Intramembrane proteolysis at a glance: from signalling to protein degradation

Kühnle, Nathalie; Dederer, Verena; Lemberg, Marius K.

doi:10.1242/jcs.217745

Cited by 48 publications

(41 citation statements)

References 79 publications

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“…With many mitochondrial proteins harboring Phe residues in their TM regions, PARL may have co-evolved a different mode of substrate recognition. This is the first substrate preference determined for any eukaryotic rhomboid protease and the preferences for others, such as the Golgi RHBDL1 and ER RHBDL4 (Kuhnle et al, 2019), remain to be determined.…”

Section: Parl Has Bulky Substrate Specificity Preferences Distinct Frmentioning

confidence: 93%

“…The PARL protease is a member of the rhomboid intramembrane protease family, which are membrane-embedded serine peptidases that are thought to be constitutively active. Their functions range from cleavage and release of membrane-tethered signaling molecules to membrane protein degradation (Kuhnle et al, 2019;Ticha et al, 2018). Regulation of PARL activity at the molecular level is thought to occur via post-translational modifications.…”

Section: Introductionmentioning

confidence: 99%

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Insights into the catalytic properties of the mitochondrial rhomboid protease PARL

Lysyk

Brassard

Arutyunova

et al. 2020

Preprint

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The rhomboid protease PARL is a critical regulator of mitochondrial homeostasis through its cleavage of substrates such as PINK1, PGAM5, and Smac, which have crucial roles in mitochondrial quality control and apoptosis. To gain insight into the catalytic properties of the PARL protease, we expressed human PARL in yeast and used FRET-based kinetic assays to measure proteolytic activity in vitro. We show PARL activity in detergent is enhanced by cardiolipin. Significantly higher turnover rates are observed for PARL reconstituted in proteoliposomes, with Smac being cleaved most rapidly at a rate of 1 min−1. PGAM5 is cleaved with the highest efficiency compared to PINK1 and Smac. In proteoliposomes, a truncated β-cleavage form of PARL is more active than the full-length enzyme for hydrolysis of PINK1, PGAM5 and Smac. Multiplex substrate profiling reveals a substrate preference for PARL with a bulky side chain Phe in P1, which is distinct from small side chain residues typically found with bacterial rhomboid proteases. This study using recombinant PARL provides fundamental insights into its catalytic activity and substrate preferences.

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Section: Parl Has Bulky Substrate Specificity Preferences Distinct Frmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Insights into the catalytic properties of the mitochondrial rhomboid protease PARL

Lysyk

Brassard

Arutyunova

et al. 2020

Preprint

Self Cite

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“…The first three families of IMPs cleave a transmembrane (TM) segment of membrane proteins (Wolfe, 2009;Strisovsky, 2016), while Rce1, the only member of the glutamyl IMPs, cleaves a soluble domain of the substrate. IMPs are involved in various cellular events in a wide range of organisms and often mediate transmembrane signaling by regulating the cleavage of a target protein in response to environmental changes (Brown et al, 2000;Kühnle et al, 2019). The S2P family is well conserved among all kingdoms of life, from prokaryotes to higher eukaryotes (Chen and Zhang, 2010;Kroos and Akiyama, 2013;Rawson, 2013;Schneider and Glickman, 2013).…”

Section: Introductionmentioning

confidence: 99%

Involvement of a Membrane-Bound Amphiphilic Helix in Substrate Discrimination and Binding by an Escherichia coli S2P Peptidase RseP

2020

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Intramembrane proteases (IMPs) are a unique class of proteases that catalyze the proteolysis within the membrane and regulate diverse cellular processes in various organisms. RseP, an Escherichia coli site-2 protease (S2P) family IMP, is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-σE) protein RseA. Extracytoplasmic stresses trigger a sequential cleavage of RseA, in which first DegS cleaves off its periplasmic domain, and RseP catalyzes the second cleavage of RseA. The two tandem-arranged periplasmic PDZ (PDZ tandem) domains of RseP serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP IMP domain. However, RseP’s substrate recognition mechanism is not fully understood. Here, we found that a periplasmic region of RseP, located downstream of the PDZ tandem, contains a segment (named H1) predicted to form an amphiphilic helix. Bacterial S2P homologs with various numbers of PDZ domains have a similar amphiphilic helix in the corresponding region. We demonstrated that the H1 segment forms a partially membrane-embedded amphiphilic helix on the periplasmic surface of the membrane. Systematic and random mutagenesis analyses revealed that the H1 helix is important for the stability and proteolytic function of RseP and that mutations in the H1 segment can affect the PDZ-mediated substrate discrimination. Cross-linking experiments suggested that H1 directly interacts with the DegS-cleaved form of RseA. We propose that H1 acts as an adaptor required for proper arrangement of the PDZ tandem domain to perform its filter function and for substrate positioning for its efficient cleavage.

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“…Such genes that are upregulated during the initial phases of UPR activation encode ER chaperones, protein disulfide isomerases (PDIs), and proteins involved in ER associated protein degradation (ERAD). ERAD is a specialized form of protein degradation that involves the retrotranslocation of misfolded proteins out of the ER lumen or membrane, followed by their ubiquitylation by ER-bound E3-ubiquitin ligases on the cytosolic face of the ER, which marks them for degradation by proteasomes, also located on the cytosolic face of the ER (Hampton, 2002;McCracken and Brodsky, 2003;Ahner and Brodsky, 2004;Meusser et al, 2005;Kuhnle et al, 2019).…”

Section: Er Stress and The Unfolded Protein Responsementioning

confidence: 99%

ATF6 as a Nodal Regulator of Proteostasis in the Heart

et al. 2020

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Proteostasis encompasses a homeostatic cellular network in all cells that maintains the integrity of the proteome, which is critical for optimal cellular function. The components of the proteostasis network include protein synthesis, folding, trafficking, and degradation. Cardiac myocytes have a specialized endoplasmic reticulum (ER) called the sarcoplasmic reticulum that is well known for its role in contractile calcium handling. However, less studied is the proteostasis network associated with the ER, which is of particular importance in cardiac myocytes because it ensures the integrity of proteins that are critical for cardiac contraction, e.g., ion channels, as well as proteins necessary for maintaining myocyte viability and interaction with other cell types, e.g., secreted hormones and growth factors. A major aspect of the ER proteostasis network is the ER unfolded protein response (UPR), which is initiated when misfolded proteins in the ER activate a group of three ER transmembrane proteins, one of which is the transcription factor, ATF6. Prior to studies in the heart, ATF6 had been shown in model cell lines to be primarily adaptive, exerting protective effects by inducing genes that encode ER proteins that fortify protein-folding in this organelle, thus establishing the canonical role for ATF6. Subsequent studies in isolated cardiac myocytes and in the myocardium, in vivo, have expanded roles for ATF6 beyond the canonical functions to include the induction of genes that encode proteins outside of the ER that do not have known functions that are obviously related to ER protein-folding. The identification of such non-canonical roles for ATF6, as well as findings that the gene programs induced by ATF6 differ depending on the stimulus, have piqued interest in further research on ATF6 as an adaptive effector in cardiac myocytes, underscoring the therapeutic potential of activating ATF6 in the heart. Moreover, discoveries of small molecule activators of ATF6 that adaptively affect the heart, as well as other organs, in vivo, have expanded the potential for development of ATF6-based therapeutics. This review focuses on the ATF6 arm of the ER UPR and its effects on the proteostasis network in the myocardium.

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Intramembrane proteolysis at a glance: from signalling to protein degradation

Cited by 48 publications

References 79 publications

Insights into the catalytic properties of the mitochondrial rhomboid protease PARL

Insights into the catalytic properties of the mitochondrial rhomboid protease PARL

Involvement of a Membrane-Bound Amphiphilic Helix in Substrate Discrimination and Binding by an Escherichia coli S2P Peptidase RseP

ATF6 as a Nodal Regulator of Proteostasis in the Heart

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