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Lopez T, Dalton K, Tomlinson A, Pande V, Frydman J. An information theoretic framework reveals a tunable allosteric network in group II chaperonins. Nat Struct Mol Biol 2017; 24:726-733. [PMID: 28741612 PMCID: PMC5986071 DOI: 10.1038/nsmb.3440] [Citation(s) in RCA: 12] [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: 10/05/2016] [Accepted: 06/22/2017] [Indexed: 12/19/2022]
Abstract
ATP-dependent allosteric regulation of the ring-shaped group II chaperonins remains ill defined, in part because their complex oligomeric topology has limited the success of structural techniques in suggesting allosteric determinants. Further, their high sequence conservation has hindered the prediction of allosteric networks using mathematical covariation approaches. Here, we develop an information theoretic strategy that is robust to residue conservation and apply it to group II chaperonins. We identify a contiguous network of covarying residues that connects all nucleotide-binding pockets within each chaperonin ring. An interfacial residue between the networks of neighboring subunits controls positive cooperativity by communicating nucleotide occupancy within each ring. Strikingly, chaperonin allostery is tunable through single mutations at this position. Naturally occurring variants at this position that double the extent of positive cooperativity are less prevalent in nature. We propose that being less cooperative than attainable allows chaperonins to support robust folding over a wider range of metabolic conditions.
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Affiliation(s)
- Tom Lopez
- Department of Biology, Stanford University, Stanford, California, USA
| | - Kevin Dalton
- Biophysics Program, Stanford University, Stanford, California, USA
| | - Anthony Tomlinson
- Department of Biology, Stanford University, Stanford, California, USA
| | - Vijay Pande
- Biophysics Program, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California, USA
- Biophysics Program, Stanford University, Stanford, California, USA
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2
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Abstract
The human chaperonin TRiC consists of eight non-identical subunits, and its protein-folding activity is critical for cellular health. Misfolded proteins are associated with many human diseases, such as amyloid diseases, cancer, and neuropathies, making TRiC a potential therapeutic target. A detailed structural understanding of its ATP-dependent folding mechanism and substrate recognition is therefore of great importance. Of particular health-related interest is the mutation Histidine 147 to Arginine (H147R) in human TRiC subunit 5 (CCT5), which has been associated with hereditary sensory neuropathy. In this paper, we describe the crystal structures of CCT5 and the CCT5-H147R mutant, which provide important structural information for this vital protein-folding machine in humans. This first X-ray crystallographic study of a single human CCT subunit in the context of a hexadecameric complex can be expanded in the future to the other 7 subunits that form the TRiC complex.
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3
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Taha, Siddiqui KS, Campanaro S, Najnin T, Deshpande N, Williams TJ, Aldrich‐Wright J, Wilkins M, Curmi PMG, Cavicchioli R. Single
TRAM
domain
RNA
‐binding proteins in
A
rchaea
: functional insight from
C
tr3 from the
A
ntarctic methanogen
M
ethanococcoides burtonii. Environ Microbiol 2016; 18:2810-24. [DOI: 10.1111/1462-2920.13229] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Taha
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - K. S. Siddiqui
- Life Sciences Department King Fahd University of Petroleum and Minerals Dhahran Kingdom of Saudi Arabia
| | - S. Campanaro
- Department of Biology University of Padua Via U. Bassi 58/B 35121 Padova Italy
| | - T. Najnin
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - N. Deshpande
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - T. J. Williams
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - J. Aldrich‐Wright
- Nanoscale Organization and Dynamic Group School of Science and Health Western Sydney University Penrith 2560 NSW Australia
| | - M. Wilkins
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - P. M. G. Curmi
- School of Physics The University of New South Wales Sydney NSW 2052 Australia
| | - R. Cavicchioli
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
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4
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Chaston JJ, Smits C, Aragão D, Wong ASW, Ahsan B, Sandin S, Molugu SK, Molugu SK, Bernal RA, Stock D, Stewart AG. Structural and Functional Insights into the Evolution and Stress Adaptation of Type II Chaperonins. Structure 2016; 24:364-74. [PMID: 26853941 DOI: 10.1016/j.str.2015.12.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 12/14/2015] [Accepted: 12/16/2015] [Indexed: 12/12/2022]
Abstract
Chaperonins are essential biological complexes assisting protein folding in all kingdoms of life. Whereas homooligomeric bacterial GroEL binds hydrophobic substrates non-specifically, the heterooligomeric eukaryotic CCT binds specifically to distinct classes of substrates. Sulfolobales, which survive in a wide range of temperatures, have evolved three different chaperonin subunits (α, β, γ) that form three distinct complexes tailored for different substrate classes at cold, normal, and elevated temperatures. The larger octadecameric β complexes cater for substrates under heat stress, whereas smaller hexadecameric αβ complexes prevail under normal conditions. The cold-shock complex contains all three subunits, consistent with greater substrate specificity. Structural analysis using crystallography and electron microscopy reveals the geometry of these complexes and shows a novel arrangement of the α and β subunits in the hexadecamer enabling incorporation of the γ subunit.
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Affiliation(s)
- Jessica J Chaston
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Callum Smits
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - David Aragão
- Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Andrew S W Wong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 637551
| | - Bilal Ahsan
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Sara Sandin
- School of Biological Sciences, Nanyang Technological University, Singapore 637551; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 637551
| | - Sudheer K Molugu
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sanjay K Molugu
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Ricardo A Bernal
- Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Daniela Stock
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia.
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia.
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5
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The Mechanism and Function of Group II Chaperonins. J Mol Biol 2015; 427:2919-30. [PMID: 25936650 DOI: 10.1016/j.jmb.2015.04.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022]
Abstract
Protein folding in the cell requires the assistance of enzymes collectively called chaperones. Among these, the chaperonins are 1-MDa ring-shaped oligomeric complexes that bind unfolded polypeptides and promote their folding within an isolated chamber in an ATP-dependent manner. Group II chaperonins, found in archaea and eukaryotes, contain a built-in lid that opens and closes over the central chamber. In eukaryotes, the chaperonin TRiC/CCT is hetero-oligomeric, consisting of two stacked rings of eight paralogous subunits each. TRiC facilitates folding of approximately 10% of the eukaryotic proteome, including many cytoskeletal components and cell cycle regulators. Folding of many cellular substrates of TRiC cannot be assisted by any other chaperone. A complete structural and mechanistic understanding of this highly conserved and essential chaperonin remains elusive. However, recent work is beginning to shed light on key aspects of chaperonin function and how their unique properties underlie their contribution to maintaining cellular proteostasis.
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Dhaunta N, Arora K, Chandrayan SK, Guptasarma P. Introduction of a thermophile-sourced ion pair network in the fourth beta/alpha unit of a psychophile-derived triosephosphate isomerase from Methanococcoides burtonii significantly increases its kinetic thermal stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1023-33. [DOI: 10.1016/j.bbapap.2013.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 12/07/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
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Williams TJ, Lauro FM, Ertan H, Burg DW, Poljak A, Raftery MJ, Cavicchioli R. Defining the response of a microorganism to temperatures that span its complete growth temperature range (-2°C to 28°C) using multiplex quantitative proteomics. Environ Microbiol 2011; 13:2186-203. [PMID: 21443741 DOI: 10.1111/j.1462-2920.2011.02467.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The growth of all microorganisms is limited to a specific temperature range. However, it has not previously been determined to what extent global protein profiles change in response to temperatures that incrementally span the complete growth temperature range of a microorganism. As a result it has remained unclear to what extent cellular processes (inferred from protein abundance profiles) are affected by growth temperature and which, in particular, constrain growth at upper and lower temperature limits. To evaluate this, 8-plex iTRAQ proteomics was performed on the Antarctic microorganism, Methanococcoides burtonii. Methanococcoides burtonii was chosen due to its importance as a model psychrophilic (cold-adapted) member of the Archaea, and the fact that proteomic methods, including subcellular fractionation procedures, have been well developed. Differential abundance patterns were obtained for cells grown at seven different growth temperatures (-2°C, 1°C, 4°C, 10°C, 16°C, 23°C, 28°C) and a principal component analysis (PCA) was performed to identify trends in protein abundances. The multiplex analysis enabled three largely distinct physiological states to be described: cold stress (-2°C), cold adaptation (1°C, 4°C, 10°C and 16°C), and heat stress (23°C and 28°C). A particular feature of the thermal extremes was the synthesis of heat- and cold-specific stress proteins, reflecting the important, yet distinct ways in which temperature-induced stress manifests in the cell. This is the first quantitative proteomic investigation to simultaneously assess the response of a microorganism to numerous growth temperatures, including the upper and lower growth temperatures limits, and has revealed a new level of understanding about cellular adaptive responses.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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