1
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Sivinski J, Ngo D, Zerio CJ, Ambrose AJ, Watson ER, Kaneko LK, Kostelic MM, Stevens M, Ray AM, Park Y, Wu C, Marty MT, Hoang QQ, Zhang DD, Lander GC, Johnson SM, Chapman E. Allosteric differences dictate GroEL complementation of E. coli. FASEB J 2022; 36:e22198. [PMID: 35199390 PMCID: PMC8887798 DOI: 10.1096/fj.202101708rr] [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: 11/10/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022]
Abstract
GroES/GroEL is the only bacterial chaperone essential under all conditions, making it a potential antibiotic target. Rationally targeting ESKAPE GroES/GroEL as an antibiotic strategy necessitates studying their structure and function. Herein, we outline the structural similarities between Escherichia coli and ESKAPE GroES/GroEL and identify significant differences in intra- and inter-ring cooperativity, required in the refolding cycle of client polypeptides. Previously, we observed that one-half of ESKAPE GroES/GroEL family members could not support cell viability when each was individually expressed in GroES/GroEL-deficient E. coli cells. Cell viability was found to be dependent on the allosteric compatibility between ESKAPE and E. coli subunits within mixed (E. coli and ESKAPE) tetradecameric GroEL complexes. Interestingly, differences in allostery did not necessarily result in differences in refolding rate for a given homotetradecameric chaperonin. Characterization of ESKAPE GroEL allostery, ATPase, and refolding rates in this study will serve to inform future studies focused on inhibitor design and mechanism of action studies.
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Affiliation(s)
- Jared Sivinski
- The University of Arizona, College of Pharmacy, Department
of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ
85721
| | - Duc Ngo
- The University of Arizona, College of Pharmacy, Department
of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ
85721
| | - Christopher J. Zerio
- The University of Arizona, College of Pharmacy, Department
of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ
85721
| | - Andrew J. Ambrose
- The University of Arizona, College of Pharmacy, Department
of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ
85721
| | - Edmond R. Watson
- Department of Integrative Structural and Computational
Biology, Scripps Research, La Jolla, CA, USA
| | - Lynn K. Kaneko
- The University of Arizona, College of Pharmacy, Department
of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ
85721
| | - Marius M. Kostelic
- The University of Arizona, Department of Chemistry and
Biochemistry, Tucson, AZ 85721
| | - Mckayla Stevens
- Indiana University School of Medicine, Department of
Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202
| | - Anne-Marie Ray
- Indiana University School of Medicine, Department of
Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202
| | - Yangshin Park
- Indiana University School of Medicine, Department of
Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202,Stark Neurosciences Research Institute, Indiana University
School of Medicine. 320 W. 15th Street, Suite 414, Indianapolis, IN 46202,Department of Neurology, Indiana University School of
Medicine. 635 Barnhill Drive, Indianapolis, IN 46202
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT 06520
| | - Michael T. Marty
- The University of Arizona, Department of Chemistry and
Biochemistry, Tucson, AZ 85721
| | - Quyen Q. Hoang
- Indiana University School of Medicine, Department of
Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202,Stark Neurosciences Research Institute, Indiana University
School of Medicine. 320 W. 15th Street, Suite 414, Indianapolis, IN 46202,Department of Neurology, Indiana University School of
Medicine. 635 Barnhill Drive, Indianapolis, IN 46202
| | - Donna D. Zhang
- The University of Arizona, College of Pharmacy, Department
of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ
85721
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational
Biology, Scripps Research, La Jolla, CA, USA
| | - Steven M. Johnson
- Indiana University School of Medicine, Department of
Biochemistry and Molecular Biology, 635 Barnhill Dr., Indianapolis, IN 46202
| | - Eli Chapman
- The University of Arizona, College of Pharmacy, Department
of Pharmacology and Toxicology, 1703 E. Mabel St., PO Box 210207, Tucson, AZ
85721,Corresponding author
, Phone: 520-626-2741
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2
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Rodriguez A, Von Salzen D, Holguin BA, Bernal RA. Complex Destabilization in the Mitochondrial Chaperonin Hsp60 Leads to Disease. Front Mol Biosci 2020; 7:159. [PMID: 32766281 PMCID: PMC7381220 DOI: 10.3389/fmolb.2020.00159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/24/2020] [Indexed: 01/21/2023] Open
Abstract
Several neurological disorders have been linked to mutations in chaperonin genes and more specifically to the HSPD1 gene. In humans, HSPD1 encodes the mitochondrial Heat Shock Protein 60 (mtHsp60) chaperonin, which carries out essential protein folding reactions that help maintain mitochondrial and cellular homeostasis. It functions as a macromolecular complex that provides client proteins an environment that favors proper folding in an ATP-dependent manner. It has been established that mtHsp60 plays a crucial role in the proper folding of mitochondrial proteins involved in ATP producing pathways. Recently, various single-point mutations in the mtHsp60 encoding gene have been directly linked to neuropathies and paraplegias. Individuals who harbor mtHsp60 mutations that negatively impact its folding ability display phenotypes with highly compromised muscle and neuron cells. Carriers of these mutations usually develop neuropathies and paraplegias at different stages of their lives mainly characterized by leg stiffness and weakness as well as degeneration of spinal cord nerves. These phenotypes are likely due to hindered energy producing pathways involved in cellular respiration resulting in ATP deprived cells. Although the complete protein folding mechanism of mtHsp60 is not well understood, recent work suggests that several of these mutations act by destabilizing the oligomeric stability of mtHsp60. Here, we discuss recent studies that highlight key aspects of the mtHsp60 mechanism with a focus on some of the known disease-causing point mutations, D29G and V98I, and their effect on the protein folding reaction cycle.
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Affiliation(s)
| | | | | | - Ricardo A. Bernal
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, United States
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3
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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.
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4
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Jain N, Knowles TJ, Lund PA, Chaudhuri TK. Minichaperone (GroEL191-345) mediated folding of MalZ proceeds by binding and release of native and functional intermediates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:941-951. [PMID: 29864530 DOI: 10.1016/j.bbapap.2018.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/02/2018] [Accepted: 05/28/2018] [Indexed: 10/14/2022]
Abstract
The isolated apical domain of GroEL consisting of residues 191-345 (known as "minichaperone") binds and assists the folding of a wide variety of client proteins without GroES and ATP, but the mechanism of its action is still unknown. In order to probe into the matter, we have examined minichaperone-mediated folding of a large aggregation prone protein Maltodextrin-glucosidase (MalZ). The key objective was to identify whether MalZ exists free in solution, or remains bound to, or cycling on and off the minichaperone during the refolding process. When GroES was introduced during refolding process, production of the native MalZ was inhibited. We also observed the same findings with a trap mutant of GroEL, which stably captures a predominantly non-native MalZ released from minichaperone during refolding process, but does not release it. Tryptophan and ANS fluorescence measurements indicated that refolded MalZ has the same structure as the native MalZ, but that its structure when bound to minichaperone is different. Surface plasmon resonance measurements provide an estimate for the equilibrium dissociation constant KD for the MalZ-minichaperone complex of 0.21 ± 0.04 μM, which are significantly higher than for most GroEL clients. This showed that minichaperone interacts loosely with MalZ to allow the protein to change its conformation and fold while bound during the refolding process. These observations suggest that the minichaperone works by carrying out repeated cycles of binding aggregation-prone protein MalZ in a relatively compact conformation and in a partially folded but active state, and releasing them to attempt to fold in solution.
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Affiliation(s)
- Neha Jain
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India; Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK
| | - Timothy J Knowles
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK
| | - Peter A Lund
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK.
| | - Tapan K Chaudhuri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India.
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5
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Bhatt JM, Enriquez AS, Wang J, Rojo HM, Molugu SK, Hildenbrand ZL, Bernal RA. Single-Ring Intermediates Are Essential for Some Chaperonins. Front Mol Biosci 2018; 5:42. [PMID: 29755985 PMCID: PMC5934643 DOI: 10.3389/fmolb.2018.00042] [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: 11/17/2017] [Accepted: 04/13/2018] [Indexed: 11/20/2022] Open
Abstract
Chaperonins are macromolecular complexes found throughout all kingdoms of life that assist unfolded proteins reach a biologically active state. Historically, chaperonins have been classified into two groups based on sequence, subunit structure, and the requirement for a co-chaperonin. Here, we present a brief review of chaperonins that can form double- and single-ring conformational intermediates in their protein-folding catalytic pathway. To date, the bacteriophage encoded chaperonins ϕ-EL and OBP, human mitochondrial chaperonin and most recently, the bacterial groEL/ES systems, have been reported to form single-ring intermediates as part of their normal protein-folding activity. These double-ring chaperonins separate into single-ring intermediates that have the ability to independently fold a protein. We discuss the structural and functional features along with the biological relevance of single-ring intermediates in cellular protein folding. Of special interest are the ϕ-EL and OBP chaperonins which demonstrate features of both group I and II chaperonins in addition to their ability to function via single-ring intermediates.
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Affiliation(s)
- Jay M Bhatt
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Adrian S Enriquez
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Jinliang Wang
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Humberto M Rojo
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Sudheer K Molugu
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | | | - Ricardo A Bernal
- Department of Chemistry, The University of Texas at El Paso, El Paso, TX, United States
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6
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Takenaka T, Nakamura T, Yanaka S, Yagi-Utsumi M, Chandak MS, Takahashi K, Paul S, Makabe K, Arai M, Kato K, Kuwajima K. Formation of the chaperonin complex studied by 2D NMR spectroscopy. PLoS One 2017; 12:e0187022. [PMID: 29059240 PMCID: PMC5653362 DOI: 10.1371/journal.pone.0187022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/11/2017] [Indexed: 11/21/2022] Open
Abstract
We studied the interaction between GroES and a single-ring mutant (SR1) of GroEL by the NMR titration of 15N-labeled GroES with SR1 at three different temperatures (20, 25 and 30°C) in the presence of 3 mM ADP in 100 mM KCl and 10 mM MgCl2 at pH 7.5. We used SR1 instead of wild-type double-ring GroEL to precisely control the stoichiometry of the GroES binding to be 1:1 ([SR1]:[GroES]). Native heptameric GroES was very flexible, showing well resolved cross peaks of the residues in a mobile loop segment (residue 17–34) and at the top of a roof hairpin (Asn51) in the heteronuclear single quantum coherence spectra. The binding of SR1 to GroES caused the cross peaks to disappear simultaneously, and hence it occurred in a single-step cooperative manner with significant immobilization of the whole GroES structure. The binding was thus entropic with a positive entropy change (219 J/mol/K) and a positive enthalpy change (35 kJ/mol), and the binding constant was estimated at 1.9×105 M−1 at 25°C. The NMR titration in 3 mM ATP also indicated that the binding constant between GroES and SR1 increased more than tenfold as compared with the binding constant in 3 mM ADP. These results will be discussed in relation to the structure and mechanisms of the chaperonin GroEL/GroES complex.
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Affiliation(s)
- Toshio Takenaka
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Takashi Nakamura
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Saeko Yanaka
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Maho Yagi-Utsumi
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
| | - Mahesh S. Chandak
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
| | - Kazunobu Takahashi
- Department of Physics, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Subhankar Paul
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Koki Makabe
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
- Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, the University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
| | - Kunihiro Kuwajima
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
- Department of Functional Molecular Science, School of Physical Sciences, the Graduate University for Advanced Studies (Sokendai), Myodaiji, Okazaki, Aichi, Japan
- Department of Physics, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
- School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Dongdaemun-gu, Seoul, Korea
- * E-mail: ,
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Creating the Functional Single-Ring GroEL-GroES Chaperonin Systems via Modulating GroEL-GroES Interaction. Sci Rep 2017; 7:9710. [PMID: 28852160 PMCID: PMC5575113 DOI: 10.1038/s41598-017-10499-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/09/2017] [Indexed: 11/08/2022] Open
Abstract
Chaperonin and cochaperonin, represented by E. coli GroEL and GroES, are essential molecular chaperones for protein folding. The double-ring assembly of GroEL is required to function with GroES, and a single-ring GroEL variant GroELSR forms a stable complex with GroES, arresting the chaperoning reaction cycle. GroES I25 interacts with GroEL; however, mutations of I25 abolish GroES-GroEL interaction due to the seven-fold mutational amplification in heptameric GroES. To weaken GroELSR-GroES interaction in a controlled manner, we used groES 7, a gene linking seven copies of groES, to incorporate I25 mutations in selected GroES modules in GroES7. We generated GroES7 variants with different numbers of GroESI25A or GroESI25D modules and different arrangements of the mutated modules, and biochemically characterized their interactions with GroELSR. GroES7 variants with two mutated modules participated in GroELSR-mediated protein folding in vitro. GroES7 variants with two or three mutated modules collaborated with GroELSR to perform chaperone function in vivo: three GroES7 variants functioned with GroELSR under both normal and heat-shock conditions. Our studies on functional single-ring bacterial chaperonin systems are informative to the single-ring human mitochondrial chaperonin mtHsp60-mtHsp10, and will provide insights into how the double-ring bacterial system has evolved to the single-ring mtHsp60-mtHsp10.
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8
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Zhuo L, Wang Y, Zhang Z, Li J, Zhang XH, Li YZ. Myxococcus xanthus DK1622 Coordinates Expressions of the Duplicate groEL and Single groES Genes for Synergistic Functions of GroELs and GroES. Front Microbiol 2017; 8:733. [PMID: 28496436 PMCID: PMC5406781 DOI: 10.3389/fmicb.2017.00733] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/10/2017] [Indexed: 11/17/2022] Open
Abstract
Chaperonin GroEL (Cpn60) requires cofactor GroES (Cpn10) for protein refolding in bacteria that possess single groEL and groES genes in a bicistronic groESL operon. Among 4,861 completely-sequenced prokaryotic genomes, 884 possess duplicate groEL genes and 770 possess groEL genes with no neighboring groES. It is unclear whether stand-alone groEL requires groES in order to function and, if required, how duplicate groEL genes and unequal groES genes balance their expressions. In Myxococcus xanthus DK1622, we determined that, while duplicate groELs were alternatively deletable, the single groES that clusters with groEL1 was essential for cell survival. Either GroEL1 or GroEL2 required interactions with GroES for in vitro and in vivo functions. Deletion of groEL1 or groEL2 resulted in decreased expressions of both groEL and groES; and ectopic complementation of groEL recovered not only the groEL but also groES expressions. The addition of an extra groES gene upstream groEL2 to form a bicistronic operon had almost no influence on groES expression and the cell survival rate, whereas over-expression of groES using a self-replicating plasmid simultaneously increased the groEL expressions. The results indicated that M. xanthus DK1622 cells coordinate expressions of the duplicate groEL and single groES genes for synergistic functions of GroELs and GroES. We proposed a potential regulation mechanism for the expression coordination.
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Affiliation(s)
- Li Zhuo
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China
| | - Yan Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China.,College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China
| | - Jian Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China
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9
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Fares MA. Evolution of Multiple Chaperonins: Innovation of Evolutionary Capacitors. PROKARYOTIC CHAPERONINS 2017:149-170. [DOI: 10.1007/978-981-10-4651-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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10
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Fares MA. Coevolution Analysis Illuminates the Evolutionary Plasticity of the Chaperonin System GroES/L. STRESS AND ENVIRONMENTAL REGULATION OF GENE EXPRESSION AND ADAPTATION IN BACTERIA 2016:796-811. [DOI: 10.1002/9781119004813.ch77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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11
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The evolution of protein moonlighting: adaptive traps and promiscuity in the chaperonins. Biochem Soc Trans 2015; 42:1709-14. [PMID: 25399594 DOI: 10.1042/bst20140225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Moonlighting proteins exhibit functions that are alternative to their main role in the cell. Heat-shock proteins, also known as molecular chaperones, are now recognized for their wide range of activities in and/or outside the cell, being prominent examples of moonlighting proteins. Chaperonins are highly conserved molecular chaperones that fold other proteins into their native conformation allowing them to carry out essential functions in the cell. Activities alternative to folding have been reported for the chaperonin (Cpn) 60 protein. Preservation of various alternative functions in one protein conflicts with the optimization of each of the functions. What evolutionary mechanisms have allowed the persistence of moonlighting proteins, and in particular the chaperonins, remains a mystery. In the present article, I argue that mechanisms that increase the resistance of phenotypes to genetic and environmental perturbations enable the persistence of a reservoir of genetic variants, each potentially codifying for a distinct function. Gene duplication is one such mechanism that has characterized the expansion and has been concomitant with the emergence of novel functions in these protein families. Indeed, Cpn60 performs a large list of folding-independent functions, including roles in the transmission of viruses from insects to plants and stimulation of the immune system, among others. In addition to the innovation promoted by gene duplication, I discuss that the Cpn60 protein comprises a hidden amino acid combinatorial code that may well be responsible for its ability to develop novel functions while maintaining an optimized folding ability. The present review points to a complex model of evolution of protein moonlighting.
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12
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Yamamoto YY, Abe Y, Moriya K, Arita M, Noguchi K, Ishii N, Sekiguchi H, Sasaki YC, Yohda M. Inter-ring communication is dispensable in the reaction cycle of group II chaperonins. J Mol Biol 2014; 426:2667-78. [PMID: 24859336 DOI: 10.1016/j.jmb.2014.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/09/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
Abstract
Chaperonins are ubiquitous molecular chaperones with the subunit molecular mass of 60kDa. They exist as double-ring oligomers with central cavities. An ATP-dependent conformational change of the cavity induces the folding of an unfolded protein that is captured in the cavity. In the group I chaperonins, which are present in eubacteria and eukaryotic organelles, inter-ring communication takes important role for the reaction cycle. However, there has been limited study on the inter-ring communication in the group II chaperonins that exist in archaea and the eukaryotic cytosol. In this study, we have constructed the asymmetric ring complex of a group II chaperonin using circular permutated covalent mutants. Although one ring of the asymmetric ring complex lacks ATPase or ATP binding activity, the other wild-type ring undergoes an ATP-dependent conformational change and maintains protein-folding activity. The results clearly demonstrate that inter-ring communication is dispensable in the reaction cycle of group II chaperonins.
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Affiliation(s)
- Yohei Y Yamamoto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka, Koganei, Tokyo 184-8588, Japan
| | - Yuki Abe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka, Koganei, Tokyo 184-8588, Japan
| | - Kazuki Moriya
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka, Koganei, Tokyo 184-8588, Japan
| | - Mayuno Arita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka, Koganei, Tokyo 184-8588, Japan
| | - Keiichi Noguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka, Koganei, Tokyo 184-8588, Japan
| | - Noriyuki Ishii
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198, Japan; CREST Sasaki Team, Japan Science and Technology Agency, Tokyo 102-0076, Japan
| | - Yuji C Sasaki
- CREST Sasaki Team, Japan Science and Technology Agency, Tokyo 102-0076, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka, Koganei, Tokyo 184-8588, Japan.
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13
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Mizuta T, Ando K, Uemura T, Kawata Y, Mizobata T. Probing the dynamic process of encapsulation in Escherichia coli GroEL. PLoS One 2013; 8:e78135. [PMID: 24205127 PMCID: PMC3813556 DOI: 10.1371/journal.pone.0078135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/16/2013] [Indexed: 11/24/2022] Open
Abstract
Kinetic analyses of GroE-assisted folding provide a dynamic sequence of molecular events that underlie chaperonin function. We used stopped-flow analysis of various fluorescent GroEL mutants to obtain details regarding the sequence of events that transpire immediately after ATP binding to GroEL and GroEL with prebound unfolded proteins. Characterization of GroEL CP86, a circularly permuted GroEL with the polypeptide ends relocated to the vicinity of the ATP binding site, showed that GroES binding and protection of unfolded protein from solution is achieved surprisingly early in the functional cycle, and in spite of greatly reduced apical domain movement. Analysis of fluorescent GroEL SR-1 and GroEL D398A variants suggested that among other factors, the presence of two GroEL rings and a specific conformational rearrangement of Helix M in GroEL contribute significantly to the rapid release of unfolded protein from the GroEL apical domain.
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Affiliation(s)
- Toshifumi Mizuta
- Department of Biotechnology, Graduate School of Engineering, Tottori, Japan
| | - Kasumi Ando
- Department of Biotechnology, Graduate School of Engineering, Tottori, Japan
| | - Tatsuya Uemura
- Department of Biomedical Science, Graduate School of Medical Sciences, Tottori University, Tottori, Japan
| | - Yasushi Kawata
- Department of Biotechnology, Graduate School of Engineering, Tottori, Japan
- Department of Biomedical Science, Graduate School of Medical Sciences, Tottori University, Tottori, Japan
| | - Tomohiro Mizobata
- Department of Biotechnology, Graduate School of Engineering, Tottori, Japan
- Department of Biomedical Science, Graduate School of Medical Sciences, Tottori University, Tottori, Japan
- * E-mail:
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Ruiz-González MX, Fares MA. Coevolution analyses illuminate the dependencies between amino acid sites in the chaperonin system GroES-L. BMC Evol Biol 2013; 13:156. [PMID: 23875653 PMCID: PMC3728108 DOI: 10.1186/1471-2148-13-156] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND GroESL is a heat-shock protein ubiquitous in bacteria and eukaryotic organelles. This evolutionarily conserved protein is involved in the folding of a wide variety of other proteins in the cytosol, being essential to the cell. The folding activity proceeds through strong conformational changes mediated by the co-chaperonin GroES and ATP. Functions alternative to folding have been previously described for GroEL in different bacterial groups, supporting enormous functional and structural plasticity for this molecule and the existence of a hidden combinatorial code in the protein sequence enabling such functions. Describing this plasticity can shed light on the functional diversity of GroEL. We hypothesize that different overlapping sets of amino acids coevolve within GroEL, GroES and between both these proteins. Shifts in these coevolutionary relationships may inevitably lead to evolution of alternative functions. RESULTS We conducted the first coevolution analyses in an extensive bacterial phylogeny, revealing complex networks of evolutionary dependencies between residues in GroESL. These networks differed among bacterial groups and involved amino acid sites with functional importance and others with previously unsuspected functional potential. Coevolutionary networks formed statistically independent units among bacterial groups and map to structurally continuous regions in the protein, suggesting their functional link. Sites involved in coevolution fell within narrow structural regions, supporting dynamic combinatorial functional links involving similar protein domains. Moreover, coevolving sites within a bacterial group mapped to regions previously identified as involved in folding-unrelated functions, and thus, coevolution may mediate alternative functions. CONCLUSIONS Our results highlight the evolutionary plasticity of GroEL across the entire bacterial phylogeny. Evidence on the functional importance of coevolving sites illuminates the as yet unappreciated functional diversity of proteins.
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Affiliation(s)
- Mario X Ruiz-González
- Integrative and Systems Biology Group, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (CSIC-UPV), Valencia, SPAIN
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Illingworth M, Ramsey A, Zheng Z, Chen L. Stimulating the substrate folding activity of a single ring GroEL variant by modulating the cochaperonin GroES. J Biol Chem 2011; 286:30401-30408. [PMID: 21757689 DOI: 10.1074/jbc.m111.255935] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In mediating protein folding, chaperonin GroEL and cochaperonin GroES form an enclosed chamber for substrate proteins in an ATP-dependent manner. The essential role of the double ring assembly of GroEL is demonstrated by the functional deficiency of the single ring GroEL(SR). The GroEL(SR)-GroES is highly stable with minimal ATPase activity. To restore the ATP cycle and the turnover of the folding chamber, we sought to weaken the GroEL(SR)-GroES interaction systematically by concatenating seven copies of groES to generate groES(7). GroES Ile-25, Val-26, and Leu-27, residues on the GroEL-GroES interface, were substituted with Asp on different groES modules of groES(7). GroES(7) variants activate ATP activity of GroEL(SR), but only some restore the substrate folding function of GroEL(SR), indicating a direct role of GroES in facilitating substrate folding through its dynamics with GroEL. Active GroEL(SR)-GroES(7) systems may resemble mammalian mitochondrial chaperonin systems.
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Affiliation(s)
- Melissa Illingworth
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
| | - Andrew Ramsey
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
| | - Zhida Zheng
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
| | - Lingling Chen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405.
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