A game-changing discovery in physiology and medicine: A cellular particle that arranges protein quaternary structure in health and disease

Proteomes are organized into protein complexes and networks (interactomes) that regulate cell function. Until recently, the formation of these entities remained largely elusive. The discovery of a molecular machine that specializes in protein complex/network arrangement has shed new light into this fundamental process. The R2TP/prefoldin-like (PFDL) complex, now PAQosome, uses unique mechanisms for substrate selection in which various components of the assembly machine and adaptors recognize specific substrates. By arranging protein quaternary structure, the PAQosome acts downstream of the ribosome in the universal process of gene expression.

In 2007, my laboratory published the discovery of a set of proteins that associate physically with human RNA polymerase II, most of them presenting either sequence homologies with or motifs found in molecular chaperones, suggesting a role for these factors in polymerase assembly and biogenesis. Four previously uncharacterized proteins were named RNA Polymerase II Associated Proteins (RPAP1-4) (Jeronimo et al 2007 Mol Cell)

Two years later, we uncovered the existence of a unique 11-subunit complex containing RPAP3 that we named RPAP3/R2TP/PFD-like (Cloutier et al 2009 Methods)

This diagram illustrates the interactions between the RPAP3/R2TP/PFD-like complex, nuclear RNA polymerases, HSP proteins, the TRiC/CCT and GimC/PFD complexes and RNA Polymerase Associated Proteins RPAP2 and RPAP4/XAB1/GPN1 (Cloutier et al 2010 Biochem Cell Biol). These RNA polymerase II-interacting factors are involved in biogenesis of this important enzyme.

In 2010 and 2013, respectively, we showed that RPAP4/XAB1/GPN1 and RPAP2 regulate nuclear import of RNA polymerase II (Forget et al 2010 Mol Cell ProteomForget et al 2013 Nucleic Acids Res). Concurrently, the group of Edouard Bertrand (Montpellier, France) reported in 2010 that the R2TP/PFD-like complex is a cofactor of HSP90 for cytoplasmic assembly of RNA polymerase II (Boulon et al 2010 Mol Cell). Our own work confirmed this conclusion and indicated a similar function in RNA polymerase I and III biogenesis (Forget et al 2014, In Emili et al (eds) Systems Analysis of Chromatin-Related Protein Complexes in Cancer, Springer NY, 227-238)

Schematic representation of R2TP/PFDL showing its R2TP module, which appears to be the active complex in yeast (Zhao et al 2005 Cell), and its Prefoldin-like module (Cloutier et al 2010 Biochem Cell Biol)

Since 2010, a number of laboratories have identified a variety of substrates requiring the R2TP/PFDL co-chaperone for assembly. Specificity factors connect R2TP/PFDL to its various substrates, including U5 snRNP, an interaction discovered in 2017 (Cloutier et al 2017 Nat CommunMalinova et al 2017 J Cell Biol). These same papers reported that the Tuberous Sclerosis tumor suppressor complex (TSC), a previously identified regulator of the TOR pathway, is a direct interactor of R2TP-PFDL, suggesting that it could act as a major regulator of anabolic processes.

In a review article co-authored by Walid Houry (Toronto), Edouard Bertrand (Montpelier) and Benoit Coulombe (Montreal), we proposed to rename the R2TP/PFDL complex as PAQosome (Particle for Arrangement of Quaternary structure). The proposed name better reflects the function of the particle in the "packing" of individual subunits into active protein complexes. How many protein complexes and networks are clients of the PAQosome remains to be determined.

How do our cells build their protein interactome? This is a question that has remained largely unanswered until the discovery and recent characterization of the PAQosome (Particle for Arrangement of Quaternary structure). Nevertheless, it seems unimaginable that a single cellular entity, the 11-subunit PAQosome, could be responsible for assembly and maturation of the whole dynamic interactome. A Comment published today in Nature Communications (Coulombe et al 2018 Nat Commun; DOI 10.1038/s41467-018-05448-2) explains how this is indeed possible based on recent discoveries demonstrating the existence of alternative PAQosomes and adaptors, which by acting together generate the various specificities required for multiple substrate selection (Maurizy et al 2018 Nat Commun 9, 2093). It now becomes clear that the PAQosome (previously known as R2TP/PFDL complex) has a much deeper impact on human cell function than expected when we first identified this modular complex as an interactor of RNA polymerase II in 2007.

© 2021 by Benoit Coulombe Lab