Article

Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein

Department of Genetics, University of Groningen, Kerklaan 30, 9751NN, Haren, The Netherlands.
Molecular Microbiology (Impact Factor: 5.03). 05/2007; 64(2):368-81. DOI: 10.1111/j.1365-2958.2007.05662.x
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ABSTRACT Competence for genetic transformation in the bacterium Bacillus subtilis is a bistable differentiation process governed by the minor groove DNA binding protein ComK. No detectable comK transcription occurs in the absence of an intact comK gene, indicating that ComK has auto-activating properties. ComK auto-stimulation, which is dependent on ComK binding to the comK promoter, is a critical step in competence development, ensuring quick and high-level expression of the late-competence genes. Auto-stimulation is also essential for the bistable expression pattern of competence. Here, we demonstrate that ComK acts as an activator at its own promoter by antagonizing the action of two repressors, Rok and CodY. Importantly, antirepression occurs without preventing binding of the repressing proteins, suggesting that ComK and the repressors might bind at distinct surfaces of the DNA helix. DegU, a DNA binding protein known to increase the affinity of ComK for its own promoter, potentiates the antirepression activity of ComK. We postulate that antirepression is primarily achieved through modulation of DNA topology. Although to our knowledge ComK is the only DNA binding protein shown to act in this novel fashion, other minor groove binding proteins may act similarly.

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Available from: Wiep Klaas Smits, Aug 29, 2015
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    • "More specifically, DegU binds in between the two ComK dimer binding sites and may possibly facilitate tetramerization of ComK at the comK promoter site by partial unwinding and bending of the DNA helix [29]. Transcription can also occur in the absence of ComK [30]. It is estimated that a cell exhibiting competence has on average 50,000 ComK dimers during stationary phase [2]. "
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    ABSTRACT: Background It is a fascinating phenomenon that in genetically identical bacteria populations of Bacillus subtilis, a distinct DNA uptake phenotype called the competence phenotype may emerge in 10–20% of the population. Many aspects of the phenomenon are believed to be due to the variable expression of critical genes: a stochastic occurrence termed “noise” which has made the phenomenon difficult to examine directly by lab experimentation. Methods To capture and model noise in this system and further understand the emergence of competence both at the intracellular and culture levels in B. subtilis, we developed a novel multi-scale, agent-based model. At the intracellular level, our model recreates the regulatory network involved in the competence phenotype. At the culture level, we simulated growth conditions, with our multi-scale model providing feedback between the two levels. Results Our model predicted three potential sources of genetic “noise”. First, the random spatial arrangement of molecules may influence the manifestation of the competence phenotype. In addition, the evidence suggests that there may be a type of epigenetic heritability to the emergence of competence, influenced by the molecular concentrations of key competence molecules inherited through cell division. Finally, the emergence of competence during the stationary phase may in part be due to the dilution effect of cell division upon protein concentrations. Conclusions The competence phenotype was easily translated into an agent-based model – one with the ability to illuminate complex cell behavior. Models such as the one described in this paper can simulate cell behavior that is otherwise unobservable in vivo, highlighting their potential usefulness as research tools.
    Theoretical Biology and Medical Modelling 04/2013; 10(1):23. DOI:10.1186/1742-4682-10-23 · 1.27 Impact Factor
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    • "comGABsu promoter [26]) or relieve transcription repression (e.g. comKBsu promoter [48]). To test whether the elements of the comGABco and comKBco promoters are functionally conserved, we assayed the effect of the ComKBsu protein on these promoter fragments in the heterologous host, B. subtilis. "
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    ABSTRACT: The genes for DNA uptake and recombination in Bacilli are commonly regulated by the transcriptional factor ComK. We have identified a ComK homologue in Bacillus coagulans, an industrial relevant organism that is recalcitrant for transformation. Introduction of B. coagulans comK gene under its own promoter region into Bacillus subtilis comK strain results in low transcriptional induction of the late competence gene comGA, but lacking bistable expression. The promoter regions of B. coagulans comK and the comGA genes are recognized in B. subtilis and expression from these promoters is activated by B. subtilis ComK. Purified ComK protein of B. coagulans showed DNA-binding ability in gel retardation assays with B. subtilis- and B. coagulans-derived probes. These experiments suggest that the function of B. coagulans ComK is similar to that of ComK of B. subtilis. When its own comK is overexpressed in B. coagulans the comGA gene expression increases 40-fold, while the expression of another late competence gene, comC is not elevated and no reproducible DNA-uptake could be observed under these conditions. Our results demonstrate that B. coagulans ComK can recognize several B. subtilis comK-responsive elements, and vice versa, but indicate that the activation of the transcription of complete sets of genes coding for a putative DNA uptake apparatus in B. coagulans might differ from that of B. subtilis.
    PLoS ONE 01/2013; 8(1):e53471. DOI:10.1371/journal.pone.0053471 · 3.23 Impact Factor
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    • "ComK functions as an anti-repressor for the transcriptional repressors Rok and CodY, and thereby allows the expression of its own gene. This permits the establishment of the bistable system pre-required for competence development (Albano et al., 2005; Smits et al., 2007). In contrast, DegU~P recruits RNA polymerase at promoter regions of genes such as yvcA and aprE to activate biofilm formation and exoprotease production respectively (Ogura et al., 2003; Verhamme et al., 2007). "
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    ABSTRACT: Bacteria control multicellular behavioural responses, including biofilm formation and swarming motility, by integrating environmental cues through a complex regulatory network. Heterogeneous gene expression within an otherwise isogenic cell population that allows for differentiation of cell fate is an intriguing phenomenon that adds to the complexity of multicellular behaviour. This review focuses on recent data about how DegU, a pleiotropic response regulator, co-ordinates multicellular behaviour in Bacillus subtilis. We review studies that challenge the conventional understanding of the molecular mechanisms underpinning the DegU regulatory system and others that describe novel targets of DegU during activation of biofilm formation by B. subtilis. We also discuss a novel role for DegU in regulating multicellular processes in the food-borne pathogen Listeria monocytogenes.
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