Stochastic Pulse Regulation in Bacterial Stress Response

Howard Hughes Medical Institute, Division of Biology and Bioengineering, Broad Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
Science (Impact Factor: 33.61). 10/2011; 334(6054):366-9. DOI: 10.1126/science.1208144
Source: PubMed


Gene regulatory circuits can use dynamic, and even stochastic, strategies to respond to environmental conditions. We examined activation of the general stress response mediated by the alternative sigma factor, σ(B), in individual Bacillus subtilis cells. We observed that energy stress activates σ(B) in discrete stochastic pulses, with increasing levels of stress leading to higher pulse frequencies. By perturbing and rewiring the endogenous system, we found that this behavior results from three key features of the σ(B) circuit: an ultrasensitive phosphorylation switch; stochasticity ("noise"), which activates that switch; and a mixed (positive and negative) transcriptional feedback, which can both amplify a pulse and switch it off. Together, these results show how prokaryotes encode signals using stochastic pulse frequency modulation through a compact regulatory architecture.

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    • "The combination of positive and negative feedback regulation provides a mechanism to regulate the strength and duration of a response [10] (Fig. 1E). For instance, the Bacillus subtilis energy stress response involving the alternative sigma factor B is temporally modulated by stochastic pulses of gene activation with the strength of the response controlled by the frequency, not the magnitude of the pulses [15]. Stochastic fluctuations in the concentration of a phosphatase serve as the pulse trigger. "
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    ABSTRACT: DNA repair safeguards the genome against a diversity of DNA damaging agents. Although the mechanisms of many repair proteins have been examined separately in vitro, far less is known about the coordinated function of the whole repair machinery in vivo. Furthermore, single-cell studies indicate that DNA damage responses generate substantial variation in repair activities across cells. This review focuses on fluorescence imaging methods that offer a quantitative description of DNA repair in single cells by measuring protein concentrations, diffusion characteristics, localizations, interactions, and enzymatic rates. Emerging single-molecule and super-resolution microscopy methods now permit direct visualization of individual proteins and DNA repair events in vivo. We expect much can be learned about the organization of DNA repair by linking cell heterogeneity to mechanistic observations at the molecular level.
    Full-text · Article · Aug 2014 · DNA repair
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    • "In our experimental system, the situation is the opposite: cell delineation is difficult, but the tracking is simple because cells grow slowly and minimally change position between two successive frames (Additional file 2). To examine if the developed algorithm is more widely applicable, we processed published time-lapse movies from three different bacterial genera: fast-growing rod-like Bacillus [28], crescent-shaped Caulobacter [7], and filamentous Streptomyces [29]. The most promising results were obtained by processing the Streptomyces time-lapse movie. "
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    Full-text · Article · Jul 2014 · BMC Bioinformatics
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    • "We used standard methods for analyzing gene expression via RT-PCR and quantitative RT-PCR, with some modifications [26]. For qRT-PCR analysis of sinI, abbA, mstX, yqxM and sigA, we used the primers listed in Table S2. "
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