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Mindrebo JT, Lander GC. Structural and mechanistic studies on human LONP1 redefine the hand-over-hand translocation mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600538. [PMID: 38979310 PMCID: PMC11230189 DOI: 10.1101/2024.06.24.600538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
AAA+ enzymes use energy from ATP hydrolysis to remodel diverse cellular targets. Structures of substrate-bound AAA+ complexes suggest that these enzymes employ a conserved hand-over-hand mechanism to thread substrates through their central pore. However, the fundamental aspects of the mechanisms governing motor function and substrate processing within specific AAA+ families remain unresolved. We used cryo-electron microscopy to structurally interrogate reaction intermediates from in vitro biochemical assays to inform the underlying regulatory mechanisms of the human mitochondrial AAA+ protease, LONP1. Our results demonstrate that substrate binding allosterically regulates proteolytic activity, and that LONP1 can adopt a configuration conducive to substrate translocation even when the ATPases are bound to ADP. These results challenge the conventional understanding of the hand-over-hand translocation mechanism, giving rise to an alternative model that aligns more closely with biochemical and biophysical data on related enzymes like ClpX, ClpA, the 26S proteasome, and Lon protease.
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Affiliation(s)
- Jeffrey T. Mindrebo
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
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2
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Li S, Hsieh KY, Kuo CI, Lin TC, Lee SH, Chen YR, Wang CH, Ho MR, Ting SY, Zhang K, Chang CI. A 5+1 assemble-to-activate mechanism of the Lon proteolytic machine. Nat Commun 2023; 14:7340. [PMID: 37957149 PMCID: PMC10643698 DOI: 10.1038/s41467-023-43035-2] [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: 09/28/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Many AAA+ (ATPases associated with diverse cellular activities) proteins function as protein or DNA remodelers by threading the substrate through the central pore of their hexameric assemblies. In this ATP-dependent translocating state, the substrate is gripped by the pore loops of the ATPase domains arranged in a universal right-handed spiral staircase organization. However, the process by which a AAA+ protein is activated to adopt this substrate-pore-loop arrangement remains unknown. We show here, using cryo-electron microscopy (cryo-EM), that the activation process of the Lon AAA+ protease may involve a pentameric assembly and a substrate-dependent incorporation of the sixth protomer to form the substrate-pore-loop contacts seen in the translocating state. Based on the structural results, we design truncated monomeric mutants that inhibit Lon activity by binding to the native pentamer and demonstrated that expressing these monomeric mutants in Escherichia coli cells containing functional Lon elicits specific phenotypes associated with lon deficiency, including the inhibition of persister cell formation. These findings uncover a substrate-dependent assembly process for the activation of a AAA+ protein and demonstrate a targeted approach to selectively inhibit its function within cells.
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Affiliation(s)
- Shanshan Li
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China.
| | - Kan-Yen Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Chiao-I Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzu-Chi Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Szu-Hui Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Ru Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - See-Yeun Ting
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kaiming Zhang
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China.
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
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Rüttermann M, Koci M, Lill P, Geladas ED, Kaschani F, Klink BU, Erdmann R, Gatsogiannis C. Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate. Nat Commun 2023; 14:5942. [PMID: 37741838 PMCID: PMC10518020 DOI: 10.1038/s41467-023-41640-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
The double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental disorders. Despite its pathophysiological importance, mechanistic details of the heterohexamer are not yet available. Here, we report cryoEM structures of Pex1/Pex6 from Saccharomyces cerevisiae, with an endogenous protein substrate trapped in the central pore of the catalytically active second ring (D2). Pairs of Pex1/Pex6(D2) subdomains engage the substrate via a staircase of pore-1 loops with distinct properties. The first ring (D1) is catalytically inactive but undergoes significant conformational changes resulting in alternate widening and narrowing of its pore. These events are fueled by ATP hydrolysis in the D2 ring and disengagement of a "twin-seam" Pex1/Pex6(D2) heterodimer from the staircase. Mechanical forces are propagated in a unique manner along Pex1/Pex6 interfaces that are not available in homo-oligomeric AAA-ATPases. Our structural analysis reveals the mechanisms of how Pex1 and Pex6 coordinate to achieve substrate translocation.
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Affiliation(s)
- Maximilian Rüttermann
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Michelle Koci
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Pascal Lill
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Ermis Dionysios Geladas
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Björn Udo Klink
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Ralf Erdmann
- Institute for Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Christos Gatsogiannis
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany.
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany.
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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4
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Structure, Substrate Specificity and Role of Lon Protease in Bacterial Pathogenesis and Survival. Int J Mol Sci 2023; 24:ijms24043422. [PMID: 36834832 PMCID: PMC9961632 DOI: 10.3390/ijms24043422] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Proteases are the group of enzymes that carry out proteolysis in all forms of life and play an essential role in cell survival. By acting on specific functional proteins, proteases affect the transcriptional and post-translational pathways in a cell. Lon, FtsH, HslVU and the Clp family are among the ATP-dependent proteases responsible for intracellular proteolysis in bacteria. In bacteria, Lon protease acts as a global regulator, governs an array of important functions such as DNA replication and repair, virulence factors, stress response and biofilm formation, among others. Moreover, Lon is involved in the regulation of bacterial metabolism and toxin-antitoxin systems. Hence, understanding the contribution and mechanisms of Lon as a global regulator in bacterial pathogenesis is crucial. In this review, we discuss the structure and substrate specificity of the bacterial Lon protease, as well as its ability to regulate bacterial pathogenesis.
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Köhrle J, Frädrich C. Deiodinases control local cellular and systemic thyroid hormone availability. Free Radic Biol Med 2022; 193:59-79. [PMID: 36206932 DOI: 10.1016/j.freeradbiomed.2022.09.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
Iodothyronine deiodinases (DIO) are a family of selenoproteins controlling systemic and local availability of the major thyroid hormone l-thyroxine (T4), a prohormone secreted by the thyroid gland. T4 is activated to the active 3,3'-5-triiodothyronine (T3) by two 5'-deiodinases, DIO1 and DIO2. DIO3, a 5-deiodinase selenoenzyme inactivates both the prohormone T4 and its active form T3. DIOs show species-specific different patterns of temporo-spatial expression, regulation and function and exhibit different mechanisms of reaction and inhibitor sensitivities. The main regulators of DIO expression and function are the thyroid hormone status, several growth factors, cytokines and altered pathophysiological conditions. Selenium (Se) status has a modest impact on DIO expression and translation. DIOs rank high in the priority of selenium supply to various selenoproteins; thus, their function is impaired only during severe selenium deficiency. DIO variants, polymorphisms, SNPs and rare mutations have been identified. Development of DIO isozyme selective drugs is ongoing. A first X-ray structure has been reported for DIO3. This review focusses on the biochemical characteristics and reaction mechanisms, the relationships between DIO selenoproteins and their importance for local and systemic provision of the active hormone T3. Nutritional, pharmacological, and environmental factors and inhibitors, such as endocrine disruptors, impact DIO functions.
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Affiliation(s)
- Josef Köhrle
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Max Rubner Center (MRC) für Kardiovaskuläre-metabolische-renale Forschung in Berlin, Institut für Experimentelle Endokrinologie, 10115, Berlin, Germany.
| | - Caroline Frädrich
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Max Rubner Center (MRC) für Kardiovaskuläre-metabolische-renale Forschung in Berlin, Institut für Experimentelle Endokrinologie, 10115, Berlin, Germany
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Kudzhaev AM, Andrianova AG, Gustchina AE, Smirnov IV, Rotanova TV. ATP-Dependent Lon Proteases in the Cellular Protein Quality Control System. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022040136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Catalytic cycling of human mitochondrial Lon protease. Structure 2022; 30:1254-1268.e7. [PMID: 35870450 DOI: 10.1016/j.str.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/21/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
Abstract
The mitochondrial Lon protease (LonP1) regulates mitochondrial health by removing redundant proteins from the mitochondrial matrix. We determined LonP1 in eight nucleotide-dependent conformational states by cryoelectron microscopy (cryo-EM). The flexible assembly of N-terminal domains had 3-fold symmetry, and its orientation depended on the conformational state. We show that a conserved structural motif around T803 with a high similarity to the trypsin catalytic triad is essential for proteolysis. We show that LonP1 is not regulated by redox potential, despite the presence of two conserved cysteines at disulfide-bonding distance in its unfoldase core. Our data indicate how sequential ATP hydrolysis controls substrate protein translocation in a 6-fold binding change mechanism. Substrate protein translocation, rather than ATP hydrolysis, is a rate-limiting step, suggesting that LonP1 is a Brownian ratchet with ATP hydrolysis preventing translocation reversal. 3-fold rocking motions of the flexible N-domain assembly may assist thermal unfolding of the substrate protein.
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8
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Wlodawer A, Sekula B, Gustchina A, Rotanova TV. Structure and the Mode of Activity of Lon Proteases from Diverse Organisms. J Mol Biol 2022; 434:167504. [PMID: 35183556 PMCID: PMC9013511 DOI: 10.1016/j.jmb.2022.167504] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/19/2022]
Abstract
Lon proteases, members of the AAA+ superfamily of enzymes, are key components of the protein quality control system in bacterial cells, as well as in the mitochondria and other specialized organelles of higher organisms. These enzymes have been subject of extensive biochemical and structural investigations, resulting in 72 crystal and solution structures, including structures of the individual domains, multi-domain constructs, and full-length proteins. However, interpretation of the latter structures still leaves some questions unanswered. Based on their amino acid sequence and details of their structure, Lon proteases can be divided into at least three subfamilies, designated as LonA, LonB, and LonC. Protomers of all Lons are single-chain polypeptides and contain two functional domains, ATPase and protease. The LonA enzymes additionally include a large N-terminal region, and different Lons may also include non-conserved inserts in the principal domains. These ATP-dependent proteases function as homohexamers, in which unfolded substrates are translocated to a large central chamber where they undergo proteolysis by a processive mechanism. X-ray crystal structures provided high-resolution models which verified that Lons are hydrolases with the rare Ser-Lys catalytic dyad. Full-length LonA enzymes have been investigated by cryo-electron microscopy (cryo-EM), providing description of the functional enzyme at different stages of the catalytic cycle, indicating extensive flexibility of their N-terminal domains, and revealing insights into the substrate translocation mechanism. Structural studies of Lon proteases provide an interesting case for symbiosis of X-ray crystallography and cryo-EM, currently the two principal techniques for determination of macromolecular structures.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA.
| | - Bartosz Sekula
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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9
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Yang J, Song AS, Wiseman RL, Lander GC. Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements. J Biol Chem 2022; 298:101694. [PMID: 35143841 PMCID: PMC8913295 DOI: 10.1016/j.jbc.2022.101694] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/26/2022] Open
Abstract
Lon protease is a conserved ATP-dependent serine protease composed of an AAA+ domain that mechanically unfolds substrates and a serine protease domain that degrades these unfolded substrates. In yeast, dysregulation of Lon protease (PIM1) attenuates lifespan and leads to gross mitochondrial morphological perturbations. Although structures of the bacterial and human Lon protease reveal a hexameric assembly, yeast PIM1 was speculated to form a heptameric assembly and is uniquely characterized by a ∼50-residue insertion between the ATPase and protease domains. To further understand the yeast-specific properties of PIM1, we determined a high-resolution cryo-electron microscopy structure of PIM1 in a substrate-translocating state. Here, we reveal that PIM1 forms a hexamer, conserved with that of bacterial and human Lon proteases, wherein the ATPase domains form a canonical closed spiral that enables pore loop residues to translocate substrates to the protease chamber. In the substrate-translocating state, PIM1 protease domains form a planar protease chamber in an active conformation and are uniquely characterized by a ∼15-residue C-terminal extension. These additional C-terminal residues form an α-helix located along the base of the protease domain. Finally, we did not observe density for the yeast-specific insertion between the ATPase and protease domains, likely due to high conformational flexibility. Biochemical studies to investigate the insertion using constructs that truncated or replaced the insertion with a glycine-serine linker suggest that the yeast-specific insertion is dispensable for PIM1's enzymatic function. Altogether, our structural and biochemical studies highlight unique components of PIM1 machinery and demonstrate evolutionary conservation of Lon protease function.
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Affiliation(s)
- Jie Yang
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, USA
| | - Albert S Song
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, USA; Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA.
| | - Gabriel C Lander
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, California, USA.
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