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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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Bertgen L, Bökenkamp JE, Schneckmann T, Koch C, Räschle M, Storchová Z, Herrmann JM. Distinct types of intramitochondrial protein aggregates protect mitochondria against proteotoxic stress. Cell Rep 2024; 43:114018. [PMID: 38551959 DOI: 10.1016/j.celrep.2024.114018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Mitochondria consist of hundreds of proteins, most of which are inaccessible to the proteasomal quality control system of the cytosol. How cells stabilize the mitochondrial proteome during challenging conditions remains poorly understood. Here, we show that mitochondria form spatially defined protein aggregates as a stress-protecting mechanism. Two different types of intramitochondrial protein aggregates can be distinguished. The mitoribosomal protein Var1 (uS3m) undergoes a stress-induced transition from a soluble, chaperone-stabilized protein that is prevalent under benign conditions to an insoluble, aggregated form upon acute stress. The formation of Var1 bodies stabilizes mitochondrial proteostasis, presumably by sequestration of aggregation-prone proteins. The AAA chaperone Hsp78 is part of a second type of intramitochondrial aggregate that transiently sequesters proteins and promotes their folding or Pim1-mediated degradation. Thus, mitochondrial proteins actively control the formation of distinct types of intramitochondrial protein aggregates, which cooperate to stabilize the mitochondrial proteome during proteotoxic stress conditions.
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Affiliation(s)
- Lea Bertgen
- Cell Biology, University of Kaiserslautern, RPTU, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Jan-Eric Bökenkamp
- Molecular Genetics, University of Kaiserslautern, RPTU, Paul-Ehrlich-Strasse 24, 67663 Kaiserslautern, Germany
| | - Tim Schneckmann
- Cell Biology, University of Kaiserslautern, RPTU, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Christian Koch
- Cell Biology, University of Kaiserslautern, RPTU, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, RPTU, Paul-Ehrlich-Strasse 24, 67663 Kaiserslautern, Germany
| | - Zuzana Storchová
- Molecular Genetics, University of Kaiserslautern, RPTU, Paul-Ehrlich-Strasse 24, 67663 Kaiserslautern, Germany
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, RPTU, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany.
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3
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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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4
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Nitika, Zheng B, Ruan L, Kline JT, Omkar S, Sikora J, Texeira Torres M, Wang Y, Takakuwa JE, Huguet R, Klemm C, Segarra VA, Winters MJ, Pryciak PM, Thorpe PH, Tatebayashi K, Li R, Fornelli L, Truman AW. Comprehensive characterization of the Hsp70 interactome reveals novel client proteins and interactions mediated by posttranslational modifications. PLoS Biol 2022; 20:e3001839. [PMID: 36269765 PMCID: PMC9629621 DOI: 10.1371/journal.pbio.3001839] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/02/2022] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
Hsp70 interactions are critical for cellular viability and the response to stress. Previous attempts to characterize Hsp70 interactions have been limited by their transient nature and the inability of current technologies to distinguish direct versus bridged interactions. We report the novel use of cross-linking mass spectrometry (XL-MS) to comprehensively characterize the Saccharomyces cerevisiae (budding yeast) Hsp70 protein interactome. Using this approach, we have gained fundamental new insights into Hsp70 function, including definitive evidence of Hsp70 self-association as well as multipoint interaction with its client proteins. In addition to identifying a novel set of direct Hsp70 interactors that can be used to probe chaperone function in cells, we have also identified a suite of posttranslational modification (PTM)-associated Hsp70 interactions. The majority of these PTMs have not been previously reported and appear to be critical in the regulation of client protein function. These data indicate that one of the mechanisms by which PTMs contribute to protein function is by facilitating interaction with chaperones. Taken together, we propose that XL-MS analysis of chaperone complexes may be used as a unique way to identify biologically important PTMs on client proteins.
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Affiliation(s)
- Nitika
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Bo Zheng
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
| | - Jake T. Kline
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States America
| | - Siddhi Omkar
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Jacek Sikora
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois, United States America
| | - Mara Texeira Torres
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
| | - Jade E. Takakuwa
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Romain Huguet
- Thermo Scientific, San Jose, California, United States America
| | - Cinzia Klemm
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Verónica A. Segarra
- Departments of Biological Sciences and Chemistry, Goucher College, Baltimore, Maryland, United States America
| | - Matthew J. Winters
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States America
| | - Peter M. Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States America
| | - Peter H. Thorpe
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Kazuo Tatebayashi
- Laboratory of Molecular Genetics, Frontier Research Unit, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States America
| | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States America
| | - Andrew W. Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
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5
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Alzandi AA, Naguib DM. Effect of yeast application on soil health and root metabolic status of corn seedlings under drought stress. Arch Microbiol 2022; 204:233. [PMID: 35357585 DOI: 10.1007/s00203-022-02843-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/05/2022] [Accepted: 03/13/2022] [Indexed: 11/30/2022]
Abstract
The soil enzymes are the heart of the biochemical reactions that occur in the soil saving the soil nutrients needed for plant growth. Recently yeast's importance as plant growth-promoting microorganisms has great attention. This study evaluated the effect of yeast application on the soil enzymes activity and root metabolic status in corn plants under drought stress. A pot experiment was performed. The pots were divided into two groups; the first group was used for yeast application, the other group was used as a non-treated group. Each group was subdivided into two groups according to water treatment. One is 75%; the other is 45% of field capacity. Soil and root samples were taken at 5, 10, and 15 days after drought application for analysis. Soil samples were subjected to NPK and soil enzymes activity analysis. The root samples were subjected to determination NPK content, the osmolytes, lipid peroxidation, and antioxidant enzymes. The present results showed that yeast application upregulated the soil enzymes under drought which protected the NPK content in the soil. Therefore NPK in the treated group was significantly higher than that in the non-treated group. Also, yeast application improved the roots' osmotic status, the treated group showed significant osmolytes accumulation. Besides that the antioxidant enzymes activity status in the treated group was significantly higher than that in the non-treated group which significantly decreased the lipid peroxidation in the treated group. Yeast application can be an effective promising tool for improving the corn plant tolerance against drought stress.
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Affiliation(s)
- Abdulrhman Ali Alzandi
- Biology Department, Faculty of Arts and Science in Qilwah, Albaha University, Qilwah, Kingdom of Saudi Arabia
| | - Deyala M Naguib
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
- Biology Department, Faculty of Arts and Science in Qilwah, Albaha University, Qilwah, Kingdom of Saudi Arabia.
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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] [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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