Regulation of the σE stress response by DegS: how the PDZ domain keeps the protease inactive in the resting state and allows integration of different OMP-derived stress signals upon folding stress

Hasselblatt, Hanna; Kurzbauer, R; Wilken, Corinna; Krojer, T.; Sawa, J.; Kurt, Juliane; Kirk, Rebecca; Hasenbein, Sonja; Ehrmann, Michael; Clausen, Tim

doi:10.1101/gad.445307

Cited by 84 publications

(94 citation statements)

References 33 publications

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“…Moreover, crystal structures of DegS ⌬PDZ closely resemble the active conformation of intact DegS (Fig. 1, B and C) and have a functional oxyanion hole (6,12). These results support an allosteric model in which the unliganded PDZ domain stabilizes the inactive protease domain conformation, whereas OMP peptide binding to the PDZ domain reduces or eliminates this inhibitory effect.…”

supporting

confidence: 70%

Allostery Is an Intrinsic Property of the Protease Domain of DegS

Sohn

Grant

Sauer

2010

Journal of Biological Chemistry

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DegS is a periplasmic Escherichia coli protease, which functions as a trimer to catalyze the initial rate-limiting step in a proteolytic cascade that ultimately activates transcription of stress response genes in the cytoplasm. Each DegS subunit consists of a protease domain and a PDZ domain. During protein folding stress, DegS is allosterically activated by peptides exposed in misfolded outer membrane porins, which bind to the PDZ domain and stabilize the active protease. Proteases are carefully regulated to ensure that these destructive enzymes are only activated under the proper circumstances. For example, most extracellular proteases are synthesized as inactive proenzymes or zymogens (1). In the trypsin proenzyme, the Ser-His-Asp catalytic triad is properly formed, but the oxyanion hole of the active site is malformed and only rearranges to the active structure following the processing event that produces the mature enzyme (2). The activities of intracellular trypsin-like proteases are also regulated by changes in active site conformation. In the DegS protease, for instance, alternative conformations of the oxyanion hole result in an equilibrium distribution of inactive and active enzymes whose populations are controlled by the binding of substrates and allosteric effectors (3-8).Escherichia coli DegS is a trimeric HtrA family enzyme consisting of a trypsin-like protease domain, a PDZ domain, and a sequence that anchors the protease to the periplasmic surface of the inner membrane (3, 9). The trimer is stabilized by interactions between the protease domains. Protein folding stress in the periplasm activates DegS cleavage of RseA, a transmembrane protein whose cytoplasmic domain binds and inhibits the E transcription factor (10, 11). DegS cleavage of RseA initiates a cascade of subsequent cleavages by other proteases, resulting in release of E and transcriptional activation of genes whose products are needed to repair damage caused by envelope stress. The PDZ domain of DegS plays a critical role in signal transduction. Specifically, C-terminal peptides of misfolded outer membrane porins (OMPs), 2 which end with a conserved Tyr-Xaa-Phe motif, bind to the PDZ domain, and activate cleavage of RseA (Fig. 1A and Ref. 3). Indeed, DegS cleavage of RseA in vitro can be accelerated more than 500-fold by OMP peptides (6, 7).OMP peptide activation of DegS appears to occur by relieving inhibitory contacts between the PDZ domain and the protease domain. For example, salt bridges between the PDZ domain and the protease domain are observed in crystal structures of peptide-free DegS, which has a malformed oxyanion hole, but these interactions are absent in peptide-bound DegS, which has a functional oxyanion hole (4, 5). Importantly, disrupting inhibitory interactions between the PDZ domain and the protease domain by point mutations or by deleting the PDZ domain entirely (DegS ⌬PDZ ) activates cleavage of RseA to levels observed with some OMP peptides (6, 7). Moreover, crystal structures of DegS ⌬PDZ closely resemble the acti...

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supporting

confidence: 70%

Allostery Is an Intrinsic Property of the Protease Domain of DegS

Sohn

Grant

Sauer

2010

Journal of Biological Chemistry

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“…Recent study showed that ligand binding to PDZ1 induces an allosteric activation of DegP (39). Similar PDZ-ligand-dependent activation has also been reported for DegS, a DegP homolog (9,10). RseP and DegP are similar in that they have tandem PDZ domains, but the roles of these domains appear to be different between these two enzymes.…”

Section: Discussionmentioning

confidence: 72%

A Pair of Circularly Permutated PDZ Domains Control RseP, the S2P Family Intramembrane Protease of Escherichia coli

Inaba

Suzuki

Maegawa

et al. 2008

Journal of Biological Chemistry

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TheE pathway of extracytoplasmic stress responses in Escherichia coli is activated through sequential cleavages of the anti-E protein, RseA, by membrane proteases DegS and RseP. Without the first cleavage by DegS, RseP is unable to cleave full-length RseA. We previously showed that a PDZ-like domain in the RseP periplasmic region is essential for this negative regulation of RseP. We now isolated additional deregulated RseP mutants. Many of the mutations affected a periplasmic region that is N-terminal to the previously defined PDZ domain. We expressed these regions and determined their crystal structures. Consistent with a recent prediction, our results indicate that RseP has tandem, circularly permutated PDZ domains (PDZ-N and PDZ-C). Strikingly, almost all the strong mutations have been mapped around the ligand binding cleft region in PDZ-N. These results together with those of an in vitro reaction reproducing the two-step RseA cleavage suggest that the proteolytic function of RseP is controlled by ligand binding to PDZ-N.

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“…3A). This finding suggests that the noncleavable ALE peptide might function as an allosteric activator like in the homologous DegS protease, where peptide binding to the PDZ domain triggers a series of conformational changes in the catalytic domain that stimulate peptidase activity (18,19). To explore further the activating effect of the ALE peptide, we preincubated DegP with saturating amounts of the potential activator and measured the rate of degradation of the ''poor'' SPM-FKGV-pNA substrate that lacks a C-terminal anchoring motif.…”

Section: Resultsmentioning

confidence: 99%

“…However, the nature of the allosteric activator is different and mirrors the degree of protease specificity. The DegS regulator is selectively activated by ligands with a XF C-terminal motif, a characteristic motif of the C termini of outer membrane proteins signaling the onset of folding stress (19). In contrast, a broad palette of peptide ligands with a rather unspecific XX C-terminal consensus can activate the housekeeping DegP protease.…”

Section: Discussionmentioning

confidence: 99%

“…This regulatory principle was first established for the DegS protease, the central regulator of the bacterial unfolded protein response (25). Upon folding stress, DegS is activated by the C termini of mislocalized outer membrane proteins (26), which interact with the PDZ domain and induce the remodeling of the catalytic domain, leading to protease activation (18,19) and subsequent cleavage of the anti-sigma factor RseA (27). Our data suggest that the DegP activity is controlled by a similar activation mechanism given that binding of an allosteric peptide to PDZ1 enhances the peptidase activity of the catalytic domain by switching the observed distorted active site (17) into an enzymatically competent conformation (Fig.…”

Section: Discussionmentioning

confidence: 99%

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Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins

Krojer

Pangerl

Kurt

et al. 2008

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

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114

118

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Aberrant proteins represent an extreme hazard to cells. Therefore, molecular chaperones and proteases have to carry out protein quality control in each cellular compartment. In contrast to the ATP-dependent cytosolic proteases and chaperones, the molecular mechanisms of extracytosolic factors are largely unknown. To address this question, we studied the protease function of DegP, the central housekeeping protein in the bacterial envelope. Our data reveal that DegP processively degrades misfolded proteins into peptides of defined size by employing a molecular ruler comprised of the PDZ1 domain and the proteolytic site. Furthermore, peptide binding to the PDZ domain transforms the resting protease into its active state. This allosteric activation mechanism ensures the regulated and rapid elimination of misfolded proteins upon folding stress. In comparison to the cytosolic proteases, the regulatory features of DegP are established by entirely different mechanisms reflecting the convergent evolution of an extracytosolic housekeeping protease.allosteric regulation ͉ chaperones ͉ HtrA ͉ protein quality control ͉ molecular ruler

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Regulation of the σE stress response by DegS: how the PDZ domain keeps the protease inactive in the resting state and allows integration of different OMP-derived stress signals upon folding stress

Cited by 84 publications

References 33 publications

Allostery Is an Intrinsic Property of the Protease Domain of DegS

Allostery Is an Intrinsic Property of the Protease Domain of DegS

A Pair of Circularly Permutated PDZ Domains Control RseP, the S2P Family Intramembrane Protease of Escherichia coli

Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins

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