent promoters in Salmonella under a single condition. These promoters are controlled by a variety of native activators and, under the condition tested, are not transcribed in the absence of the DctD AAA+ ATPase domain. We also identified a novel σ(54)-dependent promoter upstream of STM2939, a homolog of the cas1 component of a CRISPR system. ChIP-chip analysis revealed at least 70 σ(54) binding sites in the chromosome, of which 58% are located within coding sequences. Promoter-lacZ fusions with selected intragenic σ(54) binding sites suggest that many of these sites are capable of functioning as σ(54)-dependent promoters. CONCLUSION: Since the DctD AAA+ ATPase domain proved effective in activating transcription from the diverse σ(54)-dependent promoters of the S. Typhimurium LT2 σ(54) regulon under a single growth condition, this approach is likely to be valuable for examining σ(54) regulons in other bacterial species. The S. Typhimurium σ(54) regulon included a high number of intragenic σ(54) binding sites/promoters, suggesting that σ(54) may have multiple regulatory roles beyond the initiation of transcription at the start of an operon. BioMed Central 2013-09-05 /pmc/articles/PMC3844500/ /pubmed/24007446 http://dx.doi.org/10.1186/1471-2164-14-602 Text en Copyright © 2013 Samuels et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Samuels, David J Frye, Jonathan G Porwollik, Steffen McClelland, Michael Mrázek, Jan Hoover, Timothy R Karls, Anna C Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ(54) (RpoN) regulon of Salmonella Typhimurium LT2 |
title | Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ(54) (RpoN) regulon of Salmonella Typhimurium LT2 |
title_full | Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ(54) (RpoN) regulon of Salmonella Typhimurium LT2 |
title_fullStr | Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ(54) (RpoN) regulon of Salmonella Typhimurium LT2 |
title_full_unstemmed | Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ(54) (RpoN) regulon of Salmonella Typhimurium LT2 |
title_short | Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ(54) (RpoN) regulon of Salmonella Typhimurium LT2 |
title_sort | use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ(54) (rpon) regulon of salmonella typhimurium lt2 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844500/ https://www.ncbi.nlm.nih.gov/pubmed/24007446 http://dx.doi.org/10.1186/1471-2164-14-602 |
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