Quarterly Reviews of Chaperonin-assisted protein folding: Biophysics a chronologue cambridge.org/qrb Arthur L. Horwich1,2 and Wayne A. Fenton2 1Howard Hughes Medical Institute, Yale School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA and 2Department of Genetics, Yale School of Medicine, Boyer Center, 295 Congress Avenue, New Invited Review Haven, CT 06510, USA Cite this article: Horwich AL, Fenton WA (2020). Chaperonin-assisted protein folding: a Abstract chronologue. Quarterly Reviews of Biophysics This chronologue seeks to document the discovery and development of an understanding of – 53, e4, 1 127. https://doi.org/10.1017/ oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. S0033583519000143 It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these Received: 16 August 2019 ATP-utilizing machines from both in vivo and in vitro observations. The chronologue is orga- Revised: 21 November 2019 nized into various topics of physiology and mechanism, for each of which a chronologic order Accepted: 26 November 2019 is generally followed. The text is liberally illustrated to provide firsthand inspection of the key Key words: pieces of experimental data that propelled this field. Because of the length and depth of this Chaperonin; GroEL; GroES; Hsp60; protein piece, the use of the outline as a guide for selected reading is encouraged, but it should also be folding of help in pursuing the text in direct order. Author for correspondence: Arthur L. Horwich, E-mail: [email protected] Table of contents I. Foundational discovery of Anfinsen and coworkers – the amino acid sequence of a polypeptide contains all of the information required for folding to the native state 7 II. Discovery of a cellular accelerant to renaturation of RNAse A – microsomal protein disulfide isomerase 8 III. Pelham’s discovery that a cellular heat shock-induced protein, Hsp70, binds hydrophobic surfaces in heat-shocked nuclei and is released by ATP 8 A. Heat shock proteins 8 B. Hsp70 stimulates the recovery of nucleolar morphology after heat shock 9 C. Binding of Hsp70 following heat shock and ATP-driven release 9 1. Hsp70 binding to nuclei and nucleoli – hydrophobic interaction 9 2. ATP-driven release 9 3. Model of action 10 IV. Broader role of Hsp70 in protein disassembly and in maintaining an unfolded state of monomeric species 10 A. Disassembly of clathrin and of a protein complex at the λ replication origin 10 B. Maintenance of import-competent unfolded state of ER and mitochondrial precursor proteins in the cytosol 10 C. ER-localized Hsp70 is the immunoglobulin heavy chain binding protein (BiP) 11 V. Contemporary view of polypeptide binding by Hsp70 and the roles of its cooperating components 11 © The Author(s) 2020. This is an Open Access VI. Discovery of a double-ring complex in bacteria, GroEL, with a role in phage article, distributed under the terms of the assembly 11 Creative Commons Attribution licence (http:// A. Role of a host bacterial function, groE, in bacteriophage assembly in E. creativecommons.org/licenses/by/4.0/), which coli 11 permits unrestricted re-use, distribution, and ∼ reproduction in any medium, provided the B. Identification of a groE protein product of 60 kDa, GroEL 12 original work is properly cited. C. Double-ring tetradecamer structure of GroEL 12 D. Second groE gene product, GroES 13 E. GroEL and GroES are heat shock proteins 14 F. GroEL and GroES interact with each other 14 1. Genetic interaction 14 Downloaded from https://www.cambridge.org/core. IP address: 170.106.40.139, on 28 Sep 2021 at 07:43:53, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/S0033583519000143 2 Arthur L. Horwich and Wayne A. Fenton G. Physical interaction of GroEL and GroES 14 H. Potential actions of GroEL/GroES 14 VII. Discovery of a plant chloroplast double-ring complex, the Rubisco subunit binding protein, with a role in the assembly of the abundant multisubunit CO2-fixing enzyme, Rubisco 15 A. Discovery of a complex 15 B. Oligomeric complex resembling GroEL in the soluble fraction of pea leaves 15 C. Role of ATP in the release of Rubisco large subunit from the binding protein 16 D. Large subunit binding protein complex contains two subunit species 16 E. Close relatedness of Rubisco binding protein α subunit and GroEL 16 F. Assembly of two prokaryotic Rubisco enzymes in E. coli promoted by groE proteins 17 VIII. The mitochondrial double-ring chaperonin, Hsp60, mediates folding of proteins imported into mitochondria 18 A. Yeast mutant affecting folding/assembly of proteins imported to the mitochondrial matrix 18 1. Imported mitochondrial proteins are translocated in an unfolded state; could there be assistance inside mitochondria to refolding imported mitochondrial proteins to their native forms? 18 2. Production and screening of a library of temperature-sensitive yeast mutants for mutants affecting mitochondrial protein import 18 a. Design of a library of mitochondrial import mutants 18 b. Screen and initial mitochondrial import mutants 19 3. Mutant affecting refolding/assembly of OTC imported into the mitochondrial matrix 19 β B. mif4 mutant affects folding/assembly of endogenous yeast F1 subunit and folding of Rieske iron-sulfur protein 19 1. F1β subunit 19 2. Rieske Fe/S protein 20 C. mif4 mutation does not affect the translocation of precursors to the matrix compartment 20 D. Identification of a mitochondrial matrix heat shock protein of ∼60 kDa as the component affected in mif4 yeast 20 E. Preceding identification of a heat shock protein in mitochondria 20 F. Yeast gene rescuing mif4 and the gene encoding the yeast mitochondrial heat shock protein homologue are identical 21 G. Hsp60 essential under all conditions (and, similarly, GroE proteins) 21 H. Effect of mif4 mutation on Hsp60 21 IX. Complex formation of several imported proteins with Hsp60 in Neurospora mitochondria and ATP-directed release 21 A. Folding of imported DHFR, measured by protease resistance, is ATP-dependent 21 β B. Imported DHFR, Rieske Fe/S protein, and F1 subunit co-fractionate with Hsp60 22 X. Reconstitution of active dimeric Rubisco in vitro from unfolded subunits by GroEL, GroES, and MgATP 22 A. Unfolded Rubisco as substrate, and recovery of activity by GroEL/GroES/MgATP 22 B. GroEL/Rubisco binary complex formation – competition with off-pathway aggregation 23 C. GroES/MgATP-mediated discharge 23 XI. Chaperonins in all three kingdoms – identification of chaperonins in the cytoplasm of archaebacteria and a related component in the cytosol of eukaryotes 24 A. Identification of a stacked double-ring particle in thermophilic archaebacteria 24 B. A further thermophilic archaebacterial particle and primary structural relationship to TCP-1, a conserved protein of the eukaryotic cytosol implicated in microtubule biology by yeast studies 24 C. TCP-1 is a subunit of a heteromeric double-ring chaperonin complex in the eukaryotic cytosol shown to assist folding of actin and tubulin 25 1. Heteromeric TCP-1-containing cytosolic chaperonin folds actin 25 2. Heteromeric TCP-1-containing chaperonin folds tubulin subunits 25 D. Cofactors involved with post-chaperonin assembly of tubulin heterodimer, and a pre-chaperonin delivery complex, prefoldin 26 E. Further observations of TCP-1 complex – subunits are related to each other, an ATP site is likely shared with all chaperonins, and monomeric luciferase can serve as a substrate in vitro 26 XII. Early physiologic studies of GroEL 26 A. Overproduction of GroEL and GroES suppresses a number of diverse amino acid-substituted mutants of metabolic enzymes of Salmonella, indicating that such altered proteins can become GroEL substrates 26 B. Temperature-sensitive mutant of GroEL that halts growth at 37 °C exhibits aggregation of a subset of newly- translated cytoplasmic proteins 26 1. Isolation of a mutant ts for GroEL function at 37 °C, E461K 26 2. Physiological study of E461K mutant 27 Downloaded from https://www.cambridge.org/core. IP address: 170.106.40.139, on 28 Sep 2021 at 07:43:53, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/S0033583519000143 Quarterly Reviews of Biophysics 3 XIII. Early physiologic studies of Hsp60 27 A. Folding and assembly of newly imported Hsp60 is dependent on pre-existent Hsp60 27 B. Identification of a GroES-like cochaperonin partner of Hsp60 in mitochondria, Hsp10 27 1. Hsp10 in mammalian liver mitochondria 27 2. Hsp10 in S. cerevisiae mitochondria – yeast gene predicts protein related to GroES and is essential, and mutation affects folding of several imported precursors 28 3. Mammalian mitochondrial Hsp60 is isolated as a single ring that can associate with mammalian Hsp10 in vitro, and the two can mediate Rubisco folding in vitro – a minimal fully folding-active chaperonin 28 C. Additional substrates of Hsp60 identified by further studies of mif4 strain: a number of other imported proteins do not require Hsp60 to reach native form 29 1. Imported matrix proteins identified as insoluble when examined after pulse-radiolabeling mif4 cells at non- permissive temperature 29 2. Other imported proteins do not exhibit dependence on Hsp60 29 3. Folding of additional proteins imported into mif4 mitochondria monitored by protease susceptibility – rhodanese exhibits Hsp60-dependence, but several other proteins are independent 30 XIV. Cooperation of Hsp70 class chaperones with the GroEL/Hsp60 chaperonins in bacteria, mitochondrial matrix, and in vitro 30 A. Cooperation in bacteria 30 B. Sequential action of Hsp70 and Hsp60 in mitochondria 31 C. Successive actions of bacterial DnaK (Hsp70) and GroEL (Hsp60) systems in an in vitro refolding reaction 31 XV. Early mechanistic studies of GroEL/GroES 32 A. Topology studies 32 1. Back-to-back arrangement of the two GroEL rings 32 2.