1
|
Heritz JA, Backe, SJ, Mollapour M. Molecular chaperones: Guardians of tumor suppressor stability and function. Oncotarget 2024; 15:679-696. [PMID: 39352796 PMCID: PMC11444336 DOI: 10.18632/oncotarget.28653] [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: 07/26/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
The term 'tumor suppressor' describes a widely diverse set of genes that are generally involved in the suppression of metastasis, but lead to tumorigenesis upon loss-of-function mutations. Despite the protein products of tumor suppressors exhibiting drastically different structures and functions, many share a common regulatory mechanism-they are molecular chaperone 'clients'. Clients of molecular chaperones depend on an intracellular network of chaperones and co-chaperones to maintain stability. Mutations of tumor suppressors that disrupt proper chaperoning prevent the cell from maintaining sufficient protein levels for physiological function. This review discusses the role of the molecular chaperones Hsp70 and Hsp90 in maintaining the stability and functional integrity of tumor suppressors. The contribution of cochaperones prefoldin, HOP, Aha1, p23, FNIP1/2 and Tsc1 as well as the chaperonin TRiC to tumor suppressor stability is also discussed. Genes implicated in renal cell carcinoma development-VHL, TSC1/2, and FLCN-will be used as examples to explore this concept, as well as how pathogenic mutations of tumor suppressors cause disease by disrupting protein chaperoning, maturation, and function.
Collapse
Affiliation(s)
- Jennifer A. Heritz
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Sarah J. Backe,
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Syracuse VA Medical Center, New York VA Health Care, Syracuse, NY 13210, USA
| |
Collapse
|
2
|
Wagner J, Carvajal AI, Bracher A, Beck F, Wan W, Bohn S, Körner R, Baumeister W, Fernandez-Busnadiego R, Hartl FU. Visualizing chaperonin function in situ by cryo-electron tomography. Nature 2024; 633:459-464. [PMID: 39169181 PMCID: PMC11390479 DOI: 10.1038/s41586-024-07843-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/18/2024] [Indexed: 08/23/2024]
Abstract
Chaperonins are large barrel-shaped complexes that mediate ATP-dependent protein folding1-3. The bacterial chaperonin GroEL forms juxtaposed rings that bind unfolded protein and the lid-shaped cofactor GroES at their apertures. In vitro analyses of the chaperonin reaction have shown that substrate protein folds, unimpaired by aggregation, while transiently encapsulated in the GroEL central cavity by GroES4-6. To determine the functional stoichiometry of GroEL, GroES and client protein in situ, here we visualized chaperonin complexes in their natural cellular environment using cryo-electron tomography. We find that, under various growth conditions, around 55-70% of GroEL binds GroES asymmetrically on one ring, with the remainder populating symmetrical complexes. Bound substrate protein is detected on the free ring of the asymmetrical complex, defining the substrate acceptor state. In situ analysis of GroEL-GroES chambers, validated by high-resolution structures obtained in vitro, showed the presence of encapsulated substrate protein in a folded state before release into the cytosol. Based on a comprehensive quantification and conformational analysis of chaperonin complexes, we propose a GroEL-GroES reaction cycle that consists of linked asymmetrical and symmetrical subreactions mediating protein folding. Our findings illuminate the native conformational and functional chaperonin cycle directly within cells.
Collapse
Affiliation(s)
- Jonathan Wagner
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
- Research Group Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Alonso I Carvajal
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Beck
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - William Wan
- Vanderbilt University Center for Structural Biology, Nashville, TN, USA
| | - Stefan Bohn
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Structural Biology, Helmholtz Center Munich, Oberschleissheim, Germany
| | - Roman Körner
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Research Group Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Ruben Fernandez-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
- Faculty of Physics, University of Göttingen, Göttingen, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
| |
Collapse
|
3
|
Braxton JR, Shao H, Tse E, Gestwicki JE, Southworth DR. Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly. Nat Struct Mol Biol 2024:10.1038/s41594-024-01352-0. [PMID: 38951622 DOI: 10.1038/s41594-024-01352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/07/2024] [Indexed: 07/03/2024]
Abstract
The mitochondrial chaperonin, mitochondrial heat shock protein 60 (mtHsp60), promotes the folding of newly imported and transiently misfolded proteins in the mitochondrial matrix, assisted by its co-chaperone mtHsp10. Despite its essential role in mitochondrial proteostasis, structural insights into how this chaperonin progresses through its ATP-dependent client folding cycle are not clear. Here, we determined cryo-EM structures of a hyperstable disease-associated human mtHsp60 mutant, V72I. Client density is identified in three distinct states, revealing interactions with the mtHsp60 apical domains and C termini that coordinate client positioning in the folding chamber. We further identify an asymmetric arrangement of the apical domains in the ATP state, in which an alternating up/down configuration positions interaction surfaces for simultaneous recruitment of mtHsp10 and client retention. Client is then fully encapsulated in mtHsp60-10, revealing prominent contacts at two discrete sites that potentially support maturation. These results identify distinct roles for the apical domains in coordinating client capture and progression through the chaperone cycle, supporting a conserved mechanism of group I chaperonin function.
Collapse
Affiliation(s)
- Julian R Braxton
- Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hao Shao
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
4
|
Harada K, Ono Y, Sekiya R, Haino T. Selective encapsulation of carboxylic acid dimers within a size-regulable resorcinarene-based hemicarcerand. Chem Commun (Camb) 2024; 60:6603-6606. [PMID: 38836696 DOI: 10.1039/d4cc00699b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
A cavity within a resorcinarene-based hemicarcerand was contracted and expanded through conformational changes induced by the complexation and decomplexation, allowing self-sorting of homo- and heterodimeric carboxylic acid pairs.
Collapse
Affiliation(s)
- Kentaro Harada
- Department of Chemistry, Graduate School of Advanced Science and Engineering Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Yudai Ono
- Department of Chemistry, Graduate School of Advanced Science and Engineering Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan
| | - Ryo Sekiya
- Department of Chemistry, Graduate School of Advanced Science and Engineering Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Takeharu Haino
- Department of Chemistry, Graduate School of Advanced Science and Engineering Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan
| |
Collapse
|
5
|
Hertle E, Ursinus A, Martin J. Low-temperature features of the psychrophilic chaperonin from Pseudoalteromonas haloplanktis. Arch Microbiol 2024; 206:299. [PMID: 38861015 PMCID: PMC11166852 DOI: 10.1007/s00203-024-04019-y] [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: 03/28/2024] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Chaperonins from psychrophilic bacteria have been shown to exist as single-ring complexes. This deviation from the standard double-ring structure has been thought to be a beneficial adaptation to the cold environment. Here we show that Cpn60 from the psychrophile Pseudoalteromonas haloplanktis (Ph) maintains its double-ring structure also in the cold. A strongly reduced ATPase activity keeps the chaperonin in an energy-saving dormant state, until binding of client protein activates it. Ph Cpn60 in complex with co-chaperonin Ph Cpn10 efficiently assists in protein folding up to 55 °C. Moreover, we show that recombinant expression of Ph Cpn60 can provide its host Escherichia coli with improved viability under low temperature growth conditions. These properties of the Ph chaperonin may make it a valuable tool in the folding and stabilization of psychrophilic proteins.
Collapse
Affiliation(s)
- Eva Hertle
- Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Astrid Ursinus
- Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| |
Collapse
|
6
|
Dupuy E, Collet JF. Entering deeper into the mysteries of the GroEL-GroES nanomachine. Curr Opin Microbiol 2024; 79:102480. [PMID: 38714141 DOI: 10.1016/j.mib.2024.102480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/09/2024]
Abstract
In the densely populated intracellular milieu, polypeptides are at constant risk of nonspecific interactions and aggregation, posing a threat to essential cellular functions. Cells rely on a network of protein folding factors to deal with this challenge. The Hsp60 family of molecular chaperones, which depend on ATP for function, stands out in the proteostasis network by a characteristic structure comprising two multimeric rings arranged back to back. This review provides an updated overview of GroEL, the bacterial Hsp60, and its GroES (Hsp10) cofactor. Specifically, we highlight recent breakthroughs in understanding the intricate folding mechanisms of the GroEL-GroES nanomachine and explore the newly discovered interaction between GroEL and the chaperedoxin CnoX. Despite considerable research on the GroEL-GroES system, numerous questions remain to be explored.
Collapse
Affiliation(s)
- Emile Dupuy
- WELBIO department, WEL Research Institute, Avenue Pasteur 6, 1300 Wavre, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Jean-François Collet
- WELBIO department, WEL Research Institute, Avenue Pasteur 6, 1300 Wavre, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
| |
Collapse
|
7
|
Marie A, Georgescauld F, Johnson KR, Ray S, Engen JR, Ivanov AR. Native Capillary Electrophoresis-Mass Spectrometry of Near 1 MDa Non-Covalent GroEL/GroES/Substrate Protein Complexes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306824. [PMID: 38191978 PMCID: PMC10953559 DOI: 10.1002/advs.202306824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/21/2023] [Indexed: 01/10/2024]
Abstract
Protein complexes are essential for proteins' folding and biological function. Currently, native analysis of large multimeric protein complexes remains challenging. Structural biology techniques are time-consuming and often cannot monitor the proteins' dynamics in solution. Here, a capillary electrophoresis-mass spectrometry (CE-MS) method is reported to characterize, under near-physiological conditions, the conformational rearrangements of ∽1 MDa GroEL upon complexation with binding partners involved in a protein folding cycle. The developed CE-MS method is fast (30 min per run), highly sensitive (low-amol level), and requires ∽10 000-fold fewer samples compared to biochemical/biophysical techniques. The method successfully separates GroEL14 (∽800 kDa), GroEL7 (∽400 kDa), GroES7 (∽73 kDa), and NanA4 (∽130 kDa) oligomers. The non-covalent binding of natural substrate proteins with GroEL14 can be detected and quantified. The technique allows monitoring of GroEL14 conformational changes upon complexation with (ATPγS)4-14 and GroES7 (∽876 kDa). Native CE-pseudo-MS3 analyses of wild-type (WT) GroEL and two GroEL mutants result in up to 60% sequence coverage and highlight subtle structural differences between WT and mutated GroEL. The presented results demonstrate the superior CE-MS performance for multimeric complexes' characterization versus direct infusion ESI-MS. This study shows the CE-MS potential to provide information on binding stoichiometry and kinetics for various protein complexes.
Collapse
Affiliation(s)
- Anne‐Lise Marie
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Florian Georgescauld
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Kendall R. Johnson
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Somak Ray
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - John R. Engen
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Alexander R. Ivanov
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| |
Collapse
|
8
|
Agam G, Barth A, Lamb DC. Folding pathway of a discontinuous two-domain protein. Nat Commun 2024; 15:690. [PMID: 38263337 PMCID: PMC10805907 DOI: 10.1038/s41467-024-44901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
It is estimated that two-thirds of all proteins in higher organisms are composed of multiple domains, many of them containing discontinuous folds. However, to date, most in vitro protein folding studies have focused on small, single-domain proteins. As a model system for a two-domain discontinuous protein, we study the unfolding/refolding of a slow-folding double mutant of the maltose binding protein (DM-MBP) using single-molecule two- and three-color Förster Resonance Energy Transfer experiments. We observe a dynamic folding intermediate population in the N-terminal domain (NTD), C-terminal domain (CTD), and at the domain interface. The dynamic intermediate fluctuates rapidly between unfolded states and compact states, which have a similar FRET efficiency to the folded conformation. Our data reveals that the delayed folding of the NTD in DM-MBP is imposed by an entropic barrier with subsequent folding of the highly dynamic CTD. Notably, accelerated DM-MBP folding is routed through the same dynamic intermediate within the cavity of the GroEL/ES chaperone system, suggesting that the chaperonin limits the conformational space to overcome the entropic folding barrier. Our study highlights the subtle tuning and co-dependency in the folding of a discontinuous multi-domain protein.
Collapse
Affiliation(s)
- Ganesh Agam
- Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany
- Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Anders Barth
- Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany
- Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629HZ, Delft, The Netherlands
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians University Munich, Munich, Germany.
- Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany.
| |
Collapse
|
9
|
Braxton JR, Shao H, Tse E, Gestwicki JE, Southworth DR. Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540872. [PMID: 37293102 PMCID: PMC10245740 DOI: 10.1101/2023.05.15.540872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mitochondrial chaperonin, mtHsp60, promotes the folding of newly imported and transiently misfolded proteins in the mitochondrial matrix, assisted by its co-chaperone mtHsp10. Despite its essential role in mitochondrial proteostasis, structural insights into how this chaperonin binds to clients and progresses through its ATP-dependent reaction cycle are not clear. Here, we determined cryo-electron microscopy (cryo-EM) structures of a hyperstable disease-associated mtHsp60 mutant, V72I, at three stages in this cycle. Unexpectedly, client density is identified in all states, revealing interactions with mtHsp60's apical domains and C-termini that coordinate client positioning in the folding chamber. We further identify a striking asymmetric arrangement of the apical domains in the ATP state, in which an alternating up/down configuration positions interaction surfaces for simultaneous recruitment of mtHsp10 and client retention. Client is then fully encapsulated in mtHsp60/mtHsp10, revealing prominent contacts at two discrete sites that potentially support maturation. These results identify a new role for the apical domains in coordinating client capture and progression through the cycle, and suggest a conserved mechanism of group I chaperonin function.
Collapse
Affiliation(s)
- Julian R. Braxton
- Graduate Program in Chemistry and Chemical Biology; University of California, San Francisco; San Francisco, CA 94158, USA
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Hao Shao
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Jason E. Gestwicki
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Daniel R. Southworth
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics; University of California, San Francisco; San Francisco, CA 94158, USA
| |
Collapse
|
10
|
Zhu FY, Yang Q, Cao M, Zheng K, Zhang XJ, Shen Q, Cai X, Liu ZQ, Zheng YG. Tuning an efficient Escherichia coli whole-cell catalyst expressing l-pantolactone dehydrogenase for the biosynthesis of d-(-)-pantolactone. J Biotechnol 2023; 367:1-10. [PMID: 36948403 DOI: 10.1016/j.jbiotec.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/18/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023]
Abstract
d-(-)-Pantolactone (DPL) is a key intermediate for the production of d-(+)-pantothenate (vitamin B5). Deracemization of d,l-pantolactone (D,L-PL) through oxidizing l-(+)-pantolactone (LPL) to ketopantoyl lactone (KPL) and subsequently reducing KPL to DPL is a promising route for synthesizing DPL. Herein, a newly mined l-pantolactone dehydrogenase from Rhodococcus hoagie (RhoLPLDH) was used for the oxidative dehydrogenation of LPL. To alleviate inclusion bodies formed by membrane-bound RhoLPLDH intracellular expression in E. coli, strategies involving chaperone assistance and decreasing induction temperature were used to achieve RhoLPLDH soluble expression. To enhance its activity, directed evolution and hydrophilicity-based engineering yielded increased catalytic activity and thermostability. 1M LPL was efficiently converted to KPL by engineering strain CM5 co-expressing RhoLPLDHL254I/V241I/I156L/F224Q/N164K and chaperone. A "two stages in one-pot" method was employed in deracemization of 1M D,L-PL with 91.2% yield. These results demonstrated that CM5 catalyst exhibits great potential in enzyme cascade deracemization for the production of DPL.
Collapse
Affiliation(s)
- Fang-Ying Zhu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Qing Yang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Beijing Tsingke Biotechnology Co., Ltd, Beijing 100176, People's Republic of China
| | - Min Cao
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Ken Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Xiao-Jian Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Qi Shen
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Xue Cai
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhi-Qiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yu-Guo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| |
Collapse
|
11
|
Törner R, Kupreichyk T, Hoyer W, Boisbouvier J. The role of heat shock proteins in preventing amyloid toxicity. Front Mol Biosci 2022; 9:1045616. [PMID: 36589244 PMCID: PMC9798239 DOI: 10.3389/fmolb.2022.1045616] [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: 09/15/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The oligomerization of monomeric proteins into large, elongated, β-sheet-rich fibril structures (amyloid), which results in toxicity to impacted cells, is highly correlated to increased age. The concomitant decrease of the quality control system, composed of chaperones, ubiquitin-proteasome system and autophagy-lysosomal pathway, has been shown to play an important role in disease development. In the last years an increasing number of studies has been published which focus on chaperones, modulators of protein conformational states, and their effects on preventing amyloid toxicity. Here, we give a comprehensive overview of the current understanding of chaperones and amyloidogenic proteins and summarize the advances made in elucidating the impact of these two classes of proteins on each other, whilst also highlighting challenges and remaining open questions. The focus of this review is on structural and mechanistic studies and its aim is to bring novices of this field "up to speed" by providing insight into all the relevant processes and presenting seminal structural and functional investigations.
Collapse
Affiliation(s)
- Ricarda Törner
- University Grenoble Alpes, CNRS CEA Institut de Biologie Structurale (IBS), Grenoble, France,*Correspondence: Ricarda Törner, ; Jerome Boisbouvier,
| | - Tatsiana Kupreichyk
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jerome Boisbouvier
- University Grenoble Alpes, CNRS CEA Institut de Biologie Structurale (IBS), Grenoble, France,*Correspondence: Ricarda Törner, ; Jerome Boisbouvier,
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Xu H. Non-Equilibrium Protein Folding and Activation by ATP-Driven Chaperones. Biomolecules 2022; 12:832. [PMID: 35740957 PMCID: PMC9221429 DOI: 10.3390/biom12060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022] Open
Abstract
Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on available structural and biochemical evidence, I propose here a unifying principle that underlies the conversion of chemical energy from ATP hydrolysis to the conformational free energy associated with protein folding and activation. I demonstrate that non-equilibrium folding requires the chaperones to break at least one of four symmetry conditions. The Hsp70 and Hsp90 chaperones each break a different subset of these symmetries and thus they use different mechanisms for non-equilibrium protein folding. I derive an upper bound on the non-equilibrium elevation of the native concentration, which implies that non-equilibrium folding only occurs in slow-folding proteins that adopt an unstable intermediate conformation in binding to ATP-driven chaperones. Contrary to the long-held view of Anfinsen's hypothesis that proteins fold to their conformational free energy minima, my results predict that some proteins may fold into thermodynamically unstable native structures with the assistance of ATP-driven chaperones, and that the native structures of some chaperone-dependent proteins may be shaped by their chaperone-mediated folding pathways.
Collapse
Affiliation(s)
- Huafeng Xu
- Roivant Sciences, New York, NY 10036, USA
| |
Collapse
|
14
|
Sen S, Thaker A, Sirajudeen L, Williams D, Nannenga BL. Protein-Nanoparticle Complex Structure Determination by Cryo-Electron Microscopy. ACS APPLIED BIO MATERIALS 2022; 5:4696-4700. [PMID: 35587230 DOI: 10.1021/acsabm.2c00130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods that allow the study of the structure of proteins in complex with nanomaterials promise to enhance our understanding of how biological molecules interface with inorganic materials. We used single-particle cryo-electron microscopy (cryo-EM) to demonstrate the potential for cryo-EM analysis to reveal structural details of protein-nanoparticle complexes. Two protein-nanomaterial complexes, namely, GroEL bound to platinum nanoparticles (GroEL-PtNP) and ferritin bound to an iron oxide nanoparticle, were used as model samples. For the GroEL-PtNP complex, a final reconstruction was obtained to 3.93 Å, which allowed us to fit the atomic model of GroEL into the resulting map. This sets the stage for future work and improvements on the use of cryo-EM for the study of protein-nanomaterial complexes.
Collapse
Affiliation(s)
- Sagnik Sen
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| | - Amar Thaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| | - Luqmanal Sirajudeen
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| | - Dewight Williams
- John M. Cowley Center for High Resolution Electron Microscopy, Arizona State University, Tempe 85281, Arizona, United States
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe 85287, Arizona, United States
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe 85287, Arizona, United States
| |
Collapse
|
15
|
Sadat A, Tiwari S, Sunidhi S, Chaphalkar A, Kochar M, Ali M, Zaidi Z, Sharma A, Verma K, Narayana Rao KB, Tripathi M, Ghosh A, Gautam D, Atul, Ray A, Mapa K, Chakraborty K. Conserved and divergent chaperoning effects of Hsp60/10 chaperonins on protein folding landscapes. Proc Natl Acad Sci U S A 2022; 119:e2118465119. [PMID: 35486698 PMCID: PMC9170145 DOI: 10.1073/pnas.2118465119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/02/2022] [Indexed: 12/21/2022] Open
Abstract
The GroEL/ES chaperonin cavity surface charge properties, especially the negative charges, play an important role in its capacity to assist intracavity protein folding. Remarkably, the larger fraction of GroEL/ES negative charges are not conserved among different bacterial species, resulting in a large variation in negative-charge density in the GroEL/ES cavity across prokaryotes. Intriguingly, eukaryotic GroEL/ES homologs have the lowest negative-charge density in the chaperonin cavity. This prompted us to investigate if GroEL’s chaperoning mechanism changed during evolution. Using a model in vivo GroEL/ES substrate, we show that the ability of GroEL/ES to buffer entropic traps in the folding pathway of its substrate was partially dependent upon the negative-charge density inside its cavity. While this activity of GroEL/ES was found to be essential for Escherichia coli, it has been perfected in some organisms and diminished in others. However, irrespective of their charges, all the tested homologs retained their ability to regulate polypeptide chain collapse and remove enthalpic traps from folding pathways. The ability of these GroEL/ES homologs to buffer mutational variations in a model substrate correlated with their negative-charge density. Thus, Hsp60/10 chaperonins in different organisms may have changed to accommodate a different spectrum of mutations on their substrates.
Collapse
Affiliation(s)
- Anwar Sadat
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Satyam Tiwari
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - S. Sunidhi
- Department of Computational Biology, Indraprastha Institute of Information Technology–Delhi, New Delhi 110020, India
| | - Aseem Chaphalkar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Manisha Kochar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Mudassar Ali
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida 201314, India
| | - Zainab Zaidi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Akanksha Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Kanika Verma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Kannan Boosi Narayana Rao
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Manjul Tripathi
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Asmita Ghosh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Deepika Gautam
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Atul
- Department of Computational Biology, Indraprastha Institute of Information Technology–Delhi, New Delhi 110020, India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology–Delhi, New Delhi 110020, India
| | - Koyeli Mapa
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida 201314, India
| | - Kausik Chakraborty
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| |
Collapse
|
16
|
Naqvi MM, Avellaneda MJ, Roth A, Koers EJ, Roland A, Sunderlikova V, Kramer G, Rye HS, Tans SJ. Protein chain collapse modulation and folding stimulation by GroEL-ES. SCIENCE ADVANCES 2022; 8:eabl6293. [PMID: 35245117 PMCID: PMC8896798 DOI: 10.1126/sciadv.abl6293] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
The collapse of polypeptides is thought important to protein folding, aggregation, intrinsic disorder, and phase separation. However, whether polypeptide collapse is modulated in cells to control protein states is unclear. Here, using integrated protein manipulation and imaging, we show that the chaperonin GroEL-ES can accelerate the folding of proteins by strengthening their collapse. GroEL induces contractile forces in substrate chains, which draws them into the cavity and triggers a general compaction and discrete folding transitions, even for slow-folding proteins. This collapse enhancement is strongest in the nucleotide-bound states of GroEL and is aided by GroES binding to the cavity rim and by the amphiphilic C-terminal tails at the cavity bottom. Collapse modulation is distinct from other proposed GroEL-ES folding acceleration mechanisms, including steric confinement and misfold unfolding. Given the prevalence of collapse throughout the proteome, we conjecture that collapse modulation is more generally relevant within the protein quality control machinery.
Collapse
Affiliation(s)
| | | | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
| | | | | | | | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Hays S. Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
| | - Sander J. Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| |
Collapse
|
17
|
Horovitz A, Reingewertz TH, Cuéllar J, Valpuesta JM. Chaperonin Mechanisms: Multiple and (Mis)Understood? Annu Rev Biophys 2022; 51:115-133. [DOI: 10.1146/annurev-biophys-082521-113418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The chaperonins are ubiquitous and essential nanomachines that assist in protein folding in an ATP-driven manner. They consist of two back-to-back stacked oligomeric rings with cavities in which protein (un)folding can take place in a shielding environment. This review focuses on GroEL from Escherichia coli and the eukaryotic chaperonin-containing t-complex polypeptide 1, which differ considerably in their reaction mechanisms despite sharing a similar overall architecture. Although chaperonins feature in many current biochemistry textbooks after being studied intensively for more than three decades, key aspects of their reaction mechanisms remain under debate and are discussed in this review. In particular, it is unclear whether a universal reaction mechanism operates for all substrates and whether it is passive, i.e., aggregation is prevented but the folding pathway is unaltered, or active. It is also unclear how chaperonin clients are distinguished from nonclients and what are the precise roles of the cofactors with which chaperonins interact. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel; Amnon.H
| | - Tali Haviv Reingewertz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel; Amnon.H
| | - Jorge Cuéllar
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - José María Valpuesta
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| |
Collapse
|
18
|
Kaewchana A, Techaparin A, Boonchot N, Thanonkeo P, Klanrit P. Improved high-temperature ethanol production from sweet sorghum juice using Zymomonas mobilis overexpressing groESL genes. Appl Microbiol Biotechnol 2021; 105:9419-9431. [PMID: 34787692 DOI: 10.1007/s00253-021-11686-0] [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: 01/28/2021] [Revised: 10/11/2021] [Accepted: 11/07/2021] [Indexed: 10/19/2022]
Abstract
Zymomonas mobilis may encounter various types of stress during ethanol fermentation, which reduces ethanol production efficiency. This situation may be mitigated by molecular chaperones, including the chaperonin GroESL, which confers enhanced protection against various stresses. In this study, we successfully developed a Z. mobilis strain R301 that harbors groESL genes and can be used for high-temperature ethanol production from sweet sorghum juice. Sequence analyses of GroES and GroEL from Z. mobilis TISTR548 demonstrated conserved residues at specific positions within GroES and conserved glycine-glycine-methionine (GGM) repeats at the C-terminus of GroEL. The Z. mobilis wild-type and R301 strains were then evaluated for their tolerance to stresses, including high temperatures, high sugar concentrations, and high ethanol concentrations up to 40°C, 300 g/L, and 13% (v/v), respectively. Z. mobilis R301 exhibited better growth performance than the wild-type strain under all stress conditions. This is the first report on ethanol production at 40°C by recombinant Z. mobilis using sweet sorghum juice; this strain produced an ethanol concentration of 41.66 g/L, with a productivity of 0.87 g/L/h and a theoretical ethanol yield of 88.9%. Overexpression of groESL resulted in increased ethanol production, with values approximately 11% higher than those of the wild type at 40°C. Additionally, at 37°C, Z. mobilis R301 gave a higher theoretical ethanol yield (92.6%) than that shown in previous research. This work illustrates the potential for future enhancement of industrial-scale ethanol production at high temperatures utilizing Z. mobilis R301 in the bioconversion of sweet sorghum juice, a promising energy crop. KEY POINTS: • The groESL-overexpressing Z. mobilis strain was successfully constructed. • The recombinant Z. mobilis exhibited higher stress tolerance than the wild-type strain. • Overexpression of groESL genes improved ethanol production efficiency at high temperatures.
Collapse
Affiliation(s)
- Anchittha Kaewchana
- Graduate School, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Atiya Techaparin
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nongluck Boonchot
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Pornthap Thanonkeo
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand.,Fermentation Research Center for Value Added Agricultural Products (FerVAAP), Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Preekamol Klanrit
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Fermentation Research Center for Value Added Agricultural Products (FerVAAP), Khon Kaen University, Khon Kaen, 40002, Thailand.
| |
Collapse
|
19
|
Panina IS, Mamchur AA, Yaroshevich IA, Zlenko DV, Pichkur EB, Kudryavtseva SS, Muronetz VI, Sokolova OS, Stanishneva-Konovalova TB. Study of GroEL Conformational Mobility by Cryo-Electron Microscopy and Molecular Dynamics. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Bacterial chaperonin GroEL is a complex ring-shaped protein oligomer that promotes the folding of other proteins by encapsulating them in the cavity. There is very little structural information about the disordered C-terminal fragment of the GroEL subunits, which is involved in the folding of the substrate protein. A 3D reconstruction of the GroEL apo-form was obtained by cryo-electron microscopy (cryo-EM) with a resolution of 3.02 Å and supplemented by molecular dynamics (MD) calculations. The results of cryo-EM and MD are in good agreement and demonstrate a diverse mobility of the protein subunit domains. The MD results predict the dynamics and the network of intramolecular contacts of the C-terminal sections of the protein. These results are of great importance for the subsequent study of the mechanism of protein folding in the GroEL cavity.
Collapse
|
20
|
Park JC, Lee JS. Genome-wide identification of heat shock proteins in harpacticoid, cyclopoid, and calanoid copepods: Potential application in marine ecotoxicology. MARINE POLLUTION BULLETIN 2021; 169:112545. [PMID: 34111604 DOI: 10.1016/j.marpolbul.2021.112545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Constant evolution of omics-technologies has provided access to identification of various important gene families. Recently, genome assemblies on widely used ecotoxicological model species, including rotifers and copepods have been completed and representative detoxification-related gene families have been discovered for biomarker genes. However, despite ubiquitous presence of stress-response proteins, limited information on full genome-wide report on heat shock proteins (Hsps) is available. Various studies have demonstrated multiple cellular functions of Hsps in living organisms as an important biomarker in response to abiotic and biotic stressors, however, full genome-wide identification of Hsps, particularly in aquatic invertebrates, has not been reported. This is the first study to report the entire Hsps and basal gene expression levels in three regional-specific copepods: Tigriopus japonicus and kingsejongensis, Paracyclopina nana, and Eurytemora affnis, and how each Hsp family gene is regulated at a basal level.
Collapse
Affiliation(s)
- Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
21
|
The Mechanism of Rubisco Catalyzed Carboxylation Reaction: Chemical Aspects Involving Acid-Base Chemistry and Functioning of the Molecular Machine. Catalysts 2021. [DOI: 10.3390/catal11070813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In recent years, a great deal of attention has been paid by the scientific community to improving the efficiency of photosynthetic carbon assimilation, plant growth and biomass production in order to achieve a higher crop productivity. Therefore, the primary carboxylase enzyme of the photosynthetic process Rubisco has received considerable attention focused on many aspects of the enzyme function including protein structure, protein engineering and assembly, enzyme activation and kinetics. Based on its fundamental role in carbon assimilation Rubisco is also targeted by the CO2-fertilization effect, which is the increased rate of photosynthesis due to increasing atmospheric CO2-concentration. The aim of this review is to provide a framework, as complete as possible, of the mechanism of the RuBP carboxylation/hydration reaction including description of chemical events occurring at the enzyme “activating” and “catalytic” sites (which involve Broensted acid-base reactions) and the functioning of the complex molecular machine. Important research results achieved over the last few years providing substantial advancement in understanding the enzyme functioning will be discussed.
Collapse
|
22
|
Macro N, Chen L, Yang Y, Mondal T, Wang L, Horovitz A, Zhong D. Slowdown of Water Dynamics from the Top to the Bottom of the GroEL Cavity. J Phys Chem Lett 2021; 12:5723-5730. [PMID: 34129341 PMCID: PMC8687601 DOI: 10.1021/acs.jpclett.1c01216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
The GroE molecular chaperone system is a critical protein machine that assists the folding of substrate proteins in its cavity. Water in the cavity is suspected to play a role in substrate protein folding, but the mechanism is currently unknown. Herein, we report measurements of water dynamics in the equatorial and apical domains of the GroEL cavity in the apo and football states, using site-specific tryptophanyl mutagenesis as an intrinsic optical probe with femtosecond resolution combined with molecular dynamics simulations. We observed clearly different water dynamics in the two domains with a slowdown of the cavity water from the apical to equatorial region in the football state. The results suggest that the GroEL cavity provides a unique water environment that may facilitate substrate protein folding.
Collapse
Affiliation(s)
- Nicolas Macro
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Long Chen
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yushan Yang
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Tridib Mondal
- Department
of Structural Biology, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Lijuan Wang
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amnon Horovitz
- Department
of Structural Biology, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Dongping Zhong
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Chemistry and Biochemistry, Programs of Biophysics, Program of
Chemical Physics, and Program of Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
23
|
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.
Collapse
|
24
|
A novel function of
Mycobacterium tuberculosis
chaperonin paralog GroEL1 in copper homeostasis. FEBS Lett 2020; 594:3305-3323. [DOI: 10.1002/1873-3468.13906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022]
|
25
|
Korobko I, Mazal H, Haran G, Horovitz A. Measuring protein stability in the GroEL chaperonin cage reveals massive destabilization. eLife 2020; 9:56511. [PMID: 32716842 PMCID: PMC7440923 DOI: 10.7554/elife.56511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/25/2020] [Indexed: 01/29/2023] Open
Abstract
The thermodynamics of protein folding in bulk solution have been thoroughly investigated for decades. By contrast, measurements of protein substrate stability inside the GroEL/ES chaperonin cage have not been reported. Such measurements require stable encapsulation, that is no escape of the substrate into bulk solution during experiments, and a way to perturb protein stability without affecting the chaperonin system itself. Here, by establishing such conditions, we show that protein stability in the chaperonin cage is reduced dramatically by more than 5 kcal mol-1 compared to that in bulk solution. Given that steric confinement alone is stabilizing, our results indicate that hydrophobic and/or electrostatic effects in the cavity are strongly destabilizing. Our findings are consistent with the iterative annealing mechanism of action proposed for the chaperonin GroEL.
Collapse
Affiliation(s)
- Ilia Korobko
- Departments of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hisham Mazal
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Haran
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Amnon Horovitz
- Departments of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
26
|
Balchin D, Hayer-Hartl M, Hartl FU. Recent advances in understanding catalysis of protein folding by molecular chaperones. FEBS Lett 2020; 594:2770-2781. [PMID: 32446288 DOI: 10.1002/1873-3468.13844] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/27/2022]
Abstract
Molecular chaperones are highly conserved proteins that promote proper folding of other proteins in vivo. Diverse chaperone systems assist de novo protein folding and trafficking, the assembly of oligomeric complexes, and recovery from stress-induced unfolding. A fundamental function of molecular chaperones is to inhibit unproductive protein interactions by recognizing and protecting hydrophobic surfaces that are exposed during folding or following proteotoxic stress. Beyond this basic principle, it is now clear that chaperones can also actively and specifically accelerate folding reactions in an ATP-dependent manner. We focus on the bacterial Hsp70 and chaperonin systems as paradigms, and review recent work that has advanced our understanding of how these chaperones act as catalysts of protein folding.
Collapse
Affiliation(s)
- David Balchin
- Protein Biogenesis Laboratory, The Francis Crick Institute, London, UK
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| |
Collapse
|
27
|
Bracher A, Paul SS, Wang H, Wischnewski N, Hartl FU, Hayer-Hartl M. Structure and conformational cycle of a bacteriophage-encoded chaperonin. PLoS One 2020; 15:e0230090. [PMID: 32339190 PMCID: PMC7185714 DOI: 10.1371/journal.pone.0230090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/07/2020] [Indexed: 11/19/2022] Open
Abstract
Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa. ɸEL, an evolutionarily distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeFx revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionarily more ancient chaperonin prior to acquisition of the encapsulation mechanism.
Collapse
Affiliation(s)
- Andreas Bracher
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- * E-mail: (AB); (MH-H)
| | - Simanta S. Paul
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Huping Wang
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Nadine Wischnewski
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - F. Ulrich Hartl
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
- * E-mail: (AB); (MH-H)
| |
Collapse
|
28
|
De Geyter J, Portaliou AG, Srinivasu B, Krishnamurthy S, Economou A, Karamanou S. Trigger factor is a bona fide secretory pathway chaperone that interacts with SecB and the translocase. EMBO Rep 2020; 21:e49054. [PMID: 32307852 DOI: 10.15252/embr.201949054] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 03/09/2020] [Accepted: 03/19/2020] [Indexed: 11/09/2022] Open
Abstract
Bacterial secretory preproteins are translocated across the inner membrane post-translationally by the SecYEG-SecA translocase. Mature domain features and signal peptides maintain preproteins in kinetically trapped, largely soluble, folding intermediates. Some aggregation-prone preproteins require chaperones, like trigger factor (TF) and SecB, for solubility and/or targeting. TF antagonizes the contribution of SecB to secretion by an unknown molecular mechanism. We reconstituted this interaction in vitro and studied targeting and secretion of the model preprotein pro-OmpA. TF and SecB display distinct, unsuspected roles in secretion. Tightly associating TF:pro-OmpA targets the translocase at SecA, but TF prevents pro-OmpA secretion. In solution, SecB binds TF:pro-OmpA with high affinity. At the membrane, when bound to the SecA C-tail, SecB increases TF and TF:pro-OmpA affinities for the translocase and allows pro-OmpA to resume translocation. Our data reveal that TF, a main cytoplasmic folding pathway chaperone, is also a bona fide post-translational secretory chaperone that directly interacts with both SecB and the translocase to mediate regulated protein secretion. Thus, TF links the cytoplasmic folding and secretion chaperone networks.
Collapse
Affiliation(s)
- Jozefien De Geyter
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Athina G Portaliou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Bindu Srinivasu
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Srinath Krishnamurthy
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| |
Collapse
|
29
|
Singh AK, Balchin D, Imamoglu R, Hayer-Hartl M, Hartl FU. Efficient Catalysis of Protein Folding by GroEL/ES of the Obligate Chaperonin Substrate MetF. J Mol Biol 2020; 432:2304-2318. [PMID: 32135190 DOI: 10.1016/j.jmb.2020.02.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 11/16/2022]
Abstract
The cylindrical chaperonin GroEL and its cofactor GroES mediate ATP-dependent protein folding in Escherichia coli by transiently encapsulating non-native substrate in a nano-cage formed by the GroEL ring cavity and the lid-shaped GroES. Mechanistic studies of GroEL/ES with heterologous protein substrates suggested that the chaperonin is inefficient, typically requiring multiple ATP-dependent encapsulation cycles with only a few percent of protein folded per cycle. Here we analyzed the spontaneous and chaperonin-assisted folding of the essential enzyme 5,10-methylenetetrahydrofolate reductase (MetF) of E. coli, an obligate GroEL/ES substrate. We found that MetF, a homotetramer of 33-kDa subunits with (β/α)8 TIM-barrel fold, populates a kinetically trapped folding intermediate(s) (MetF-I) upon dilution from denaturant that fails to convert to the native state, even in the absence of aggregation. GroEL/ES recognizes MetF-I and catalyzes rapid folding, with ~50% of protein folded in a single round of encapsulation. Analysis by hydrogen/deuterium exchange at peptide resolution showed that the MetF subunit folds to completion in the GroEL/ES nano-cage and binds its cofactor flavin adenine dinucleotide. Rapid folding required the net negative charge character of the wall of the chaperonin cavity. These findings reveal a remarkable capacity of GroEL/ES to catalyze folding of an endogenous substrate protein that would have coevolved with the chaperonin system.
Collapse
Affiliation(s)
- Amit K Singh
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - David Balchin
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - Rahmi Imamoglu
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany.
| |
Collapse
|
30
|
Abstract
This chronologue seeks to document the discovery and development of an understanding of oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these ATP-utilizing machines from both in vivo and in vitro observations. The chronologue is organized into various topics of physiology and mechanism, for each of which a chronologic order is generally followed. The text is liberally illustrated to provide firsthand inspection of the key pieces of experimental data that propelled this field. Because of the length and depth of this piece, the use of the outline as a guide for selected reading is encouraged, but it should also be of help in pursuing the text in direct order.
Collapse
|
31
|
Imamoglu R, Balchin D, Hayer-Hartl M, Hartl FU. Bacterial Hsp70 resolves misfolded states and accelerates productive folding of a multi-domain protein. Nat Commun 2020; 11:365. [PMID: 31953415 PMCID: PMC6969021 DOI: 10.1038/s41467-019-14245-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022] Open
Abstract
The ATP-dependent Hsp70 chaperones (DnaK in E. coli) mediate protein folding in cooperation with J proteins and nucleotide exchange factors (E. coli DnaJ and GrpE, respectively). The Hsp70 system prevents protein aggregation and increases folding yields. Whether it also enhances the rate of folding remains unclear. Here we show that DnaK/DnaJ/GrpE accelerate the folding of the multi-domain protein firefly luciferase (FLuc) ~20-fold over the rate of spontaneous folding measured in the absence of aggregation. Analysis by single-pair FRET and hydrogen/deuterium exchange identified inter-domain misfolding as the cause of slow folding. DnaK binding expands the misfolded region and thereby resolves the kinetically-trapped intermediates, with folding occurring upon GrpE-mediated release. In each round of release DnaK commits a fraction of FLuc to fast folding, circumventing misfolding. We suggest that by resolving misfolding and accelerating productive folding, the bacterial Hsp70 system can maintain proteins in their native states under otherwise denaturing stress conditions.
Collapse
Affiliation(s)
- Rahmi Imamoglu
- Max Planck Institute of Biochemistry, Department of Cellular Biochemistry, Martinsried, Germany
| | - David Balchin
- Max Planck Institute of Biochemistry, Department of Cellular Biochemistry, Martinsried, Germany.
| | - Manajit Hayer-Hartl
- Max Planck Institute of Biochemistry, Department of Cellular Biochemistry, Martinsried, Germany.
| | - F Ulrich Hartl
- Max Planck Institute of Biochemistry, Department of Cellular Biochemistry, Martinsried, Germany.
| |
Collapse
|
32
|
The Hsp70 Chaperone System Stabilizes a Thermo-sensitive Subproteome in E. coli. Cell Rep 2019; 28:1335-1345.e6. [DOI: 10.1016/j.celrep.2019.06.081] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/01/2019] [Accepted: 06/21/2019] [Indexed: 01/05/2023] Open
|
33
|
Zhao Q, Zhang X, Sommer F, Ta N, Wang N, Schroda M, Cong Y, Liu C. Hetero-oligomeric CPN60 resembles highly symmetric group-I chaperonin structure revealed by Cryo-EM. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:798-812. [PMID: 30735603 DOI: 10.1111/tpj.14273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/07/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
The chloroplast chaperonin system is indispensable for the biogenesis of Rubisco, the key enzyme in photosynthesis. Using Chlamydomonas reinhardtii as a model system, we found that in vivo the chloroplast chaperonin consists of CPN60α, CPN60β1 and CPN60β2 and the co-chaperonin of the three subunits CPN20, CPN11 and CPN23. In Escherichia coli, CPN20 homo-oligomers and all possible other chloroplast co-chaperonin hetero-oligomers are functional, but only that consisting of CPN11/20/23-CPN60αβ1β2 can fully replace GroES/GroEL under stringent stress conditions. Endogenous CPN60 was purified and its stoichiometry was determined to be 6:2:6 for CPN60α:CPN60β1:CPN60β2. The cryo-EM structures of endogenous CPN60αβ1β2/ADP and CPN60αβ1β2/co-chaperonin/ADP were solved at resolutions of 4.06 and 3.82 Å, respectively. In both hetero-oligomeric complexes the chaperonin subunits within each ring are highly symmetric. Through hetero-oligomerization, the chloroplast co-chaperonin CPN11/20/23 forms seven GroES-like domains, which symmetrically interact with CPN60αβ1β2. Our structure also reveals an uneven distribution of roof-forming domains in the dome-shaped CPN11/20/23 co-chaperonin and potentially diversified surface properties in the folding cavity of the CPN60αβ1β2 chaperonin that might enable the chloroplast chaperonin system to assist in the folding of specific substrates.
Collapse
Affiliation(s)
- Qian Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang Zhang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Frederik Sommer
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Na Ta
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Ning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Erwin-Schroedinger Str. 70, 67663, Kaiserslautern, Germany
| | - Yao Cong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Cuimin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
34
|
Gestaut D, Limatola A, Joachimiak L, Frydman J. The ATP-powered gymnastics of TRiC/CCT: an asymmetric protein folding machine with a symmetric origin story. Curr Opin Struct Biol 2019; 55:50-58. [PMID: 30978594 DOI: 10.1016/j.sbi.2019.03.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
Abstract
The eukaryotic chaperonin TRiC/CCT is a large hetero-oligomeric complex that plays an essential role assisting cellular protein folding and suppressing protein aggregation. It consists of two rings, and each composed of eight different subunits; non-native polypeptides bind and fold in an ATP-dependent manner within their central chamber. Here, we review recent advances in our understanding of TRiC structure and mechanism enabled by application of hybrid structural methods including the integration of cryo-electron microscopy with distance constraints from crosslinking mass spectrometry. These new insights are revealing how the different TRiC/CCT subunits create asymmetry in its ATP-driven conformational cycle and its interaction with non-native polypeptides, which ultimately underlie its unique ability to fold proteins that cannot be folded by other chaperones.
Collapse
Affiliation(s)
- Daniel Gestaut
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA
| | - Antonio Limatola
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA
| | - Lukasz Joachimiak
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305-5430, USA.
| |
Collapse
|
35
|
Abstract
The genome-wide occurrence of G-quadruplexes and their demonstrated biological activities call for detailed understanding on the stability and transition kinetics of the structures. Although the core structural element in a G-quadruplex is simple and requires only four tandem repeats of Guanine rich sequences, there is rather rich conformational diversity in this structure. Corresponding to this structural diversity, it displays involved transition kinetics within individual G-quadruplexes and complicated interconversion among different G-quadruplex species. Due to the inherently high signal-to-noise ratio in the measurement, single-molecule tools offer a unique capability to investigate the thermodynamic, kinetic, and mechanical properties of G-quadruplexes with dynamic conformations. In this chapter, we describe different single molecule methods such as atomic-force microscopy (AFM), single-molecule fluorescence resonance energy transfer (smFRET), optical, magnetic, and magneto-optical tweezers to investigate G-quadruplex structures as well as their interactions with small-molecule ligands.
Collapse
Affiliation(s)
- Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA
| | | | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA.
| |
Collapse
|
36
|
Dahiya V, Buchner J. Functional principles and regulation of molecular chaperones. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:1-60. [PMID: 30635079 DOI: 10.1016/bs.apcsb.2018.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To be able to perform their biological function, a protein needs to be correctly folded into its three dimensional structure. The protein folding process is spontaneous and does not require the input of energy. However, in the crowded cellular environment where there is high risk of inter-molecular interactions that may lead to protein molecules sticking to each other, hence forming aggregates, protein folding is assisted. Cells have evolved robust machinery called molecular chaperones to deal with the protein folding problem and to maintain proteins in their functional state. Molecular chaperones promote efficient folding of newly synthesized proteins, prevent their aggregation and ensure protein homeostasis in cells. There are different classes of molecular chaperones functioning in a complex interplay. In this review, we discuss the principal characteristics of different classes of molecular chaperones, their structure-function relationships, their mode of regulation and their involvement in human disorders.
Collapse
Affiliation(s)
- Vinay Dahiya
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany.
| |
Collapse
|
37
|
Motojima F, Fujii K, Yoshida M. Chaperonin facilitates protein folding by avoiding initial polypeptide collapse. J Biochem 2018; 164:369-379. [PMID: 30053017 PMCID: PMC6190516 DOI: 10.1093/jb/mvy061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 07/12/2018] [Indexed: 11/14/2022] Open
Abstract
Chaperonins assist folding of many cellular proteins, including essential proteins for cell viability. However, it remains unclear how chaperonin-assisted folding is different from spontaneous folding. Chaperonin GroEL/GroES facilitates folding of denatured protein encapsulated in its central cage but the denatured protein often escapes from the cage to the outside during reaction. Here, we show evidence that the in-cage-folding and the escape occur diverging from the same intermediate complex in which polypeptide is tethered loosely to the cage and partly protrudes out of the cage. Furthermore, denatured proteins in the chaperonin cage are kept in more extended conformation than those initially formed in spontaneous folding. We propose that the formation of tethered intermediate of polypeptide is necessary to prevent polypeptide collapse at the expense of polypeptide escape. The tethering of polypeptide would allow freely mobile portions of tethered polypeptide to fold segmentally.
Collapse
Affiliation(s)
- Fumihiro Motojima
- Department of Molecular Biosciences, Kyoto Sangyo University Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, Japan
| | - Katsuya Fujii
- Department of Molecular Biosciences, Kyoto Sangyo University Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| | - Masasuke Yoshida
- Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, Japan
| |
Collapse
|
38
|
Wang C, Piroozan N, Javidpour L, Sahimi M. Effect of the geometry of confining media on the stability and folding rate of α -helix proteins. J Chem Phys 2018; 148:194305. [PMID: 30307193 DOI: 10.1063/1.5020841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein folding in confined media has attracted wide attention over the past 15 years due to its importance to both in vivo and in vitro applications. It is generally believed that protein stability increases by decreasing the size of the confining medium, if the medium's walls are repulsive, and that the maximum folding temperature in confinement is in a pore whose size D 0 is only slightly larger than the smallest dimension of a protein's folded state. Until recently, the stability of proteins in pores with a size very close to that of the folded state has not received the attention it deserves. In a previous paper [L. Javidpour and M. Sahimi, J. Chem. Phys. 135, 125101 (2011)], we showed that, contrary to the current theoretical predictions, the maximum folding temperature occurs in larger pores for smaller α-helices. Moreover, in very tight pores, the free energy surface becomes rough, giving rise to a new barrier for protein folding close to the unfolded state. In contrast to unbounded domains, in small nanopores proteins with an α-helical native state that contain the β structures are entropically stabilized implying that folding rates decrease notably and that the free energy surface becomes rougher. In view of the potential significance of such results to interpretation of many sets of experimental data that could not be explained by the current theories, particularly the reported anomalously low rates of folding and the importance of entropic effects on proteins' misfolded states in highly confined environments, we address the following question in the present paper: To what extent the geometry of a confined medium affects the stability and folding rates of proteins? Using millisecond-long molecular dynamics simulations, we study the problem in three types of confining media, namely, cylindrical and slit pores and spherical cavities. Most importantly, we find that the prediction of the previous theories that the dependence of the maximum folding temperature T f on the size D of a confined medium occurs in larger media for larger proteins is correct only in spherical geometry, whereas the opposite is true in the two other geometries that we study. Also studied is the effect of the strength of the interaction between the confined media's walls and the proteins. If the walls are only weakly or moderately attractive, a complex behavior emerges that depends on the size of the confining medium.
Collapse
Affiliation(s)
- Congyue Wang
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Nariman Piroozan
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Leili Javidpour
- Departments of Energy Engineering and Physics, Amirkabir University of Technology, Tehran 15875-4413, Iran
| | - Muhammad Sahimi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| |
Collapse
|
39
|
Piana S, Shaw DE. Atomic-Level Description of Protein Folding inside the GroEL Cavity. J Phys Chem B 2018; 122:11440-11449. [PMID: 30277396 DOI: 10.1021/acs.jpcb.8b07366] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chaperonins (ubiquitous facilitators of protein folding) sequester misfolded proteins within an internal cavity, thus preventing protein aggregation during the process of refolding. GroEL, a tetradecameric bacterial chaperonin, is one of the most studied chaperonins, but the role of the internal cavity in the refolding process is still unclear. It has been suggested that rather than simply isolating proteins while they refold, the GroEL cavity actively promotes protein folding. A detailed characterization of the folding dynamics and thermodynamics of protein substrates encapsulated within the cavity, however, has been difficult to obtain by experimental means, due to the system's complexity and the many steps in the folding cycle. Here, we examine the influence of the GroEL cavity on protein folding based on the results of unbiased, atomistic molecular dynamics simulations. We first verified that the computational setup, which uses a recently developed state-of-the-art force field that more accurately reproduces the aggregation propensity of unfolded states, could recapitulate the essential structural dynamics of GroEL. In these simulations, the GroEL tetradecamer was highly dynamic, transitioning among states corresponding to most of the structures that have been observed experimentally. We then simulated a small, unfolded protein both in the GroEL cavity and in bulk solution and compared the protein's folding process within these two environments. Inside the GroEL cavity, the unfolded protein interacted strongly with the disordered residues in GroEL's C-terminal tails. These interactions stabilized the protein's unfolded states relative to its compact states and increased the roughness of its folding free-energy surface, resulting in slower folding compared to the rate in solution. For larger proteins, which are more typical GroEL substrates, we speculate that these interactions may allow substrates to more quickly escape kinetic traps associated with compact, misfolded states, thereby actively promoting folding.
Collapse
Affiliation(s)
- Stefano Piana
- D. E. Shaw Research , New York , New York 10036 , United States
| | - David E Shaw
- D. E. Shaw Research , New York , New York 10036 , United States.,Department of Biochemistry and Molecular Biophysics , Columbia University , New York , New York 10032 , United States
| |
Collapse
|
40
|
Yi J, Wu H, Liu J, Lai X, Guo J, Li D, Zhang G. Molecular characterization and expression of six heat shock protein genes in relation to development and temperature in Trichogramma chilonis. PLoS One 2018; 13:e0203904. [PMID: 30226893 PMCID: PMC6143235 DOI: 10.1371/journal.pone.0203904] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/29/2018] [Indexed: 11/26/2022] Open
Abstract
Trichogramma is a kind of egg parasitoid wasp that is widely used to control lepidopterous pests. Temperature is one of the main factors that determines the various life activities of this species, including development, reproduction and parasitism efficiency. Heat shock proteins (HSPs) are highly conserved and ubiquitous proteins that are best known for their responsiveness to temperature and other stresses. To explore the potential role of HSPs in Trichogramma species, we obtained the full-length cDNAs of six HSP genes (Tchsp10, Tchsp21.6, Tchsp60, Tchsp70, Tchsc70-3, and Tchsp90) from T. chilonis and analyzed their expression patterns during development and exposure to temperature stress. The deduced amino acid sequences of these HSP genes contained the typical signatures of their corresponding protein family and showed high homology to their counterparts in other species. The expression levels of Tchsp10, Tchsp21.6 and Tchsp60 decreased during development. However, the expression of Tchsc70-3 increased from the pupal stage to the adult stage. Tchsp70 and Tchsp90 exhibited the highest expression levels in the adult stage. The expression of six Tchsps was dramatically upregulated after 1 h of exposure to 32 and 40°C but did not significantly change after 1 h of exposure to 10 and 17°C. This result indicated that heat stress, rather than cold stress, induced the expression of HSP genes. Furthermore, the expression of these genes was time dependent, and the expression of each gene reached its peak after 1 h of heat exposure (40°C). Tchsp10 and Tchsp70 exhibited a low-intensity cold response after 4 and 8 h of exposure to 10°C, respectively, but the other genes did not respond to cold at any time points. These results suggested that HSPs may play different roles in the development of this organism and in its response to temperature stress.
Collapse
Affiliation(s)
- Jiequn Yi
- State Key Laboratory for Biocontrol & Institute of Entomology, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Han Wu
- State Key Laboratory for Biocontrol & Institute of Entomology, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jianbai Liu
- State Key Laboratory for Biocontrol & Institute of Entomology, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xueshuang Lai
- State Key Laboratory for Biocontrol & Institute of Entomology, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jixing Guo
- State Key Laboratory for Biocontrol & Institute of Entomology, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Dunsong Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection/Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
- * E-mail: (DL); (GZ)
| | - Guren Zhang
- State Key Laboratory for Biocontrol & Institute of Entomology, Sun Yat-Sen University, Guangzhou, Guangdong, China
- * E-mail: (DL); (GZ)
| |
Collapse
|
41
|
Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures. Proc Natl Acad Sci U S A 2018; 115:9539-9544. [PMID: 30181280 DOI: 10.1073/pnas.1805939115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Due to the small size of a nanoconfinement, the property of water contained inside is rather challenging to probe. Herein, we measured the amount of water molecules released during the folding of individual G-quadruplex and i-motif structures, from which water activities are estimated in the DNA nanocages prepared by 5 × 5 to 7 × 7 helix bundles (cross-sections, 9 × 9 to 15 × 15 nm). We found water activities decrease with reducing cage size. In the 9 × 9-nm cage, water activity was reduced beyond the reach of regular cosolutes such as polyethylene glycol (PEG). With this set of nanocages, we were able to retrieve the change in water molecules throughout the folding trajectory of G-quadruplex or i-motif. We found that water molecules absorbed from the unfolded to the transition states are much fewer than those lost from the transition to the folded states. The overall loss of water therefore drives the folding of G-quadruplex or i-motif in nanocages with reduced water activities.
Collapse
|
42
|
Wang Q, Chen M, Zhang W. A two-component signal transduction system contributes to the virulence of Riemerella anatipestifer. J Vet Sci 2018; 19:260-270. [PMID: 29284206 PMCID: PMC5879074 DOI: 10.4142/jvs.2018.19.2.260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/25/2017] [Accepted: 11/24/2017] [Indexed: 11/20/2022] Open
Abstract
Similar to other studies of bacterial pathogens, current studies of the pathogenesis of Riemerella anatipestifer (RA) are focused mainly on in vitro culture conditions. To elucidate further the pathogenesis of RA in vivo, bacterial RNA was extracted from overnight tryptic soy broth cultures (in vitro) and from the blood of infected ducks (in vivo) for comparative RNA sequencing analysis. In total, 682 upregulated genes were identified in vivo. Among the upregulated genes, a signal transduction response regulator (ArsR) and a signal transduction histidine kinase (SthK) were predicted to be located on the same operon. A mutant was constructed by deletion of both of these genes. Duck infection tests showed that genes ArsR and SthK were related to the virulence of the pathogen in vivo. Differentially expressed genes identified by comparison of in vitro and in vivo conditions provided an insight into the physiological process of RA infection and provided an opportunity to identify additional virulence factors.
Collapse
Affiliation(s)
- Qing Wang
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mianmian Chen
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Zhang
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
43
|
Structure-Function Analysis of the Curli Accessory Protein CsgE Defines Surfaces Essential for Coordinating Amyloid Fiber Formation. mBio 2018; 9:mBio.01349-18. [PMID: 30018113 PMCID: PMC6050966 DOI: 10.1128/mbio.01349-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Curli amyloid fibers are produced as part of the extracellular biofilm matrix and are composed primarily of the major structural subunit CsgA. The CsgE chaperone facilitates the secretion of CsgA through CsgG by forming a cap at the base of the nonameric CsgG outer membrane pore. We elucidated a series of finely tuned nonpolar and charge-charge interactions that facilitate the oligomerization of CsgE and its ability to transport unfolded CsgA to CsgG for translocation. CsgE oligomerization in vitro is temperature dependent and is disrupted by mutations in the W48 and F79 residues. Using nuclear magnetic resonance (NMR), we identified two regions of CsgE involved in the CsgE-CsgA interaction: a head comprising a positively charged patch centered around R47 and a stem comprising a negatively charged patch containing E31 and E85. Negatively charged residues in the intrinsically disordered N- and C-terminal "tails" were not implicated in this interaction. Head and stem residues were mutated and interrogated using in vivo measurements of curli production and in vitro amyloid polymerization assays. The R47 head residue of CsgE is required for stabilization of CsgA- and CsgE-mediated curli fiber formation. Mutation of the E31 and E85 stem residues to positively charged side chains decreased CsgE-mediated curli fiber formation but increased CsgE-mediated stabilization of CsgA. No single-amino-acid substitutions in the head, stem, or tail regions affected the ability of CsgE to cap the CsgG pore as determined by a bile salt sensitivity assay. These mechanistic insights into the directed assembly of functional amyloids in extracellular biofilms elucidate possible targets for biofilm-associated bacterial infections.IMPORTANCE Curli represent a class of functional amyloid fibers produced by Escherichia coli and other Gram-negative bacteria that serve as protein scaffolds in the extracellular biofilm matrix. Despite the lack of sequence conservation among different amyloidogenic proteins, the structural and biophysical properties of functional amyloids such as curli closely resemble those of amyloids associated with several common neurodegenerative diseases. These parallels are underscored by the observation that certain proteins and chemicals can prevent amyloid formation by the major curli subunit CsgA and by alpha-synuclein, the amyloid-forming protein found in Lewy bodies during Parkinson's disease. CsgA subunits are targeted to the CsgG outer membrane pore by CsgE prior to secretion and assembly into fibers. Here, we use biophysical, biochemical, and genetic approaches to elucidate a mechanistic understanding of CsgE function in curli biogenesis.
Collapse
|
44
|
Johnston CL, Marzano NR, van Oijen AM, Ecroyd H. Using Single-Molecule Approaches to Understand the Molecular Mechanisms of Heat-Shock Protein Chaperone Function. J Mol Biol 2018; 430:4525-4546. [PMID: 29787765 DOI: 10.1016/j.jmb.2018.05.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/11/2018] [Accepted: 05/13/2018] [Indexed: 02/01/2023]
Abstract
The heat-shock proteins (Hsp) are a family of molecular chaperones, which collectively form a network that is critical for the maintenance of protein homeostasis. Traditional ensemble-based measurements have provided a wealth of knowledge on the function of individual Hsps and the Hsp network; however, such techniques are limited in their ability to resolve the heterogeneous, dynamic and transient interactions that molecular chaperones make with their client proteins. Single-molecule techniques have emerged as a powerful tool to study dynamic biological systems, as they enable rare and transient populations to be identified that would usually be masked in ensemble measurements. Thus, single-molecule techniques are particularly amenable for the study of Hsps and have begun to be used to reveal novel mechanistic details of their function. In this review, we discuss the current understanding of the chaperone action of Hsps and how gaps in the field can be addressed using single-molecule methods. Specifically, this review focuses on the ATP-independent small Hsps and the broader Hsp network and describes how these dynamic systems are amenable to single-molecule techniques.
Collapse
Affiliation(s)
- Caitlin L Johnston
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Nicholas R Marzano
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Antoine M van Oijen
- School of Chemistry, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| | - Heath Ecroyd
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| |
Collapse
|
45
|
Ansari MY, Mande SC. A Glimpse Into the Structure and Function of Atypical Type I Chaperonins. Front Mol Biosci 2018; 5:31. [PMID: 29696145 PMCID: PMC5904260 DOI: 10.3389/fmolb.2018.00031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/21/2018] [Indexed: 12/22/2022] Open
Abstract
Chaperonins are a subclass of molecular chaperones that assist cellular proteins to fold and assemble into their native shape. Much work has been done on Type I chaperonins, which has elucidated their elegant mechanism. Some debate remains about the details in these mechanisms, but nonetheless the roles of these in helping protein folding have been understood in great depth. In this review we discuss the known functions of atypical Type I chaperonins, highlighting evolutionary aspects that might lead chaperonins to perform alternate functions.
Collapse
|
46
|
Chen LJ, Chen S, Qin Y, Xu L, Yin GQ, Zhu JL, Zhu FF, Zheng W, Li X, Yang HB. Construction of Porphyrin-Containing Metallacycle with Improved Stability and Activity within Mesoporous Carbon. J Am Chem Soc 2018; 140:5049-5052. [PMID: 29625011 DOI: 10.1021/jacs.8b02386] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The successful construction of porphyrin functionalized metallacycle in the confined cavity of mesoporous carbon FDU-16 (3⊂C) is presented in this study. Because of high dispersity of metallacycles within the mesoporous cavities, the stability and activity of porphyrin-containing metallacycles were obviously improved. For example, 1O2 generation efficiency of 3⊂C is ca. 6-fold faster than that of free metallaycles in solution. Thus, the resultant hybrid material has been successfully employed as a heterogeneous catalyst for photooxidation of sulfides.
Collapse
Affiliation(s)
- Li-Jun Chen
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , People's Republic of China
| | - Shangjun Chen
- Department of Chemistry , Shanghai Normal University , Shanghai 200234 , People's Republic of China
| | - Yi Qin
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , People's Republic of China
| | - Lin Xu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , People's Republic of China
| | - Guang-Qiang Yin
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , People's Republic of China.,Department of Chemistry , University of South Florida Tampa , Florida 33620 , United States
| | - Jun-Long Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , People's Republic of China
| | - Fan-Fan Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , People's Republic of China
| | - Wei Zheng
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , People's Republic of China
| | - Xiaopeng Li
- Department of Chemistry , University of South Florida Tampa , Florida 33620 , United States
| | - Hai-Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , People's Republic of China
| |
Collapse
|
47
|
Chi H, Xu B, Liu Z, Wei J, Li S, Ren H, Xu Y, Lu X, Wang X, Wang X, Huang F. Combined thermodynamic and kinetic analysis of GroEL interacting with CXCR4 transmembrane peptides. Biochim Biophys Acta Gen Subj 2018; 1862:1576-1583. [PMID: 29627450 DOI: 10.1016/j.bbagen.2018.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 04/03/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
Abstract
GroEL along with ATP and its co-chaperonin GroES has been demonstrated to significantly enhance the folding of newly translated G-protein-coupled receptors (GPCRs). This work extends the previous studies to explore the guest capture and release processes in GroEL-assisted folding of GPCRs, by the reduced approach of employing CXCR4 transmembrane peptides as model substrates. Each of the CXCR4-derived peptides exhibited high affinity for GroEL with a binding stoichiometry near seven. It is found that the peptides interact with the paired α helices in the apical domain of the chaperonin which are similar with the binding sites of SBP (strongly binding peptide: SWMTTPWGFLHP). Complementary binding study with a single-ring version of GroEL indicates that each of the two chaperonin rings is competent for accommodating all the seven CXCR4 peptides bound to GroEL under saturation condition. Meanwhile, the binding kinetics of CXCR4 peptides with GroEL was also examined; ATP alone, or in combination of GroES evidently promoted the release of the peptide substrates from the chaperonin. The results obtained would be beneficial to understand the thermodynamic and kinetic nature of GroEL-GPCRs interaction which is the central molecular event in the assisted folding process.
Collapse
Affiliation(s)
- Haixia Chi
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; Qingdao Langoo Oceantec Co., Ltd, Qingdao 266235, PR China
| | - Baomei Xu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Zhenzhen Liu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Junting Wei
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Yan Xu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Xinwei Lu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Xiaoqiang Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; College of Science, China University of Petroleum (East China), Qingdao 266580, PR China.
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China.
| |
Collapse
|
48
|
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), a ∼530 kDa complex of 8 large (RbcL) and 8 small subunits (RbcS), mediates the fixation of atmospheric CO2 into usable sugars during photosynthesis. Despite its fundamental role, Rubisco is a remarkably inefficient enzyme and thus is produced by plants in huge amounts. It has long been a key target for bioengineering with the goal to increase crop yields. However, such efforts have been hampered by the complex requirement of Rubisco biogenesis for molecular chaperones. Recent studies have identified an array of auxiliary factors needed for the folding and assembly of the Rubisco subunits. The folding of plant RbcL subunits is mediated by the cylindrical chloroplast chaperonin, Cpn60, and its cofactor Cpn20. Folded RbcL requires a number of additional Rubisco specific assembly chaperones, including RbcX, Rubisco accumulation factors 1 (Raf1) and 2 (Raf2), and the Bundle sheath defective-2 (BSD2), to mediate the assembly of the RbcL8 intermediate complex. Incorporation of the RbcS and displacement of the assembly factors generates the active holoenzyme. An Escherichia coli strain expressing the chloroplast chaperonin and auxiliary factors now allows the expression of functional plant Rubisco, paving the way for Rubisco engineering by large scale mutagenesis. Here, we review our current understanding on how these chaperones cooperate to produce one of the most important enzymes in nature.
Collapse
Affiliation(s)
- Robert H Wilson
- Department of Cellular Biochemistry , Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry , Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| |
Collapse
|
49
|
Abstract
Protein folding in the cell was originally assumed to be a spontaneous process, based on Anfinsen's discovery that purified proteins can fold on their own after removal from denaturant. Consequently cell biologists showed little interest in the protein folding process. This changed only in the mid and late 1980s, when the chaperone story began to unfold. As a result, we now know that in vivo, protein folding requires assistance by a complex machinery of molecular chaperones. To ensure efficient folding, members of different chaperone classes receive the nascent protein chain emerging from the ribosome and guide it along an ordered pathway toward the native state. I was fortunate to contribute to these developments early on. In this short essay, I will describe some of the critical steps leading to the current concept of protein folding as a highly organized cellular process.
Collapse
Affiliation(s)
- F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
50
|
GroEL Ring Separation and Exchange in the Chaperonin Reaction. Cell 2018; 172:605-617.e11. [PMID: 29336887 DOI: 10.1016/j.cell.2017.12.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/16/2017] [Accepted: 12/06/2017] [Indexed: 11/24/2022]
Abstract
The bacterial chaperonin GroEL and its cofactor, GroES, form a nano-cage for a single molecule of substrate protein (SP) to fold in isolation. GroEL and GroES undergo an ATP-regulated interaction cycle to close and open the folding cage. GroEL consists of two heptameric rings stacked back to back. Here, we show that GroEL undergoes transient ring separation, resulting in ring exchange between complexes. Ring separation occurs upon ATP-binding to the trans ring of the asymmetric GroEL:7ADP:GroES complex in the presence or absence of SP and is a consequence of inter-ring negative allostery. We find that a GroEL mutant unable to perform ring separation is folding active but populates symmetric GroEL:GroES2 complexes, where both GroEL rings function simultaneously rather than sequentially. As a consequence, SP binding and release from the folding chamber is inefficient, and E. coli growth is impaired. We suggest that transient ring separation is an integral part of the chaperonin mechanism.
Collapse
|