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Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ54 (RpoN) regulon of Salmonella Typhimurium LT2
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  • 作者：David J Samuels (6)
    Jonathan G Frye (7)
    Steffen Porwollik (8)
    Michael McClelland (8)
    Jan Mrázek (6) (9)
    Timothy R Hoover (6)
    Anna C Karls (6)
  • 关键词：Sigma54 ; RpoN ; Bacterial enhancer ; binding protein ; Regulon ; Sigma factor ; Salmonella
  • 刊名：BMC Genomics
  • 出版年：2013
  • 出版时间：December 2013
  • 年：2013
  • 卷：14
  • 期：1
  • 全文大小：696KB
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  • 作者单位：David J Samuels (6)
    Jonathan G Frye (7)
    Steffen Porwollik (8)
    Michael McClelland (8)
    Jan Mrázek (6) (9)
    Timothy R Hoover (6)
    Anna C Karls (6)

    6. Department of Microbiology, University of Georgia, 30602, Athens, GA, USA
    7. US Department of Agriculture, Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Richard B. Russell Research Center, Agricultural Research Service, 30605, Athens, GA, USA
    8. Department of Microbiology and Molecular Genetics, University of California, 92697, Irvine, CA, USA
    9. Institute of Bioinformatics, University of Georgia, 30602, Athens, GA, USA
文摘
Background Sigma54, or RpoN, is an alternative σ factor found widely in eubacteria. A significant complication in analysis of the global σ54 regulon in a bacterium is that the σ54 RNA polymerase holoenzyme requires interaction with an active bacterial enhancer-binding protein (bEBP) to initiate transcription at a σ54-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 σ54-dependent promoters for the characterization of the σ54 regulon of Salmonella Typhimurium LT2. Results The AAA+?ATPase domain of DctD was able to drive transcription from nearly all previously characterized or predicted σ54-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 σ54-dependent promoter upstream of STM2939, a homolog of the cas1 component of a CRISPR system. ChIP-chip analysis revealed at least 70 σ54 binding sites in the chromosome, of which 58% are located within coding sequences. Promoter-lacZ fusions with selected intragenic σ54 binding sites suggest that many of these sites are capable of functioning as σ54-dependent promoters. Conclusion Since the DctD AAA+?ATPase domain proved effective in activating transcription from the diverse σ54-dependent promoters of the S. Typhimurium LT2 σ54 regulon under a single growth condition, this approach is likely to be valuable for examining σ54 regulons in other bacterial species. The S. Typhimurium σ54 regulon included a high number of intragenic σ54 binding sites/promoters, suggesting that σ54 may have multiple regulatory roles beyond the initiation of transcription at the start of an operon.

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