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Identification of regulatory activities and binding sites for σ54 (RpoN) in Salmonella Typhimurium ATCC14028

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

PROVIDER: GSE75180 | GEO | 2017/03/27

SECONDARY ACCESSION(S): PRJNA302717

REPOSITORIES: GEO

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Novel DNA Binding and Regulatory Activities for σ54 (RpoN) in Salmonella enterica Serovar Typhimurium 14028s.

Project description:The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. Salmonella enterica serovar Typhimurium utilizes the housekeeping σ70 and five alternative sigma factors, including σ54 The σ54-RNAP differs from other σ-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription. In S. Typhimurium, σ54-dependent promoters normally respond to one of 13 different bEBPs, each of which is activated under a specific growth condition. Here, we utilized a constitutively active, promiscuous bEBP to perform a genome-wide identification of σ54-RNAP DNA binding sites and the transcriptome of the σ54 regulon of S. Typhimurium. The position and context of many of the identified σ54 RNAP DNA binding sites suggest regulatory roles for σ54-RNAP that connect the σ54 regulon to regulons of other σ factors to provide a dynamic response to rapidly changing environmental conditions.IMPORTANCE The alternative sigma factor σ54 (RpoN) is required for expression of genes involved in processes with significance in agriculture, bioenergy production, bioremediation, and host-microbe interactions. The characterization of the σ54 regulon of the versatile pathogen S. Typhimurium has expanded our understanding of the scope of the σ54 regulon and how it links to other σ regulons within the complex regulatory network for gene expression in bacteria.

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Identification of regulatory activities for σ54 (RpoN) in Salmonella Typhimurium ATCC14028 [expression]

Project description:Transcriptional profiles of mid-exponentially growing Salmonella enterica sv Typhimurium ATCC14028 wild type and ΔrpoN mutant cultures containing plasmid pPBHP192 expressing protein DctD250

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Identification of binding sites for σ54 (RpoN) in Salmonella Typhimurium ATCC14028 [ChIP]

Project description:ChIP-chip analysis of DNA specifically bound to anti-σ54 from mid-exponentially growing Salmonella enterica sv Typhimurium ATCC14028 wild type and ΔrpoN mutant cultures containing plasmid pPBHP192 expressing protein DctD250

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Identification of regulatory activities and binding sites for σ54 (RpoN) in Salmonella Typhimurium ATCC14028

Project description:Identification of regulatory activities and binding sites for σ54 (RpoN) in Salmonella Typhimurium ATCC14028

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Sfh and H-NS binding sites in the Salmonella Typhimurium genome

Project description:This SuperSeries is composed of the SubSeries listed below.

2009-12-07 | GSE19356 | GEO

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Project description:Sigma54, or RpoN, is an alternative ? factor found widely in eubacteria. A significant complication in analysis of the global ??? regulon in a bacterium is that the ??? RNA polymerase holoenzyme requires interaction with an active bacterial enhancer-binding protein (bEBP) to initiate transcription at a ???-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 ???-dependent promoters for the characterization of the ??? regulon of Salmonella Typhimurium LT2.The AAA+?ATPase domain of DctD was able to drive transcription from nearly all previously characterized or predicted ???-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 ???-dependent promoter upstream of STM2939, a homolog of the cas1 component of a CRISPR system. ChIP-chip analysis revealed at least 70 ??? binding sites in the chromosome, of which 58% are located within coding sequences. Promoter-lacZ fusions with selected intragenic ??? binding sites suggest that many of these sites are capable of functioning as ???-dependent promoters.Since the DctD AAA + ATPase domain proved effective in activating transcription from the diverse ???-dependent promoters of the S. Typhimurium LT2 ??? regulon under a single growth condition, this approach is likely to be valuable for examining ??? regulons in other bacterial species. The S. Typhimurium ??? regulon included a high number of intragenic ??? binding sites/promoters, suggesting that ??? may have multiple regulatory roles beyond the initiation of transcription at the start of an operon.

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Project description:Conventional cancer therapies are often limited in effectiveness and exhibit strong side effects. Therefore, alternative therapeutic strategies are demanded. The employment of tumor-colonizing bacteria that exert anticancer effects is such a novel approach that attracts increasing attention. For instance, Salmonella enterica serovar Typhimurium has been used in many animal tumor models as well as in first clinical studies. These bacteria exhibit inherent tumoricidal effects. In addition, they can be used to deliver therapeutic agents. However, bacterial expression has to be restricted to the tumor to prevent toxic substances from harming healthy tissue. Therefore, we screened an S. Typhimurium promoter-trap library to identify promoters that exclusively drive gene expression in the cancerous tissue. Twelve elements could be detected that show reporter gene expression in tumors but not in spleen and liver. In addition, a DNA motif was identified that appears to be necessary for tumor specificity. Now, such tumor-specific promoters can be used to safely express therapeutic proteins by tumor-colonizing S. Typhimurium directly in the neoplasia.

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Genome-scale mapping reveals complex regulatory activities of RpoN in Yersinia pseudotuberculosis

Project description:This SuperSeries is composed of the SubSeries listed below.

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