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

Yam, Alice; Xia, Yu; Lin, Hen-Tzu Jill; Burlingame, Alma L.; Gerstein, Mark; Frydman, Judith

doi:10.1038/nsmb.1515

Cited by 365 publications

(386 citation statements)

References 60 publications

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“…A recent study of the TRiC interactome suggests that ~ 10% of newly synthesized cellular proteins, including actin, tubulin, cell cycle regulators and tumor suppressors are TRiC substrates. Generally, multidomain proteins ranging from 40-75 kDa are ideal substrates (Yam et al, 2008). This study also showed that proteins belonging to oligomeric assemblies are highly enriched in the interactome and this suggests a role of TRiC in facilitating protein complex assembly in cells.…”

Section: Ii4113 the Chaperoninssupporting

confidence: 58%

“…Unlike GroEL/ES which can act only post-translationally, TRiC has been shown to fold the discrete domains of firefly luciferase co-translationally (Frydman et al, 1994). From biochemical studies using unfolded firefly luciferase, actin and tubulin, it has been shown that while GroEL/ES failed to fold these model proteins, TRiC was able to mediate their folding, suggesting that it can interact with a different range of substrates via mechanism distinct from class I chaperonins (Frydman et al, 1992;Tian et al, 1995;Yam et al, 2008). A recent study of the TRiC interactome suggests that ~ 10% of newly synthesized cellular proteins, including actin, tubulin, cell cycle regulators and tumor suppressors are TRiC substrates.…”

Section: Ii4113 the Chaperoninsmentioning

confidence: 99%

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Firefly luciferase mutants as sensors of proteome stress

et al. 2011

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Section: Ii4113 the Chaperoninssupporting

confidence: 58%

Section: Ii4113 the Chaperoninsmentioning

confidence: 99%

Firefly luciferase mutants as sensors of proteome stress

et al. 2011

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“…TRiC also appears important for the prevention of protein aggregation and toxicity (6)(7)(8). TRiC is essential for cell viability, as it assists the folding of many essential proteins, including actin, tubulin, and many cell cycle regulators and signaling molecules (9,10). Notably, a number of TRiC substrates cannot be folded by other chaperonins, suggesting that TRiC possesses unique structural and mechanistic properties that distinguish it functionally from other chaperonins (11,12).…”

mentioning

confidence: 99%

4.0-Å resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement

Yao

Baker

Jakana

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of ∼5-10% of the cellular proteome. Many TRiC substrates cannot be folded by other chaperonins from prokaryotes or archaea. These unique folding properties are likely linked to TRiC's unique heterooligomeric subunit organization, whereby each ring consists of eight different paralogous subunits in an arrangement that remains uncertain. Using single particle cryo-EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7-Å resolution. This revealed the existence of a 2-fold axis between its two rings resulting in two homotypic subunit interactions across the rings. A subsequent 2-fold symmetrized map yielded a 4.0-Å resolution structure that evinces the densities of a large fraction of side chains, loops, and insertions. These features permitted unambiguous identification of all eight individual subunits, despite their sequence similarity. Independent biochemical near-neighbor analysis supports our cryo-EM derived TRiC subunit arrangement. We obtained a Cα backbone model for each subunit from an initial homology model refined against the cryo-EM density. A subsequently optimized atomic model for a subunit showed ∼95% of the main chain dihedral angles in the allowable regions of the Ramachandran plot. The determination of the TRiC subunit arrangement opens the way to understand its unique function and mechanism. In particular, an unevenly distributed positively charged wall lining the closed folding chamber of TRiC differs strikingly from that of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity.asymmetric reconstruction | atomic model | subunit structure

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“…The open state of the complex binds the polypeptide substrate (4,5), whereupon closing the substrate is sequestered into a large interior cavity where folding can occur. TRiC has been implicated in the folding pathways of many cytosolic proteins (6), most notably actin and tubulin (7,8).…”

mentioning

confidence: 99%

Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling

Kalisman

Adams

Levitt

2012

Proc. Natl. Acad. Sci. U.S.A.

164

178

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The TRiC/CCTchaperonin is a 1-MDa hetero-oligomer of 16 subunits that assists the folding of proteins in eukaryotes. Low-resolution structural studies confirmed the TRiC particle to be composed of two stacked octameric rings enclosing a folding cavity. The exact arrangement of the different proteins in the rings underlies the functionality of TRiC and is likely to be conserved across all eukaryotes. Yet despite its importance it has not been determined conclusively, mainly because the different subunits appear nearly identical under low resolution. This work successfully addresses the arrangement problem by the emerging technique of cross-linking, mass spectrometry, and modeling. We cross-linked TRiC under native conditions with a cross-linker that is primarily reactive toward exposed lysine side chains that are spatially close in the context of the particle. Following digestion and mass spectrometry we were able to identify over 60 lysine pairs that underwent crosslinking, thus providing distance restraints between specific residues in the complex. Independently of the cross-link set, we constructed 40,320 (¼8 factorial) computational models of the TRiC particle, which exhaustively enumerate all the possible arrangements of the different subunits. When we assessed the compatibility of each model with the cross-link set, we discovered that one specific model is significantly more compatible than any other model. Furthermore, bootstrapping analysis confirmed that this model is 10 times more likely to result from this cross-link set than the next best-fitting model. Our subunit arrangement is very different than any of the previously reported models and changes the context of existing and future findings on TRiC.group II chaperonins | protein folding | violation distances I n eukaryotes and archaea the folding of nascent and mis-folded polypeptide chains is assisted by a group II chaperonin system known as the thermosome in archea and TRiC (or CCT) in eukaryotes (1). These large protein complexes consist of two stacked octameric rings (2) The open state of the complex binds the polypeptide substrate (4, 5), whereupon closing the substrate is sequestered into a large interior cavity where folding can occur. TRiC has been implicated in the folding pathways of many cytosolic proteins (6), most notably actin and tubulin (7,8).Many archaeal species have just one thermosome gene and a simple homo-oligomeric architecture (9). Other archaeal species have at most three different types of subunits, and there is evidence that the multiple genes are redundant (10). In stark contrast, the eukaryotic TRiC consists of eight different subunit types (CCT1 to CCT8), all of which are essential. The subunit specialization occurred very early in eukaryote evolution (11) and is conserved to such an extent that the sequence identity between mammalian and yeast subunits of the same type is nearly 60%, whereas the sequence identity between the different subunit types in the same organism is only 30%. The diversity of eight distinct subun...

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

Cited by 365 publications

References 60 publications

Firefly luciferase mutants as sensors of proteome stress

Firefly luciferase mutants as sensors of proteome stress

4.0-Å resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement

Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling

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