1
|
Cooney I, Schubert HL, Cedeno K, Fisher ON, Carson R, Price JC, Hill CP, Shen PS. Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway. Nat Commun 2024; 15:7505. [PMID: 39209885 PMCID: PMC11362554 DOI: 10.1038/s41467-024-51835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase motor domains, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of native structures of Cdc48 affinity purified from budding yeast lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data uncover elements of Shp1-Cdc48 interactions and support a 'hand-over-hand' mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by the D2 motor in substrate translocation/unfolding.
Collapse
Affiliation(s)
- Ian Cooney
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Karina Cedeno
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Olivia N Fisher
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Richard Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
| | - Peter S Shen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
2
|
Zhan J, Zeher A, Huang R, Tang WK, Jenkins LM, Xia D. Conformations of Bcs1L undergoing ATP hydrolysis suggest a concerted translocation mechanism for folded iron-sulfur protein substrate. Nat Commun 2024; 15:4655. [PMID: 38821922 PMCID: PMC11143374 DOI: 10.1038/s41467-024-49029-y] [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: 10/10/2023] [Accepted: 05/20/2024] [Indexed: 06/02/2024] Open
Abstract
The human AAA-ATPase Bcs1L translocates the fully assembled Rieske iron-sulfur protein (ISP) precursor across the mitochondrial inner membrane, enabling respiratory Complex III assembly. Exactly how the folded substrate is bound to and released from Bcs1L has been unclear, and there has been ongoing debate as to whether subunits of Bcs1L act in sequence or in unison hydrolyzing ATP when moving the protein cargo. Here, we captured Bcs1L conformations by cryo-EM during active ATP hydrolysis in the presence or absence of ISP substrate. In contrast to the threading mechanism widely employed by AAA proteins in substrate translocation, subunits of Bcs1L alternate uniformly between ATP and ADP conformations without detectable intermediates that have different, co-existing nucleotide states, indicating that the subunits act in concert. We further show that the ISP can be trapped by Bcs1 when its subunits are all in the ADP-bound state, which we propose to be released in the apo form.
Collapse
Affiliation(s)
- Jingyu Zhan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Allison Zeher
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- NIH Intramural Cryo-EM Consortium (NICE), Bethesda, MD, USA
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- NIH Intramural Cryo-EM Consortium (NICE), Bethesda, MD, USA
| | - Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
3
|
Waters ER, Bezanilla M, Vierling E. ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages. PLANT & CELL PHYSIOLOGY 2024; 65:493-502. [PMID: 37859594 DOI: 10.1093/pcp/pcad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
ATPase family AAA domain-containing 3 (ATAD3) proteins are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent in Fungi and Amoebozoa. These ∼600-amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal ATPases Associated with a variety of cellular Activities (AAA+) matrix domain and an ATAD3_N domain, which is located primarily in the inner membrane space but potentially extends to the cytosol to interact with the ER. Sequence and structural alignments indicate that ATAD3 proteins are most similar to classic chaperone unfoldases in the AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here, we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants and the challenges in determining their essential roles in mitochondria.
Collapse
Affiliation(s)
- Elizabeth R Waters
- Department of Biology, San Diego State University, 5500 Campanille Dr., San Diego, CA 92182, USA
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, 78 College St., Hanover, NH 03755, USA
| | - Elizabeth Vierling
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003, USA
| |
Collapse
|
4
|
Silberberg JM, Ketter S, Böhm PJN, Jordan K, Wittenberg M, Grass J, Hänelt I. KdpD is a tandem serine histidine kinase that controls K + pump KdpFABC transcriptionally and post-translationally. Nat Commun 2024; 15:3223. [PMID: 38622146 PMCID: PMC11018627 DOI: 10.1038/s41467-024-47526-8] [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: 12/19/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Two-component systems, consisting of a histidine kinase and a response regulator, serve signal transduction in bacteria, often regulating transcription in response to environmental stimuli. Here, we identify a tandem serine histidine kinase function for KdpD, previously described as a histidine kinase of the KdpDE two-component system, which controls production of the potassium pump KdpFABC. We show that KdpD additionally mediates an inhibitory serine phosphorylation of KdpFABC at high potassium levels, using not its C-terminal histidine kinase domain but an N-terminal atypical serine kinase domain. Sequence analysis of KdpDs from different species highlights that some KdpDs are much shorter than others. We show that, while Escherichia coli KdpD's atypical serine kinase domain responds directly to potassium levels, a shorter version from Deinococcus geothermalis is controlled by second messenger cyclic di-AMP. Our findings add to the growing functional diversity of sensor kinases while simultaneously expanding the framework for regulatory mechanisms in bacterial potassium homeostasis.
Collapse
Affiliation(s)
- Jakob M Silberberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Sophie Ketter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Paul J N Böhm
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Kristin Jordan
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Marcel Wittenberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Julia Grass
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany.
| |
Collapse
|
5
|
Cho C, Ganser C, Uchihashi T, Kato K, Song JJ. Structure of the human ATAD2 AAA+ histone chaperone reveals mechanism of regulation and inter-subunit communication. Commun Biol 2023; 6:993. [PMID: 37770645 PMCID: PMC10539301 DOI: 10.1038/s42003-023-05373-1] [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: 01/18/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
ATAD2 is a non-canonical ATP-dependent histone chaperone and a major cancer target. Despite widespread efforts to design drugs targeting the ATAD2 bromodomain, little is known about the overall structural organization and regulation of ATAD2. Here, we present the 3.1 Å cryo-EM structure of human ATAD2 in the ATP state, showing a shallow hexameric spiral that binds a peptide substrate at the central pore. The spiral conformation is locked by an N-terminal linker domain (LD) that wedges between the seam subunits, thus limiting ATP-dependent symmetry breaking of the AAA+ ring. In contrast, structures of the ATAD2-histone H3/H4 complex show the LD undocked from the seam, suggesting that H3/H4 binding unlocks the AAA+ spiral by allosterically releasing the LD. These findings, together with the discovery of an inter-subunit signaling mechanism, reveal a unique regulatory mechanism for ATAD2 and lay the foundation for developing new ATAD2 inhibitors.
Collapse
Affiliation(s)
- Carol Cho
- Department of Biological Sciences, KAIST Stem Cell Center, Basic Science 4.0 Institute, and KI for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
| | - Christian Ganser
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Department of Physics and Institute for Glyco-core Research (iGCORE), Nagoya University, Chikusa-ku, Furo-cho, Nagoya, Aichi, 464-8602, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Ji-Joon Song
- Department of Biological Sciences, KAIST Stem Cell Center, Basic Science 4.0 Institute, and KI for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
Collapse
Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
8
|
Wu D, Liu Y, Dai Y, Wang G, Lu G, Chen Y, Li N, Lin J, Gao N. Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization. PLoS Biol 2023; 21:e3001987. [PMID: 36745679 PMCID: PMC9934407 DOI: 10.1371/journal.pbio.3001987] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 02/16/2023] [Accepted: 01/04/2023] [Indexed: 02/07/2023] Open
Abstract
The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of-function CLPB mutations are associated with a few human diseases with neutropenia and neurological disorders. Unlike canonical AAA+ proteins, CLPB contains a unique ankyrin repeat domain (ANK) at its N-terminus. How CLPB functions as a disaggregase and the role of its ANK domain are currently unclear. Herein, we report a comprehensive structural characterization of human CLPB in both the apo- and substrate-bound states. CLPB assembles into homo-tetradecamers in apo-state and is remodeled into homo-dodecamers upon substrate binding. Conserved pore-loops (PLs) on the ATPase domains form a spiral staircase to grip and translocate the substrate in a step-size of 2 amino acid residues. The ANK domain is not only responsible for maintaining the higher-order assembly but also essential for the disaggregase activity. Interactome analysis suggests that the ANK domain may directly interact with a variety of mitochondrial substrates. These results reveal unique properties of CLPB as a general disaggregase in mitochondria and highlight its potential as a target for the treatment of various mitochondria-related diseases.
Collapse
Affiliation(s)
- Damu Wu
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Yan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuhao Dai
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Academy of Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Guopeng Wang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Guoliang Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yan Chen
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- * E-mail: (JL); (NG)
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
- National Biomedical Imaging Center, Peking University, Beijing, China
- * E-mail: (JL); (NG)
| |
Collapse
|
9
|
Kocaman S, Lo YH, Krahn JM, Sobhany M, Dandey VP, Petrovich ML, Etigunta SK, Williams JG, Deterding LJ, Borgnia MJ, Stanley RE. Communication network within the essential AAA-ATPase Rix7 drives ribosome assembly. PNAS NEXUS 2022; 1:pgac118. [PMID: 36090660 PMCID: PMC9437592 DOI: 10.1093/pnasnexus/pgac118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/08/2022] [Indexed: 02/06/2023]
Abstract
Rix7 is an essential AAA+ ATPase that functions during the early stages of ribosome biogenesis. Rix7 is composed of three domains including an N-terminal domain (NTD) and two AAA+ domains (D1 and D2) that assemble into an asymmetric stacked hexamer. It was recently established that Rix7 is a presumed protein translocase that removes substrates from preribosomes by translocating them through its central pore. However, how the different domains of Rix7 coordinate their activities within the overall hexameric structure was unknown. We captured cryo-electron microscopy (EM) structures of single and double Walker B variants of full length Rix7. The disordered NTD was not visible in the cryo-EM reconstructions, but cross-linking mass spectrometry revealed that the NTD can associate with the central channel in vitro. Deletion of the disordered NTD enabled us to obtain a structure of the Rix7 hexamer to 2.9 Å resolution, providing high resolution details of critical motifs involved in substrate translocation and interdomain communication. This structure coupled with cell-based assays established that the linker connecting the D1 and D2 domains as well as the pore loops lining the central channel are essential for formation of the large ribosomal subunit. Together, our work shows that Rix7 utilizes a complex communication network to drive ribosome biogenesis.
Collapse
Affiliation(s)
- Seda Kocaman
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Yu-Hua Lo
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mack Sobhany
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Venkata P Dandey
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Matthew L Petrovich
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Suhas K Etigunta
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jason G Williams
- Department of Health and Human Services, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Leesa J Deterding
- Department of Health and Human Services, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| |
Collapse
|
10
|
Prattes M, Grishkovskaya I, Hodirnau VV, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nat Struct Mol Biol 2022; 29:942-953. [PMID: 36097293 PMCID: PMC9507969 DOI: 10.1038/s41594-022-00832-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 08/03/2022] [Indexed: 11/23/2022]
Abstract
The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.
Collapse
Affiliation(s)
- Michael Prattes
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | | | | | - Gertrude Zisser
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Carolin Sailer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Vasileios Kargas
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Mathias Loibl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Lisa Kofler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Alan J Warren
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Florian Stengel
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
| | - Helmut Bergler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
- Field of Excellence BioHealth - University of Graz, Graz, Austria.
| |
Collapse
|
11
|
Judy RM, Sheedy CJ, Gardner BM. Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis. Cells 2022; 11:2067. [PMID: 35805150 PMCID: PMC9265785 DOI: 10.3390/cells11132067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 02/01/2023] Open
Abstract
The AAA-ATPases Pex1 and Pex6 are required for the formation and maintenance of peroxisomes, membrane-bound organelles that harbor enzymes for specialized metabolism. Together, Pex1 and Pex6 form a heterohexameric AAA-ATPase capable of unfolding substrate proteins via processive threading through a central pore. Here, we review the proposed roles for Pex1/Pex6 in peroxisome biogenesis and degradation, discussing how the unfolding of potential substrates contributes to peroxisome homeostasis. We also consider how advances in cryo-EM, computational structure prediction, and mechanisms of related ATPases are improving our understanding of how Pex1/Pex6 converts ATP hydrolysis into mechanical force. Since mutations in PEX1 and PEX6 cause the majority of known cases of peroxisome biogenesis disorders such as Zellweger syndrome, insights into Pex1/Pex6 structure and function are important for understanding peroxisomes in human health and disease.
Collapse
Affiliation(s)
| | | | - Brooke M. Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (R.M.J.); (C.J.S.)
| |
Collapse
|
12
|
Abstract
The p97 AAA+ATPase is an essential and abundant regulator of protein homeostasis that plays a central role in unfolding ubiquitylated substrates. Here we report two cryo-EM structures of human p97 in complex with its p47 adaptor. One of the conformations is six-fold symmetric, corresponds to previously reported structures of p97, and lacks bound substrate. The other structure adopts a helical conformation, displays substrate running in an extended conformation through the pore of the p97 hexamer, and resembles structures reported for other AAA unfoldases. These findings support the model that p97 utilizes a "hand-over-hand" mechanism in which two residues of the substrate are translocated for hydrolysis of two ATPs, one in each of the two p97 AAA ATPase rings. Proteomics analysis supports the model that one p97 complex can bind multiple substrate adaptors or binding partners, and can process substrates with multiple types of ubiquitin modification.
Collapse
|
13
|
AAA+ protease-adaptor structures reveal altered conformations and ring specialization. Nat Struct Mol Biol 2022; 29:1068-1079. [PMID: 36329286 PMCID: PMC9663308 DOI: 10.1038/s41594-022-00850-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022]
Abstract
ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here we present high-resolution cryo-EM structures of Escherichia coli ClpAPS complexes, showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze the protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated, tucked away from the channel and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies show additional structures and functions for key AAA+ elements. Pore-loop tucking may be used broadly by AAA+ unfoldases, for example, during enzyme pausing/unloading.
Collapse
|
14
|
Khan YA, White KI, Brunger AT. The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines. Crit Rev Biochem Mol Biol 2021; 57:156-187. [PMID: 34632886 DOI: 10.1080/10409238.2021.1979460] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.
Collapse
Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| |
Collapse
|
15
|
Prattes M, Grishkovskaya I, Hodirnau VV, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nat Commun 2021; 12:3483. [PMID: 34108481 PMCID: PMC8190095 DOI: 10.1038/s41467-021-23854-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/20/2021] [Indexed: 02/01/2023] Open
Abstract
The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2'-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.
Collapse
Affiliation(s)
- Michael Prattes
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | | | - Ingrid Rössler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Isabella Klein
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Gertrude Zisser
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
| | - Helmut Bergler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
- Field of Excellence BioHealth - University of Graz, Graz, Austria.
| |
Collapse
|
16
|
Creekmore BC, Chang YW, Lee EB. The Cryo-EM Effect: Structural Biology of Neurodegenerative Disease Proteostasis Factors. J Neuropathol Exp Neurol 2021; 80:494-513. [PMID: 33860329 PMCID: PMC8177850 DOI: 10.1093/jnen/nlab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases are characterized by the accumulation of misfolded proteins. This protein aggregation suggests that abnormal proteostasis contributes to aging-related neurodegeneration. A better fundamental understanding of proteins that regulate proteostasis may provide insight into the pathophysiology of neurodegenerative disease and may perhaps reveal novel therapeutic opportunities. The 26S proteasome is the key effector of the ubiquitin-proteasome system responsible for degrading polyubiquitinated proteins. However, additional factors, such as valosin-containing protein (VCP/p97/Cdc48) and C9orf72, play a role in regulation and trafficking of substrates through the normal proteostasis systems of a cell. Nonhuman AAA+ ATPases, such as the disaggregase Hsp104, also provide insights into the biochemical processes that regulate protein aggregation. X-ray crystallography and cryo-electron microscopy (cryo-EM) structures not bound to substrate have provided meaningful information about the 26S proteasome, VCP, and Hsp104. However, recent cryo-EM structures bound to substrate have provided new information about the function and mechanism of these proteostasis factors. Cryo-EM and cryo-electron tomography data combined with biochemical data have also increased the understanding of C9orf72 and its role in maintaining proteostasis. These structural insights provide a foundation for understanding proteostasis mechanisms with near-atomic resolution upon which insights can be gleaned regarding the pathophysiology of neurodegenerative diseases.
Collapse
Affiliation(s)
- Benjamin C Creekmore
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yi-Wei Chang
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
17
|
Sobhany M, Stanley RE. Polysome Profiling without Gradient Makers or Fractionation Systems. J Vis Exp 2021. [PMID: 34152326 DOI: 10.3791/62680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Polysome fractionation by sucrose density gradient centrifugation is a powerful tool that can be used to create ribosome profiles, identify specific mRNAs being translated by ribosomes, and analyze polysome associated factors. While automated gradient makers and gradient fractionation systems are commonly used with this technique, these systems are generally expensive and can be cost-prohibitive for laboratories that have limited resources or cannot justify the expense due to their infrequent or occasional need to perform this method for their research. Here, a protocol is presented to reproducibly generate polysome profiles using standard equipment available in most molecular biology laboratories without specialized fractionation instruments. Moreover, a comparison of polysome profiles generated with and without a gradient fractionation system is provided. Strategies to optimize and produce reproducible polysome profiles are discussed. Saccharomyces cerevisiae is utilized as a model organism in this protocol. However, this protocol can be easily modified and adapted to generate ribosome profiles for many different organisms and cell types.
Collapse
Affiliation(s)
- Mack Sobhany
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health;
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health;
| |
Collapse
|
18
|
Frazier MN, Pillon MC, Kocaman S, Gordon J, Stanley RE. Structural overview of macromolecular machines involved in ribosome biogenesis. Curr Opin Struct Biol 2021; 67:51-60. [PMID: 33099228 PMCID: PMC8058114 DOI: 10.1016/j.sbi.2020.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022]
Abstract
The production of ribosomes is essential for ensuring the translational capacity of cells. Because of its high energy demand ribosome production is subject to stringent cellular controls. Hundreds of ribosome assembly factors are required to facilitate assembly of nascent ribosome particles with high fidelity. Many ribosome assembly factors organize into macromolecular machines that drive complex steps of the production pathway. Recent advances in structural biology, in particular cryo-EM, have provided detailed information about the structure and function of these higher order enzymatic assemblies. Here, we summarize recent structures revealing molecular insight into these macromolecular machines with an emphasis on the interplay between discrete active sites.
Collapse
Affiliation(s)
- Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Seda Kocaman
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jacob Gordon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
19
|
Glynn SE, Kardon JR, Mueller-Cajar O, Cho C. AAA+ proteins: converging mechanisms, diverging functions. Nat Struct Mol Biol 2020; 27:515-518. [PMID: 32461632 DOI: 10.1038/s41594-020-0444-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Steven E Glynn
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.
| | - Julia R Kardon
- Department of Biochemistry, Brandeis University, Waltham, MA, USA.
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Carol Cho
- Research Center for Natural Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
| |
Collapse
|
20
|
Xia D. Structural snapshots of the cellular folded protein translocation machinery Bcs1. FEBS J 2020; 288:2870-2883. [PMID: 32979284 PMCID: PMC7994207 DOI: 10.1111/febs.15576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/05/2020] [Accepted: 09/22/2020] [Indexed: 11/29/2022]
Abstract
Proteins destined to various intra‐ and extra‐cellular locations must traverse membranes most frequently in an unfolded form. When the proteins being translocated need to remain in a folded state, specialized cellular transport machinery is used. One such machine is the membrane‐bound AAA protein Bcs1 (Bcs1), which assists the iron‐sulfur protein, an essential subunit of the respiratory Complex III, across the mitochondrial inner membrane. Recent structure determinations of mouse and yeast Bcs1 in three different nucleotide states reveal its homo‐heptameric association and at least two dramatically different conformations. The apo and ADP‐bound structures are similar, both containing a large substrate‐binding cavity accessible to the mitochondrial matrix space, which contracts by concerted motion of the ATPase domains upon ATP binding, suggesting that bound substrate could then be pushed across the membrane. ATP hydrolysis drives substrate release and resets Bcs1 conformation back to the apo/ADP form. These structures shed new light on the mechanism of folded protein translocation across a membrane, provide better understanding on the assembly process of the respiratory Complex III, and correlate clinical presentations of disease‐associated mutations with their locations in the 3D structure.
Collapse
Affiliation(s)
- Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
21
|
Urae S, Harita Y, Udagawa T, Ode KL, Nagahama M, Kajiho Y, Kanda S, Saito A, Ueda HR, Nangaku M, Oka A. A cellular model of albumin endocytosis uncovers a link between membrane and nuclear proteins. J Cell Sci 2020; 133:jcs242859. [PMID: 32482797 DOI: 10.1242/jcs.242859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/20/2020] [Indexed: 12/21/2022] Open
Abstract
Cubilin (CUBN) and amnionless (AMN), expressed in kidney and intestine, form a multiligand receptor complex called CUBAM that plays a crucial role in albumin absorption. To date, the mechanism of albumin endocytosis mediated by CUBAM remains to be elucidated. Here, we describe a quantitative assay to evaluate albumin uptake by CUBAM using cells expressing full-length CUBN and elucidate the crucial roles of the C-terminal part of CUBN and the endocytosis signal motifs of AMN in albumin endocytosis. We also demonstrate that nuclear valosin-containing protein-like 2 (NVL2), an interacting protein of AMN, is involved in this process. Although NVL2 was mainly localized in the nucleolus in cells without AMN expression, it was translocated to the extranuclear compartment when coexpressed with AMN. NVL2 knockdown significantly impaired internalization of the CUBN-albumin complex in cultured cells, demonstrating an involvement of NVL2 in endocytic regulation. These findings uncover a link between membrane and nucleolar proteins that is involved in endocytic processes.
Collapse
Affiliation(s)
- Seiya Urae
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
- Division of Nephrology and Endocrinology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yutaka Harita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Tomohiro Udagawa
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Masami Nagahama
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose-shi, Tokyo 204-8588, Japan
| | - Yuko Kajiho
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Shoichiro Kanda
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Akihiko Saito
- Department of Applied Molecular Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata-shi, Niigata 951-8510, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Wako-shi, Saitama 351-0198, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| |
Collapse
|
22
|
A spiral path to unfolding. Nat Struct Mol Biol 2020; 26:763-765. [PMID: 31427794 DOI: 10.1038/s41594-019-0284-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
23
|
Structures of AAA protein translocase Bcs1 suggest translocation mechanism of a folded protein. Nat Struct Mol Biol 2020; 27:202-209. [PMID: 32042153 DOI: 10.1038/s41594-020-0373-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/07/2020] [Indexed: 01/17/2023]
Abstract
The mitochondrial membrane-bound AAA protein Bcs1 translocate substrates across the mitochondrial inner membrane without previous unfolding. One substrate of Bcs1 is the iron-sulfur protein (ISP), a subunit of the respiratory Complex III. How Bcs1 translocates ISP across the membrane is unknown. Here we report structures of mouse Bcs1 in two different conformations, representing three nucleotide states. The apo and ADP-bound structures reveal a homo-heptamer and show a large putative substrate-binding cavity accessible to the matrix space. ATP binding drives a contraction of the cavity by concerted motion of the ATPase domains, which could push substrate across the membrane. Our findings shed light on the potential mechanism of translocating folded proteins across a membrane, offer insights into the assembly process of Complex III and allow mapping of human disease-associated mutations onto the Bcs1 structure.
Collapse
|
24
|
Gates SN, Martin A. Stairway to translocation: AAA+ motor structures reveal the mechanisms of ATP-dependent substrate translocation. Protein Sci 2020; 29:407-419. [PMID: 31599052 PMCID: PMC6954725 DOI: 10.1002/pro.3743] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 09/28/2019] [Accepted: 09/30/2019] [Indexed: 12/31/2022]
Abstract
Translocases of the AAA+ (ATPases Associated with various cellular Activities) family are powerful molecular machines that use the mechano-chemical coupling of ATP hydrolysis and conformational changes to thread DNA or protein substrates through their central channel for many important biological processes. These motors comprise hexameric rings of ATPase subunits, in which highly conserved nucleotide-binding domains form active-site pockets near the subunit interfaces and aromatic pore-loop residues extend into the central channel for substrate binding and mechanical pulling. Over the past 2 years, 41 cryo-EM structures have been solved for substrate-bound AAA+ translocases that revealed spiral-staircase arrangements of pore-loop residues surrounding substrate polypeptides and indicating a conserved hand-over-hand mechanism for translocation. The subunits' vertical positions within the spiral arrangements appear to be correlated with their nucleotide states, progressing from ATP-bound at the top to ADP or apo states at the bottom. Studies describing multiple conformations for a particular motor illustrate the potential coupling between ATP-hydrolysis steps and subunit movements to propel the substrate. Experiments with double-ring, Type II AAA+ motors revealed an offset of hydrolysis steps between the two ATPase domains of individual subunits, and the upper ATPase domains lacking aromatic pore loops frequently form planar rings. This review summarizes the critical advances provided by recent studies to our structural and functional understanding of hexameric AAA+ translocases, as well as the important outstanding questions regarding the underlying mechanisms for coordinated ATP-hydrolysis and mechano-chemical coupling.
Collapse
Affiliation(s)
- Stephanie N. Gates
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- California Institute for Quantitative BiosciencesUniversity of California at BerkeleyBerkeleyCalifornia
- Howard Hughes Medical InstituteUniversity of California at BerkeleyBerkeleyCalifornia
| | - Andreas Martin
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCalifornia
- California Institute for Quantitative BiosciencesUniversity of California at BerkeleyBerkeleyCalifornia
- Howard Hughes Medical InstituteUniversity of California at BerkeleyBerkeleyCalifornia
| |
Collapse
|
25
|
Wang L, Myasnikov A, Pan X, Walter P. Structure of the AAA protein Msp1 reveals mechanism of mislocalized membrane protein extraction. eLife 2020; 9:e54031. [PMID: 31999255 PMCID: PMC7018516 DOI: 10.7554/elife.54031] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/29/2020] [Indexed: 01/03/2023] Open
Abstract
The AAA protein Msp1 extracts mislocalized tail-anchored membrane proteins and targets them for degradation, thus maintaining proper cell organization. How Msp1 selects its substrates and firmly engages them during the energetically unfavorable extraction process remains a mystery. To address this question, we solved cryo-EM structures of Msp1-substrate complexes at near-atomic resolution. Akin to other AAA proteins, Msp1 forms hexameric spirals that translocate substrates through a central pore. A singular hydrophobic substrate recruitment site is exposed at the spiral's seam, which we propose positions the substrate for entry into the pore. There, a tight web of aromatic amino acids grips the substrate in a sequence-promiscuous, hydrophobic milieu. Elements at the intersubunit interfaces coordinate ATP hydrolysis with the subunits' positions in the spiral. We present a comprehensive model of Msp1's mechanism, which follows general architectural principles established for other AAA proteins yet specializes Msp1 for its unique role in membrane protein extraction.
Collapse
Affiliation(s)
- Lan Wang
- Howard Hughes Medical InstituteChevy Chase, MarylandUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Alexander Myasnikov
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Centre for Integrative Biology, Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de StrasbourgIllkirchFrance
| | - Xingjie Pan
- UCSF/UCB Graduate Program in Bioengineering, University of California, San FranciscoSan FranciscoUnited States
| | - Peter Walter
- Howard Hughes Medical InstituteChevy Chase, MarylandUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| |
Collapse
|
26
|
Shaping the Nascent Ribosome: AAA-ATPases in Eukaryotic Ribosome Biogenesis. Biomolecules 2019; 9:biom9110715. [PMID: 31703473 PMCID: PMC6920918 DOI: 10.3390/biom9110715] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 02/08/2023] Open
Abstract
AAA-ATPases are molecular engines evolutionarily optimized for the remodeling of proteins and macromolecular assemblies. Three AAA-ATPases are currently known to be involved in the remodeling of the eukaryotic ribosome, a megadalton range ribonucleoprotein complex responsible for the translation of mRNAs into proteins. The correct assembly of the ribosome is performed by a plethora of additional and transiently acting pre-ribosome maturation factors that act in a timely and spatially orchestrated manner. Minimal disorder of the assembly cascade prohibits the formation of functional ribosomes and results in defects in proliferation and growth. Rix7, Rea1, and Drg1, which are well conserved across eukaryotes, are involved in different maturation steps of pre-60S ribosomal particles. These AAA-ATPases provide energy for the efficient removal of specific assembly factors from pre-60S particles after they have fulfilled their function in the maturation cascade. Recent structural and functional insights have provided the first glimpse into the molecular mechanism of target recognition and remodeling by Rix7, Rea1, and Drg1. Here we summarize current knowledge on the AAA-ATPases involved in eukaryotic ribosome biogenesis. We highlight the latest insights into their mechanism of mechano-chemical complex remodeling driven by advanced cryo-EM structures and the use of highly specific AAA inhibitors.
Collapse
|
27
|
Gatsogiannis C, Balogh D, Merino F, Sieber SA, Raunser S. Cryo-EM structure of the ClpXP protein degradation machinery. Nat Struct Mol Biol 2019; 26:946-954. [PMID: 31582852 PMCID: PMC6783313 DOI: 10.1038/s41594-019-0304-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/19/2019] [Indexed: 12/23/2022]
Abstract
The ClpXP machinery is a two component protease complex performing
targeted protein degradation in bacteria and mitochondria. The complex consists
of the AAA+ chaperone ClpX and the peptidase ClpP. The hexameric ClpX utilizes
the energy of ATP binding and hydrolysis to engage, unfold and translocate
substrates into the catalytic chamber of tetradecameric ClpP where they are
degraded. Formation of the complex involves a symmetry mismatch, since hexameric
AAA+ rings bind axially to the opposing stacked heptameric rings of the
tetradecameric ClpP. Here we present the cryo-EM structure of ClpXP from
Listeria monocytogenes. We unravel the heptamer-hexamer
binding interface and provide novel insights into the ClpX-ClpP crosstalk and
activation mechanism. The comparison with available crystal structures of ClpP
and ClpX in different states allows us to understand important aspects of
ClpXP’s complex mode of action and provides a structural framework for
future pharmacological applications.
Collapse
Affiliation(s)
- Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dora Balogh
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany
| | - Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| |
Collapse
|
28
|
Twomey EC, Ji Z, Wales TE, Bodnar NO, Ficarro SB, Marto JA, Engen JR, Rapoport TA. Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Science 2019; 365:science.aax1033. [PMID: 31249135 DOI: 10.1126/science.aax1033] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/13/2019] [Indexed: 12/13/2022]
Abstract
The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded substrates is unclear. Here, we report cryo-electron microscopy structures of the Cdc48 ATPase in complex with Ufd1/Npl4 and polyubiquitinated substrate. The structures show that the Cdc48 complex initiates substrate processing by unfolding a ubiquitin molecule. The unfolded ubiquitin molecule binds to Npl4 and projects its N-terminal segment through both hexameric ATPase rings. Pore loops of the second ring form a staircase that acts as a conveyer belt to move the polypeptide through the central pore. Inducing the unfolding of ubiquitin allows the Cdc48 ATPase complex to process a broad range of substrates.
Collapse
Affiliation(s)
- Edward C Twomey
- Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Zhejian Ji
- Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Nicholas O Bodnar
- Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Tom A Rapoport
- Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|