title: Integration of global regulation of two aromatic-responsive sigma(54)-dependent systems: a common phenotype by different mechanisms.
abstract: Pseudomonas-derived regulators DmpR and XylR are structurally and mechanistically related sigma(54)-dependent activators that control transcription of genes involved in catabolism of aromatic compounds. The binding of distinct sets of aromatic effectors to these regulatory proteins results in release of a repressive interdomain interaction and consequently allows the activators to promote transcription from their cognate target promoters. The DmpR-controlled Po promoter region and the XylR-controlled Pu promoter region are also similar, although homology is limited to three discrete DNA signatures for binding sigma(54) RNA polymerase, the integration host factor, and the regulator. These common properties allow cross-regulation of Pu and Po by DmpR and XylR in response to appropriate aromatic effectors. In vivo, transcription of both the DmpR/Po and XylR/Pu regulatory circuits is subject to dominant global regulation, which results in repression of transcription during growth in rich media. Here, we comparatively assess the contribution of (p)ppGpp, the FtsH protease, and a component of an alternative phosphoenolpyruvate-sugar phosphotransferase system, which have been independently implicated in mediating this level of regulation. Further, by exploiting the cross-regulatory abilities of these two circuits, we identify the target component(s) that are intercepted in each case. The results show that (i) contrary to previous speculation, FtsH is not universally required for transcription of sigma(54)-dependent systems; (ii) the two factors found to impact the XylR/Pu regulatory circuit do not intercept the DmpR/Po circuit; and (iii) (p)ppGpp impacts the DmpR/Po system to a greater extent than the XylR/Pu system in both the native Pseudomonas putida and a heterologous Escherichia coli host. The data demonstrate that, despite the similarities of the specific regulatory circuits, the host global regulatory network latches onto and dominates over these specific circuits by exploiting their different properties. The mechanistic implications of how each of the host factors exerts its action are discussed.
authors.affiliation: Department of Cell and Molecular Biology, Umeå University, S-901 87 Umeå, Sweden.
authors.forename: Chun Chau
authors.initials: CC
authors.lastname: Sze
authors.forename: Lisandro M D
authors.initials: LM
authors.lastname: Bernardo
authors.forename: Victoria
authors.initials: V
authors.lastname: Shingler
mesh_terms: D049069:ATP-Dependent Proteases; D001426:Bacterial Proteins / Q000378:metabolism; D001592:Benzyl Alcohols / Q000494:pharmacology; D003408:Cresols / Q000494:pharmacology; D004268:DNA-Binding Proteins / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter; D006159:Guanosine Tetraphosphate / Q000378:metabolism; D008565:Membrane Proteins / Q000378:metabolism; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000378:metabolism; D016958:Pseudomonas putida / Q000235:genetics*; D051877:RNA Polymerase Sigma 54; D012808:Sigma Factor / Q000378:metabolism*; D015398:Signal Transduction; D015534:Trans-Activators / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D001592:Benzyl Alcohols; D003408:Cresols; D004268:DNA-Binding Proteins; C080133:DmpR protein, Pseudomonas; D029968:Escherichia coli Proteins; D008565:Membrane Proteins; C423631:PtsN protein, Pseudomonas putida; D012808:Sigma Factor; D015534:Trans-Activators; D014157:Transcription Factors; C074322:XylR protein, Pseudomonas; C497751:rpoN protein, E coli; D006159:Guanosine Tetraphosphate; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54; D049069:ATP-Dependent Proteases; C513383:FtsH protein, E coli; C042289:3-methylbenzyl alcohol; C034047:2-cresol