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Wan T, Zhuo L, Pan Z, Chen RY, Ma H, Cao Y, Wang J, Wang JJ, Hu WF, Lai YJ, Hayat M, Li YZ. Dosage constraint of the ribosome-associated molecular chaperone drives the evolution and fates of its duplicates in bacteria. mBio 2024:e0199424. [PMID: 39373534 DOI: 10.1128/mbio.01994-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 09/17/2024] [Indexed: 10/08/2024] Open
Abstract
Gene duplication events happen prevalently during evolution, and the mechanisms governing the loss or retention of duplicated genes are mostly elusive. Our genome scanning analysis revealed that trigger factor (TF), the one and only bacterial ribosome-associated molecular chaperone, is singly copied in virtually every bacterium except for a very few that possess two or more copies. However, even in these exceptions, only one complete TF copy exists, while other homologs lack the N-terminal domain that contains the conserved ribosome binding site (RBS) motif. Consistently, we demonstrated that the overproduction of the N-terminal complete TF proteins is detrimental to the cell, which can be rescued by removing the N-terminal domain. Our findings also indicated that TF overproduction leads to a decrease in protein productivity and profile changes in proteome due to its characteristic ribosome binding and holdase activities. Additionally, these N-terminal deficient TF homologs in bacteria with multiple TF homologs partition the function of TF via subfunctionalization. Our results revealed that TF is subjected to a dosage constraint that originates from its own intrinsic functions, which may drive the evolution and fates of duplicated TFs in bacteria. IMPORTANCE Gene duplication events presumably occur in tig, which encodes the ribosome-associated molecular chaperone trigger factor (TF). However, TF is singly copied in virtually every bacterium, and these exceptions with multiple TF homologs always retain only one complete copy while other homologs lack the N-terminal domain. Here, we reveal the manner and mechanism underlying the evolution and fates of TF duplicates in bacteria. We discovered that the mutation-to-loss or retention-to-sub/neofunctionalization of TF duplicates is associated with the dosage constraint of N-terminal complete TF. The dosage constraint of TF is attributed to its characteristic ribosome binding and substrate-holding activities, causing a decrease in protein productivity and profile changes in cellular proteome.
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Affiliation(s)
- Tianyu Wan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
- Shenzhen Research Institute, Shandong University, Shenzhen, China
- Suzhou Research Institute, Shandong University, Suzhou, China
| | - Zhuo Pan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Rui-Yun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Han Ma
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ying Cao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Wei-Feng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ya-Jun Lai
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Muhammad Hayat
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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2
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Banerjee A, Ataman M, Smialek MJ, Mookherjee D, Rabl J, Mironov A, Mues L, Enkler L, Coto-Llerena M, Schmidt A, Boehringer D, Piscuoglio S, Spang A, Mittal N, Zavolan M. Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains. Nucleic Acids Res 2024; 52:9028-9048. [PMID: 39041433 PMCID: PMC11347166 DOI: 10.1093/nar/gkae630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
Increasingly many studies reveal how ribosome composition can be tuned to optimally translate the transcriptome of individual cell types. In this study, we investigated the expression pattern, structure within the ribosome and effect on protein synthesis of the ribosomal protein paralog 39L (RPL39L). With a novel mass spectrometric approach we revealed the expression of RPL39L protein beyond mouse germ cells, in human pluripotent cells, cancer cell lines and tissue samples. We generated RPL39L knock-out mouse embryonic stem cell (mESC) lines and demonstrated that RPL39L impacts the dynamics of translation, to support the pluripotency and differentiation, spontaneous and along the germ cell lineage. Most differences in protein abundance between WT and RPL39L KO lines were explained by widespread autophagy. By CryoEM analysis of purified RPL39 and RPL39L-containing ribosomes we found that, unlike RPL39, RPL39L has two distinct conformations in the exposed segment of the nascent peptide exit tunnel, creating a distinct hydrophobic patch that has been predicted to support the efficient co-translational folding of alpha helices. Our study shows that ribosomal protein paralogs provide switchable modular components that can tune translation to the protein production needs of individual cell types.
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Affiliation(s)
| | - Meric Ataman
- Biozentrum, University of Basel, Basel, Switzerland
| | - Maciej Jerzy Smialek
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Julius Rabl
- Cryo-EM Knowledge Hub (CEMK), ETH Zürich, Switzerland
| | | | - Lea Mues
- Biozentrum, University of Basel, Basel, Switzerland
| | - Ludovic Enkler
- Biozentrum, University of Basel, Basel, Switzerland
- University of Strasbourg, UMR7156 GMGM, Strasbourg, France
| | - Mairene Coto-Llerena
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | | | | | - Salvatore Piscuoglio
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland
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3
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Herling TW, Cassaignau AME, Wentink AS, Peter QAE, Kumar PC, Kartanas T, Schneider MM, Cabrita LD, Christodoulou J, Knowles TPJ. Thermodynamic profiles for cotranslational trigger factor substrate recognition. SCIENCE ADVANCES 2024; 10:eadn4824. [PMID: 38985872 PMCID: PMC11235164 DOI: 10.1126/sciadv.adn4824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Molecular chaperones are central to the maintenance of proteostasis in living cells. A key member of this protein family is trigger factor (TF), which acts throughout the protein life cycle and has a ubiquitous role as the first chaperone encountered by proteins during synthesis. However, our understanding of how TF achieves favorable interactions with such a diverse substrate base remains limited. Here, we use microfluidics to reveal the thermodynamic determinants of this process. We find that TF binding to empty 70S ribosomes is enthalpy-driven, with micromolar affinity, while nanomolar affinity is achieved through a favorable entropic contribution for both intrinsically disordered and folding-competent nascent chains. These findings suggest a general mechanism for cotranslational TF function, which relies on occupation of the exposed TF-substrate binding groove rather than specific complementarity between chaperone and nascent chain. These insights add to our wider understanding of how proteins can achieve broad substrate specificity.
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Affiliation(s)
- Therese W. Herling
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Anaïs M. E. Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Anne S. Wentink
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Quentin A. E. Peter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Pavan C. Kumar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Tadas Kartanas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Matthias M. Schneider
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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4
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Roeselová A, Maslen SL, Shivakumaraswamy S, Pellowe GA, Howell S, Joshi D, Redmond J, Kjær S, Skehel JM, Balchin D. Mechanism of chaperone coordination during cotranslational protein folding in bacteria. Mol Cell 2024; 84:2455-2471.e8. [PMID: 38908370 DOI: 10.1016/j.molcel.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/12/2024] [Accepted: 06/01/2024] [Indexed: 06/24/2024]
Abstract
Protein folding is assisted by molecular chaperones that bind nascent polypeptides during mRNA translation. Several structurally distinct classes of chaperones promote de novo folding, suggesting that their activities are coordinated at the ribosome. We used biochemical reconstitution and structural proteomics to explore the molecular basis for cotranslational chaperone action in bacteria. We found that chaperone binding is disfavored close to the ribosome, allowing folding to precede chaperone recruitment. Trigger factor recognizes compact folding intermediates that expose an extensive unfolded surface, and dictates DnaJ access to nascent chains. DnaJ uses a large surface to bind structurally diverse intermediates and recruits DnaK to sequence-diverse solvent-accessible sites. Neither Trigger factor, DnaJ, nor DnaK destabilize cotranslational folding intermediates. Instead, the chaperones collaborate to protect incipient structure in the nascent polypeptide well beyond the ribosome exit tunnel. Our findings show how the chaperone network selects and modulates cotranslational folding intermediates.
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Affiliation(s)
- Alžběta Roeselová
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Grant A Pellowe
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Steven Howell
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Dhira Joshi
- Chemical Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Joanna Redmond
- Chemical Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - J Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - David Balchin
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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5
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Masse MM, Guzman-Luna V, Varela AE, Mahfuza Shapla U, Hutchinson RB, Srivastava A, Wei W, Fuchs AM, Cavagnero S. Nascent chains derived from a foldable protein sequence interact with specific ribosomal surface sites near the exit tunnel. Sci Rep 2024; 14:12324. [PMID: 38811604 PMCID: PMC11137106 DOI: 10.1038/s41598-024-61274-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
In order to become bioactive, proteins must be translated and protected from aggregation during biosynthesis. The ribosome and molecular chaperones play a key role in this process. Ribosome-bound nascent chains (RNCs) of intrinsically disordered proteins and RNCs bearing a signal/arrest sequence are known to interact with ribosomal proteins. However, in the case of RNCs bearing foldable protein sequences, not much information is available on these interactions. Here, via a combination of chemical crosslinking and time-resolved fluorescence-anisotropy, we find that nascent chains of the foldable globin apoHmp1-140 interact with ribosomal protein L23 and have a freely-tumbling non-interacting N-terminal compact region comprising 63-94 residues. Longer RNCs (apoHmp1-189) also interact with an additional yet unidentified ribosomal protein, as well as with chaperones. Surprisingly, the apparent strength of RNC/r-protein interactions does not depend on nascent-chain sequence. Overall, foldable nascent chains establish and expand interactions with selected ribosomal proteins and chaperones, as they get longer. These data are significant because they reveal the interplay between independent conformational sampling and nascent-protein interactions with the ribosomal surface.
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Affiliation(s)
- Meranda M Masse
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Angela E Varela
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ummay Mahfuza Shapla
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Rachel B Hutchinson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Aniruddha Srivastava
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- McGaw Medical Center, Northwestern University, Chicago, IL, 60611, USA
| | - Wanting Wei
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- AIDS Vaccine Research Laboratory, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Andrew M Fuchs
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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6
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Lauer SM, Reepmeyer M, Berendes O, Klepacki D, Gasse J, Gabrielli S, Grubmüller H, Bock LV, Krizsan A, Nikolay R, Spahn CMT, Hoffmann R. Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88. Nat Commun 2024; 15:3945. [PMID: 38730238 PMCID: PMC11087509 DOI: 10.1038/s41467-024-48027-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
Proline-rich antimicrobial peptides (PrAMPs) inhibit bacterial protein biosynthesis by binding to the polypeptide exit tunnel (PET) near the peptidyl transferase center. Api137, an optimized derivative of honeybee PrAMP apidaecin, inhibits protein expression by trapping release factors (RFs), which interact with stop codons on ribosomes to terminate translation. This study uses cryo-EM, functional assays and molecular dynamic (MD) simulations to show that Api137 additionally occupies a second binding site near the exit of the PET and can repress translation independently of RF-trapping. Api88, a C-terminally amidated (-CONH2) analog of Api137 (-COOH), binds to the same sites, occupies a third binding pocket and interferes with the translation process presumably without RF-trapping. In conclusion, apidaecin-derived PrAMPs inhibit bacterial ribosomes by multimodal mechanisms caused by minor structural changes and thus represent a promising pool for drug development efforts.
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Affiliation(s)
- Simon M Lauer
- Institute of Medical Physics and Biophysics, Charité - Berlin University of medicine, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Humboldt-Universität zu Berlin, Institut für Biologie, 10099, Berlin, Germany
| | - Maren Reepmeyer
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
| | - Ole Berendes
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Dorota Klepacki
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Jakob Gasse
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
| | - Sara Gabrielli
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Andor Krizsan
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
| | - Rainer Nikolay
- Institute of Medical Physics and Biophysics, Charité - Berlin University of medicine, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Department of Genome Regulation, Ihnestrasse 63-73, 14195, Berlin, Germany.
| | - Christian M T Spahn
- Institute of Medical Physics and Biophysics, Charité - Berlin University of medicine, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany.
- Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany.
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7
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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] [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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8
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Chan C, Groisman EA. Chaperone Hsp70 helps Salmonella survive infection-relevant stress by reducing protein synthesis. PLoS Biol 2024; 22:e3002560. [PMID: 38574172 PMCID: PMC10994381 DOI: 10.1371/journal.pbio.3002560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024] Open
Abstract
In all domains of life, Hsp70 chaperones preserve protein homeostasis by promoting protein folding and degradation and preventing protein aggregation. We now report that the Hsp70 from the bacterial pathogen Salmonella enterica serovar Typhimurium-termed DnaK-independently reduces protein synthesis in vitro and in S. Typhimurium facing cytoplasmic Mg2+ starvation, a condition encountered during infection. This reduction reflects a 3-fold increase in ribosome association with DnaK and a 30-fold decrease in ribosome association with trigger factor, the chaperone normally associated with translating ribosomes. Surprisingly, this reduction does not involve J-domain cochaperones, unlike previously known functions of DnaK. Removing the 74 C-terminal amino acids of the 638-residue long DnaK impeded DnaK association with ribosomes and reduction of protein synthesis, rendering S. Typhimurium defective in protein homeostasis during cytoplasmic Mg2+ starvation. DnaK-dependent reduction in protein synthesis is critical for survival against Mg2+ starvation because inhibiting protein synthesis in a dnaK-independent manner overcame the 10,000-fold loss in viability resulting from DnaK truncation. Our results indicate that DnaK protects bacteria from infection-relevant stresses by coordinating protein synthesis with protein folding capacity.
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Affiliation(s)
- Carissa Chan
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
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9
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Žoldák G, Knappe TA, Geitner AJ, Scholz C, Dobbek H, Schmid FX, Jakob RP. Bacterial Chaperone Domain Insertions Convert Human FKBP12 into an Excellent Protein-Folding Catalyst-A Structural and Functional Analysis. Molecules 2024; 29:1440. [PMID: 38611720 PMCID: PMC11013033 DOI: 10.3390/molecules29071440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Many folding enzymes use separate domains for the binding of substrate proteins and for the catalysis of slow folding reactions such as prolyl isomerization. FKBP12 is a small prolyl isomerase without a chaperone domain. Its folding activity is low, but it could be increased by inserting the chaperone domain from the homolog SlyD of E. coli near the prolyl isomerase active site. We inserted two other chaperone domains into human FKBP12: the chaperone domain of SlpA from E. coli, and the chaperone domain of SlyD from Thermococcus sp. Both stabilized FKBP12 and greatly increased its folding activity. The insertion of these chaperone domains had no influence on the FKBP12 and the chaperone domain structure, as revealed by two crystal structures of the chimeric proteins. The relative domain orientations differ in the two crystal structures, presumably representing snapshots of a more open and a more closed conformation. Together with crystal structures from SlyD-like proteins, they suggest a path for how substrate proteins might be transferred from the chaperone domain to the prolyl isomerase domain.
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Affiliation(s)
- Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, Pavol Jozef Šafárik University in Košice, 040 11 Kosice, Slovakia
| | - Thomas A. Knappe
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Anne-Juliane Geitner
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | | | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany;
| | - Franz X. Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Roman P. Jakob
- Departement Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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10
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Muraoka T, Okumura M, Saio T. Enzymatic and synthetic regulation of polypeptide folding. Chem Sci 2024; 15:2282-2299. [PMID: 38362427 PMCID: PMC10866363 DOI: 10.1039/d3sc05781j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Proper folding is essential for the biological functions of all proteins. The folding process is intrinsically error-prone, and the misfolding of a polypeptide chain can cause the formation of toxic aggregates related to pathological outcomes such as neurodegenerative disease and diabetes. Chaperones and some enzymes are involved in the cellular proteostasis systems that assist polypeptide folding to diminish the risk of aggregation. Elucidating the molecular mechanisms of chaperones and related enzymes is important for understanding proteostasis systems and protein misfolding- and aggregation-related pathophysiology. Furthermore, mechanistic studies of chaperones and related enzymes provide important clues to designing chemical mimics, or chemical chaperones, that are potentially useful for recovering proteostasis activities as therapeutic approaches for treating and preventing protein misfolding-related diseases. In this Perspective, we provide a comprehensive overview of the latest understanding of the folding-promotion mechanisms by chaperones and oxidoreductases and recent progress in the development of chemical mimics that possess activities comparable to enzymes, followed by a discussion of future directions.
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Affiliation(s)
- Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology Koganei Tokyo 184-8588 Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC) Kanagawa 243-0435 Japan
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University Sendai Miyagi 980-8578 Japan
| | - Tomohide Saio
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University Tokushima 770-8503 Japan
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11
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Thommen BT, Dziekan JM, Achcar F, Tjia S, Passecker A, Buczak K, Gumpp C, Schmidt A, Rottmann M, Grüring C, Marti M, Bozdech Z, Brancucci NMB. Genetic validation of PfFKBP35 as an antimalarial drug target. eLife 2023; 12:RP86975. [PMID: 37934560 PMCID: PMC10629825 DOI: 10.7554/elife.86975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Plasmodium falciparum accounts for the majority of over 600,000 malaria-associated deaths annually. Parasites resistant to nearly all antimalarials have emerged and the need for drugs with alternative modes of action is thus undoubted. The FK506-binding protein PfFKBP35 has gained attention as a promising drug target due to its high affinity to the macrolide compound FK506 (tacrolimus). Whilst there is considerable interest in targeting PfFKBP35 with small molecules, a genetic validation of this factor as a drug target is missing and its function in parasite biology remains elusive. Here, we show that limiting PfFKBP35 levels are lethal to P. falciparum and result in a delayed death-like phenotype that is characterized by defective ribosome homeostasis and stalled protein synthesis. Our data furthermore suggest that FK506, unlike the action of this drug in model organisms, exerts its antiproliferative activity in a PfFKBP35-independent manner and, using cellular thermal shift assays, we identify putative FK506-targets beyond PfFKBP35. In addition to revealing first insights into the function of PfFKBP35, our results show that FKBP-binding drugs can adopt non-canonical modes of action - with major implications for the development of FK506-derived molecules active against Plasmodium parasites and other eukaryotic pathogens.
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Affiliation(s)
- Basil T Thommen
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Jerzy M Dziekan
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Fiona Achcar
- Wellcome Center for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of GlasgowGlasgowUnited Kingdom
- Institute for Parasitology, University of ZurichZurichSwitzerland
| | - Seth Tjia
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Armin Passecker
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | | | - Christin Gumpp
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | | | - Matthias Rottmann
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Christof Grüring
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Matthias Marti
- Wellcome Center for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of GlasgowGlasgowUnited Kingdom
- Institute for Parasitology, University of ZurichZurichSwitzerland
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Nicolas MB Brancucci
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
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12
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Chen X, Kaiser CM. AP profiling resolves co-translational folding pathway and chaperone interactions in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555749. [PMID: 37693575 PMCID: PMC10491307 DOI: 10.1101/2023.09.01.555749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Natural proteins have evolved to fold robustly along specific pathways. Folding begins during synthesis, guided by interactions of the nascent protein with the ribosome and molecular chaperones. However, the timing and progression of co-translational folding remain largely elusive, in part because the process is difficult to measure in the natural environment of the cytosol. We developed a high-throughput method to quantify co-translational folding in live cells that we term Arrest Peptide profiling (AP profiling). We employed AP profiling to delineate co-translational folding for a set of GTPase domains with very similar structures, defining how topology shapes folding pathways. Genetic ablation of major nascent chain-binding chaperones resulted in localized folding changes that suggest how functional redundancies among chaperones are achieved by distinct interactions with the nascent protein. Collectively, our studies provide a window into cellular folding pathways of complex proteins and pave the way for systematic studies on nascent protein folding at unprecedented resolution and throughput.
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Affiliation(s)
- Xiuqi Chen
- CMDB Graduate Program, Johns Hopkins University, Baltimore, MD, United States
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Present address: Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Christian M. Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
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13
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Taguchi H, Koike-Takeshita A. In vivo client proteins of the chaperonin GroEL-GroES provide insight into the role of chaperones in protein evolution. Front Mol Biosci 2023; 10:1091677. [PMID: 36845542 PMCID: PMC9950496 DOI: 10.3389/fmolb.2023.1091677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Protein folding is often hampered by intermolecular protein aggregation, which can be prevented by a variety of chaperones in the cell. Bacterial chaperonin GroEL is a ring-shaped chaperone that forms complexes with its cochaperonin GroES, creating central cavities to accommodate client proteins (also referred as substrate proteins) for folding. GroEL and GroES (GroE) are the only indispensable chaperones for bacterial viability, except for some species of Mollicutes such as Ureaplasma. To understand the role of chaperonins in the cell, one important goal of GroEL research is to identify a group of obligate GroEL/GroES clients. Recent advances revealed hundreds of in vivo GroE interactors and obligate chaperonin-dependent clients. This review summarizes the progress on the in vivo GroE client repertoire and its features, mainly for Escherichia coli GroE. Finally, we discuss the implications of the GroE clients for the chaperone-mediated buffering of protein folding and their influences on protein evolution.
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Affiliation(s)
- Hideki Taguchi
- Cell Biology Center, Tokyo Institute of Technology, Yokohama, Japan,*Correspondence: Hideki Taguchi,
| | - Ayumi Koike-Takeshita
- Department of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
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14
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Matavacas J, Hallgren J, von Wachenfeldt C. Bacillus subtilis forms twisted cells with cell wall integrity defects upon removal of the molecular chaperones DnaK and trigger factor. Front Microbiol 2023; 13:988768. [PMID: 36726573 PMCID: PMC9886141 DOI: 10.3389/fmicb.2022.988768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023] Open
Abstract
The protein homeostasis network ensures a proper balance between synthesis, folding, and degradation of all cellular proteins. DnaK and trigger factor (TF) are ubiquitous bacterial molecular chaperones that assist in protein folding, as well as preventing protein misfolding and aggregation. In Escherichia coli, DnaK and TF possess partially overlapping functions. Their combined depletion results in proteostasis collapse and is synthetically lethal at temperatures above 30°C. To increase our understanding on how proteostasis is maintained in Gram-positive bacteria, we have investigated the physiological effects of deleting dnaK and tig (encoding for DnaK and TF) in Bacillus subtilis. We show that combined deletion of dnaK and tig in B. subtilis is non-lethal, but causes a severe pleiotropic phenotype, including an aberrant twisted and filamentous cell morphology, as well as decreased tolerance to heat and to cell wall active antibiotics and hydrolytic enzymes, indicative of defects in cell wall integrity. In addition, cells lacking DnaK and TF have a much smaller colony size due to defects in motility. Despite these physiological changes, we observed no major compromises in important cellular processes such as cell growth, FtsZ localization and division and only moderate defects in spore formation. Finally, through suppressor analyses, we found that the wild-type cell shape can be partially restored by mutations in genes involved in metabolism or in other diverse cellular processes.
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15
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M.tb-Rv2462c of Mycobacterium tuberculosis Shows Chaperone-like Activity and Plays a Role in Stress Adaptation and Immunomodulation. BIOLOGY 2022; 12:biology12010069. [PMID: 36671761 PMCID: PMC9855790 DOI: 10.3390/biology12010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023]
Abstract
Mycobacterium tuberculosis (M.tb)-encoded factors protect it against host-generated stresses and support its survival in the hostile host environment. M.tb possesses two peptidyl-prolyl cis-trans isomerases and a probable trigger factor encoded by Rv2462c which has an FKBP-like PPIase domain. PPIases are known to assist the folding of peptidyl-prolyl bonds and are involved in various cellular processes important for bacterial survival in host-generated stresses. In this study, we aim to functionally characterize Rv2462c of M.tb. Our data suggest that the trigger factor of M.tb exhibits chaperone activity both in vitro and in vivo. Heterologous expression of M.tb-Rv2462c locus into Mycobacterium smegmatis enhanced its survival within macrophages, adaptation to oxidative stress and biofilm formation. M.tb-trigger factor has strong immunomodulatory potential and modifies the cytokine profile of the host towards the proinflammatory axis.
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16
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Rief M, Žoldák G. Single-molecule mechanical studies of chaperones and their clients. BIOPHYSICS REVIEWS 2022; 3:041301. [PMID: 38505517 PMCID: PMC10903372 DOI: 10.1063/5.0098033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/12/2022] [Indexed: 03/21/2024]
Abstract
Single-molecule force spectroscopy provides access to the mechanics of biomolecules. Recently, magnetic and laser optical tweezers were applied in the studies of chaperones and their interaction with protein clients. Various aspects of the chaperone-client interactions can be revealed based on the mechanical probing strategies. First, when a chaperone is probed under load, one can examine the inner workings of the chaperone while it interacts with and works on the client protein. Second, when protein clients are probed under load, the action of chaperones on folding clients can be studied in great detail. Such client folding studies have given direct access to observing actions of chaperones in real-time, like foldase, unfoldase, and holdase activity. In this review, we introduce the various single molecule mechanical techniques and summarize recent single molecule mechanical studies on heat shock proteins, chaperone-mediated folding on the ribosome, SNARE folding, and studies of chaperones involved in the folding of membrane proteins. An outlook on significant future developments is given.
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Affiliation(s)
- Matthias Rief
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Ernst-Otto-Fischer-Str., 8, D-85748 Garching, Germany
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Trieda SNP 1, 040 11 Košice, Slovakia
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17
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Carius Y, Ries F, Gries K, Trentmann O, Lancaster CRD, Willmund F. Structural features of chloroplast trigger factor determined at 2.6 Å resolution. Acta Crystallogr D Struct Biol 2022; 78:1259-1272. [PMID: 36189745 PMCID: PMC9527764 DOI: 10.1107/s2059798322009068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/11/2022] [Indexed: 11/21/2022] Open
Abstract
The folding of newly synthesized polypeptides requires the coordinated action of molecular chaperones. Prokaryotic cells and the chloroplasts of plant cells possess the ribosome-associated chaperone trigger factor, which binds nascent polypeptides at their exit stage from the ribosomal tunnel. The structure of bacterial trigger factor has been well characterized and it has a dragon-shaped conformation, with flexible domains responsible for ribosome binding, peptidyl-prolyl cis-trans isomerization (PPIase) activity and substrate protein binding. Chloroplast trigger-factor sequences have diversified from those of their bacterial orthologs and their molecular mechanism in plant organelles has been little investigated to date. Here, the crystal structure of the plastidic trigger factor from the green alga Chlamydomonas reinhardtii is presented at 2.6 Å resolution. Due to the high intramolecular flexibility of the protein, diffraction to this resolution was only achieved using a protein that lacked the N-terminal ribosome-binding domain. The eukaryotic trigger factor from C. reinhardtii exhibits a comparable dragon-shaped conformation to its bacterial counterpart. However, the C-terminal chaperone domain displays distinct charge distributions, with altered positioning of the helical arms and a specifically altered charge distribution along the surface responsible for substrate binding. While the PPIase domain shows a highly conserved structure compared with other PPIases, its rather weak activity and an unusual orientation towards the C-terminal domain points to specific adaptations of eukaryotic trigger factor for function in chloroplasts.
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Affiliation(s)
- Yvonne Carius
- Department of Structural Biology, Saarland University, Center of Human and Molecular Biology (ZHMB), Faculty of Medicine, Building 60, 66421 Homburg, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663 Kaiserslautern, Germany
| | - Karin Gries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663 Kaiserslautern, Germany
| | - Oliver Trentmann
- Molecular Botany, University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663 Kaiserslautern, Germany
| | - C. Roy D. Lancaster
- Department of Structural Biology, Saarland University, Center of Human and Molecular Biology (ZHMB), Faculty of Medicine, Building 60, 66421 Homburg, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663 Kaiserslautern, Germany
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18
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Mecha MF, Hutchinson RB, Lee JH, Cavagnero S. Protein folding in vitro and in the cell: From a solitary journey to a team effort. Biophys Chem 2022; 287:106821. [PMID: 35667131 PMCID: PMC9636488 DOI: 10.1016/j.bpc.2022.106821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 12/22/2022]
Abstract
Correct protein folding is essential for the health and function of living organisms. Yet, it is not well understood how unfolded proteins reach their native state and avoid aggregation, especially within the cellular milieu. Some proteins, especially small, single-domain and apparent two-state folders, successfully attain their native state upon dilution from denaturant. Yet, many more proteins undergo misfolding and aggregation during this process, in a concentration-dependent fashion. Once formed, native and aggregated states are often kinetically trapped relative to each other. Hence, the early stages of protein life are absolutely critical for proper kinetic channeling to the folded state and for long-term solubility and function. This review summarizes current knowledge on protein folding/aggregation mechanisms in buffered solution and within the bacterial cell, highlighting early stages. Remarkably, teamwork between nascent chain, ribosome, trigger factor and Hsp70 molecular chaperones enables all proteins to overcome aggregation propensities and reach a long-lived bioactive state.
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Affiliation(s)
- Miranda F Mecha
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States of America
| | - Rachel B Hutchinson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States of America
| | - Jung Ho Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States of America
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States of America.
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19
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Kaushik S, He H, Dalbey RE. Bacterial Signal Peptides- Navigating the Journey of Proteins. Front Physiol 2022; 13:933153. [PMID: 35957980 PMCID: PMC9360617 DOI: 10.3389/fphys.2022.933153] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022] Open
Abstract
In 1971, Blobel proposed the first statement of the Signal Hypothesis which suggested that proteins have amino-terminal sequences that dictate their export and localization in the cell. A cytosolic binding factor was predicted, and later the protein conducting channel was discovered that was proposed in 1975 to align with the large ribosomal tunnel. The 1975 Signal Hypothesis also predicted that proteins targeted to different intracellular membranes would possess distinct signals and integral membrane proteins contained uncleaved signal sequences which initiate translocation of the polypeptide chain. This review summarizes the central role that the signal peptides play as address codes for proteins, their decisive role as targeting factors for delivery to the membrane and their function to activate the translocation machinery for export and membrane protein insertion. After shedding light on the navigation of proteins, the importance of removal of signal peptide and their degradation are addressed. Furthermore, the emerging work on signal peptidases as novel targets for antibiotic development is described.
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20
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Abstract
The folding of proteins into their native structure is crucial for the functioning of all biological processes. Molecular chaperones are guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity. ATP-independent chaperones do not require ATP to regulate their functional cycle. Although these chaperones have been traditionally regarded as passive holdases that merely prevent aggregation, recent work has shown that they can directly affect the folding energy landscape by tuning their affinity to various folding states of the client. This review focuses on emerging paradigms in the mechanism of action of ATP-independent chaperones and on the various modes of regulating client binding and release.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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21
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Fedorov AN. Biosynthetic Protein Folding and Molecular Chaperons. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S128-S19. [PMID: 35501992 DOI: 10.1134/s0006297922140115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The problem of linear polypeptide chain folding into a unique tertiary structure is one of the fundamental scientific challenges. The process of folding cannot be fully understood without its biological context, especially for big multidomain and multisubunit proteins. The principal features of biosynthetic folding are co-translational folding of growing nascent polypeptide chains and involvement of molecular chaperones in the process. The review summarizes available data on the early events of nascent chain folding, as well as on later advanced steps, including formation of elements of native structure. The relationship between the non-uniformity of translation rate and folding of the growing polypeptide is discussed. The results of studies on the effect of biosynthetic folding features on the parameters of folding as a physical process, its kinetics and mechanisms, are presented. Current understanding and hypotheses on the relationship of biosynthetic folding with the fundamental physical parameters and current views on polypeptide folding in the context of energy landscapes are discussed.
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Affiliation(s)
- Alexey N Fedorov
- Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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22
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Mercier E, Wang X, Bögeholz LAK, Wintermeyer W, Rodnina MV. Cotranslational Biogenesis of Membrane Proteins in Bacteria. Front Mol Biosci 2022; 9:871121. [PMID: 35573737 PMCID: PMC9099147 DOI: 10.3389/fmolb.2022.871121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/12/2022] [Indexed: 12/26/2022] Open
Abstract
Nascent polypeptides emerging from the ribosome during translation are rapidly scanned and processed by ribosome-associated protein biogenesis factors (RPBs). RPBs cleave the N-terminal formyl and methionine groups, assist cotranslational protein folding, and sort the proteins according to their cellular destination. Ribosomes translating inner-membrane proteins are recognized and targeted to the translocon with the help of the signal recognition particle, SRP, and SRP receptor, FtsY. The growing nascent peptide is then inserted into the phospholipid bilayer at the translocon, an inner-membrane protein complex consisting of SecY, SecE, and SecG. Folding of membrane proteins requires that transmembrane helices (TMs) attain their correct topology, the soluble domains are inserted at the correct (cytoplasmic or periplasmic) side of the membrane, and – for polytopic membrane proteins – the TMs find their interaction partner TMs in the phospholipid bilayer. This review describes the recent progress in understanding how growing nascent peptides are processed and how inner-membrane proteins are targeted to the translocon and find their correct orientation at the membrane, with the focus on biophysical approaches revealing the dynamics of the process. We describe how spontaneous fluctuations of the translocon allow diffusion of TMs into the phospholipid bilayer and argue that the ribosome orchestrates cotranslational targeting not only by providing the binding platform for the RPBs or the translocon, but also by helping the nascent chains to find their correct orientation in the membrane. Finally, we present the auxiliary role of YidC as a chaperone for inner-membrane proteins. We show how biophysical approaches provide new insights into the dynamics of membrane protein biogenesis and raise new questions as to how translation modulates protein folding.
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23
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Matavacas J, von Wachenfeldt C. Update on the Protein Homeostasis Network in Bacillus subtilis. Front Microbiol 2022; 13:865141. [PMID: 35350626 PMCID: PMC8957991 DOI: 10.3389/fmicb.2022.865141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Protein homeostasis is fundamental to cell function and survival. It relies on an interconnected network of processes involving protein synthesis, folding, post-translational modification and degradation as well as regulators of these processes. Here we provide an update on the roles, regulation and subcellular localization of the protein homeostasis machinery in the Gram-positive model organism Bacillus subtilis. We discuss emerging ideas and current research gaps in the field that, if tackled, increase our understanding of how Gram-positive bacteria, including several human pathogens, maintain protein homeostasis and cope with stressful conditions that challenge their survival.
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24
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Cyclophilin anaCyp40 regulates photosystem assembly and phycobilisome association in a cyanobacterium. Nat Commun 2022; 13:1690. [PMID: 35354803 PMCID: PMC8967839 DOI: 10.1038/s41467-022-29211-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/28/2022] [Indexed: 11/08/2022] Open
Abstract
Cyclophilins, or immunophilins, are proteins found in many organisms including bacteria, plants and humans. Most of them display peptidyl-prolyl cis-trans isomerase activity, and play roles as chaperones or in signal transduction. Here, we show that cyclophilin anaCyp40 from the cyanobacterium Anabaena sp. PCC 7120 is enzymatically active, and seems to be involved in general stress responses and in assembly of photosynthetic complexes. The protein is associated with the thylakoid membrane and interacts with phycobilisome and photosystem components. Knockdown of anacyp40 leads to growth defects under high-salt and high-light conditions, and reduced energy transfer from phycobilisomes to photosystems. Elucidation of the anaCyp40 crystal structure at 1.2-Å resolution reveals an N-terminal helical domain with similarity to PsbQ components of plant photosystem II, and a C-terminal cyclophilin domain with a substrate-binding site. The anaCyp40 structure is distinct from that of other multi-domain cyclophilins (such as Arabidopsis thaliana Cyp38), and presents features that are absent in single-domain cyclophilins.
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25
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Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding. Int J Mol Sci 2022; 23:ijms23052485. [PMID: 35269628 PMCID: PMC8910466 DOI: 10.3390/ijms23052485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/10/2022] Open
Abstract
Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics-activity relationships to explain the mechanism of functional diversity of molecular chaperones.
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26
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Zinc-Dependent Oligomerization of Thermus thermophilus Trigger Factor Chaperone. BIOLOGY 2021; 10:biology10111106. [PMID: 34827099 PMCID: PMC8614707 DOI: 10.3390/biology10111106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Metal ions often play important roles in biological processes. Thermus thermophilus trigger factor (TtTF) is a zinc-dependent molecular chaperone where Zn2+ has been shown to enhance its folding-arrest activity. However, the mechanisms of how Zn2+ binds to TtTF and how Zn2+ affects the activity of TtTF are yet to be elucidated. As a first step in understanding the mechanism, we performed in vitro biophysical experiments on TtTF to investigate the zinc-binding site on TtTF and unveil how Zn2+ alters the physical properties of TtTF, including secondary structure, thermal stability, and oligomeric state. Our results showed that TtTF binds Zn2+ in a 1:1 ratio, and all three domains of TtTF are involved in zinc-binding. We found that Zn2+ does not affect the thermal stability of TtTF, whereas it does induce partial structural change and promote the oligomerization of TtTF. Given that the folding-arrest activity of Escherichia coli TF (EcTF) is regulated by its oligomerization, our results imply that TtTF exploits Zn2+ to modulate its oligomeric state to regulate the activity. Abstract Thermus thermophilus trigger factor (TtTF) is a zinc-dependent molecular chaperone whose folding-arrest activity is regulated by Zn2+. However, little is known about the mechanism of zinc-dependent regulation of the TtTF activity. Here we exploit in vitro biophysical experiments to investigate zinc-binding, the oligomeric state, the secondary structure, and the thermal stability of TtTF in the absence and presence of Zn2+. The data show that full-length TtTF binds Zn2+, but the isolated domains and tandem domains of TtTF do not bind to Zn2+. Furthermore, circular dichroism (CD) and nuclear magnetic resonance (NMR) spectra suggested that Zn2+-binding induces the partial structural changes of TtTF, and size exclusion chromatography-multi-angle light scattering (SEC-MALS) showed that Zn2+ promotes TtTF oligomerization. Given the previous work showing that the activity regulation of E. coli trigger factor is accompanied by oligomerization, the data suggest that TtTF exploits zinc ions to induce the structural change coupled with the oligomerization to assemble the client-binding site, thereby effectively preventing proteins from misfolding in the thermal environment.
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Nikolaeva DD, Gelfand MS, Garushyants SK. Simplification of Ribosomes in Bacteria with Tiny Genomes. Mol Biol Evol 2021; 38:58-66. [PMID: 32681797 PMCID: PMC7782861 DOI: 10.1093/molbev/msaa184] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine-Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.
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Affiliation(s)
- Daria D Nikolaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sofya K Garushyants
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
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Macošek J, Mas G, Hiller S. Redefining Molecular Chaperones as Chaotropes. Front Mol Biosci 2021; 8:683132. [PMID: 34195228 PMCID: PMC8237284 DOI: 10.3389/fmolb.2021.683132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/20/2021] [Indexed: 01/27/2023] Open
Abstract
Molecular chaperones are the key instruments of bacterial protein homeostasis. Chaperones not only facilitate folding of client proteins, but also transport them, prevent their aggregation, dissolve aggregates and resolve misfolded states. Despite this seemingly large variety, single chaperones can perform several of these functions even on multiple different clients, thus suggesting a single biophysical mechanism underlying. Numerous recently elucidated structures of bacterial chaperone–client complexes show that dynamic interactions between chaperones and their client proteins stabilize conformationally flexible non-native client states, which results in client protein denaturation. Based on these findings, we propose chaotropicity as a suitable biophysical concept to rationalize the generic activity of chaperones. We discuss the consequences of applying this concept in the context of ATP-dependent and -independent chaperones and their functional regulation.
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Huang CT, Lai YC, Chen SY, Ho MR, Chiang YW, Hsu ST. Structural polymorphism and substrate promiscuity of a ribosome-associated molecular chaperone. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:375-386. [PMID: 37904759 PMCID: PMC10539794 DOI: 10.5194/mr-2-375-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/02/2021] [Indexed: 11/01/2023]
Abstract
Trigger factor (TF) is a highly conserved multi-domain molecular chaperone that exerts its chaperone activity at the ribosomal tunnel exit from which newly synthesized nascent chains emerge. TF also displays promiscuous substrate binding for a large number of cytosolic proteins independent of ribosome binding. We asked how TF recognizes a variety of substrates while existing in a monomer-dimer equilibrium. Paramagnetic nuclear magnetic resonance (NMR) and electron spin resonance (ESR) spectroscopy were used to show that dimeric TF displays a high degree of structural polymorphism in solution. A series of peptides has been generated to quantify their TF binding affinities in relation with their sequence compositions. The results confirmed a previous predication that TF preferentially binds to peptide fragments that are rich in aromatic and positively charged amino acids. NMR paramagnetic relaxation enhancement analysis showed that TF utilizes multiple binding sites, located in the chaperone domain and part of the prolyl trans-cis isomerization domain, to interact with these peptides. Dimerization of TF effectively sequesters most of the substrate binding sites, which are expected to become accessible upon binding to the ribosome as a monomer. As TF lacks ATPase activity, which is commonly used to trigger conformational changes within molecular chaperones in action, the ribosome-binding-associated disassembly and conformational rearrangements may be the underlying regulatory mechanism of its chaperone activity.
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Affiliation(s)
- Chih-Ting Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yei-Chen Lai
- Department of Chemistry, National Tsing Hua University, Hsichu 30013, Taiwan
| | - Szu-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsichu 30013, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
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Fatima K, Naqvi F, Younas H. A Review: Molecular Chaperone-mediated Folding, Unfolding and Disaggregation of Expressed Recombinant Proteins. Cell Biochem Biophys 2021; 79:153-174. [PMID: 33634426 DOI: 10.1007/s12013-021-00970-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/01/2021] [Indexed: 12/26/2022]
Abstract
The advancements in biotechnology over time have led to an increase in the demand of pure, soluble and functionally active proteins. Recombinant protein production has thus been employed to obtain high expression of purified proteins in bulk. E. coli is considered as the most desirable host for recombinant protein production due to its inexpensive and fast cultivation, simple nutritional requirements and known genetics. Despite all these benefits, recombinant protein production often comes with drawbacks, such as, the most common being the formation of inclusion bodies due to improper protein folding. Consequently, this can lead to the loss of the structure-function relationship of a protein. Apart from various strategies, one major strategy to resolve this issue is the use of molecular chaperones that act as folding modulators for proteins. Molecular chaperones assist newly synthesized, aggregated or misfolded proteins to fold into their native conformations. Chaperones have been widely used to improve the expression of various proteins which are otherwise difficult to produce in E. coli. Here, we discuss the structure, function, and role of major E. coli molecular chaperones in recombinant technology such as trigger factor, GroEL, DnaK and ClpB.
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Affiliation(s)
- Komal Fatima
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan
| | - Fatima Naqvi
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan
| | - Hooria Younas
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan.
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The multi-drug efflux system AcrABZ-TolC is essential for infection of Salmonella Typhimurium by the flagellum-dependent bacteriophage Chi. J Virol 2021; 95:JVI.00394-21. [PMID: 33731456 PMCID: PMC8139690 DOI: 10.1128/jvi.00394-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteriophages are the most abundant biological entities in the biosphere. Due to their host specificity and ability to kill bacteria rapidly, bacteriophages have many potential healthcare applications, including therapy against antibiotic-resistant bacteria. Infection by flagellotropic bacteriophages requires a properly rotating bacterial flagellar filament. The flagella-dependent phage χ (Chi) infects serovars of the pathogenic enterobacterium Salmonella enterica However, cell surface receptors and proteins involved in other stages of χ infection have not been discovered to date. We screened a multi-gene deletion library of S. enterica serovar Typhimurium by spotting mutants on soft agar plates seeded with bacteriophage χ and monitoring their ability to grow and form a swim ring, a characteristic of bacteriophage-resistant motile mutants. Those multi-gene deletion regions identified to be important for χ infectivity were further investigated by characterizing the phenotypes of corresponding single-gene deletion mutants. This way, we identified motile mutants with varying degrees of resistance to χ. Deletions in individual genes encoding the AcrABZ-TolC multi-drug efflux system drastically reduced infection by bacteriophage χ. Furthermore, an acrABtolC triple deletion strain was fully resistant to χ. Infection was severely reduced but not entirely blocked by the deletion of the gene tig encoding the molecular chaperone trigger factor. Finally, deletion in genes encoding enzymes involved in the synthesis of the antioxidants glutathione (GSH) and uric acid resulted in reduced infectivity. Our findings begin to elucidate poorly understood processes involved in later stages of flagellotropic bacteriophage infection and informs research aimed at the use of bacteriophages to combat antibiotic-resistant bacterial infections.IMPORTANCEAntimicrobial resistance is a large concern in the healthcare field. With more multi-drug resistant bacterial pathogens emerging, other techniques for eliminating bacterial infections are being explored. Among these is phage therapy, where combinations of specific phages are used to treat infections. Generally, phages utilize cell appendages and surface receptors for the initial attachment to their host. Phages that are flagellotropic are of particular interest because flagella are often important in bacterial virulence, making resistance to attachment of these phages harder to achieve without reducing virulence. This study discovered the importance of a multi-drug efflux pump for the infection of Salmonella enterica by a flagellotropic phage. In theory, if a bacterial pathogen develops phage resistance by altering expression of the efflux pump then the pathogen would simultaneously become more susceptible to the antibiotic substrates of the pump. Thus, co-administering antibiotics and flagellotropic phage may be a particularly potent antibacterial therapy.
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32
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Xia L, Luo G, Wu M, Wang L, Zhang N, Wu C, Yin Y. Self-assembled raccoon dog parvovirus VP2 protein confers immunity against RDPV disease in raccoon dogs: in vitro and in vivo studies. Virol J 2021; 18:79. [PMID: 33858464 PMCID: PMC8047598 DOI: 10.1186/s12985-021-01549-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/07/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Raccoon dog parvovirus (RDPV) causes acute infectious diseases in raccoon dogs and may cause death in severe cases. The current treatment strategy relies on the extensive usage of classical inactivated vaccine which is marred by large doses, short immunization cycles and safety concerns. METHODS The present study aimed at optimization of RDPV VP2 gene, subcloning the gene into plasmid pET30a, and its subsequent transfer to Escherichia coli with trigger factor 16 for co-expression. The protein thus expressed was purified with ammonium sulfate precipitation, hydrophobic chromatography, and endotoxin extraction procedures. VLPs were examined by transmission electron microscopy, dynamic light scattering, and the efficacy of VLPs vaccine was tested in vivo. RESULTS Results indicated that RDPV VP2 protein could be expressed soluble. Transmission electron microscopy and dynamic light scattering results indicated that RDPV VP2 self-assembled into VLPs. Hemagglutination inhibition antibody titers elicited by Al(OH)3 adjuvanted RDPV VLPs were comparable with RDPV inactivated vaccines, and the viral loads in the blood of the struck raccoon dogs were greatly reduced. Hematoxylin and eosin and Immunohistochemical results indicated that RDPV VLPs vaccine could protect raccoon dogs against RDPV infections. CONCLUSIONS These results suggest that RDPV VLPs can become a potential vaccine candidate for RDPV therapy.
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Affiliation(s)
- Linya Xia
- School of Life Sciences, Changchun University of Technology, Changchun, 130012, China
| | - Guoliang Luo
- Institute of Special Animal and Plant Sciences of CAAS, Changchun, 130012, China
| | - Mingjie Wu
- School of Life Sciences, Changchun University of Technology, Changchun, 130012, China
| | - Lei Wang
- School of Life Sciences, Changchun University of Technology, Changchun, 130012, China
| | - Ning Zhang
- School of Life Sciences, Changchun University of Technology, Changchun, 130012, China
| | - Congmei Wu
- School of Life Sciences, Changchun University of Technology, Changchun, 130012, China
| | - Yuhe Yin
- School of Life Sciences, Changchun University of Technology, Changchun, 130012, China.
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Jiang C, Wynne M, Huber D. How Quality Control Systems AID Sec-Dependent Protein Translocation. Front Mol Biosci 2021; 8:669376. [PMID: 33928127 PMCID: PMC8076867 DOI: 10.3389/fmolb.2021.669376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The evolutionarily conserved Sec machinery is responsible for transporting proteins across the cytoplasmic membrane. Protein substrates of the Sec machinery must be in an unfolded conformation in order to be translocated across (or inserted into) the cytoplasmic membrane. In bacteria, the requirement for unfolded proteins is strict: substrate proteins that fold (or misfold) prematurely in the cytoplasm prior to translocation become irreversibly trapped in the cytoplasm. Partially folded Sec substrate proteins and stalled ribosomes containing nascent Sec substrates can also inhibit translocation by blocking (i.e., “jamming”) the membrane-embedded Sec machinery. To avoid these issues, bacteria have evolved a complex network of quality control systems to ensure that Sec substrate proteins do not fold in the cytoplasm. This quality control network can be broken into three branches, for which we have defined the acronym “AID”: (i) avoidance of cytoplasmic intermediates through cotranslationally channeling newly synthesized Sec substrates to the Sec machinery; (ii) inhibition of folding Sec substrate proteins that transiently reside in the cytoplasm by molecular chaperones and the requirement for posttranslational modifications; (iii) destruction of products that could potentially inhibit translocation. In addition, several stress response pathways help to restore protein-folding homeostasis when environmental conditions that inhibit translocation overcome the AID quality control systems.
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Affiliation(s)
- Chen Jiang
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Max Wynne
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Damon Huber
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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34
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Akbar S, Bhakta S, Sengupta J. Structural insights into the interplay of protein biogenesis factors with the 70S ribosome. Structure 2021; 29:755-767.e4. [PMID: 33761323 DOI: 10.1016/j.str.2021.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/16/2021] [Accepted: 03/02/2021] [Indexed: 11/28/2022]
Abstract
Bacterial co-translational N-terminal methionine excision, an early event of nascent polypeptide chain processing, is mediated by two enzymes: peptide deformylase (PDF) and methionine aminopeptidase (MetAP). Trigger factor (TF), the only ribosome-associated bacterial chaperone, offers co-translational chaperoning assistance. Here, we present two high-resolution cryoelectron microscopy structures of tRNA-bound E. coli ribosome complexes showing simultaneous binding of PDF and TF, in the absence (3.4 Å) and presence of MetAP (4.1 Å). These structures establish molecular details of the interactions of the factors with the ribosome, and thereby reveal the structural basis of nascent chain processing. Our results suggest that simultaneous binding of all three factors is not a functionally favorable mechanism of nascent chain processing. Strikingly, an unusual structural distortion of the 70S ribosome, potentially driven by binding of multiple copies of MetAP, is observed when MetAP is incubated with a pre-formed PDF-TF-bound ribosome complex.
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Affiliation(s)
- Shirin Akbar
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Sayan Bhakta
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Jayati Sengupta
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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35
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Rey M, Dhenin J, Kong Y, Nouchikian L, Filella I, Duchateau M, Dupré M, Pellarin R, Duménil G, Chamot-Rooke J. Advanced In Vivo Cross-Linking Mass Spectrometry Platform to Characterize Proteome-Wide Protein Interactions. Anal Chem 2021; 93:4166-4174. [DOI: 10.1021/acs.analchem.0c04430] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Martial Rey
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Jonathan Dhenin
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Youxin Kong
- Pathogenesis of Vascular Infections, Department of Cell Biology and Infection, Institut Pasteur, INSERM U1225, 28 rue du Docteur Roux, 75015 Paris France
| | - Lucienne Nouchikian
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Isaac Filella
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, 75015 Paris, France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Mathieu Dupré
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Riccardo Pellarin
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, 75015 Paris, France
| | - Guillaume Duménil
- Pathogenesis of Vascular Infections, Department of Cell Biology and Infection, Institut Pasteur, INSERM U1225, 28 rue du Docteur Roux, 75015 Paris France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
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36
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Choudhury M, Dhara A, Kumar M. Trigger Factor in Association with the ClpP1P2 Heterocomplex of Leptospira Promotes Protease/Peptidase Activity. ACS OMEGA 2021; 6:1400-1409. [PMID: 33490799 PMCID: PMC7818586 DOI: 10.1021/acsomega.0c05057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/28/2020] [Indexed: 05/07/2023]
Abstract
The genomic analysis of Leptospira reveals a trigger factor (TF) encoding gene (tig) to be colocalized along with the clpP1 and clpX. The TF is a crouching dragon-like protein known to be a ribosome-associated chaperone that is involved in cotranslational protein folding in bacteria in an ATP-independent mode. In Leptospira, tig is localized upstream of the clpP1 with a short (4 bp) overlap. In the present study, we document the distinctive role of Leptospira TF (LinTF) in the caseinolytic protease (ClpP) system. The recombinant LinTF (rLinTF) was found to improve the peptidase or protease activity of the ClpP1P2 heterocomplex and ClpXP1P2 complex, respectively, on model substrates. In addition, on supplementation of rLinTF to rClpP1P2 bound to its physiological ATPase chaperone ClpX or the antibiotic analogue acyldepsipeptide (ADEP), an augmentation in the activity of ClpP1P2 was observed. These studies underscore the novel role of LinTF in aiding the caseinolytic protease activity of Leptospira. Supplementation of rLinTF to a peptidase assay of rClpP1P2 conditionally in the presence of a salt (sodium citrate) with high Hofmeister strength led us to speculate that rLinTF may have a role in the assembly of multimeric proteins. The deletion of one of the arms (arm-2) of the LinTF structure from the carboxy terminal domain indicated a reduction in its capacity to stimulate rClpP1P2 activity. Thus, the C-terminal domain of LinTF may have a role in the assembly of multimeric ClpP protein, leading to enhancement of ClpP activity.
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Affiliation(s)
| | | | - Manish Kumar
- . Phone: +91-361-258-2230. Fax: +91-361-258-2249
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37
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Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex. Nat Commun 2021; 12:281. [PMID: 33436616 PMCID: PMC7804408 DOI: 10.1038/s41467-020-20553-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
A functional association is uncovered between the ribosome-associated trigger factor (TF) chaperone and the ClpXP degradation complex. Bioinformatic analyses demonstrate conservation of the close proximity of tig, the gene coding for TF, and genes coding for ClpXP, suggesting a functional interaction. The effect of TF on ClpXP-dependent degradation varies based on the nature of substrate. While degradation of some substrates are slowed down or are unaffected by TF, surprisingly, TF increases the degradation rate of a third class of substrates. These include λ phage replication protein λO, master regulator of stationary phase RpoS, and SsrA-tagged proteins. Globally, TF acts to enhance the degradation of about 2% of newly synthesized proteins. TF is found to interact through multiple sites with ClpX in a highly dynamic fashion to promote protein degradation. This chaperone-protease cooperation constitutes a unique and likely ancestral aspect of cellular protein homeostasis in which TF acts as an adaptor for ClpXP.
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38
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Nikolaeva DD, Gelfand MS, Garushyants SK. Simplification of Ribosomes in Bacteria with Tiny Genomes. Mol Biol Evol 2021. [PMID: 32681797 DOI: 10.1101/755876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine-Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.
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Affiliation(s)
- Daria D Nikolaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sofya K Garushyants
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
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39
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Hiller S. Molecular chaperones and their denaturing effect on client proteins. JOURNAL OF BIOMOLECULAR NMR 2021; 75:1-8. [PMID: 33136251 PMCID: PMC7897196 DOI: 10.1007/s10858-020-00353-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/23/2020] [Indexed: 05/05/2023]
Abstract
Advanced NMR methods combined with biophysical techniques have recently provided unprecedented insight into structure and dynamics of molecular chaperones and their interaction with client proteins. These studies showed that several molecular chaperones are able to dissolve aggregation-prone polypeptides in aqueous solution. Furthermore, chaperone-bound clients often feature fluid-like backbone dynamics and chaperones have a denaturing effect on clients. Interestingly, these effects that chaperones have on client proteins resemble the effects of known chaotropic substances. Following this analogy, chaotropicity could be a fruitful concept to describe, quantify and rationalize molecular chaperone function. In addition, the observations raise the possibility that at least some molecular chaperones might share functional similarities with chaotropes. We discuss these concepts and outline future research in this direction.
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Affiliation(s)
- Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstr. 70, 4056, Basel, Switzerland.
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40
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Jia M, Wu B, Yang Z, Chen C, Zhao M, Hou X, Niu X, Jin C, Hu Y. Conformational Dynamics of the Periplasmic Chaperone SurA. Biochemistry 2020; 59:3235-3246. [PMID: 32786408 DOI: 10.1021/acs.biochem.0c00507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The periplasmic protein SurA is the primary chaperone involved in the biogenesis of bacterial outer membrane proteins and is a potential antibacterial drug target. The three-dimensional structure of SurA can be divided into three parts, a core module formed by the N- and C-terminal regions and two peptidyl-prolyl isomerase (PPIase) domains, P1 and P2. Despite the determination of the structures of several SurA-peptide complexes, the functional mechanism of this chaperone remains elusive and the roles of the two PPIase domains are yet unclear. Herein, we characterize the conformational dynamics of SurA by using solution nuclear magnetic resonance and single-molecule fluorescence resonance energy transfer methods. We demonstrate a "closed-to-open" structural transition of the P1 domain that is correlated with both chaperone activity and peptide binding and show that the flexible P2 domain can also occupy conformations that closely contact the NC core module. Our results offer a structural basis for the counteracting roles of the two PPIase domains in regulating the SurA chaperone activity.
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Affiliation(s)
- Moye Jia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bo Wu
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.,MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.,MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xianhui Hou
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Yunfei Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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41
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Hu X, Fan G, Liao H, Fu Z, Ma C, Ni H, Li X. Optimized soluble expression of a novel endoglucanase from Burkholderia pyrrocinia in Escherichia coli. 3 Biotech 2020; 10:387. [PMID: 32832337 DOI: 10.1007/s13205-020-02327-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022] Open
Abstract
Burkholderia pyrrocinia B1213, a novel microbe isolated from a Baijiu-producing environment, displayed strong cellulolytic activity on agar plates with glucan as the carbon source and had an activity of 674.5 U/mL after culturing with barley. Genome annotation of B. pyrrocinia identificated a single endoglucanase (EG)-encoding gene, designated as BpEG01790. The endoglucanase BpEG01790 shows 98.28% sequence similarity with an endo-β-1,4-glucanase (EC 3.2.1.4) from Burkholderia stabilis belonging to glycoside hydrolase family 8 (GH8). The gene BpEG01790 has an open reading frame of 1218 bp encoding a 406 amino acid (AA) residue protein (43.0 kDa) with a 40-AA signal peptide. BpEG01790 was successfully cloned into pET28a( +) with and without the signal peptide; however, attempts to overexpress this protein in Escherichia coli BL21(DE3) cells using this expression system failed. BpEG01790 was also cloned into the pCold TF vector. Active BpEG01790 was successfully overexpressed with or without the signal peptide using the pCold TF vector expression system and E. coli BL21 (DE3) cells. Overexpression of recombinant BpEG01790 without the signal peptide was higher compared with the construct that included the signal peptide. Optimization of culture conditions improved the enzyme activity by 12.5-fold. This is the first report describing the heterologous soluble overexpression of an EG belonging to GH8 from B. pyrrocinia using TF as a molecular chaperone.
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Affiliation(s)
- Xiaoqing Hu
- College of Food and Biological Engineering, Jimei University, Yindou Road, Jimei District, Xiamen, 361021 Fujian China
| | - Guangsen Fan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), No 11 Fucheng Street, Haidian District, Beijing, 100048 China
| | - Hui Liao
- College of Food and Biological Engineering, Jimei University, Yindou Road, Jimei District, Xiamen, 361021 Fujian China
| | - Zhilei Fu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
| | - Chao Ma
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Yindou Road, Jimei District, Xiamen, 361021 Fujian China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, 100048 China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), No 11 Fucheng Street, Haidian District, Beijing, 100048 China
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Tüting C, Iacobucci C, Ihling CH, Kastritis PL, Sinz A. Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity. Sci Rep 2020; 10:12618. [PMID: 32724211 PMCID: PMC7387497 DOI: 10.1038/s41598-020-69313-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
The ribosome is not only a highly complex molecular machine that translates the genetic information into proteins, but also an exceptional specimen for testing and optimizing cross-linking/mass spectrometry (XL-MS) workflows. Due to its high abundance, ribosomal proteins are frequently identified in proteome-wide XL-MS studies of cells or cell extracts. Here, we performed in-depth cross-linking of the E. coli ribosome using the amine-reactive cross-linker disuccinimidyl diacetic urea (DSAU). We analyzed 143 E. coli ribosomal structures, mapping a total of 10,771 intramolecular distances for 126 cross-link-pairs and 3,405 intermolecular distances for 97 protein pairs. Remarkably, 44% of intermolecular cross-links covered regions that have not been resolved in any high-resolution E. coli ribosome structure and point to a plasticity of cross-linked regions. We systematically characterized all cross-links and discovered flexible regions, conformational changes, and stoichiometric variations in bound ribosomal proteins, and ultimately remodeled 2,057 residues (15,794 atoms) in total. Our working model explains more than 95% of all cross-links, resulting in an optimized E. coli ribosome structure based on the cross-linking data obtained. Our study might serve as benchmark for conducting biochemical experiments on newly modeled protein regions, guided by XL-MS. Data are available via ProteomeXchange with identifier PXD018935.
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Affiliation(s)
- Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
- Corporate Preclinical R&D, Analytics and Early Formulations Department, CHIESI FARMACEUTICI S.P.A., Via Palermo 26/A, 43122, Parma, Italy
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
- Center for Structural Mass Spectrometry, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany.
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany.
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120, Halle/Saale, Germany.
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany.
- Center for Structural Mass Spectrometry, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany.
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43
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Ramakrishnan R, Houben B, Rousseau F, Schymkowitz J. Differential proteostatic regulation of insoluble and abundant proteins. Bioinformatics 2020; 35:4098-4107. [PMID: 30903148 PMCID: PMC6792106 DOI: 10.1093/bioinformatics/btz214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 12/19/2022] Open
Abstract
Motivation Despite intense effort, it has been difficult to explain chaperone dependencies of proteins from sequence or structural properties. Results We constructed a database collecting all publicly available data of experimental chaperone interaction and dependency data for the Escherichia coli proteome, and enriched it with an extensive set of protein-specific as well as cell-context-dependent proteostatic parameters. Employing this new resource, we performed a comprehensive meta-analysis of the key determinants of chaperone interaction. Our study confirms that GroEL client proteins are biased toward insoluble proteins of low abundance, but for client proteins of the Trigger Factor/DnaK axis, we instead find that cellular parameters such as high protein abundance, translational efficiency and mRNA turnover are key determinants. We experimentally confirmed the finding that chaperone dependence is a function of translation rate and not protein-intrinsic parameters by tuning chaperone dependence of Green Fluorescent Protein (GFP) in E.coli by synonymous mutations only. The juxtaposition of both protein-intrinsic and cell-contextual chaperone triage mechanisms explains how the E.coli proteome achieves combining reliable production of abundant and conserved proteins, while also enabling the evolution of diverging metabolic functions. Availability and implementation The database will be made available via http://phdb.switchlab.org. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Reshmi Ramakrishnan
- Switch Laboratory, Center for Brain and Disease Research, VIB.,Department of Cellular and Molecular Medicine, KULeuven, Leuven Belgium
| | - Bert Houben
- Switch Laboratory, Center for Brain and Disease Research, VIB.,Department of Cellular and Molecular Medicine, KULeuven, Leuven Belgium
| | - Frederic Rousseau
- Switch Laboratory, Center for Brain and Disease Research, VIB.,Department of Cellular and Molecular Medicine, KULeuven, Leuven Belgium
| | - Joost Schymkowitz
- Switch Laboratory, Center for Brain and Disease Research, VIB.,Department of Cellular and Molecular Medicine, KULeuven, Leuven Belgium
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Identification of Substrates of Cytoplasmic Peptidyl-Prolyl Cis/Trans Isomerases and Their Collective Essentiality in Escherichia Coli. Int J Mol Sci 2020; 21:ijms21124212. [PMID: 32545723 PMCID: PMC7353009 DOI: 10.3390/ijms21124212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 11/16/2022] Open
Abstract
Protein folding often requires molecular chaperones and folding catalysts, such as peptidyl-prolyl cis/trans isomerases (PPIs). The Escherichia coli cytoplasm contains six well-known PPIs, although a requirement of their PPIase activity, the identity of their substrates and relative enzymatic contribution is unknown. Thus, strains lacking all periplasmic and one of the cytoplasmic PPIs were constructed. Measurement of their PPIase activity revealed that PpiB is the major source of PPIase activity in the cytoplasm. Furthermore, viable Δ6ppi strains could be constructed only on minimal medium in the temperature range of 30-37 °C, but not on rich medium. To address the molecular basis of essentiality of PPIs, proteins that aggregate in their absence were identified. Next, wild-type and putative active site variants of FkpB, FklB, PpiB and PpiC were purified and in pull-down experiments substrates specific to each of these PPIs identified, revealing an overlap of some substrates. Substrates of PpiC were validated by immunoprecipitations using extracts from wild-type and PpiC-H81A strains carrying a 3xFLAG-tag appended to the C-terminal end of the ppiC gene on the chromosome. Using isothermal titration calorimetry, RpoE, RseA, S2, and AhpC were established as FkpB substrates and PpiC's PPIase activity was shown to be required for interaction with AhpC.
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Rein T. Peptidylprolylisomerases, Protein Folders, or Scaffolders? The Example of FKBP51 and FKBP52. Bioessays 2020; 42:e1900250. [DOI: 10.1002/bies.201900250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/12/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Theo Rein
- Department of Translational Science in Psychiatry, MunichMax Planck Institute of Psychiatry Munich 80804 Germany
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46
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Rojano-Nisimura AM, Haning K, Janovsky J, Vasquez KA, Thompson JP, Contreras LM. Codon Selection Affects Recruitment of Ribosome-Associating Factors during Translation. ACS Synth Biol 2020; 9:329-342. [PMID: 31769967 DOI: 10.1021/acssynbio.9b00344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An intriguing aspect of protein synthesis is how cotranslational events are managed inside the cell. In this study, we developed an in vivo bimolecular fluorescence complementation assay coupled to SecM stalling (BiFC-SecM) to study how codon usage influences the interactions of ribosome-associating factors that occur cotranslationally. We profiled ribosomal associations of a number of proteins, and observed differential association of chaperone proteins TF, DnaK, GroEL, and translocation factor Ffh as a result of introducing synonymous codon substitutions that change the affinity of the translating sequence to the ribosomal anti-Shine-Dalgarno (aSD) sequence. The use of pausing sequences within proteins regulates their transit within the translating ribosome. Our results indicate that the dynamics between cellular factors and the new polypeptide chain are affected by how codon composition is designed. Furthermore, associating factors may play a role in processes including protein quality control (folding and degradation) and cellular respiration.
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Affiliation(s)
- Alejandra M. Rojano-Nisimura
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Stop A4800, Austin, Texas 78712, United States
| | - Katie Haning
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Justin Janovsky
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Stop A4800, Austin, Texas 78712, United States
| | - Kevin A. Vasquez
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Jeffrey P. Thompson
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
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Wild K, Aleksić M, Lapouge K, Juaire KD, Flemming D, Pfeffer S, Sinning I. MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments. Nat Commun 2020; 11:776. [PMID: 32034140 PMCID: PMC7005732 DOI: 10.1038/s41467-020-14603-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature 80S ribosomes for translational control. Here, we present a cryo-EM single particle analysis reconstruction of Ebp1 bound to non-translating human 80S ribosomes at a resolution range from 3.3 to ~8 Å. Ebp1 blocks the tunnel exit with major interactions to the general uL23/uL29 docking site for nascent chain-associated factors complemented by eukaryote-specific eL19 and rRNA helix H59. H59 is defined as dynamic adaptor undergoing significant remodeling upon Ebp1 binding. Ebp1 recruits rRNA expansion segment ES27L to the tunnel exit via specific interactions with rRNA consensus sequences. The Ebp1-ribosome complex serves as a template for MetAP binding and provides insights into the structural principles for spatial coordination of co-translational events and molecular triage at the ribosomal tunnel exit. The ErbB3 receptor binding protein Ebp1 binds to ribosomes and is linked to translational control. Here, the authors present the cryo-EM structure of human Ebp1 bound to a non-translating 80S ribosome and find that Ebp1 blocks the tunnel exit and recruits the rRNA expansion segment ES27L to the tunnel exit.
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Affiliation(s)
- Klemens Wild
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Milan Aleksić
- Zentrum für Molekulare Biologie der Universität Heidelberg, INF282, D-69120, Heidelberg, Germany
| | - Karine Lapouge
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Keven D Juaire
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Dirk Flemming
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, INF282, D-69120, Heidelberg, Germany.
| | - Irmgard Sinning
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany.
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Co-Translational Protein Folding and Sorting in Chloroplasts. PLANTS 2020; 9:plants9020214. [PMID: 32045984 PMCID: PMC7076657 DOI: 10.3390/plants9020214] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 01/22/2023]
Abstract
Cells depend on the continuous renewal of their proteome composition during the cell cycle and in order to replace aberrant proteins or to react to changing environmental conditions. In higher eukaryotes, protein synthesis is achieved by up to five million ribosomes per cell. With the fast kinetics of translation, the large number of newly made proteins generates a substantial burden for protein homeostasis and requires a highly orchestrated cascade of factors promoting folding, sorting and final maturation. Several of the involved factors directly bind to translating ribosomes for the early processing of emerging nascent polypeptides and the translocation of ribosome nascent chain complexes to target membranes. In plant cells, protein synthesis also occurs in chloroplasts serving the expression of a relatively small set of 60–100 protein-coding genes. However, most of these proteins, together with nucleus-derived subunits, form central complexes majorly involved in the essential processes of photosynthetic light reaction, carbon fixation, metabolism and gene expression. Biogenesis of these heterogenic complexes adds an additional level of complexity for protein biogenesis. In this review, we summarize the current knowledge about co-translationally binding factors in chloroplasts and discuss their role in protein folding and ribosome translocation to thylakoid membranes.
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Electrostatics of Prokaryotic Ribosome and Its Biological Implication. Biophys J 2020; 118:1205-1212. [PMID: 32023436 DOI: 10.1016/j.bpj.2020.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/26/2019] [Accepted: 01/09/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes are essential machines for protein synthesis in cells. Their structures are very complex but conserved in different species. Because most parts of a ribosome are composed of negatively charged RNAs, its electrostatics should play a fundamental role in the realization of its functions. However, a complete picture of the electrostatics of ribosomes is still absent at present. Here, assisted by the latest version of DelPhi (version 8.4), we illustrate a picture of the electrostatics of a prokaryotic ribosome as well as its molecular chaperones. The revealed electrostatics features are consistent with available experimental data as well as the functions of the ribosome and its molecular chaperones and provides a basis for further studying the mechanism underlying these functions.
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Abstract
Neurodegeneration in Parkinson’s disease is correlated with the occurrence of Lewy bodies, intracellular inclusions containing aggregates of the intrinsically disordered protein (IDP) α-Synuclein1. The aggregation propensity of α-Synuclein in cells is modulated by specific factors including posttranslational modifications2,3, Abelson-kinase-mediated phosphorylation4,5 and interactions with intracellular machineries such as molecular chaperones, although the underlying mechanisms are unclear6–8. Here, we systematically characterize the interaction of molecular chaperones with α-Synuclein in vitro as well as in cells at the atomic level. We find that six vastly different molecular chaperones commonly recognize a canonical motif in α-Synuclein, consisting of the amino-terminus and a segment around Tyr39, hindering its aggregation. In-cell NMR experiments9 show the same transient interaction pattern preserved inside living mammalian cells. Specific inhibition of the interactions between α-Synuclein and the chaperones Hsc70 and Hsp90 yields transient membrane binding and triggers a remarkable re-localization of α-Synuclein to mitochondria and concomitant aggregate formation. Phosphorylation of α-Synuclein at Tyr39 directly impairs the chaperone interaction, thus providing a functional explanation for the role of Abelson kinase in Parkinson’s disease progression. Our results establish a master regulatory mechanism of α-Synuclein function and aggregation in mammalian cells, extending the functional repertoire of molecular chaperones and opening new perspectives for therapeutic interventions for Parkinson’s disease.
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