Blue Light Activates the σ
            <sup>B</sup>
            -Dependent Stress Response of
            <i>Bacillus subtilis</i>
            via YtvA

Ávila-Pérez, Marcela; Hellingwerf, Klaas J.; Kort, Remco

doi:10.1128/jb.00716-06

Cited by 150 publications

(149 citation statements)

References 17 publications

(19 reference statements)

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“…To focus on the environmental stress response pathways, and avoid potential cross-talk from the energy stress pathways, we deleted the energy stress phosphatase, rsbQP (26). We also deleted the blue-light sensor, ytvA, to avoid inadvertent activation of σ B by microscope illumination (SI Text) (29,30). We then used quantitative time-lapse microscopy to examine σ B activation in individual cells of this strain over time on agarose pads or using the CellASIC microfluidic culturing system (31-33).…”

Section: Resultsmentioning

confidence: 99%

Rate of environmental change determines stress response specificity

Young

Locke

Elowitz

2013

Proc. Natl. Acad. Sci. U.S.A.

115

142

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Cells use general stress response pathways to activate diverse target genes in response to a variety of stresses. However, general stress responses coexist with more specific pathways that are activated by individual stresses, provoking the fundamental question of whether and how cells control the generality or specificity of their response to a particular stress. Here we address this issue using quantitative time-lapse microscopy of the Bacillus subtilis environmental stress response, mediated by σ B . We analyzed σ B activation in response to stresses such as salt and ethanol imposed at varying rates of increase. Dynamically, σ B responded to these stresses with a single adaptive activity pulse, whose amplitude depended on the rate at which the stress increased. This rate-responsive behavior can be understood from mathematical modeling of a key negative feedback loop in the underlying regulatory circuit. Using RNAseq we analyzed the effects of both rapid and gradual increases of ethanol and salt stress across the genome. Because of the rate responsiveness of σ B activation, salt and ethanol regulons overlap under rapid, but not gradual, increases in stress. Thus, the cell responds specifically to individual stresses that appear gradually, while using σ B to broaden the cellular response under more rapidly deteriorating conditions. Such dynamic control of specificity could be a critical function of other general stress response pathways.systems biology | single-cell dynamics | computational biology C ells must respond to, and anticipate, a wide range of stresses that occur on multiple timescales. For this purpose, many species use general stress response pathways, which activate a diverse set of target regulons in response to a variety of stresses. For example, in mammals, p53 is activated by DNA damage (1-4) and hypoxia (5, 6), among others, and activates genes that impact cell cycle progression (7), DNA repair (8, 9), apoptosis, and angiogenesis (10, 11). In yeast, Msn2/4 responds to nutritional stress (12), as well as to salt (13), calcium (14), heat, and other stresses (15). Bacteria also contain general stress response pathways, including the alternative sigma factors RpoS in Escherichia coli (16) and σ B in Bacillus subtilis (17).It has been proposed that general stress response pathways enable cells to cross-protect, by anticipating stresses that may not be present at the moment, but are likely to occur soon (18). For example, preexposure to specific stresses is known to enhance bacterial resistance to different stresses applied subsequently (19)(20)(21). This raises a basic question: How do cells determine when to use the general stress response rather than activating more specific individual pathways?The σ B -mediated general stress response of B. subtilis provides an ideal model system to address these issues. σ B is activated by diverse stresses through a well-characterized and conserved transcriptional and posttranscriptional circuit mechanism (17). In response to stress, it activates ∼200 target ge...

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Section: Resultsmentioning

confidence: 99%

Rate of environmental change determines stress response specificity

Young

Locke

Elowitz

2013

Proc. Natl. Acad. Sci. U.S.A.

115

142

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“…The B. subtilis stressosome is an~1.8 MDa supramolecular complex that consists of multiple copies of RsbR and RsbS (Chen et al, 2003;Delumeau et al, 2006;Dufour et al, 1996;Marles-Wright et al, 2008). Different environmental stresses and signals are thought to stimulate RsbT kinase activity towards its stressosome substrates (Akbar et al, 2001;Á vila-Pé rez et al, 2006;Gaidenko et al, 2006;Kim et al, 2004;Voelker et al, 1995). This leads to dissociation of RsbT from the stressosome to activate RsbU and subsequently s B .…”

Section: Introductionmentioning

confidence: 99%

Novel σ B regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases

et al. 2011

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A common bacterial strategy to cope with stressful conditions is the activation of alternative sigma factors that control specific regulons enabling targeted responses. In the human pathogen Bacillus cereus, activation of the major stress-responsive sigma factor s B is controlled by a signalling route that involves the multi-sensor hybrid histidine kinase RsbK. RsbK-type kinases are not restricted to the B. cereus group, but occur in a wide variety of other bacterial species, including members of the the low-GC Gram-positive genera Geobacillus and Paenibacillus as well as the high-GC actinobacteria. Genome context and protein sequence analyses of 118 RsbK homologues revealed extreme variability in N-terminal sensory as well as C-terminal regulatory domains and suggested that RsbK-type kinases are subject to complex fine-tuning systems, including sensitization and desensitization via methylation and demethylation within the helical domain preceding the H-box. The RsbK-mediated stress-responsive sigma factor activation mechanism that has evolved in B. cereus and the other species differs markedly from the extensively studied and highly conserved RsbRST-mediated s B activation route found in Bacillus subtilis and other low-GC Gram-positive bacteria. Implications for future research on sigma factor control mechanisms are presented and current knowledge gaps are briefly discussed.

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“…These studies identify that LOV proteins are implicated in adaptation to general stress responses and osmotic stress in diverse organisms (bacteria (48,49), plants (50), and fungi (11)). Currently a direct sensing mechanism by LOV proteins in these responses has remained elusive, and most focus on two-component signal transduction pathways, where LOV proteins act to attenuate kinase function in a light-dependent manner.…”

mentioning

confidence: 99%

A Native Threonine Coordinates Ordered Water to Tune Light-Oxygen-Voltage (LOV) Domain Photocycle Kinetics and Osmotic Stress Signaling in Trichoderma reesei ENVOY

Lokhandwala

Vega

Hopkins

et al. 2016

Journal of Biological Chemistry

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Light-oxygen-voltage (LOV)3 domain-containing photoreceptors are widely distributed in nature, where they couple blue light absorption to regulation of a diverse array of signal transduction pathways (1). In general, LOV proteins can be divided into two subclasses: 1) short LOV proteins (sLOV) that exist as the isolated LOV domain with short ancillary N-or C-terminal caps (2-4) and 2) modular LOV proteins that couple blue light activation to allosteric regulation of effector domains (1). Although the modular LOV proteins are present in plants, bacteria, and all fungi, the sLOV variety are predominantly found in bacteria and only some fungi (4). Currently, LOV proteins have received widespread attention because of their important roles in regulation of circadian function (3, 5, 6), growth and development (7,8), stress responses (9 -11), and adaptation to and regulation of pathogenicity (12). In addition, their wide ranging utility has led to the development of optogenetic tools that harness their modular design (13,14). Despite substantial research, key questions involving LOV photocycles remain.LOV domain chemistry is characterized by blue light-induced formation of a covalent adduct between a bound flavin cofactor (FMN, FAD, or riboflavin) and a conserved Cys residue in a GXNCRFLQ motif. Concomitant with adduct formation is protonation of the N5 position of the isoalloxazine ring. Current models indicate that signal transduction is coupled to N5 protonation via allosteric regulation of N-or C-terminal effector elements remote from the flavin active site (3,15,16). The covalent adduct is defined by a broad UV-visible absorption band centered at ϳ390 nm (LOV 390 ). Upon return to the dark, the adduct state spontaneously decays to an oxidized flavin (LOV 450 ) on a timescale of seconds to days (17,18). Currently the biological role of the wide range in photocycle lifetimes is unknown; however, several studies have suggested that the range facilitates adaptation to changing levels of light intensity (17,19,20). For these reasons, chemical tuning of the LOV photocycle lifetime through understanding of the adduct decay mechanism has been attempted in several systems (2,17,18,(21)(22)(23)(24).Several lines of reasoning have led to a general mechanism of adduct decay. First, solvent isotope effect experiments indicate that a single proton abstraction event is rate-limiting (17, 18). Second, adduct decay can be catalyzed by the presence of small molecule bases such as imidazole (25). Third, residue substitutions at regions that regulate solvent access to the flavin active site have a substantial effect on LOV photocycle lifetimes (18,26). Combined, these experiments implicate N5 deprotonation as the rate-determining step in adduct decay. Consistent with such a model, mutation of residues that regulate accessibility of small molecules to the N5 position or that tune hydrogen bonding characteristics affect kinetics of LOV proteins (17,18,21,22,24,26,27). Importantly, the natural base responsible for N5 deprotonation remai...

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Blue Light Activates the σ ^B -Dependent Stress Response of Bacillus subtilis via YtvA

Cited by 150 publications

References 17 publications

Rate of environmental change determines stress response specificity

Rate of environmental change determines stress response specificity

Novel σ B regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases

A Native Threonine Coordinates Ordered Water to Tune Light-Oxygen-Voltage (LOV) Domain Photocycle Kinetics and Osmotic Stress Signaling in Trichoderma reesei ENVOY

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Blue Light Activates the σ B -Dependent Stress Response of Bacillus subtilis via YtvA

Cited by 150 publications

References 17 publications

Rate of environmental change determines stress response specificity

Rate of environmental change determines stress response specificity

Novel σ B regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases

A Native Threonine Coordinates Ordered Water to Tune Light-Oxygen-Voltage (LOV) Domain Photocycle Kinetics and Osmotic Stress Signaling in Trichoderma reesei ENVOY

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Blue Light Activates the σ ^B -Dependent Stress Response of Bacillus subtilis via YtvA