1
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Jánosi B, Liewald JF, Seidenthal M, Yu SC, Umbach S, Redzovic J, Rentsch D, Alcantara IC, Bergs ACF, Schneider MW, Shao J, Gottschalk A. RIM and RIM-Binding Protein Localize Synaptic CaV2 Channels to Differentially Regulate Transmission in Neuronal Circuits. J Neurosci 2024; 44:e0535222024. [PMID: 38951038 PMCID: PMC11293454 DOI: 10.1523/jneurosci.0535-22.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/16/2024] [Accepted: 05/05/2024] [Indexed: 07/03/2024] Open
Abstract
At chemical synapses, voltage-gated Ca2+ channels (VGCCs) translate electrical signals into a trigger for synaptic vesicle (SV) fusion. VGCCs and the Ca2+ microdomains they elicit must be located precisely to primed SVs to evoke rapid transmitter release. Localization is mediated by Rab3-interacting molecule (RIM) and RIM-binding proteins, which interact and bind to the C terminus of the CaV2 VGCC α-subunit. We studied this machinery at the mixed cholinergic/GABAergic neuromuscular junction of Caenorhabditis elegans hermaphrodites. rimb-1 mutants had mild synaptic defects, through loosening the anchoring of UNC-2/CaV2 and delaying the onset of SV fusion. UNC-10/RIM deletion much more severely affected transmission. Although postsynaptic depolarization was reduced, rimb-1 mutants had increased cholinergic (but reduced GABAergic) transmission, to compensate for the delayed release. This did not occur when the excitation-inhibition (E-I) balance was altered by removing GABA transmission. Further analyses of GABA defective mutants and GABAA or GABAB receptor deletions, as well as cholinergic rescue of RIMB-1, emphasized that GABA neurons may be more affected than cholinergic neurons. Thus, RIMB-1 function differentially affects excitation-inhibition balance in the different motor neurons, and RIMB-1 thus may differentially regulate transmission within circuits. Untethering the UNC-2/CaV2 channel by removing its C-terminal PDZ ligand exacerbated the rimb-1 defects, and similar phenotypes resulted from acute degradation of the CaV2 β-subunit CCB-1. Therefore, untethering of the CaV2 complex is as severe as its elimination, yet it does not abolish transmission, likely due to compensation by CaV1. Thus, robustness and flexibility of synaptic transmission emerge from VGCC regulation.
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Affiliation(s)
- Barbara Jánosi
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Jana F Liewald
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Marius Seidenthal
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Szi-Chieh Yu
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Simon Umbach
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Jasmina Redzovic
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Dennis Rentsch
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Ivan C Alcantara
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Amelie C F Bergs
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Martin W Schneider
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Jiajie Shao
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt D-60438, Germany
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt D-60438, Germany
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2
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Inter-subunit crosstalk via PDZ synergistically governs allosteric activation of proapoptotic HtrA2. Structure 2022; 30:1307-1320.e5. [PMID: 35738282 DOI: 10.1016/j.str.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/28/2022] [Accepted: 05/30/2022] [Indexed: 01/19/2023]
Abstract
The mitochondrial serine protease High-temperature requirement A2 (HtrA2) is associated with various diseases including neurodegenerative disorders and cancer. Despite availability of structural details, the reports on HtrA2's mechanistic regulation that varies with the type of activation signals still remain non-concordant. To expound the role of regulatory PDZ (Postsynaptic density-95/Discs large/Zonula occludens-1) domains in multimodal activation of HtrA2, we generated heterotrimeric HtrA2 variants comprising different numbers of PDZs and/or active-site mutations. Sequential deletion of PDZs from the trimeric ensemble significantly affected its residual activity in a way that proffered a hypothesis advocating inter-molecular allosteric crosstalk via PDZs in HtrA2. Furthermore, structural and computational snapshots affirmed the role of PDZs in secondary structural element formation around the regulatory loops and coordinated reorganization of the N-terminal region. Therefore, apart from providing cues for devising structure-guided therapeutic strategies, this study establishes a physiologically relevant working model of complex allosteric regulation through a trans-mediated cooperatively shared energy landscape.
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3
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Šulskis D, Thoma J, Burmann BM. Structural basis of DegP protease temperature-dependent activation. SCIENCE ADVANCES 2021; 7:eabj1816. [PMID: 34878848 PMCID: PMC8654288 DOI: 10.1126/sciadv.abj1816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/16/2021] [Indexed: 05/21/2023]
Abstract
Protein quality control is an essential cellular function mainly executed by a vast array of different proteases and molecular chaperones. One of the bacterial high temperature requirement A (HtrA) protein family members, the homo-oligomeric DegP protease, plays a crucial role in the Escherichia coli protein quality control machinery by removing unfolded proteins or preventing their aggregation and chaperoning them to their final folded state within the periplasm. DegP contains two regulatory PDZ domains, which play key roles in substrate recognition and in the transformation of DegP between inactive hexameric and proteolytic active cage-like structures. Here, we analyze the interaction and dynamics of the DegP PDZ domains underlying this transformation by high-resolution NMR spectroscopy complemented with biochemical cleavage assays. We identify an interdomain molecular lock, which controls the interactions between the two PDZ domains, regulated by fine-tuned temperature-dependent protein dynamics, and which is potentially conserved in proteins harboring tandem PDZ domains.
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Affiliation(s)
- Darius Šulskis
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Johannes Thoma
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
- Corresponding author.
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4
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Hart EM, O'Connell A, Tang K, Wzorek JS, Grabowicz M, Kahne D, Silhavy TJ. Fine-Tuning of σ E Activation Suppresses Multiple Assembly-Defective Mutations in Escherichia coli. J Bacteriol 2019; 201:e00745-18. [PMID: 30858299 PMCID: PMC6509652 DOI: 10.1128/jb.00745-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/25/2019] [Indexed: 12/19/2022] Open
Abstract
The Gram-negative outer membrane (OM) is a selectively permeable asymmetric bilayer that allows vital nutrients to diffuse into the cell but prevents toxins and hydrophobic molecules from entering. Functionally and structurally diverse β-barrel outer membrane proteins (OMPs) build and maintain the permeability barrier, making the assembly of OMPs crucial for cell viability. In this work, we characterize an assembly-defective mutant of the maltoporin LamB, LamBG439D We show that the folding defect of LamBG439D results in an accumulation of unfolded substrate that is toxic to the cell when the periplasmic protease DegP is removed. Selection for suppressors of this toxicity identified the novel mutant degSA323E allele. The mutant DegSA323E protein contains an amino acid substitution at the PDZ/protease domain interface that results in a partially activated conformation of this protein. This activation increases basal levels of downstream σE stress response signaling. Furthermore, the enhanced σE activity of DegSA323E suppresses a number of other assembly-defective conditions without exhibiting the toxicity associated with high levels of σE activity. We propose that the increased basal levels of σE signaling primes the cell to respond to envelope stress before OMP assembly defects threaten cell viability. This finding addresses the importance of envelope stress responses in monitoring the OMP assembly process and underpins the critical balance between envelope defects and stress response activation.IMPORTANCE Gram-negative bacteria, such as Escherichia coli, inhabit a natural environment that is prone to flux. In order to cope with shifting growth conditions and the changing availability of nutrients, cells must be capable of quickly responding to stress. Stress response pathways allow cells to rapidly shift gene expression profiles to ensure survival in this unpredictable environment. Here we describe a mutant that partially activates the σE stress response pathway. The elevated basal level of this stress response allows the cell to quickly respond to overwhelming stress to ensure cell survival.
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Affiliation(s)
- Elizabeth M Hart
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Aileen O'Connell
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Kimberly Tang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Joseph S Wzorek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- Novartis Institute for BioMedical Research, Inc., Cambridge, Massachusetts, USA
| | - Marcin Grabowicz
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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5
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Cabrera AC, Melo E, Roth D, Topp A, Delobel F, Stucki C, Chen CY, Jakob P, Banfai B, Dunkley T, Schilling O, Huber S, Iacone R, Petrone P. HtrA1 activation is driven by an allosteric mechanism of inter-monomer communication. Sci Rep 2017; 7:14804. [PMID: 29093542 PMCID: PMC5666011 DOI: 10.1038/s41598-017-14208-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/04/2017] [Indexed: 11/26/2022] Open
Abstract
The human protease family HtrA is responsible for preventing protein misfolding and mislocalization, and a key player in several cellular processes. Among these, HtrA1 is implicated in several cancers, cerebrovascular disease and age-related macular degeneration. Currently, HtrA1 activation is not fully characterized and relevant for drug-targeting this protease. Our work provides a mechanistic step-by-step description of HtrA1 activation and regulation. We report that the HtrA1 trimer is regulated by an allosteric mechanism by which monomers relay the activation signal to each other, in a PDZ-domain independent fashion. Notably, we show that inhibitor binding is precluded if HtrA1 monomers cannot communicate with each other. Our study establishes how HtrA1 trimerization plays a fundamental role in proteolytic activity. Moreover, it offers a structural explanation for HtrA1-defective pathologies as well as mechanistic insights into the degradation of complex extracellular fibrils such as tubulin, amyloid beta and tau that belong to the repertoire of HtrA1.
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Affiliation(s)
- Alvaro Cortes Cabrera
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Esther Melo
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Doris Roth
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Andreas Topp
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Frederic Delobel
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Corinne Stucki
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Chia-Yi Chen
- Institute of Molecular Medicine and Cell Research, University of Freiburg, 79104, Freiburg, Germany
| | - Peter Jakob
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Balazs Banfai
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
- Soladis GmbH, 4052, Basel, Switzerland
| | - Tom Dunkley
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104, Freiburg, Germany
| | - Sylwia Huber
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Roberto Iacone
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Paula Petrone
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland.
- Barcelonabeta Brain Research Center, Fundacion Pascual Maragall. Carrer de Wellington, 30, 08005, Barcelona, Spain.
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6
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Lu C, Stock G, Knecht V. Mechanisms for allosteric activation of protease DegS by ligand binding and oligomerization as revealed from molecular dynamics simulations. Proteins 2016; 84:1690-1705. [PMID: 27556733 DOI: 10.1002/prot.25154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/03/2016] [Accepted: 08/08/2016] [Indexed: 12/18/2022]
Abstract
A local perturbation of a protein may lead to functional changes at some distal site, a phenomenon denoted as allostery. Here, we study the allosteric control of a protease using molecular dynamics simulations. The system considered is the bacterial protein DegS which includes a protease domain activated on ligand binding to an adjacent PDZ domain. Starting from crystallographic structures of DegS homo-trimers, we perform simulations of the ligand-free and -bound state of DegS at equilibrium. Considering a single protomer only, the trimeric state was mimicked by applying restraints on the residues in contact with other protomers in the DegS trimer. In addition, the bound state was also simulated without any restraints to mimic the monomer. Our results suggest that not only ligand release but also disassembly of a DegS trimer inhibits proteolytic activity. Considering various observables for structural changes, we infer allosteric pathways from the interface with other protomers to the active site. Moreover, we study how ligand release leads to (i) catalytically relevant changes involving residues 199-201 and (ii) a transition from a stretched to a bent conformation for residues 217-219 (which prohibits proper substrate binding). Finally, based on ligand-induced Cα shifts we identify residues in contact with other protomers in the DegS trimer that likely transduce the perturbation from ligand release from a given protomer to adjacent protomers. These residues likely play a key role in the experimentally known effect of ligand release from a protomer on the proteolytic activity of the other protomers. Proteins 2016; 84:1690-1705. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Cheng Lu
- Biomolecular Dynamics Group, Institute of Physics, Albert Ludwigs University, Hermann-Herder-Str. 3, Freiburg, 79104, Germany
| | - Gerhard Stock
- Biomolecular Dynamics Group, Institute of Physics, Albert Ludwigs University, Hermann-Herder-Str. 3, Freiburg, 79104, Germany
| | - Volker Knecht
- Biomolecular Dynamics Group, Institute of Physics, Albert Ludwigs University, Hermann-Herder-Str. 3, Freiburg, 79104, Germany.
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7
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Hershey DM, Browne PJ, Iavarone AT, Teyra J, Lee EH, Sidhu SS, Komeili A. Magnetite Biomineralization in Magnetospirillum magneticum Is Regulated by a Switch-like Behavior in the HtrA Protease MamE. J Biol Chem 2016; 291:17941-52. [PMID: 27302060 DOI: 10.1074/jbc.m116.731000] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 11/06/2022] Open
Abstract
Magnetotactic bacteria are aquatic organisms that produce subcellular magnetic particles in order to orient in the earth's geomagnetic field. MamE, a predicted HtrA protease required to produce magnetite crystals in the magnetotactic bacterium Magnetospirillum magneticum AMB-1, was recently shown to promote the proteolytic processing of itself and two other biomineralization factors in vivo Here, we have analyzed the in vivo processing patterns of three proteolytic targets and used this information to reconstitute proteolysis with a purified form of MamE. MamE cleaves a custom peptide substrate with positive cooperativity, and its autoproteolysis can be stimulated with exogenous substrates or peptides that bind to either of its PDZ domains. A misregulated form of the protease that circumvents specific genetic requirements for proteolysis causes biomineralization defects, showing that proper regulation of its activity is required during magnetite biosynthesis in vivo Our results represent the first reconstitution of the proteolytic activity of MamE and show that its behavior is consistent with the previously proposed checkpoint model for biomineralization.
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Affiliation(s)
| | | | - Anthony T Iavarone
- the California Institute for Quantitative Biosciences, and the QB3/Chemistry Mass Spectrometry Facility, and the University of California, Berkeley, California 94720 and
| | - Joan Teyra
- the Department of Molecular Genetics, Terrance Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | | | - Sachdev S Sidhu
- the Department of Molecular Genetics, Terrance Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Arash Komeili
- From the Departments of Plant and Microbial Biology and the California Institute for Quantitative Biosciences, and Molecular and Cell Biology,
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8
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Jarzab M, Wenta T, Zurawa-Janicka D, Polit A, Gieldon AJ, Wysocka M, Glaza P, Skorko-Glonek J, Ciarkowski J, Lesner A, Lipinska B. Intra- and intersubunit changes accompanying thermal activation of the HtrA2(Omi) protease homotrimer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:283-296. [PMID: 26702898 DOI: 10.1016/j.bbapap.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/26/2015] [Accepted: 12/14/2015] [Indexed: 01/16/2023]
Abstract
HtrA2(Omi) protease is involved in the maintenance of mitochondrial homeostasis and stimulation of apoptosis as well as in development of cancer and neurodegenerative disorders. The protein is a homotrimer whose subunits comprise serine protease domain (PD) and PDZ regulatory domain. In the basal, inactive state, a tight interdomain interface limits access both to the PDZ peptide (carboxylate) binding site and to the PD catalytic center. The molecular mechanism of activation is not well understood. To further the knowledge of HtrA2 thermal activation we monitored the dynamics of the PDZ-PD interactions during temperature increase using tryptophan-induced quenching (TrIQ) method. The TrIQ results suggested that during activation the PDZ domain changed its position versus PD inside a subunit, including a prominent change affecting the L3 regulatory loop of PD, and also changed its interactions with the PD of the adjacent subunit (PD*), specifically with its L1* regulatory loop containing the active site serine. The α5 helix of PDZ was involved in both, the intra- and intersubunit changes of interactions and thus seems to play an important role in HtrA2 activation. The amino acid substitutions designed to decrease the PDZ interactions with the PD or PD* promoted protease activity at a wide range of temperatures, which supports the conclusions based on the TrIQ analysis. The model presented in this work describes PDZ movement in relation to PD and PD*, resulting in an increased access to the peptide binding and active sites, and conformational changes of the L3 and L1* loops.
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Affiliation(s)
- Miroslaw Jarzab
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Tomasz Wenta
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dorota Zurawa-Janicka
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Agnieszka Polit
- Department of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Artur J Gieldon
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Magdalena Wysocka
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Przemyslaw Glaza
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Joanna Skorko-Glonek
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jerzy Ciarkowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Barbara Lipinska
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
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9
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Using total internal reflection fluorescence microscopy to visualize rhodopsin-containing cells. Appl Environ Microbiol 2015; 81:3442-50. [PMID: 25769822 DOI: 10.1128/aem.00230-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/04/2015] [Indexed: 01/03/2023] Open
Abstract
Sunlight is captured and converted to chemical energy in illuminated environments. Although (bacterio)chlorophyll-based photosystems have been characterized in detail, retinal-based photosystems, rhodopsins, have only recently been identified as important mediators of light energy capture and conversion. Recent estimates suggest that up to 70% of cells in some environments harbor rhodopsins. However, because rhodopsin autofluorescence is low-comparable to that of carotenoids and significantly less than that of (bacterio)chlorophylls-these estimates are based on metagenomic sequence data, not direct observation. We report here the use of ultrasensitive total internal reflection fluorescence (TIRF) microscopy to distinguish between unpigmented, carotenoid-producing, and rhodopsin-expressing bacteria. Escherichia coli cells were engineered to produce lycopene, β-carotene, or retinal. A gene encoding an uncharacterized rhodopsin, actinorhodopsin, was cloned into retinal-producing E. coli. The production of correctly folded and membrane-incorporated actinorhodopsin was confirmed via development of pink color in E. coli and SDS-PAGE. Cells expressing carotenoids or actinorhodopsin were imaged by TIRF microscopy. The 561-nm excitation laser specifically illuminated rhodopsin-containing cells, allowing them to be differentiated from unpigmented and carotenoid-containing cells. Furthermore, water samples collected from the Delaware River were shown by PCR to have rhodopsin-containing organisms and were examined by TIRF microscopy. Individual microorganisms that fluoresced under illumination from the 561-nm laser were identified. These results verify the sensitivity of the TIRF microscopy method for visualizing and distinguishing between different molecules with low autofluorescence, making it useful for analyzing natural samples.
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10
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Steric clashes with bound OMP peptides activate the DegS stress-response protease. Proc Natl Acad Sci U S A 2015; 112:3326-31. [PMID: 25733864 DOI: 10.1073/pnas.1502372112] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Escherichia coli senses envelope stress using a signaling cascade initiated when DegS cleaves a transmembrane inhibitor of a transcriptional activator for response genes. Each subunit of the DegS trimer contains a protease domain and a PDZ domain. During stress, unassembled outer-membrane proteins (OMPs) accumulate in the periplasm and their C-terminal peptides activate DegS by binding to its PDZ domains. In the absence of stress, autoinhibitory interactions, mediated by the L3 loop, stabilize inactive DegS, but it is not known how this autoinhibition is reversed during activation. Here, we show that OMP peptides initiate a steric clash between the PDZ domain and the L3 loop that results in a structural rearrangement of the loop and breaking of autoinhibitory interactions. Many different L3-loop sequences are compatible with activation but those that relieve the steric clash reduce OMP activation dramatically. Our results provide a compelling molecular mechanism for allosteric activation of DegS by OMP-peptide binding.
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11
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de Regt AK, Kim S, Sohn J, Grant RA, Baker TA, Sauer RT. A conserved activation cluster is required for allosteric communication in HtrA-family proteases. Structure 2015; 23:517-526. [PMID: 25703375 DOI: 10.1016/j.str.2015.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 12/16/2022]
Abstract
In E. coli, outer-membrane stress causes a transcriptional response through a signaling cascade initiated by DegS cleavage of a transmembrane antisigma factor. Each subunit of DegS, an HtrA-family protease, contains a protease domain and a PDZ domain. The trimeric protease domain is autoinhibited by the unliganded PDZ domains. Allosteric activation requires binding of unassembled outer-membrane proteins (OMPs) to the PDZ domains and protein substrate binding. Here, we identify a set of DegS residues that cluster together at subunit-subunit interfaces in the trimer, link the active sites and substrate binding sites, and are crucial for stabilizing the active enzyme conformation in response to OMP signaling. These residues are conserved across the HtrA-protease family, including orthologs linked to human disease, supporting a common mechanism of allosteric activation. Indeed, mutation of residues at homologous positions in the DegP quality-control protease also eliminates allosteric activation.
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Affiliation(s)
- Anna K de Regt
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Seokhee Kim
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Jungsan Sohn
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA.
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Ascenzi P, Gianni S. Functional role of transient conformations: Rediscovering “chronosteric effects” thirty years later. IUBMB Life 2013; 65:836-44. [DOI: 10.1002/iub.1208] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/22/2013] [Accepted: 08/19/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy; University Roma Tre; I-00146 Roma Italy
| | - Stefano Gianni
- Department of Biochemical Sciences “Alessandro Rossi Fanelli,”; La Sapienza University; I-00185 Roma Italy
- Department of Chemistry; University of Cambridge; Lensfield Road, Cambridge CB2 1EW United Kingdom
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Chaganti LK, Kuppili RR, Bose K. Intricate structural coordination and domain plasticity regulate activity of serine protease HtrA2. FASEB J 2013; 27:3054-66. [DOI: 10.1096/fj.13-227256] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Lalith K. Chaganti
- Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC)Tata Memorial CentreNavi MumbaiIndia
| | - Raja Reddy Kuppili
- Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC)Tata Memorial CentreNavi MumbaiIndia
| | - Kakoli Bose
- Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC)Tata Memorial CentreNavi MumbaiIndia
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