A Conserved Structural Module Regulates Transcriptional Responses to Diverse Stress Signals in Bacteria

Campbell, Elizabeth A.; Greenwell, Roger; Anthony, Jennifer R.; Wang, Sheng; Lim, Lionel; Das, Kalyan; Sofia, Heidi J.; Donohue, Timothy J.; Darst, Seth A.

doi:10.1016/j.molcel.2007.07.009

Cited by 139 publications

(322 citation statements)

References 50 publications

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“…An analysis of different σ/anti-σ complex structures in the Protein Data Bank (PDB) reveals that interaction between a σ factor and its cognate anti-σ factor can occur in a number of different ways (23)(24)(25). A flexible linker between regions σ 2 and σ 4 has been described as important for anti-σ interaction but also as a general structural feature required for proper association of σ with RNAP and with -10 and -35 sequences in the promoter (16,(26)(27)(28)(29). In the case of PhyR, the SL domain is missing critical sequence required for it to function as a bona fide σ factor (4) yet retains the flexible loop (α3-α4) between regions σ 2 and σ 4 .…”

Section: Discussionmentioning

confidence: 99%

Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria

Herrou¹,

Rotskoff²,

Luo³

et al. 2012

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

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α-Proteobacteria uniquely integrate features of two-component signal transduction (TCS) and alternative sigma factor (σ) regulation to control transcription in response to general stress. The core of this regulatory system is the PhyR protein, which contains a σ-like (SL) domain and a TCS receiver domain. Aspartyl phosphorylation of the PhyR receiver in response to stress signals promotes binding of the anti-σ factor, NepR, to PhyR-SL. This mechanism, whereby NepR switches binding between its cognate σ factor and phospho-PhyR (PhyR∼P), controls transcription of the general stress regulon. We have defined the structural basis of the PhyR∼P/NepR interaction in Caulobacter crescentus and characterized the effect of aspartyl phosphorylation on PhyR structure by molecular dynamics simulations. Our data support a model in which phosphorylation of the PhyR receiver domain promotes its dissociation from the PhyR-SL domain, which exposes the NepR binding site. A highly dynamic loop–helix region (α3-α4) of the PhyR-SL domain plays an important role in PhyR∼P binding to NepR in vitro, and in stress-dependent activation of transcription in vivo. This study provides a foundation for understanding the protein-protein interactions and protein structural dynamics that underpin general stress adaptation in a large and metabolically diverse clade of the bacterial kingdom.

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Section: Discussionmentioning

confidence: 99%

Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria

Herrou¹,

Rotskoff²,

Luo³

et al. 2012

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

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“…Likewise, Rhodobacter sphaeroides E interacts with its zinc-containing anti-(ChrR) by using residues in region 2.1 (29). Indeed, structural homology modeling suggests that many -anti-pairs may interact in a similar manner (30). Region 2.1 of has many surface-exposed residues and does not itself contact either core RNA polymerase or DNA.…”

Section: Discussionmentioning

confidence: 99%

Analysis of σ ³² mutants defective in chaperone-mediated feedback control reveals unexpected complexity of the heat shock response

Yura

Guisbert²,

Poritz

et al. 2007

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

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Protein quality control is accomplished by inducing chaperones and proteases in response to an altered cellular folding state. In Escherichia coli, expression of chaperones and proteases is positively regulated by 32 . Chaperone-mediated negative feedback control of 32 activity allows this transcription factor to sense the cellular folding state. We identified point mutations in 32 altered in feedback control. Surprisingly, such mutants are resistant to inhibition by both the DnaK/J and GroEL/S chaperones in vivo and also show dramatically increased stability. Further characterization of the most defective mutant revealed that it has almost normal binding to chaperones and RNA polymerase and is competent for chaperone-mediated inactivation in vitro. We suggest that the mutants identify a regulatory step downstream of chaperone binding that is required for both inactivation and degradation of 32 .heat shock transcription factor ͉ proteolysis ͉ GroEL ͉ DnaK ͉ stress response T he heat shock response is a major homeostatic mechanism for controlling the state of protein folding and degradation in all cells (1-3). Upon heat stress, a set of highly conserved heat shock proteins (hsps), including chaperones and proteases, is rapidly and transiently induced. Hsps maintain optimal states of protein folding and turnover during normal growth and also minimize cellular damage from stress-induced protein misfolding and aggregation (4, 5). The level of hsps is controlled primarily by heat shock transcription factors that sense the cellular folding environment through negative feedback control mediated by chaperones (6-9). Understanding this mode of regulation is central to our understanding of protein quality control as well as cellular stress responses. Here, we report the determinants required for chaperone regulation of 32 , the heat shock transcription factor in Escherichia coli (10-12).32 regulon members control both the activity and stability of 32 . The DnaK/J/GrpE and GroEL/S chaperone machines each constitute a negative feedback loop that couples 32 activity to cellular protein folding state: overexpression of either chaperone machine decreases 32 activity; conversely, chaperone depletion or overexpression of chaperone substrates increases 32 activity (13-16). The chaperones are likely to act directly on 32 because they bind to 32 and inhibit its activity in a purified in vitro transcription system (17-19). Regulated degradation of 32 is mediated by the FtsH protease and facilitated by DnaK/J/GrpE and GroEL/S in vivo, but this process has not been completely recapitulated in vitro, where degradation of 32 by FtsH is slow and not facilitated by chaperones (20,21).We selected and characterized feedback-resistant mutants of 32 . The residues altered by the mutations map to a small patch in 32 . Surprisingly, most mutants simultaneously diminished all three negative feedback loops operative in vivo; the most severe mutant essentially eliminated chaperone-mediated activity control and degradation by FtsH protease. In stri...

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“…These mutations are likely to destabilize the folded structure of the protein, leading to increased degradation by proteases. The L10P and A60P mutations introduce prolines in the first position of a turn and in the middle of an ␣ helix, respectively (30,31). An isoleucine substitution at position 155 likely exposes a hydrophobic residue on the surface of the protein, and V170 is buried in the hydrophobic core (15,29).…”

Section: Figmentioning

confidence: 99%

Appropriate Regulation of the σ ^E -Dependent Envelope Stress Response Is Necessary To Maintain Cell Envelope Integrity and Stationary-Phase Survival in Escherichia coli

2017

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The alternative sigma factor E is a key component of the Escherichia coli response to cell envelope stress and is required for viability even in the absence of stress. The activity of E increases during entry into stationary phase, suggesting an important role for E when nutrients are limiting. Elevated E activity has been proposed to activate a pathway leading to the lysis of nonculturable cells that accumulate during early stationary phase. To better understand E -directed cell lysis and the role of E in stationary phase, we investigated the effects of elevated E activity in cultures grown for 10 days. We demonstrate that high E activity is lethal for all cells in stationary phase, not only those that are nonculturable. Spontaneous mutants with reduced E activity, due primarily to point mutations in the region of E that binds the Ϫ35 promoter motif, arise and take over cultures within 5 to 6 days after entry into stationary phase. High E activity leads to large reductions in the levels of outer membrane porins and increased membrane permeability, indicating membrane defects. These defects can be counteracted and stationary-phase lethality delayed significantly by stabilizing membranes with Mg 2ϩ and buffering the growth medium or by deleting the E -dependent small RNAs (sRNAs) MicA, RybB, and MicL, which inhibit the expression of porins and Lpp. Expression of these sRNAs also reverses the loss of viability following depletion of E activity. Our results demonstrate that appropriate regulation of E activity, ensuring that it is neither too high nor too low, is critical for envelope integrity and cell viability.IMPORTANCE The Gram-negative cell envelope and cytoplasm differ significantly, and separate responses have evolved to combat stress in each compartment. An array of cell envelope stress responses exist, each of which is focused on different parts of the envelope. The E response is conserved in many enterobacteria and is tuned to monitor pathways for the maturation and delivery of outer membrane porins, lipoproteins, and lipopolysaccharide to the outer membrane. The activity of E is tightly regulated to match the production of E regulon members to the needs of the cell. In E. coli, loss of E results in lethality. Here we demonstrate that excessive E activity is also lethal and results in decreased membrane integrity, the very phenotype the system is designed to prevent.KEYWORDS cell envelope, stress response, transcriptional regulation S tress responses allow cells to rapidly adapt their gene expression to cope with changing conditions. Signal transduction pathways sense an inducing stress and transduce that information to a transcription factor, which, in turn, regulates the expression of specialized sets of genes required to combat the stress. Once the stress Citation Nicoloff H, Gopalkrishnan S, Ades SE. 2017. Appropriate regulation of the σ Edependent envelope stress response is necessary to maintain cell envelope integrity and stationary-phase survival in Escherichia coli.

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A Conserved Structural Module Regulates Transcriptional Responses to Diverse Stress Signals in Bacteria

Cited by 139 publications

References 50 publications

Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria

Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria

Analysis of σ ³² mutants defective in chaperone-mediated feedback control reveals unexpected complexity of the heat shock response

Appropriate Regulation of the σ ^E -Dependent Envelope Stress Response Is Necessary To Maintain Cell Envelope Integrity and Stationary-Phase Survival in Escherichia coli

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A Conserved Structural Module Regulates Transcriptional Responses to Diverse Stress Signals in Bacteria

Cited by 139 publications

References 50 publications

Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria

Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria

Analysis of σ 32 mutants defective in chaperone-mediated feedback control reveals unexpected complexity of the heat shock response

Appropriate Regulation of the σ E -Dependent Envelope Stress Response Is Necessary To Maintain Cell Envelope Integrity and Stationary-Phase Survival in Escherichia coli

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Product

Resources

About

Analysis of σ ³² mutants defective in chaperone-mediated feedback control reveals unexpected complexity of the heat shock response

Appropriate Regulation of the σ ^E -Dependent Envelope Stress Response Is Necessary To Maintain Cell Envelope Integrity and Stationary-Phase Survival in Escherichia coli