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Khawary M, Pandey S, Sharma O, Raunak R, Sharma M, Malik R, Tripathi D. Identification of novel inhibitors for trigger factor (TF) of M. tb: an in silico investigation. J Biomol Struct Dyn 2024; 42:4064-4071. [PMID: 37286383 DOI: 10.1080/07391102.2023.2218937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 05/21/2023] [Indexed: 06/09/2023]
Abstract
Trigger factor, as a chaperone protein, is required for survival of Mycobacterium tuberculosis (M.tb) in a stressed environment. This protein interacts with various partners in both the pre- and the post-translation processes, yet the crystal structures of the M.tb trigger factor remain unresolved. In this study, we developed a homology model of M.tb trigger factor to facilitate the discovery and design of inhibitors. To validate the model, we employed several methodologies, including Ramachandran plot and molecular dynamics simulations. The simulations showed a stable trajectory, indicating the accuracy of the model. The active site of M.tb Trigger Factor was identified based on site scores, and virtual screening of over 70,000 compounds led to the identification of two potential hits: HTS02984 (ethyl 2-(3-(4-fluorophenyl)ureido)-6-methyl-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate) and S06856 ((E)-N-(4-((2-(4-(tert-butyl)benzoyl)hydrazono)methyl)phenyl) acetamide). These compounds showed strong binding affinity and energy scores, and their chemical descriptors were evaluated. Our study provides a reliable computational model for M.tb Trigger Factor and identifies two potential inhibitors for this crucial protein, which could aid in the development of novel therapies against tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Masuma Khawary
- Microbial Pathogenesis Research Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Saurabh Pandey
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Omprakash Sharma
- Department of Pharmacy, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Raunak Raunak
- Microbial Pathogenesis Research Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Manish Sharma
- The University for Innovation, Koba Institutional Area, Gandhinagar, India
| | - Ruchi Malik
- Department of Pharmacy, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Deeksha Tripathi
- Microbial Pathogenesis Research Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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2
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Jiang J, Natarajan K, Margulies DH. Chaperone-mediated MHC-I peptide exchange in antigen presentation. IUCrJ 2024; 11:S2052252524002768. [PMID: 38656309 DOI: 10.1107/s2052252524002768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Zhao P, Wang C, Sun S, Wang X, Balch WE. Tracing genetic diversity captures the molecular basis of misfolding disease. Nat Commun 2024; 15:3333. [PMID: 38637533 PMCID: PMC11026414 DOI: 10.1038/s41467-024-47520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Genetic variation in human populations can result in the misfolding and aggregation of proteins, giving rise to systemic and neurodegenerative diseases that require management by proteostasis. Here, we define the role of GRP94, the endoplasmic reticulum Hsp90 chaperone paralog, in managing alpha-1-antitrypsin deficiency on a residue-by-residue basis using Gaussian process regression-based machine learning to profile the spatial covariance relationships that dictate protein folding arising from sequence variants in the population. Covariance analysis suggests a role for the ATPase activity of GRP94 in controlling the N- to C-terminal cooperative folding of alpha-1-antitrypsin responsible for the correction of liver aggregation and lung-disease phenotypes of alpha-1-antitrypsin deficiency. Gaussian process-based spatial covariance profiling provides a standard model built on covariant principles to evaluate the role of proteostasis components in guiding information flow from genome to proteome in response to genetic variation, potentially allowing us to intervene in the onset and progression of complex multi-system human diseases.
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Affiliation(s)
- Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Shuhong Sun
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- Department of Nutrition and Food Hygiene, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Collaborative Innovation Center for Cancer Personalized Medicine, and Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Xi Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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Adupa V, Ustyantseva E, Kampinga HH, Onck PR. Tertiary structure and conformational dynamics of the anti-amyloidogenic chaperone DNAJB6b at atomistic resolution. Nat Commun 2024; 15:3285. [PMID: 38627370 PMCID: PMC11021509 DOI: 10.1038/s41467-024-46587-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024] Open
Abstract
DNAJB6b is a molecular chaperone of the heat shock protein network, shown to play a crucial role in preventing aggregation of several disease-related intrinsically disordered proteins. Using homology modeling and microsecond-long all-atom molecular dynamics (MD) simulations, we show that monomeric DNAJB6b is a transiently interconverting protein cycling between three states: a closed state, an open state (both abundant), and a less abundant extended state. Interestingly, the reported regulatory autoinhibitory anchor between helix V in the G/F1 region and helices II/III of the J-domain, which obstructs the access of Hsp70 to the J-domain remains present in all three states. This possibly suggests a mechanistically intriguing regulation in which DNAJB6b only becomes exposed when loaded with substrates that require Hsp70 processing. Our MD results of DNAJB6b carrying mutations in the G/F1 region that are linked to limb-girdle muscular dystrophy type D1 (LGMDD1) show that this G/F1 region becomes highly dynamic, pointing towards a spontaneous release of the autoinhibitory helix V from helices II/III. This would increase the probability of non-functional Hsp70 interactions to DNAJB6b without substrates. Our cellular data indeed confirm that non-substrate loaded LGMDD1 mutants have aberrant interactions with Hsp70.
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Affiliation(s)
- Vasista Adupa
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Elizaveta Ustyantseva
- Department of Biomedical Sciences, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harm H Kampinga
- Department of Biomedical Sciences, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
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6
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Vetter J, Papa G, Tobler K, Rodriguez JM, Kley M, Myers M, Wiesendanger M, Schraner EM, Luque D, Burrone OR, Fraefel C, Eichwald C. The recruitment of TRiC chaperonin in rotavirus viroplasms correlates with virus replication. mBio 2024; 15:e0049924. [PMID: 38470055 PMCID: PMC11005421 DOI: 10.1128/mbio.00499-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Rotavirus (RV) replication takes place in the viroplasms, cytosolic inclusions that allow the synthesis of virus genome segments and their encapsidation in the core shell, followed by the addition of the second layer of the virion. The viroplasms are composed of several viral proteins, including NSP5, which serves as the main building block. Microtubules, lipid droplets, and miRNA-7 are among the host components recruited in viroplasms. We investigated the interaction between RV proteins and host components of the viroplasms by performing a pull-down assay of lysates from RV-infected cells expressing NSP5-BiolD2. Subsequent tandem mass spectrometry identified all eight subunits of the tailless complex polypeptide I ring complex (TRiC), a cellular chaperonin responsible for folding at least 10% of the cytosolic proteins. Our confirmed findings reveal that TRiC is brought into viroplasms and wraps around newly formed double-layered particles. Chemical inhibition of TRiC and silencing of its subunits drastically reduced virus progeny production. Through direct RNA sequencing, we show that TRiC is critical for RV replication by controlling dsRNA genome segment synthesis, particularly negative-sense single-stranded RNA. Importantly, cryo-electron microscopy analysis shows that TRiC inhibition results in defective virus particles lacking genome segments and polymerase complex (VP1/VP3). Moreover, TRiC associates with VP2 and NSP5 but not with VP1. Also, VP2 is shown to be essential for recruiting TRiC in viroplasms and preserving their globular morphology. This study highlights the essential role of TRiC in viroplasm formation and in facilitating virion assembly during the RV life cycle. IMPORTANCE The replication of rotavirus takes place in cytosolic inclusions termed viroplasms. In these inclusions, the distinct 11 double-stranded RNA genome segments are co-packaged to complete a genome in newly generated virus particles. In this study, we show for the first time that the tailless complex polypeptide I ring complex (TRiC), a cellular chaperonin responsible for the folding of at least 10% of the cytosolic proteins, is a component of viroplasms and is required for the synthesis of the viral negative-sense single-stranded RNA. Specifically, TRiC associates with NSP5 and VP2, the cofactor involved in RNA replication. Our study adds a new component to the current model of rotavirus replication, where TRiC is recruited to viroplasms to assist replication.
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Affiliation(s)
- Janine Vetter
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Guido Papa
- Molecular Immunology Lab, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Kurt Tobler
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Javier M. Rodriguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Cantoblanco, Madrid, Spain
| | - Manuel Kley
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Michael Myers
- Proteomics Lab, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Mahesa Wiesendanger
- Institute of Virology, University of Zurich, Zurich, Switzerland
- Institute of Veterinary Anatomy, University of Zurich, Zurich, Switzerland
| | - Elisabeth M. Schraner
- Institute of Virology, University of Zurich, Zurich, Switzerland
- Institute of Veterinary Anatomy, University of Zurich, Zurich, Switzerland
| | - Daniel Luque
- School of Biomedical Sciences, The University of New South Wales, Sydney, New South Wales, Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, New South Wales, Australia
| | - Oscar R. Burrone
- Molecular Immunology Lab, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
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7
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Zyla DS, Wiegand T, Bachmann P, Zdanowicz R, Giese C, Meier BH, Waksman G, Hospenthal MK, Glockshuber R. The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili. Nat Commun 2024; 15:3032. [PMID: 38589417 PMCID: PMC11001860 DOI: 10.1038/s41467-024-47212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
Type 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of copies of the main structural subunit FimA and is assembled in vivo by the assembly platform FimD. Although type 1 pilus rods can self-assemble from FimA in vitro, this reaction is slower and produces structures with lower kinetic stability against denaturants compared to in vivo-assembled rods. Our study reveals that FimD-catalysed in vitro-assembled type 1 pilus rods attain a similar stability as pilus rods assembled in vivo. Employing structural, biophysical and biochemical analyses, we show that in vitro assembly reactions lacking FimD produce pilus rods with structural defects, reducing their stability against dissociation. Overall, our results indicate that FimD is not only required for the catalysis of pilus assembly, but also to control the assembly of the most stable quaternary structure.
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Affiliation(s)
- Dawid S Zyla
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
- La Jolla Institute for Immunology, 9420 Athena Cir, La Jolla, CA, 92037, USA
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim/Ruhr, Germany
| | - Paul Bachmann
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Rafal Zdanowicz
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK
| | - Manuela K Hospenthal
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland.
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK.
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
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8
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Wickenberg M, Mercier R, Yap M, Walker J, Baker K, LaPointe P. Hsp90 inhibition leads to an increase in surface expression of multiple immunological receptors in cancer cells. Front Mol Biosci 2024; 11:1334876. [PMID: 38645275 PMCID: PMC11027010 DOI: 10.3389/fmolb.2024.1334876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone important for maintaining protein homeostasis (proteostasis) in the cell. Hsp90 inhibitors are being explored as cancer therapeutics because of their ability to disrupt proteostasis. Inhibiting Hsp90 increases surface density of the immunological receptor Major Histocompatibility Complex 1 (MHC1). Here we show that this increase occurs across multiple cancer cell lines and with both cytosol-specific and pan-Hsp90 inhibitors. We demonstrate that Hsp90 inhibition also alters surface expression of both IFNGR and PD-L1, two additional immunological receptors that play a significant role in anti-tumour or anti-immune activity in the tumour microenvironment. Hsp90 also negatively regulates IFN-γ activity in cancer cells, suggesting it has a unique role in mediating the immune system's response to cancer. Our data suggests a strong link between Hsp90 activity and the pathways that govern anti-tumour immunity. This highlights the potential for the use of an Hsp90 inhibitor in combination with another currently available cancer treatment, immune checkpoint blockade therapy, which works to prevent immune evasion of cancer cells. Combination checkpoint inhibitor therapy and the use of an Hsp90 inhibitor may potentiate the therapeutic benefits of both treatments and improve prognosis for cancer patients.
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Affiliation(s)
- Madison Wickenberg
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Rebecca Mercier
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Megan Yap
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - John Walker
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Kristi Baker
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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9
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Maneix L, Iakova P, Lee CG, Moree SE, Lu X, Datar GK, Hill CT, Spooner E, King JCK, Sykes DB, Saez B, Di Stefano B, Chen X, Krause DS, Sahin E, Tsai FTF, Goodell MA, Berk BC, Scadden DT, Catic A. Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing. Nat Cell Biol 2024; 26:593-603. [PMID: 38553595 PMCID: PMC11021199 DOI: 10.1038/s41556-024-01387-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 02/23/2024] [Indexed: 04/11/2024]
Abstract
Loss of protein function is a driving force of ageing. We have identified peptidyl-prolyl isomerase A (PPIA or cyclophilin A) as a dominant chaperone in haematopoietic stem and progenitor cells. Depletion of PPIA accelerates stem cell ageing. We found that proteins with intrinsically disordered regions (IDRs) are frequent PPIA substrates. IDRs facilitate interactions with other proteins or nucleic acids and can trigger liquid-liquid phase separation. Over 20% of PPIA substrates are involved in the formation of supramolecular membrane-less organelles. PPIA affects regulators of stress granules (PABPC1), P-bodies (DDX6) and nucleoli (NPM1) to promote phase separation and increase cellular stress resistance. Haematopoietic stem cell ageing is associated with a post-transcriptional decrease in PPIA expression and reduced translation of IDR-rich proteins. Here we link the chaperone PPIA to the synthesis of intrinsically disordered proteins, which indicates that impaired protein interaction networks and macromolecular condensation may be potential determinants of haematopoietic stem cell ageing.
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Affiliation(s)
- Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Polina Iakova
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Charles G Lee
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Shannon E Moree
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Xuan Lu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gandhar K Datar
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Cedric T Hill
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric Spooner
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Jordon C K King
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Borja Saez
- Center for Applied Medical Research, Hematology-Oncology Unit, Pamplona, Navarra, Spain
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Daniela S Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Ergun Sahin
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Francis T F Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Bradford C Berk
- Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - André Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA.
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA.
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10
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Kazzaz SA, Tawil J, Harhaj EW. The aryl hydrocarbon receptor-interacting protein in cancer and immunity: Beyond a chaperone protein for the dioxin receptor. J Biol Chem 2024; 300:107157. [PMID: 38479600 PMCID: PMC11002312 DOI: 10.1016/j.jbc.2024.107157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
The aryl hydrocarbon receptor (AhR)-interacting protein (AIP) is a ubiquitously expressed, immunophilin-like protein best known for its role as a co-chaperone in the AhR-AIP-Hsp90 cytoplasmic complex. In addition to regulating AhR and the xenobiotic response, AIP has been linked to various aspects of cancer and immunity that will be the focus of this review article. Loss-of-function AIP mutations are associated with pituitary adenomas, suggesting that AIP acts as a tumor suppressor in the pituitary gland. However, the tumor suppressor mechanisms of AIP remain unclear, and AIP can exert oncogenic functions in other tissues. While global deletion of AIP in mice yields embryonically lethal cardiac malformations, heterozygote, and tissue-specific conditional AIP knockout mice have revealed various physiological roles of AIP. Emerging studies have established the regulatory roles of AIP in both innate and adaptive immunity. AIP interacts with and inhibits the nuclear translocation of the transcription factor IRF7 to inhibit type I interferon production. AIP also interacts with the CARMA1-BCL10-MALT1 complex in T cells to enhance IKK/NF-κB signaling and T cell activation. Taken together, AIP has diverse functions that vary considerably depending on the client protein, the tissue, and the species.
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Affiliation(s)
- Sarah A Kazzaz
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA; Medical Scientist Training Program, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - John Tawil
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Edward W Harhaj
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA.
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11
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Kong YX, Chiu J, Passam FH. "Sticki-ER": Functions of the Platelet Endoplasmic Reticulum. Antioxid Redox Signal 2024. [PMID: 38284332 DOI: 10.1089/ars.2024.0566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Significance: The primary role of platelets is to generate a thrombus by platelet activation. Platelet activation relies on calcium mobilization from the endoplasmic reticulum (ER). ER resident proteins, which are externalized upon platelet activation, are essential for the function of platelet surface receptors and intercellular interactions. Recent Advances: The platelet ER is a conduit for changes in cellular function in response to the extracellular milieu. ER homeostasis is maintained by an appropriate redox balance, regulated calcium stores and normal protein folding. Alterations in ER function and ER stress results in ER proteins externalizing to the cell surface, including members of the protein disulfide isomerase family (PDIs) and chaperones. Critical Issues: The platelet ER is central to platelet function, but our understanding of its regulation is incomplete. Previous studies have focused on the function of PDIs in the extracellular space, and much less on their intracellular role. How platelets maintain ER homeostasis and how they direct ER chaperone proteins to facilitate intercellular signalling is unknown. Future Directions: An understanding of ER functions in the platelet is essential as these may determine critical platelet activities such as secretion and adhesion. Studies are necessary to understand the redox reactions of PDIs in the intracellular versus extracellular space, as these differentially affect platelet function. An unresolved question is how platelet ER proteins control calcium release. Regulation of protein folding in the platelet and downstream pathways of ER stress require further evaluation. Targeting the platelet ER may have therapeutic application in metabolic and neoplastic disease.
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Affiliation(s)
- Yvonne X Kong
- Haematology Research Group, Charles Perkins Centre; The University of Sydney, Camperdown, New South Wales, Australia
- Central Clinical School, Faculty of Medicine and Health; The University of Sydney, Camperdown, New South Wales, Australia
- Department of Haematology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Joyce Chiu
- ACRF Centenary Cancer Research Centre, The Centenary Institute; The University of Sydney, Camperdown, New South Wales, Australia
| | - Freda H Passam
- Haematology Research Group, Charles Perkins Centre; The University of Sydney, Camperdown, New South Wales, Australia
- Central Clinical School, Faculty of Medicine and Health; The University of Sydney, Camperdown, New South Wales, Australia
- Department of Haematology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
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12
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Nair ZJ, Gao IH, Firras A, Chong KKL, Hill ED, Choo PY, Colomer-Winter C, Chen Q, Manzano C, Pethe K, Kline KA. An essential protease, FtsH, influences daptomycin resistance acquisition in Enterococcus faecalis. Mol Microbiol 2024. [PMID: 38527904 DOI: 10.1111/mmi.15253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
Daptomycin is a last-line antibiotic commonly used to treat vancomycin-resistant Enterococci, but resistance evolves rapidly and further restricts already limited treatment options. While genetic determinants associated with clinical daptomycin resistance (DAPR) have been described, information on factors affecting the speed of DAPR acquisition is limited. The multiple peptide resistance factor (MprF), a phosphatidylglycerol-modifying enzyme involved in cationic antimicrobial resistance, is linked to DAPR in pathogens such as methicillin-resistant Staphylococcus aureus. Since Enterococcus faecalis encodes two paralogs of mprF and clinical DAPR mutations do not map to mprF, we hypothesized that functional redundancy between the paralogs prevents mprF-mediated resistance and masks other evolutionary pathways to DAPR. Here, we performed in vitro evolution to DAPR in mprF mutant background. We discovered that the absence of mprF results in slowed DAPR evolution and is associated with inactivating mutations in ftsH, resulting in the depletion of the chaperone repressor HrcA. We also report that ftsH is essential in the parental, but not in the ΔmprF, strain where FtsH depletion results in growth impairment in the parental strain, a phenotype associated with reduced extracellular acidification and reduced ability for metabolic reduction. This presents FtsH and HrcA as enticing targets for developing anti-resistance strategies.
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Affiliation(s)
- Zeus Jaren Nair
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Iris Hanxing Gao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Aslam Firras
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
| | - Eric D Hill
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Pei Yi Choo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Cristina Colomer-Winter
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Qingyan Chen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Caroline Manzano
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kevin Pethe
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
| | - Kimberly A Kline
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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13
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Tregub PP, Kulikov VP, Ibrahimli I, Tregub OF, Volodkin AV, Ignatyuk MA, Kostin AA, Atiakshin DA. Molecular Mechanisms of Neuroprotection after the Intermittent Exposures of Hypercapnic Hypoxia. Int J Mol Sci 2024; 25:3665. [PMID: 38612476 PMCID: PMC11011936 DOI: 10.3390/ijms25073665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
The review introduces the stages of formation and experimental confirmation of the hypothesis regarding the mutual potentiation of neuroprotective effects of hypoxia and hypercapnia during their combined influence (hypercapnic hypoxia). The main focus is on the mechanisms and signaling pathways involved in the formation of ischemic tolerance in the brain during intermittent hypercapnic hypoxia. Importantly, the combined effect of hypoxia and hypercapnia exerts a more pronounced neuroprotective effect compared to their separate application. Some signaling systems are associated with the predominance of the hypoxic stimulus (HIF-1α, A1 receptors), while others (NF-κB, antioxidant activity, inhibition of apoptosis, maintenance of selective blood-brain barrier permeability) are mainly modulated by hypercapnia. Most of the molecular and cellular mechanisms involved in the formation of brain tolerance to ischemia are due to the contribution of both excess carbon dioxide and oxygen deficiency (ATP-dependent potassium channels, chaperones, endoplasmic reticulum stress, mitochondrial metabolism reprogramming). Overall, experimental studies indicate the dominance of hypercapnia in the neuroprotective effect of its combined action with hypoxia. Recent clinical studies have demonstrated the effectiveness of hypercapnic-hypoxic training in the treatment of childhood cerebral palsy and diabetic polyneuropathy in children. Combining hypercapnic hypoxia with pharmacological modulators of neuro/cardio/cytoprotection signaling pathways is likely to be promising for translating experimental research into clinical medicine.
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Affiliation(s)
- Pavel P. Tregub
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Brain Science Institute, Research Center of Neurology, 125367 Moscow, Russia
- Scientific and Educational Resource Center “Innovative Technologies of Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis”, RUDN University, 117198 Moscow, Russia; (A.V.V.); (M.A.I.); (A.A.K.); (D.A.A.)
| | - Vladimir P. Kulikov
- Department of Ultrasound and Functional Diagnostics, Altay State Medical University, 656040 Barnaul, Russia;
| | - Irada Ibrahimli
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | | | - Artem V. Volodkin
- Scientific and Educational Resource Center “Innovative Technologies of Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis”, RUDN University, 117198 Moscow, Russia; (A.V.V.); (M.A.I.); (A.A.K.); (D.A.A.)
| | - Michael A. Ignatyuk
- Scientific and Educational Resource Center “Innovative Technologies of Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis”, RUDN University, 117198 Moscow, Russia; (A.V.V.); (M.A.I.); (A.A.K.); (D.A.A.)
| | - Andrey A. Kostin
- Scientific and Educational Resource Center “Innovative Technologies of Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis”, RUDN University, 117198 Moscow, Russia; (A.V.V.); (M.A.I.); (A.A.K.); (D.A.A.)
| | - Dmitrii A. Atiakshin
- Scientific and Educational Resource Center “Innovative Technologies of Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis”, RUDN University, 117198 Moscow, Russia; (A.V.V.); (M.A.I.); (A.A.K.); (D.A.A.)
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14
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Finci LI, Chakrabarti M, Gulten G, Finney J, Grose C, Fox T, Yang R, Nissley DV, McCormick F, Esposito D, Balius TE, Simanshu DK. Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements. Commun Biol 2024; 7:260. [PMID: 38431713 PMCID: PMC10908828 DOI: 10.1038/s42003-024-05959-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/22/2024] [Indexed: 03/05/2024] Open
Abstract
RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular interactions governing RAF1 folding is crucial for comprehending this process. Here, we present a cryo-EM structure of the closed-state RAF1-HSP90-CDC37 complex, where the C-lobe of the RAF1 kinase domain binds to one side of the HSP90 dimer, and an unfolded N-lobe segment of the RAF1 kinase domain threads through the center of the HSP90 dimer. CDC37 binds to the kinase C-lobe, mimicking the N-lobe with its HxNI motif. We also describe structures of HSP90 dimers without RAF1 and CDC37, displaying only N-terminal and middle domains, which we term the semi-open state. Employing 1 μs atomistic simulations, energetic decomposition, and comparative structural analysis, we elucidate the dynamics and interactions within these complexes. Our quantitative analysis reveals that CDC37 bridges the HSP90-RAF1 interaction, RAF1 binds HSP90 asymmetrically, and that HSP90 structural elements engage RAF1's unfolded region. Additionally, N- and C-terminal interactions stabilize HSP90 dimers, and molecular interactions in HSP90 dimers rearrange between the closed and semi-open states. Our findings provide valuable insight into the contributions of HSP90 and CDC37 in mediating client folding.
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Affiliation(s)
- Lorenzo I Finci
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mayukh Chakrabarti
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gulcin Gulten
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph Finney
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Carissa Grose
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tara Fox
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Renbin Yang
- Center for Molecular Microscopy, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Trent E Balius
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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15
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Dawar S, Benitez MC, Lim Y, Dite TA, Yousef JM, Thio N, Garciaz S, Jackson TD, Milne JV, Dagley LF, Phillips WA, Kumar S, Clemons NJ. Caspase-2 protects against ferroptotic cell death. Cell Death Dis 2024; 15:182. [PMID: 38429264 PMCID: PMC10907636 DOI: 10.1038/s41419-024-06560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 03/03/2024]
Abstract
Caspase-2, one of the most evolutionarily conserved members of the caspase family, is an important regulator of the cellular response to oxidative stress. Given that ferroptosis is suppressed by antioxidant defense pathways, such as that involving selenoenzyme glutathione peroxidase 4 (GPX4), we hypothesized that caspase-2 may play a role in regulating ferroptosis. This study provides the first demonstration of an important and unprecedented function of caspase-2 in protecting cancer cells from undergoing ferroptotic cell death. Specifically, we show that depletion of caspase-2 leads to the downregulation of stress response genes including SESN2, HMOX1, SLC7A11, and sensitizes mutant-p53 cancer cells to cell death induced by various ferroptosis-inducing compounds. Importantly, the canonical catalytic activity of caspase-2 is not required for its role and suggests that caspase-2 regulates ferroptosis via non-proteolytic interaction with other proteins. Using an unbiased BioID proteomics screen, we identified novel caspase-2 interacting proteins (including heat shock proteins and co-chaperones) that regulate cellular responses to stress. Finally, we demonstrate that caspase-2 limits chaperone-mediated autophagic degradation of GPX4 to promote the survival of mutant-p53 cancer cells. In conclusion, we document a novel role for caspase-2 as a negative regulator of ferroptosis in cells with mutant p53. Our results provide evidence for a novel function of caspase-2 in cell death regulation and open potential new avenues to exploit ferroptosis in cancer therapy.
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Affiliation(s)
- Swati Dawar
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Mariana C Benitez
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yoon Lim
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5001, Australia
| | - Toby A Dite
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jumana M Yousef
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Niko Thio
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Sylvain Garciaz
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Thomas D Jackson
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Julia V Milne
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Wayne A Phillips
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Surgery (St Vincent's Hospital), The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5001, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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16
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Marie A, Georgescauld F, Johnson KR, Ray S, Engen JR, Ivanov AR. Native Capillary Electrophoresis-Mass Spectrometry of Near 1 MDa Non-Covalent GroEL/GroES/Substrate Protein Complexes. Adv Sci (Weinh) 2024; 11:e2306824. [PMID: 38191978 PMCID: PMC10953559 DOI: 10.1002/advs.202306824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/21/2023] [Indexed: 01/10/2024]
Abstract
Protein complexes are essential for proteins' folding and biological function. Currently, native analysis of large multimeric protein complexes remains challenging. Structural biology techniques are time-consuming and often cannot monitor the proteins' dynamics in solution. Here, a capillary electrophoresis-mass spectrometry (CE-MS) method is reported to characterize, under near-physiological conditions, the conformational rearrangements of ∽1 MDa GroEL upon complexation with binding partners involved in a protein folding cycle. The developed CE-MS method is fast (30 min per run), highly sensitive (low-amol level), and requires ∽10 000-fold fewer samples compared to biochemical/biophysical techniques. The method successfully separates GroEL14 (∽800 kDa), GroEL7 (∽400 kDa), GroES7 (∽73 kDa), and NanA4 (∽130 kDa) oligomers. The non-covalent binding of natural substrate proteins with GroEL14 can be detected and quantified. The technique allows monitoring of GroEL14 conformational changes upon complexation with (ATPγS)4-14 and GroES7 (∽876 kDa). Native CE-pseudo-MS3 analyses of wild-type (WT) GroEL and two GroEL mutants result in up to 60% sequence coverage and highlight subtle structural differences between WT and mutated GroEL. The presented results demonstrate the superior CE-MS performance for multimeric complexes' characterization versus direct infusion ESI-MS. This study shows the CE-MS potential to provide information on binding stoichiometry and kinetics for various protein complexes.
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Affiliation(s)
- Anne‐Lise Marie
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Florian Georgescauld
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Kendall R. Johnson
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Somak Ray
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - John R. Engen
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Alexander R. Ivanov
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
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17
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Almeida MC, Eger SJ, He C, Audouard M, Nikitina A, Glasauer SMK, Han D, Mejía-Cupajita B, Acosta-Uribe J, Villalba-Moreno ND, Littau JL, Elcheikhali M, Rivera EK, Carrettiero DC, Villegas-Lanau CA, Sepulveda-Falla D, Lopera F, Kosik KS. Single-nucleus RNA sequencing demonstrates an autosomal dominant Alzheimer's disease profile and possible mechanisms of disease protection. Neuron 2024:S0896-6273(24)00093-X. [PMID: 38417436 DOI: 10.1016/j.neuron.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 01/07/2024] [Accepted: 02/09/2024] [Indexed: 03/01/2024]
Abstract
Highly penetrant autosomal dominant Alzheimer's disease (ADAD) comprises a distinct disease entity as compared to the far more prevalent form of AD in which common variants collectively contribute to risk. The downstream pathways that distinguish these AD forms in specific cell types have not been deeply explored. We compared single-nucleus transcriptomes among a set of 27 cases divided among PSEN1-E280A ADAD carriers, sporadic AD, and controls. Autophagy genes and chaperones clearly defined the PSEN1-E280A cases compared to sporadic AD. Spatial transcriptomics validated the activation of chaperone-mediated autophagy genes in PSEN1-E280A. The PSEN1-E280A case in which much of the brain was spared neurofibrillary pathology and harbored a homozygous APOE3-Christchurch variant revealed possible explanations for protection from AD pathology including overexpression of LRP1 in astrocytes, increased expression of FKBP1B, and decreased PSEN1 expression in neurons. The unique cellular responses in ADAD and sporadic AD require consideration when designing clinical trials.
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Affiliation(s)
- Maria Camila Almeida
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Center for Natural and Humans Sciences, Federal University of ABC, Sao Bernardo do Campo, SP 09608020, Brazil
| | - Sarah J Eger
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Caroline He
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Morgane Audouard
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Arina Nikitina
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stella M K Glasauer
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Dasol Han
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Barbara Mejía-Cupajita
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia
| | - Juliana Acosta-Uribe
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia
| | - Nelson David Villalba-Moreno
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jessica Lisa Littau
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Megan Elcheikhali
- Department of Statistics and Applied Probability, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Erica Keane Rivera
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Daniel Carneiro Carrettiero
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Center for Natural and Humans Sciences, Federal University of ABC, Sao Bernardo do Campo, SP 09608020, Brazil
| | | | - Diego Sepulveda-Falla
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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18
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Minoia M, Quintana-Cordero J, Jetzinger K, Kotan IE, Turnbull KJ, Ciccarelli M, Masser AE, Liebers D, Gouarin E, Czech M, Hauryliuk V, Bukau B, Kramer G, Andréasson C. Chp1 is a dedicated chaperone at the ribosome that safeguards eEF1A biogenesis. Nat Commun 2024; 15:1382. [PMID: 38360885 PMCID: PMC10869706 DOI: 10.1038/s41467-024-45645-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Cotranslational protein folding depends on general chaperones that engage highly diverse nascent chains at the ribosomes. Here we discover a dedicated ribosome-associated chaperone, Chp1, that rewires the cotranslational folding machinery to assist in the challenging biogenesis of abundantly expressed eukaryotic translation elongation factor 1A (eEF1A). Our results indicate that during eEF1A synthesis, Chp1 is recruited to the ribosome with the help of the nascent polypeptide-associated complex (NAC), where it safeguards eEF1A biogenesis. Aberrant eEF1A production in the absence of Chp1 triggers instant proteolysis, widespread protein aggregation, activation of Hsf1 stress transcription and compromises cellular fitness. The expression of pathogenic eEF1A2 variants linked to epileptic-dyskinetic encephalopathy is protected by Chp1. Thus, eEF1A is a difficult-to-fold protein that necessitates a biogenesis pathway starting with dedicated folding factor Chp1 at the ribosome to protect the eukaryotic cell from proteostasis collapse.
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Affiliation(s)
- Melania Minoia
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jany Quintana-Cordero
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Katharina Jetzinger
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ilgin Eser Kotan
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kathryn Jane Turnbull
- Department of Clinical Microbiology, Rigshospitalet, 2200, Copenhagen, Denmark
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Michela Ciccarelli
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Anna E Masser
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Dorina Liebers
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Eloïse Gouarin
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marius Czech
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vasili Hauryliuk
- Science for Life Laboratory, Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, 50411, Tartu, Estonia
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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19
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Rendón-Luna DF, Arroyo-Mosso IA, De Luna-Valenciano H, Campos F, Segovia L, Saab-Rincón G, Cuevas-Velazquez CL, Reyes JL, Covarrubias AA. Alternative conformations of a group 4 Late Embryogenesis Abundant protein associated to its in vitro protective activity. Sci Rep 2024; 14:2770. [PMID: 38307936 PMCID: PMC10837141 DOI: 10.1038/s41598-024-53295-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/30/2024] [Indexed: 02/04/2024] Open
Abstract
Late Embryogenesis Abundant (LEA) proteins are a group of intrinsically disordered proteins implicated in plant responses to water deficit. In vitro studies revealed that LEA proteins protect reporter enzymes from inactivation during low water availability. Group 4 LEA proteins constitute a conserved protein family, displaying in vitro protective capabilities. Under water deficiency or macromolecular crowding, the N-terminal of these proteins adopts an alpha-helix conformation. This region has been identified as responsible for the protein in vitro protective activity. This study investigates whether the attainment of alpha-helix conformation and/or particular amino acid residues are required for the in vitro protective activity. The LEA4-5 protein from Arabidopsis thaliana was used to generate mutant proteins. The mutations altered conserved residues, deleted specific conserved regions, or introduced prolines to hinder alpha-helix formation. The results indicate that conserved residues are not essential for LEA4-5 protective function. Interestingly, the C-terminal region was found to contribute to this function. Moreover, alpha-helix conformation is necessary for the protective activity only when the C-terminal region is deleted. Overall, LEA4-5 shows the ability to adopt alternative functional conformations under the tested conditions. These findings shed light on the in vitro mechanisms by which LEA proteins protect against water deficit stress.
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Affiliation(s)
- David F Rendón-Luna
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Inti A Arroyo-Mosso
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Haydee De Luna-Valenciano
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México
- Programa de Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Francisco Campos
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Lorenzo Segovia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Gloria Saab-Rincón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Cesar L Cuevas-Velazquez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - José Luis Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México.
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20
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Park J, Kim H, Gestaut D, Lim S, Opoku-Nsiah KA, Leitner A, Frydman J, Roh SH. A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle. Nat Commun 2024; 15:1007. [PMID: 38307855 PMCID: PMC10837153 DOI: 10.1038/s41467-024-45242-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. PhLP2A binds to open apo-TRiC through polyvalent domain-specific contacts with its chamber's equatorial and apical regions. PhLP2A N-terminal H3-domain binding to subunits CCT3/4 apical domains displace PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to positively charged inner surface residues from CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding.
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Affiliation(s)
- Junsun Park
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Hyunmin Kim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Daniel Gestaut
- Dept of Biology and Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Seyeon Lim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | | | - Alexander Leitner
- Institute of Molecular Systems Biology, Dept of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Judith Frydman
- Dept of Biology and Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Soung-Hun Roh
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.
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21
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Kumar R, Le Marchand T, Adam L, Bobrovs R, Chen G, Fridmanis J, Kronqvist N, Biverstål H, Jaudzems K, Johansson J, Pintacuda G, Abelein A. Identification of potential aggregation hotspots on Aβ42 fibrils blocked by the anti-amyloid chaperone-like BRICHOS domain. Nat Commun 2024; 15:965. [PMID: 38302480 PMCID: PMC10834949 DOI: 10.1038/s41467-024-45192-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
Protein misfolding can generate toxic intermediates, which underlies several devastating diseases, such as Alzheimer's disease (AD). The surface of AD-associated amyloid-β peptide (Aβ) fibrils has been suggested to act as a catalyzer for self-replication and generation of potentially toxic species. Specifically tailored molecular chaperones, such as the BRICHOS protein domain, were shown to bind to amyloid fibrils and break this autocatalytic cycle. Here, we identify a site on the Aβ42 fibril surface, consisting of three C-terminal β-strands and particularly the solvent-exposed β-strand stretching from residues 26-28, which is efficiently sensed by a designed variant of Bri2 BRICHOS. Remarkably, while only a low amount of BRICHOS binds to Aβ42 fibrils, fibril-catalyzed nucleation processes are effectively prevented, suggesting that the identified site acts as a catalytic aggregation hotspot, which can specifically be blocked by BRICHOS. Hence, these findings provide an understanding how toxic nucleation events can be targeted by molecular chaperones.
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Affiliation(s)
- Rakesh Kumar
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Tanguy Le Marchand
- Université de Lyon, Centre de Resonance Magnétique Nucléaire (CRMN) à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1), 69100, Villeurbanne, France
| | - Laurène Adam
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Raitis Bobrovs
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Jēkabs Fridmanis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Nina Kronqvist
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Henrik Biverstål
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Guido Pintacuda
- Université de Lyon, Centre de Resonance Magnétique Nucléaire (CRMN) à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1), 69100, Villeurbanne, France
| | - Axel Abelein
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden.
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22
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Mansour HM, Mohamed AF, Khattab MM, El-Khatib AS. Heat Shock Protein 90 in Parkinson's Disease: Profile of a Serial Killer. Neuroscience 2024; 537:32-46. [PMID: 38040085 DOI: 10.1016/j.neuroscience.2023.11.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/18/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease, characterized by abnormal α-synuclein misfolding and aggregation, mitochondrial dysfunction, oxidative stress, as well as progressive death of dopaminergic neurons in the substantia nigra. Molecular chaperones play a role in stabilizing proteins and helping them achieve their proper structure. Previous studies have shown that overexpression of heat shock protein 90 (HSP90) can lead to the death of dopaminergic neurons associated with PD. Inhibiting HSP90 is considered a potential treatment approach for neurodegenerative disorders, as it may reduce protein aggregation and related toxicity, as well as suppress various forms of regulated cell death (RCD). This review provides an overview of HSP90 and its role in PD, focusing on its modulation of proteostasis and quality control of LRRK2. The review also explores the effects of HSP90 on different types of RCD, such as apoptosis, chaperone-mediated autophagy (CMA), necroptosis, and ferroptosis. Additionally, it discusses HSP90 inhibitors that have been tested in PD models. We will highlight the under-investigated neuroprotective effects of HSP90 inhibition, including modulation of oxidative stress, mitochondrial dysfunction, PINK/PARKIN, heat shock factor 1 (HSF1), histone deacetylase 6 (HDAC6), and the PHD2-HSP90 complex-mediated mitochondrial stress pathway. By examining previous literature, this review uncovers overlooked neuroprotective mechanisms and emphasizes the need for further research on HSP90 inhibitors as potential therapeutic strategies for PD. Finally, the review discusses the potential limitations and possibilities of using HSP90 inhibitors in PD therapy.
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Affiliation(s)
- Heba M Mansour
- Central Administration of Biological, Innovative Products, and Clinical Studies (BIO-INN), Egyptian Drug Authority, EDA, Giza, Egypt.
| | - Ahmed F Mohamed
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Cairo, Egypt; Faculty of Pharmacy, King Salman International University (KSIU), South Sinai 46612, Egypt
| | - Mahmoud M Khattab
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Aiman S El-Khatib
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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23
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Agam G, Barth A, Lamb DC. Folding pathway of a discontinuous two-domain protein. Nat Commun 2024; 15:690. [PMID: 38263337 PMCID: PMC10805907 DOI: 10.1038/s41467-024-44901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
It is estimated that two-thirds of all proteins in higher organisms are composed of multiple domains, many of them containing discontinuous folds. However, to date, most in vitro protein folding studies have focused on small, single-domain proteins. As a model system for a two-domain discontinuous protein, we study the unfolding/refolding of a slow-folding double mutant of the maltose binding protein (DM-MBP) using single-molecule two- and three-color Förster Resonance Energy Transfer experiments. We observe a dynamic folding intermediate population in the N-terminal domain (NTD), C-terminal domain (CTD), and at the domain interface. The dynamic intermediate fluctuates rapidly between unfolded states and compact states, which have a similar FRET efficiency to the folded conformation. Our data reveals that the delayed folding of the NTD in DM-MBP is imposed by an entropic barrier with subsequent folding of the highly dynamic CTD. Notably, accelerated DM-MBP folding is routed through the same dynamic intermediate within the cavity of the GroEL/ES chaperone system, suggesting that the chaperonin limits the conformational space to overcome the entropic folding barrier. Our study highlights the subtle tuning and co-dependency in the folding of a discontinuous multi-domain protein.
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Affiliation(s)
- Ganesh Agam
- Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany
- Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Anders Barth
- Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany
- Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629HZ, Delft, The Netherlands
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany.
- Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany.
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24
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Xiao X, Fay A, Molina PS, Kovach A, Glickman MS, Li H. Structure of the M. tuberculosis DnaK-GrpE complex reveals how key DnaK roles are controlled. Nat Commun 2024; 15:660. [PMID: 38253530 PMCID: PMC10803776 DOI: 10.1038/s41467-024-44933-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The molecular chaperone DnaK is essential for viability of Mycobacterium tuberculosis (Mtb). DnaK hydrolyzes ATP to fold substrates, and the resulting ADP is exchanged for ATP by the nucleotide exchange factor GrpE. It has been unclear how GrpE couples DnaK's nucleotide exchange with substrate release. Here we report a cryo-EM analysis of GrpE bound to an intact Mtb DnaK, revealing an asymmetric 1:2 DnaK-GrpE complex. The GrpE dimer ratchets to modulate both DnaK nucleotide-binding domain and the substrate-binding domain. We further show that the disordered GrpE N-terminus is critical for substrate release, and that the DnaK-GrpE interface is essential for protein folding activity both in vitro and in vivo. Therefore, the Mtb GrpE dimer allosterically regulates DnaK to concomitantly release ADP in the nucleotide-binding domain and substrate peptide in the substrate-binding domain.
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Affiliation(s)
- Xiansha Xiao
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Amanda Kovach
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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25
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Vollmar L, Schimpf J, Hermann B, Hugel T. Co chaperones convey the energy of ATP hydrolysis for directional action of Hsp90. Nat Commun 2024; 15:569. [PMID: 38233436 PMCID: PMC10794413 DOI: 10.1038/s41467-024-44847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
The molecular chaperone and heat shock protein Hsp90 is part of many protein complexes in eukaryotic cells. Together with its cochaperones, Hsp90 is responsible for the maturation of hundreds of clients. Although having been investigated for decades, it still is largely unknown which components are necessary for a functional complex and how the energy of ATP hydrolysis is used to enable cyclic operation. Here we use single-molecule FRET to show how cochaperones introduce directionality into Hsp90's conformational changes during its interaction with the client kinase Ste11. Three cochaperones are needed to couple ATP turnover to these conformational changes. All three are therefore essential for a functional cyclic operation, which requires coupling to an energy source. Finally, our findings show how the formation of sub-complexes in equilibrium followed by a directed selection of the functional complex can be the most energy efficient pathway for kinase maturation.
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Affiliation(s)
- Leonie Vollmar
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Julia Schimpf
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Bianca Hermann
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany.
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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26
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Manisha Y, Srinivasan M, Jobichen C, Rosenshine I, Sivaraman J. Sensing for survival: specialised regulatory mechanisms of Type III secretion systems in Gram-negative pathogens. Biol Rev Camb Philos Soc 2024. [PMID: 38217090 DOI: 10.1111/brv.13047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/15/2024]
Abstract
For centuries, Gram-negative pathogens have infected the human population and been responsible for numerous diseases in animals and plants. Despite advancements in therapeutics, Gram-negative pathogens continue to evolve, with some having developed multi-drug resistant phenotypes. For the successful control of infections caused by these bacteria, we need to widen our understanding of the mechanisms of host-pathogen interactions. Gram-negative pathogens utilise an array of effector proteins to hijack the host system to survive within the host environment. These proteins are secreted into the host system via various secretion systems, including the integral Type III secretion system (T3SS). The T3SS spans two bacterial membranes and one host membrane to deliver effector proteins (virulence factors) into the host cell. This multifaceted process has multiple layers of regulation and various checkpoints. In this review, we highlight the multiple strategies adopted by these pathogens to regulate or maintain virulence via the T3SS, encompassing the regulation of small molecules to sense and communicate with the host system, as well as master regulators, gatekeepers, chaperones, and other effectors that recognise successful host contact. Further, we discuss the regulatory links between the T3SS and other systems, like flagella and metabolic pathways including the tricarboxylic acid (TCA) cycle, anaerobic metabolism, and stringent cell response.
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Affiliation(s)
- Yadav Manisha
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Mahalashmi Srinivasan
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
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27
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Cho H, Liu Y, Chung S, Chandrasekar S, Weiss S, Shan SO. Dynamic stability of Sgt2 enables selective and privileged client handover in a chaperone triad. Nat Commun 2024; 15:134. [PMID: 38167697 PMCID: PMC10761869 DOI: 10.1038/s41467-023-44260-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Membrane protein biogenesis poses acute challenges to protein homeostasis, and how they are selectively escorted to the target membrane is not well understood. Here we address this question in the guided-entry-of-tail-anchored protein (GET) pathway, in which tail-anchored membrane proteins (TAs) are relayed through an Hsp70-Sgt2-Get3 chaperone triad for targeting to the endoplasmic reticulum. We show that the Hsp70 ATPase cycle and TA substrate drive dimeric Sgt2 from a wide-open conformation to a closed state, in which TAs are protected by both substrate binding domains of Sgt2. Get3 is privileged to receive TA from closed Sgt2, whereas off-pathway chaperones remove TAs from open Sgt2. Sgt2 closing is less favorable with suboptimal GET substrates, which are rejected during or after the Hsp70-to-Sgt2 handover. Our results demonstrate how fine-tuned conformational dynamics in Sgt2 enable hydrophobic TAs to be effectively funneled onto their dedicated targeting factor while also providing a mechanism for substrate selection.
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Affiliation(s)
- Hyunju Cho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Center for Biomolecular and Cellular Structure, Institute for Basic Science, Daejeon, 34126, Republic of Korea
| | - Yumeng Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Biochemistry and Molecular Biotechnology Department, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Sowmya Chandrasekar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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Cortés-Avalos D, Borges Farias A, Romero-González LE, Lara-Ochoa C, Villa-Tanaca L, García-Del Portillo F, López-Guerrero V, Bustamante VH, Pérez-Rueda E, Ibarra JA. Interactions between the AraC/XylS-like transcriptional activator InvF of Salmonella Typhimurium, the RNA polymerase alpha subunit and the chaperone SicA. Sci Rep 2024; 14:156. [PMID: 38167847 PMCID: PMC10761746 DOI: 10.1038/s41598-023-50636-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Salmonella enterica serovar Typhimurium causes gastroenteritis and systemic infections in humans. For this bacterium the expression of a type III secretion system (T3SS) and effector proteins encoded in the Salmonella pathogenicity island-1 (SPI-1), is keystone for the virulence of this bacterium. Expression of these is controlled by a regulatory cascade starting with the transcriptional regulators HilD, HilC and RtsA that induce the expression of HilA, which then activates expression of the regulator InvF, a transcriptional regulator of the AraC/XylS family. InvF needs to interact with the chaperone SicA to activate transcription of SPI-1 genes including sicA, sopB, sptP, sopE, sopE2, and STM1239. InvF very likely acts as a classical activator; however, whether InvF interacts with the RNA polymerase alpha subunit RpoA has not been determined. Results from this study confirm the interaction between InvF with SicA and reveal that both proteins interact with the RNAP alpha subunit. Thus, our study further supports that the InvF/SicA complex acts as a classical activator. Additionally, we showed for the first time an interaction between a chaperone of T3SS effectors (SicA) and the RNAP.
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Affiliation(s)
- Daniel Cortés-Avalos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala S/N, Col. Santo Tomás 11340, Mexico City, Mexico
| | - André Borges Farias
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Mexico
| | - Luis E Romero-González
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala S/N, Col. Santo Tomás 11340, Mexico City, Mexico
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Cristina Lara-Ochoa
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Lourdes Villa-Tanaca
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala S/N, Col. Santo Tomás 11340, Mexico City, Mexico
| | - Francisco García-Del Portillo
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, Darwin, 3, 28049, Madrid, Spain
| | - Vanessa López-Guerrero
- Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Mexico
| | - J Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala S/N, Col. Santo Tomás 11340, Mexico City, Mexico.
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Velasco-Carneros L, Cuéllar J, Dublang L, Santiago C, Maréchal JD, Martín-Benito J, Maestro M, Fernández-Higuero JÁ, Orozco N, Moro F, Valpuesta JM, Muga A. Author Correction: The self-association equilibrium of DNAJA2 regulates its interaction with unfolded substrate proteins and with Hsc70. Nat Commun 2024; 15:99. [PMID: 38167402 PMCID: PMC10762187 DOI: 10.1038/s41467-023-44499-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Affiliation(s)
- Lorea Velasco-Carneros
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Jorge Cuéllar
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Leire Dublang
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - César Santiago
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, (UAB), 08193, Bellaterra (Barcelona), Spain
| | - Jaime Martín-Benito
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Moisés Maestro
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - José Ángel Fernández-Higuero
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Natalia Orozco
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
| | - Fernando Moro
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - José María Valpuesta
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain.
| | - Arturo Muga
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain.
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain.
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30
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Pechmann S. Single-cell expression predicts neuron-specific protein homeostasis networks. Open Biol 2024; 14:230386. [PMID: 38262604 PMCID: PMC10805596 DOI: 10.1098/rsob.230386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 11/17/2023] [Indexed: 01/25/2024] Open
Abstract
The protein homeostasis network keeps proteins in their correct shapes and avoids unwanted aggregation. In turn, the accumulation of aberrantly misfolded proteins has been directly associated with the onset of ageing-associated neurodegenerative diseases such as Alzheimer's and Parkinson's. However, a detailed and rational understanding of how protein homeostasis is achieved in health, and how it can be targeted for therapeutic intervention in diseases remains missing. Here, large-scale single-cell expression data from the Allen Brain Map are analysed to investigate the transcription regulation of the core protein homeostasis network across the human brain. Remarkably, distinct expression profiles suggest specialized protein homeostasis networks with systematic adaptations in excitatory neurons, inhibitory neurons and non-neuronal cells. Moreover, several chaperones and Ubiquitin ligases are found transcriptionally coregulated with genes important for synapse formation and maintenance, thus linking protein homeostasis to the regulation of neuronal function. Finally, evolutionary analyses highlight the conservation of an elevated interaction density in the chaperone network, suggesting that one of the most exciting aspects of chaperone action may yet be discovered in their collective action at the systems level. More generally, our work highlights the power of computational analyses for breaking down complexity and gaining complementary insights into fundamental biological problems.
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Zhang X, Ma S, Gu C, Hu M, Miao M, Quan Y, Yu W. K64 acetylation of heat shock protein 90 suppresses nucleopolyhedrovirus replication in Bombyx mori. Arch Insect Biochem Physiol 2024; 115:e22079. [PMID: 38288491 DOI: 10.1002/arch.22079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/03/2023] [Accepted: 12/13/2023] [Indexed: 02/01/2024]
Abstract
HSP90 is a highly conserved chaperone that facilitates the proliferation of many viruses, including silkworm (bombyx mori) nucleopolyhedrovirus (BmNPV), but the underlying regulatory mechanism was unclear. We found that suppression of HSP90 by 17-AAG, a HSP90-specific inhibitor, significantly reduced the expression of BmNPV capsid protein gp64 and viral genome replication, whereas overexpression of B. mori HSP90(BmHSP90) promoted BmNPV replication. Furthermore, in a recent study of the lysine acetylome of B. mori infected with BmNPV, we focused on the reduced viral proliferation due to changes of BmHSP90 lysine acetylation. Site-directed introduction of acetylated (K/Q) or deacetylated (K/R) mimic mutations into BmHSP90 revealed that lysine 64 (K64) acetylation activated the JAK/STAT pathway and reduced BmHSP90 ATPase activity, leading to diminished chaperone activity and ultimately inhibiting BmNPV proliferation. In this study, a single lysine 64 acetylation change of BmHSP90 was elucidated as a model of posttranslational modifications occurring in the wake of host-virus interactions, providing novel insights into potential antiviral strategies.
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Affiliation(s)
- Xizhen Zhang
- Department of Biopharmaceuticals, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Shiyi Ma
- Department of Biopharmaceuticals, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Chaoguang Gu
- Department of Biopharmaceuticals, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Miao Hu
- Department of Biopharmaceuticals, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Meng Miao
- Department of Biopharmaceuticals, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Yanping Quan
- Department of Biopharmaceuticals, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Wei Yu
- Department of Biopharmaceuticals, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
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Manole A, Wong T, Rhee A, Novak S, Chin SM, Tsimring K, Paucar A, Williams A, Newmeyer TF, Schafer ST, Rosh I, Kaushik S, Hoffman R, Chen S, Wang G, Snyder M, Cuervo AM, Andrade L, Manor U, Lee K, Jones JR, Stern S, Marchetto MC, Gage FH. NGLY1 mutations cause protein aggregation in human neurons. Cell Rep 2023; 42:113466. [PMID: 38039131 PMCID: PMC10826878 DOI: 10.1016/j.celrep.2023.113466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 08/04/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023] Open
Abstract
Biallelic mutations in the gene that encodes the enzyme N-glycanase 1 (NGLY1) cause a rare disease with multi-symptomatic features including developmental delay, intellectual disability, neuropathy, and seizures. NGLY1's activity in human neural cells is currently not well understood. To understand how NGLY1 gene loss leads to the specific phenotypes of NGLY1 deficiency, we employed direct conversion of NGLY1 patient-derived induced pluripotent stem cells (iPSCs) to functional cortical neurons. Transcriptomic, proteomic, and functional studies of iPSC-derived neurons lacking NGLY1 function revealed several major cellular processes that were altered, including protein aggregate-clearing functionality, mitochondrial homeostasis, and synaptic dysfunctions. These phenotypes were rescued by introduction of a functional NGLY1 gene and were observed in iPSC-derived mature neurons but not astrocytes. Finally, laser capture microscopy followed by mass spectrometry provided detailed characterization of the composition of protein aggregates specific to NGLY1-deficient neurons. Future studies will harness this knowledge for therapeutic development.
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Affiliation(s)
- Andreea Manole
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Thomas Wong
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Amanda Rhee
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sammy Novak
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shao-Ming Chin
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Katya Tsimring
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andres Paucar
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - April Williams
- The Razavi Newman Integrative Genomics and Bioinformatics Core Facility, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Traci Fang Newmeyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Idan Rosh
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Susmita Kaushik
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rene Hoffman
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Songjie Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Guangwen Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Leo Andrade
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Uri Manor
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kevin Lee
- Grace Science Foundation, Menlo Park, CA 94025, USA
| | - Jeffrey R Jones
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shani Stern
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Maria C Marchetto
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Heidari H, Lawrence DA. Climate Stressors and Physiological Dysregulations: Mechanistic Connections to Pathologies. Int J Environ Res Public Health 2023; 21:28. [PMID: 38248493 PMCID: PMC10815632 DOI: 10.3390/ijerph21010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024]
Abstract
This review delves into the complex relationship between environmental factors, their mechanistic cellular and molecular effects, and their significant impact on human health. Climate change is fueled by industrialization and the emission of greenhouse gases and leads to a range of effects, such as the redistribution of disease vectors, higher risks of disease transmission, and shifts in disease patterns. Rising temperatures pose risks to both food supplies and respiratory health. The hypothesis addressed is that environmental stressors including a spectrum of chemical and pathogen exposures as well as physical and psychological influences collectively impact genetics, metabolism, and cellular functions affecting physical and mental health. The objective is to report the mechanistic associations linking environment and health. As environmental stressors intensify, a surge in health conditions, spanning from allergies to neurodegenerative diseases, becomes evident; however, linkage to genetic-altered proteomics is more hidden. Investigations positing that environmental stressors cause mitochondrial dysfunction, metabolic syndrome, and oxidative stress, which affect missense variants and neuro- and immuno-disorders, are reported. These disruptions to homeostasis with dyslipidemia and misfolded and aggregated proteins increase susceptibility to cancers, infections, and autoimmune diseases. Proposed interventions, such as vitamin B supplements and antioxidants, target oxidative stress and may aid mitochondrial respiration and immune balance. The mechanistic interconnections of environmental stressors and disruptions in health need to be unraveled to develop strategies to protect public health.
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Affiliation(s)
- Hajar Heidari
- Department of Biomedical Sciences, University at Albany School of Public Health, Rensselaer, NY 12144, USA;
| | - David A. Lawrence
- Department of Biomedical Sciences, University at Albany School of Public Health, Rensselaer, NY 12144, USA;
- Department of Environmental Health Sciences, University at Albany School of Public Health, Rensselaer, NY 12144, USA
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
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Hendershot LM, Buck TM, Brodsky JL. The Essential Functions of Molecular Chaperones and Folding Enzymes in Maintaining Endoplasmic Reticulum Homeostasis. J Mol Biol 2023:168418. [PMID: 38143019 DOI: 10.1016/j.jmb.2023.168418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
It has been estimated that up to one-third of the proteins encoded by the human genome enter the endoplasmic reticulum (ER) as extended polypeptide chains where they undergo covalent modifications, fold into their native structures, and assemble into oligomeric protein complexes. The fidelity of these processes is critical to support organellar, cellular, and organismal health, and is perhaps best underscored by the growing number of disease-causing mutations that reduce the fidelity of protein biogenesis in the ER. To meet demands encountered by the diverse protein clientele that mature in the ER, this organelle is populated with a cadre of molecular chaperones that prevent protein aggregation, facilitate protein disulfide isomerization, and lower the activation energy barrier of cis-trans prolyl isomerization. Components of the lectin (glycan-binding) chaperone system also reside within the ER and play numerous roles during protein biogenesis. In addition, the ER houses multiple homologs of select chaperones that can recognize and act upon diverse peptide signatures. Moreover, redundancy helps ensure that folding-compromised substrates are unable to overwhelm essential ER-resident chaperones and enzymes. In contrast, the ER in higher eukaryotic cells possesses a single member of the Hsp70, Hsp90, and Hsp110 chaperone families, even though several homologs of these molecules reside in the cytoplasm. In this review, we discuss specific functions of the many factors that maintain ER quality control, highlight some of their interactions, and describe the vulnerabilities that arise from the absence of multiple members of some chaperone families.
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Affiliation(s)
- Linda M Hendershot
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
| | - Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
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Kohler V, Arunagiri A, Ventura S, Kroschwald S, Ranganathan S. Editorial: Molecular determinants of protein assemblies in health and disease, Volume II. Front Mol Biosci 2023; 10:1343082. [PMID: 38146534 PMCID: PMC10749430 DOI: 10.3389/fmolb.2023.1343082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Affiliation(s)
- Verena Kohler
- Department of Molecular Biology, Faculty of Medicine, Umeå University, Umeå, Sweden
| | - Anoop Arunagiri
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sonja Kroschwald
- Department of Biology, Institute of Biochemistry, Zürich, Switzerland
| | - Srivastav Ranganathan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
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Karaś P, Kochanowicz K, Pitek M, Domanski P, Obuchowski I, Tomiczek B, Liberek K. Evolution towards simplicity in bacterial small heat shock protein system. eLife 2023; 12:RP89813. [PMID: 38063373 PMCID: PMC10708888 DOI: 10.7554/elife.89813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Evolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either two proteins with different functions (IbpA and IbpB) or a secondarily single sHsp that performs both functions in an equally efficient way. Secondarily single sHsp evolved from IbpA, an ancestor specialized in strong substrate binding. Evolution of an intermolecular binding site drove the alteration of substrate binding properties, as well as the formation of higher-order oligomers. Upon two mutations in the α-crystallin domain, secondarily single sHsp interacts with aggregated substrates less tightly. Paradoxically, less efficient binding positively influences the ability of sHsp to stimulate substrate refolding, since the dissociation of sHps from aggregates is required to initiate Hsp70-Hsp100-dependent substrate refolding. After the loss of a partner, IbpA took over its role in facilitating the sHsp dissociation from an aggregate by weakening the interaction with the substrate, which became beneficial for the refolding process. We show that the same two amino acids introduced in modern-day systems define whether the IbpA acts as a single sHsp or obligatorily cooperates with an IbpB partner. Our discoveries illuminate how one sequence has evolved to encode functions previously performed by two distinct proteins.
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Affiliation(s)
- Piotr Karaś
- Intercollegiate Faculty of Biotechnology UG-MUG, University of GdanskGdańskPoland
| | - Klaudia Kochanowicz
- Intercollegiate Faculty of Biotechnology UG-MUG, University of GdanskGdańskPoland
| | - Marcin Pitek
- Intercollegiate Faculty of Biotechnology UG-MUG, University of GdanskGdańskPoland
| | - Przemyslaw Domanski
- Intercollegiate Faculty of Biotechnology UG-MUG, University of GdanskGdańskPoland
| | - Igor Obuchowski
- Intercollegiate Faculty of Biotechnology UG-MUG, University of GdanskGdańskPoland
| | - Barlomiej Tomiczek
- Intercollegiate Faculty of Biotechnology UG-MUG, University of GdanskGdańskPoland
| | - Krzysztof Liberek
- Intercollegiate Faculty of Biotechnology UG-MUG, University of GdanskGdańskPoland
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Noddings CM, Johnson JL, Agard DA. Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the glucocorticoid receptor. Nat Struct Mol Biol 2023; 30:1867-1877. [PMID: 37945740 PMCID: PMC10716051 DOI: 10.1038/s41594-023-01128-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 09/18/2023] [Indexed: 11/12/2023]
Abstract
Hsp90 is an essential molecular chaperone responsible for the folding and activation of hundreds of 'client' proteins, including the glucocorticoid receptor (GR). Previously, we revealed that Hsp70 and Hsp90 remodel the conformation of GR to regulate ligand binding, aided by co-chaperones. In vivo, the co-chaperones FKBP51 and FKBP52 antagonistically regulate GR activity, but a molecular understanding is lacking. Here we present a 3.01 Å cryogenic electron microscopy structure of the human GR:Hsp90:FKBP52 complex, revealing how FKBP52 integrates into the GR chaperone cycle and directly binds to the active client, potentiating GR activity in vitro and in vivo. We also present a 3.23 Å cryogenic electron microscopy structure of the human GR:Hsp90:FKBP51 complex, revealing how FKBP51 competes with FKBP52 for GR:Hsp90 binding and demonstrating how FKBP51 can act as a potent antagonist to FKBP52. Altogether, we demonstrate how FKBP51 and FKBP52 integrate into the GR chaperone cycle to advance GR to the next stage of maturation.
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Affiliation(s)
- Chari M Noddings
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Jill L Johnson
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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Aschenbrenner I, Siebenmorgen T, Lopez A, Parr M, Ruckgaber P, Kerle A, Rührnößl F, Catici D, Haslbeck M, Frishman D, Sattler M, Zacharias M, Feige MJ. Assembly-dependent Structure Formation Shapes Human Interleukin-23 versus Interleukin-12 Secretion. J Mol Biol 2023; 435:168300. [PMID: 37805067 DOI: 10.1016/j.jmb.2023.168300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/09/2023]
Abstract
Interleukin 12 (IL-12) family cytokines connect the innate and adaptive branches of the immune system and regulate immune responses. A unique characteristic of this family is that each member is anα:βheterodimer. For human αsubunits it has been shown that they depend on theirβsubunit for structure formation and secretion from cells. Since subunits are shared within the family and IL-12 as well as IL-23 use the same βsubunit, subunit competition may influence cytokine secretion and thus downstream immunological functions. Here, we rationally design a folding-competent human IL-23α subunit that does not depend on itsβsubunit for structure formation. This engineered variant still forms a functional heterodimeric cytokine but shows less chaperone dependency and stronger affinity in assembly with its βsubunit. It forms IL-23 more efficiently than its natural counterpart, skewing the balance of IL-12 and IL-23 towards more IL-23 formation. Together, our study shows that folding-competent human IL-12 familyαsubunits are obtainable by only few mutations and compatible with assembly and function of the cytokine. These findings might suggest that human α subunits have evolved for assembly-dependent folding to maintain and regulate correct IL-12 family member ratios in the light of subunit competition.
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Affiliation(s)
- Isabel Aschenbrenner
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Till Siebenmorgen
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany; Helmholtz Munich, Molecular Targets & Therapeutics Center, Institute of Structural Biology, Neuherberg, Germany
| | - Abraham Lopez
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, Germany; Helmholtz Munich, Molecular Targets & Therapeutics Center, Institute of Structural Biology, Neuherberg, Germany
| | - Marina Parr
- Technical University of Munich, TUM School of Life Sciences, Department of Bioinformatics, Freising, Germany
| | - Philipp Ruckgaber
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Anna Kerle
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Florian Rührnößl
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Dragana Catici
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Martin Haslbeck
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Dmitrij Frishman
- Technical University of Munich, TUM School of Life Sciences, Department of Bioinformatics, Freising, Germany
| | - Michael Sattler
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, Germany; Helmholtz Munich, Molecular Targets & Therapeutics Center, Institute of Structural Biology, Neuherberg, Germany
| | - Martin Zacharias
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Matthias J Feige
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany.
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Braxton JR, Altobelli CR, Tucker MR, Tse E, Thwin AC, Arkin MR, Southworth DR. The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions. Nat Struct Mol Biol 2023; 30:2009-2019. [PMID: 37945741 PMCID: PMC10716044 DOI: 10.1038/s41594-023-01126-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/14/2023] [Indexed: 11/12/2023]
Abstract
p97, also known as valosin-containing protein, is an essential cytosolic AAA+ (ATPases associated with diverse cellular activities) hexamer that unfolds substrate polypeptides to support protein homeostasis and macromolecular disassembly. Distinct sets of p97 adaptors guide cellular functions but their roles in direct control of the hexamer are unclear. The UBXD1 adaptor localizes with p97 in critical mitochondria and lysosome clearance pathways and contains multiple p97-interacting domains. Here we identify UBXD1 as a potent p97 ATPase inhibitor and report structures of intact human p97-UBXD1 complexes that reveal extensive UBXD1 contacts across p97 and an asymmetric remodeling of the hexamer. Conserved VIM, UBX and PUB domains tether adjacent protomers while a connecting strand forms an N-terminal domain lariat with a helix wedged at the interprotomer interface. An additional VIM-connecting helix binds along the second (D2) AAA+ domain. Together, these contacts split the hexamer into a ring-open conformation. Structures, mutagenesis and comparisons to other adaptors further reveal how adaptors containing conserved p97-remodeling motifs regulate p97 ATPase activity and structure.
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Affiliation(s)
- Julian R Braxton
- Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chad R Altobelli
- Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Maxwell R Tucker
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Graduate Program in Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Eric Tse
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Aye C Thwin
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA.
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
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40
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Abayev-Avraham M, Salzberg Y, Gliksberg D, Oren-Suissa M, Rosenzweig R. DNAJB6 mutants display toxic gain of function through unregulated interaction with Hsp70 chaperones. Nat Commun 2023; 14:7066. [PMID: 37923706 PMCID: PMC10624832 DOI: 10.1038/s41467-023-42735-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Molecular chaperones are essential cellular components that aid in protein folding and preventing the abnormal aggregation of disease-associated proteins. Mutations in one such chaperone, DNAJB6, were identified in patients with LGMDD1, a dominant autosomal disorder characterized by myofibrillar degeneration and accumulations of aggregated protein within myocytes. The molecular mechanisms through which such mutations cause this dysfunction, however, are not well understood. Here we employ a combination of solution NMR and biochemical assays to investigate the structural and functional changes in LGMDD1 mutants of DNAJB6. Surprisingly, we find that DNAJB6 disease mutants show no reduction in their aggregation-prevention activity in vitro, and instead differ structurally from the WT protein, affecting their interaction with Hsp70 chaperones. While WT DNAJB6 contains a helical element regulating its ability to bind and activate Hsp70, in LGMDD1 disease mutants this regulation is disrupted. These variants can thus recruit and hyperactivate Hsp70 chaperones in an unregulated manner, depleting Hsp70 levels in myocytes, and resulting in the disruption of proteostasis. Interfering with DNAJB6-Hsp70 binding, however, reverses the disease phenotype, suggesting future therapeutic avenues for LGMDD1.
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Affiliation(s)
- Meital Abayev-Avraham
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Yehuda Salzberg
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Dar Gliksberg
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Meital Oren-Suissa
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 761000, Israel.
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Bellanger T, da Silva Barreira D, Wien F, Delarue P, Senet P, Rieu A, Neiers F, Varela PF, Combet S, Weidmann S. Significant influence of four highly conserved amino-acids in lipochaperon-active sHsps on the structure and functions of the Lo18 protein. Sci Rep 2023; 13:19036. [PMID: 37923897 PMCID: PMC10624808 DOI: 10.1038/s41598-023-46306-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023] Open
Abstract
To cope with environmental stresses, bacteria have developed different strategies, including the production of small heat shock proteins (sHSP). All sHSPs are described for their role as molecular chaperones. Some of them, like the Lo18 protein synthesized by Oenococcus oeni, also have the particularity of acting as a lipochaperon to maintain membrane fluidity in its optimal state following cellular stresses. Lipochaperon activity is poorly characterized and very little information is available on the domains or amino-acids key to this activity. The aim in this paper is to investigate the importance at the protein structure and function level of four highly conserved residues in sHSP exhibiting lipochaperon activity. Thus, by combining in silico, in vitro and in vivo approaches the importance of three amino-acids present in the core of the protein was shown to maintain both the structure of Lo18 and its functions.
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Affiliation(s)
- Tiffany Bellanger
- Procédés Alimentaires et Microbiologiques (PAM), AgroSup Dijon, PAM UMR A 02.102, Laboratoire VAlMiS-IUVV, Dijon, France
| | - David da Silva Barreira
- Procédés Alimentaires et Microbiologiques (PAM), AgroSup Dijon, PAM UMR A 02.102, Laboratoire VAlMiS-IUVV, Dijon, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, 91192, Gif-sur-Yvette, France
| | - Patrice Delarue
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303, CNRS, Université de Bourgogne Franche-Comté, 21078, Dijon, France
| | - Patrick Senet
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303, CNRS, Université de Bourgogne Franche-Comté, 21078, Dijon, France
| | - Aurélie Rieu
- Procédés Alimentaires et Microbiologiques (PAM), AgroSup Dijon, PAM UMR A 02.102, Laboratoire VAlMiS-IUVV, Dijon, France
| | - Fabrice Neiers
- Laboratory: Flavour Perception: Molecular Mechanisms (Flavours), INRAE, CNRS, Institut Agro, Université de Bourgogne Franche-Comté, 21000, Dijon, France
| | - Paloma Fernández Varela
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Sophie Combet
- Laboratoire Léon-Brillouin (LLB), UMR12 CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette CEDEX, France
| | - Stéphanie Weidmann
- Procédés Alimentaires et Microbiologiques (PAM), AgroSup Dijon, PAM UMR A 02.102, Laboratoire VAlMiS-IUVV, Dijon, France.
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Wang Y, Wang B, Gao Y, Nakanishi H, Gao XD, Li Z. Highly efficient expression and secretion of human lysozyme using multiple strategies in Pichia pastoris. Biotechnol J 2023; 18:e2300259. [PMID: 37470505 DOI: 10.1002/biot.202300259] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Human lysozyme (hLYZ), an emerging antibacterial agent, has extensive application in the food and pharmaceutical industries. However, the source of hLYZ is particularly limited. RESULTS To achieve highly efficient expression and secretion of hLYZ in Pichia pastoris, multiple strategies including G418 sulfate screening, signal sequence optimization, vacuolar sorting receptor VPS10 disruption, and chaperones/transcription factors co-expression were applied. The maximal enzyme activity of extracellular hLYZ in a shaking flask was 81,600 ± 5230 U mL-1 , which was about five times of original strain. To further reduce the cost, the optimal medium RDMY was developed and the highest hLYZ activity reached 352,000 ± 16,696.5 U mL-1 in a 5 L fermenter. CONCLUSION This research provides a very useful and cost-effective approach for the hLYZ production in P. pastoris and can also be applied to the production of other recombinant proteins.
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Affiliation(s)
- Yasen Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Buqing Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Yahui Gao
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
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43
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Ries F, Weil HL, Herkt C, Mühlhaus T, Sommer F, Schroda M, Willmund F. Competition co-immunoprecipitation reveals the interactors of the chloroplast CPN60 chaperonin machinery. Plant Cell Environ 2023; 46:3371-3391. [PMID: 37606545 DOI: 10.1111/pce.14697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/28/2023] [Accepted: 08/11/2023] [Indexed: 08/23/2023]
Abstract
The functionality of all metabolic processes in chloroplasts depends on a balanced integration of nuclear- and chloroplast-encoded polypeptides into the plastid's proteome. The chloroplast chaperonin machinery is an essential player in chloroplast protein folding under ambient and stressful conditions, with a more intricate structure and subunit composition compared to the orthologous GroEL/ES chaperonin of Escherichia coli. However, its exact role in chloroplasts remains obscure, mainly because of very limited knowledge about the interactors. We employed the competition immunoprecipitation method for the identification of the chaperonin's interactors in Chlamydomonas reinhardtii. Co-immunoprecipitation of the target complex in the presence of increasing amounts of isotope-labelled competitor epitope and subsequent mass spectrometry analysis specifically allowed to distinguish true interactors from unspecifically co-precipitated proteins. Besides known substrates such as RbcL and the expected complex partners, we revealed numerous new interactors with high confidence. Proteins that qualify as putative substrate proteins differ from bulk chloroplast proteins by a higher content of beta-sheets, lower alpha-helical conformation and increased aggregation propensity. Immunoprecipitations targeted against a subunit of the co-chaperonin lid revealed the ClpP protease as a specific partner complex, pointing to a close collaboration of these machineries to maintain protein homeostasis in the chloroplast.
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Affiliation(s)
- Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Heinrich Lukas Weil
- Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Plant Physiology/Synmikro, University of Marburg, Marburg, Germany
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Kim M, McDonald EF, Sabusap CMP, Timalsina B, Joshi D, Hong JS, Rab A, Sorscher EJ, Plate L. Elexacaftor/VX-445-mediated CFTR interactome remodeling reveals differential correction driven by mutation-specific translational dynamics. J Biol Chem 2023; 299:105242. [PMID: 37690692 PMCID: PMC10579539 DOI: 10.1016/j.jbc.2023.105242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023] Open
Abstract
Cystic fibrosis (CF) is one of the most prevalent lethal genetic diseases with over 2000 identified mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Pharmacological chaperones such as lumacaftor (VX-809), tezacaftor (VX-661), and elexacaftor (VX-445) treat mutation-induced defects by stabilizing CFTR and are called correctors. These correctors improve proper folding and thus facilitate processing and trafficking to increase the amount of functional CFTR on the cell surface. Yet, CFTR variants display differential responses to each corrector. Here, we report that variants P67L and L206W respond similarly to VX-809 but divergently to VX-445 with P67L exhibiting little rescue when treated with VX-445. We investigate the underlying cellular mechanisms of how CFTR biogenesis is altered by correctors in these variants. Affinity purification-mass spectrometry multiplexed with isobaric tandem mass tags was used to quantify CFTR protein-protein interaction changes between variants P67L and L206W. VX-445 facilitates unique proteostasis factor interactions especially in translation, folding, and degradation pathways in a CFTR variant-dependent manner. A number of these interacting proteins knocked down by siRNA, such as ribosomal subunit proteins, moderately rescued fully glycosylated P67L. Importantly, these knockdowns sensitize P67L to VX-445 and further enhance the trafficking correction of this variant. Partial inhibition of protein translation also mildly sensitizes P67L CFTR to VX-445 correction, supporting a role for translational dynamics in the rescue mechanism of VX-445. Our results provide a better understanding of VX-445 biological mechanism of action and reveal cellular targets that may sensitize nonresponsive CFTR variants to known and available correctors.
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Affiliation(s)
- Minsoo Kim
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Bibek Timalsina
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Disha Joshi
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Jeong S Hong
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Andras Rab
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Eric J Sorscher
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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45
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Kwon Y, Kim J, Cho SY, Kang YJ, Lee J, Kwon J, Rhee H, Bauer S, Kim HS, Lee E, Kim HS, Jung JH, Kim H, Kim WK. Identification of novel pathogenic roles of BLZF1/ATF6 in tumorigenesis of gastrointestinal stromal tumor showing Golgi-localized mutant KIT. Cell Death Differ 2023; 30:2309-2321. [PMID: 37704840 PMCID: PMC10589262 DOI: 10.1038/s41418-023-01220-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
Gastrointestinal stromal tumors (GISTs) frequently show KIT mutations, accompanied by overexpression and aberrant localization of mutant KIT (MT-KIT). As previously established by multiple studies, including ours, we confirmed that MT-KIT initiates downstream signaling in the Golgi complex. Basic leucine zipper nuclear factor 1 (BLZF1) was identified as a novel MT-KIT-binding partner that tethers MT-KIT to the Golgi complex. Sustained activation of activated transcription factor 6 (ATF6), which belongs to the unfolded protein response (UPR) family, alleviates endoplasmic reticulum (ER) stress by upregulating chaperone expression, including heat shock protein 90 (HSP90), which assists in MT-KIT folding. BLZF1 knockdown and ATF6 inhibition suppressed both imatinib-sensitive and -resistant GIST in vitro. ATF6 inhibitors further showed potent antitumor effects in GIST xenografts, and the effect was enhanced with ER stress-inducing drugs. ATF6 activation was frequently observed in 67% of patients with GIST (n = 42), and was significantly associated with poorer relapse-free survival (P = 0.033). Overall, GIST bypasses ER quality control (QC) and ER stress-mediated cell death via UPR activation and uses the QC-free Golgi to initiate signaling.
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Affiliation(s)
- Yujin Kwon
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Jiyoon Kim
- Department of Pharmacology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Su-Yeon Cho
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Yoon Jin Kang
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
- Department of Marine Life Sciences, College of Life Science, Gangneung-Wonju National University, Gangneung, 25457, South Korea
| | - Jongsoo Lee
- Department of Urology, Urologic Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jaeyoung Kwon
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, South Korea
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
| | - Hyungjin Rhee
- Department of Radiology, Research Institute of Radiological Science, Center for Clinical Imaging Data Science, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Sebastian Bauer
- Sarcoma Center, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Germany and German Cancer Consortium (DKTK), Essen, 45141, Germany
| | - Hyung-Sik Kim
- Department of Oral Biochemistry; Dental and Life Science Institute, School of Dentistry, Pusan National University, Yangsan, 50612, South Korea
| | - Esak Lee
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Han Sang Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jae Hung Jung
- Department of Urology, Yonsei University Wonju College of Medicine/Center of Evidence Based Medicine Institute of Convergence Science, Wonju, 26426, South Korea
| | - Hoguen Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Won Kyu Kim
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea.
- Department of Convergence Medicine, Yonsei University Wonju College of Medicine, Wonju, 26426, South Korea.
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46
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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47
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Roy M, Fleisher RC, Alexandrov AI, Horovitz A. Author Correction: Reduced ADP off-rate by the yeast CCT2 double mutation T394P/R510H which causes Leber congenital amaurosis in humans. Commun Biol 2023; 6:957. [PMID: 37730860 PMCID: PMC10511531 DOI: 10.1038/s42003-023-05357-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023] Open
Affiliation(s)
- Mousam Roy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rachel C Fleisher
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Alexander I Alexandrov
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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48
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Sanghai N, Tranmer GK. Biochemical and Molecular Pathways in Neurodegenerative Diseases: An Integrated View. Cells 2023; 12:2318. [PMID: 37759540 PMCID: PMC10527779 DOI: 10.3390/cells12182318] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/05/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Neurodegenerative diseases (NDDs) like Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are defined by a myriad of complex aetiologies. Understanding the common biochemical molecular pathologies among NDDs gives an opportunity to decipher the overlapping and numerous cross-talk mechanisms of neurodegeneration. Numerous interrelated pathways lead to the progression of neurodegeneration. We present evidence from the past pieces of literature for the most usual global convergent hallmarks like ageing, oxidative stress, excitotoxicity-induced calcium butterfly effect, defective proteostasis including chaperones, autophagy, mitophagy, and proteosome networks, and neuroinflammation. Herein, we applied a holistic approach to identify and represent the shared mechanism across NDDs. Further, we believe that this approach could be helpful in identifying key modulators across NDDs, with a particular focus on AD, PD, and ALS. Moreover, these concepts could be applied to the development and diagnosis of novel strategies for diverse NDDs.
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Affiliation(s)
- Nitesh Sanghai
- College of Pharmacy, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada;
| | - Geoffrey K. Tranmer
- College of Pharmacy, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada;
- Department of Chemistry, Faculty of Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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49
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McQuown AJ, Nelliat AR, Reif D, Sabbarini IM, Membreno BS, Wu CCC, Denic V. A Zpr1 co-chaperone mediates folding of eukaryotic translation elongation factor 1A via a GTPase cycle. Mol Cell 2023; 83:3108-3122.e13. [PMID: 37597513 PMCID: PMC10528422 DOI: 10.1016/j.molcel.2023.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/23/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023]
Abstract
General protein folding is mediated by chaperones that utilize ATP hydrolysis to regulate client binding and release. Zinc-finger protein 1 (Zpr1) is an essential ATP-independent chaperone dedicated to the biogenesis of eukaryotic translation elongation factor 1A (eEF1A), a highly abundant GTP-binding protein. How Zpr1-mediated folding is regulated to ensure rapid Zpr1 recycling remains an unanswered question. Here, we use yeast genetics and microscopy analysis, biochemical reconstitution, and structural modeling to reveal that folding of eEF1A by Zpr1 requires GTP hydrolysis. Furthermore, we identify the highly conserved altered inheritance of mitochondria 29 (Aim29) protein as a Zpr1 co-chaperone that recognizes eEF1A in the GTP-bound, pre-hydrolysis conformation. This interaction dampens Zpr1⋅eEF1A GTPase activity and facilitates client exit from the folding cycle. Our work reveals that a bespoke ATP-independent chaperone system has mechanistic similarity to ATPase chaperones but unexpectedly relies on client GTP hydrolysis to regulate the chaperone-client interaction.
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Affiliation(s)
- Alexander J McQuown
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anjali R Nelliat
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dvir Reif
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ibrahim M Sabbarini
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Britnie Santiago Membreno
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Colin Chih-Chien Wu
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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50
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Velasco-Carneros L, Cuéllar J, Dublang L, Santiago C, Maréchal JD, Martín-Benito J, Maestro M, Fernández-Higuero JÁ, Orozco N, Moro F, Valpuesta JM, Muga A. The self-association equilibrium of DNAJA2 regulates its interaction with unfolded substrate proteins and with Hsc70. Nat Commun 2023; 14:5436. [PMID: 37670029 PMCID: PMC10480186 DOI: 10.1038/s41467-023-41150-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
J-domain proteins tune the specificity of Hsp70s, engaging them in precise functions. Despite their essential role, the structure and function of many J-domain proteins remain largely unknown. We explore human DNAJA2, finding that it reversibly forms highly-ordered, tubular structures that can be dissociated by Hsc70, the constitutively expressed Hsp70 isoform. Cryoelectron microscopy and mutational studies reveal that different domains are involved in self-association. Oligomer dissociation into dimers potentiates its interaction with unfolded client proteins. The J-domains are accessible to Hsc70 within the tubular structure. They allow binding of closely spaced Hsc70 molecules that could be transferred to the unfolded substrate for its cooperative remodelling, explaining the efficient recovery of DNAJA2-bound clients. The disordered C-terminal domain, comprising the last 52 residues, regulates its holding activity and productive interaction with Hsc70. These in vitro findings suggest that the association equilibrium of DNAJA2 could regulate its interaction with client proteins and Hsc70.
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Affiliation(s)
- Lorea Velasco-Carneros
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Jorge Cuéllar
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Leire Dublang
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - César Santiago
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, (UAB), 08193, Bellaterra (Barcelona), Spain
| | - Jaime Martín-Benito
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Moisés Maestro
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - José Ángel Fernández-Higuero
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Natalia Orozco
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
| | - Fernando Moro
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - José María Valpuesta
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain.
| | - Arturo Muga
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain.
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain.
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