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

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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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, H. 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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