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Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies

Nature Structural & Molecular Biology volume 15, pages 1255–1262 (2008)Cite this article

Abstract

Folding within the crowded cellular milieu often requires assistance from molecular chaperones that prevent inappropriate interactions leading to aggregation and toxicity. The contribution of individual chaperones to folding the proteome remains elusive. Here we demonstrate that the eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) has broad binding specificity in vitro, similar to the prokaryotic chaperonin GroEL. However, in vivo, TRiC substrate selection is not based solely on intrinsic determinants; instead, specificity is dictated by factors present during protein biogenesis. The identification of cellular substrates revealed that TRiC interacts with folding intermediates of a subset of structurally and functionally diverse polypeptides. Bioinformatics analysis revealed an enrichment in multidomain proteins and regions of β-strand propensity that are predicted to be slow folding and aggregation prone. Thus, TRiC may have evolved to protect complex protein topologies within its central cavity during biosynthesis and folding.

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Figure 1: Principles of TRiC substrate selection in the eukaryotic cytosol.
Figure 2: Screening for the TRiC interactome in the context of translation.
Figure 3: In vivo analysis of the TRiC interactome reveals distinct kinetics of substrate flux through the chaperonin.
Figure 4: Physical and structural properties of the TRiC interactome.
Figure 5: Function of TRiC during de novo protein folding.

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Acknowledgements

The authors thank members of the Frydman laboratory and R. Andino for comments and discussion. The cDNA library was a generous gift from W. Zhao and G. Fang (Department of Biology, Stanford University). We thank W. Harper (Department of Pathology, Harvard Medical School), T. Kinzy (Department of Molecular Genetics & Microbiology, Rutgers University), and Michael Rexach (Department of Biological Sciences, Stanford University) for gifts of plasmids and antibodies. This work was supported by grants from the US National Institutes of Health and the W.M. Keck Foundation.

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Author notes

  1. Alice Y Yam & Yu Xia

    Present address: Present addresses: Novartis Vaccines and Diagnostics, Inc., 4560 Horton Street, M/S 4.3, Emeryville, California 94608, USA (A.Y.Y.); Department of Chemistry, 44 Cummington Street, Boston University, Boston, Massachusetts 02215, USA (Y.X.).,

Authors and Affiliations

  1. Department of Biology and BioX Program, E200A James Clark Center, 318 Campus Drive, Stanford University, Stanford, 94043, California, USA

    Alice Y Yam & Judith Frydman

  2. Department of Molecular Biophysics & Biochemistry, PO Box 208114, Yale University, New Haven, 06520, Connecticut, USA

    Yu Xia & Mark Gerstein

  3. Department of Pharmaceutical Chemistry, 600 16th Street, MC 2240, Genentech Hall, Suite N472A, University of California at San Francisco, San Francisco, 94143, California, USA

    Hen-Tzu Jill Lin & Alma Burlingame

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Contributions

J.F. directed the project; A.Y.Y. and J.F. designed the project, analyzed the data and wrote the manuscript; A.Y.Y. carried out all experiments; H.-T.J.L. and A.B. carried out MS analysis; and Y.X. and M.G. carried out bioinformatics data analysis and contributed to the manuscript.

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Correspondence to Judith Frydman.

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Yam, A., Xia, Y., Lin, HT. et al. Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nat Struct Mol Biol 15, 1255–1262 (2008). https://doi.org/10.1038/nsmb.1515

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