Biology subjects

Shen, P. S.

Publications and source records attributed to Shen, P. S..

8 recordsLinked to original sources

bioRxiv2026

C. elegans Dicer stacks with the RIG-I-like receptor DRH-1 to cleave dsRNA

In prior studies we showed that the nematode ancestor of Dicer's helicase domain had minimal ATP hydrolysis, translocation and dsRNA binding activity, and in extant C. elegans the RIG-I like receptor (RLR) DRH-1, and the dsRNA binding protein RDE-4, were co-opted to provide these activities. Here we report cleavage-competent cryo-EM structures of the antiviral complex (AVC; DCR-1{middle dot}DRH-1{middle dot}RDE-4), in the absence (3.2[A]) and presence (3.0[A] of ATP. A key feature of both structures is stacking of DCR-1's helicase with the helicases of two DRH-1 molecules, reminiscent of oligomerization of mammalian RLRs. dsRNA threads through all three helicases with a widened major groove at helicase-helicase interfaces and where the conserved Hel2 loop inserts into the major groove. The presence of nucleotide redistributed helicase-helicase and helicase-RNA contacts in the AVC, as for MDA5, albeit specific interactions and remodeling differed. MDA5 and RIG-I RLRs contain an unstructured linker between their CARDs and helicase domain, but the analogous linker in DRH-1 has a short-structured region positioned to interact with DCR-1. These findings provide a structural framework for understanding how DCR-1, DRH-1, and RDE-4 cooperate to cleave viral dsRNA and elucidate unique features required for antiviral defense in different animals.

immunology↗

bioRxiv2025

Disease-causing mutations in the G protein β5 β-propeller disrupt its chaperonin-mediated folding trajectory

The Chaperonin Containing Tailless polypeptide 1 (CCT or TRiC) is an essential cytosolic chaperone that folds multiple protein substrates, including many with {beta}-propeller folds. One {beta}-propeller substrate is the G protein {beta}5 subunit (G{beta}5) of Regulator of G protein Signaling (RGS) complexes that determine the duration of G protein signals in neurons. In recent work, we used cryo-electron microscopy (cryo-EM) to visualize the complete CCT-mediated folding trajectory for G{beta}5, from an initiating electrostatic interaction of a single {beta}-strand in G{beta}5 with the CCT5 subunit to a completely folded {beta}-propeller structure. Here, we employed biochemistry and cryo-EM to determine key interactions with CCT that initiate G{beta}5 folding and how missense mutations in G{beta}5 that cause severe neurological diseases alter the G{beta}5 folding trajectory and lead to incompletely folded, trapped intermediates. These findings highlight how CCT recognizes folding substrates, how defects in chaperonin-mediated folding contribute to disease, and how strategies might be designed to stabilize misfolded proteins to restore function. SignificanceElectrostatic interactions between the CCT chaperonin and its protein substrates initiate the folding process. Using cryo-EM structure determinations, we found a striking specificity for these interactions that allow CCT-mediated G{beta}5 folding. Moreover, certain missense mutations in G{beta}5 lead to misfolding and are associated with neurological disorders. We tracked how these mutations disrupt the normal folding of G{beta}5 by CCT. Although mutant G{beta}5 still binds the complex, folding stalls mid-process, leaving the protein trapped in partially folded, non-functional states. These defects arise from disrupted packing of the G{beta}5 core that interferes with formation of the native structure. Our findings reveal a molecular basis for G{beta}5 misfolding in disease and suggest pharmacological chaperones that stabilize the folded state might restore proper function.

biochemistry↗

bioRxiv2025

Biochemical and structural basis of Dicer helicase function unveiled by resurrecting ancient proteins

A fully functional Dicer helicase, present in the modern arthropod, uses energy generated during ATP hydrolysis to power translocation on bound dsRNA, enabling the processive dsRNA cleavage required for efficient antiviral defense. However, modern Dicer orthologs exhibit divergent helicase functions that affect their ability to contribute to antiviral defense, and moreover, mechanisms that couple ATP hydrolysis to Dicer helicase movement on dsRNA remain enigmatic. Here, we used biochemical and structural analyses of ancestrally reconstructed Dicer helicases to map evolution of dsRNA binding affinity, ATP hydrolysis and translocation. We found that loss of affinity for dsRNA occurred early in Dicer evolution, coinciding with a decline in translocation activity, despite preservation of ATP hydrolysis activity, exemplified by the ancient deuterostome Dicer. Ancestral nematode Dicer also exhibited significant decline in ATP hydrolysis and translocation, but studies of antiviral activities in the modern nematode C. elegans indicate Dicer retained a role in antiviral defense by recruiting a second helicase. Cryo-EM analyses of an ancient metazoan Dicer allowed capture of multiple helicase states revealing the mechanism that connects each step of ATP hydrolysis to unidirectional movement along dsRNA. Overall, our study rationalizes the diversity in modern Dicer helicases by connecting ancestral functions to observations in extant enzymes. Significance StatementAmong invertebrates, the contribution of Dicers helicase to recognition and elimination of viral double-stranded RNA varies from phylum to phylum. At the extreme end of the spectrum, vertebrate Dicers show no helicase activity. On the other end, an arthropod ortholog uses helicase translocation to efficiently move double-stranded RNA into Dicers cleavage site. The biochemical and structural basis of Dicers helicase function, as well as the evolutionary events that contribute to a divergence in function, have remained unknown. This study shows how ancient Dicer helicase tightly binds double-stranded RNA and couples ATP hydrolysis to movement along this substrate. In addition, the data reveal how components of this intricate system declined along different clades of animal evolution.

biochemistry↗

bioRxiv2023

ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97

The t(X,17) chromosomal translocation, generating the ASPSCR1-TFE3 fusion oncoprotein, is the singular genetic driver of alveolar soft part sarcoma (ASPS) and some Xp11-rearranged renal cell carcinomas (RCC), frustrating efforts to identify therapeutic targets for these rare cancers. Proteomic analysis showed that VCP/p97, an AAA+ ATPase with known segregase function, was strongly enriched in co-immunoprecipitated nuclear complexes with ASPSCR1-TFE3. We demonstrate that VCP is a likely obligate co-factor of ASPSCR1-TFE3, one of the only such fusion oncoprotein co-factors identified in cancer biology. Specifically, VCP co-distributed with ASPSCR1-TFE3 across chromatin in association with enhancers genome-wide. VCP presence, its hexameric assembly, and its enzymatic function orchestrated the oncogenic transcriptional signature of ASPSCR1-TFE3, by facilitating assembly of higher-order chromatin conformation structures as demonstrated by HiChIP. Finally, ASPSCR1-TFE3 and VCP demonstrated co-dependence for cancer cell proliferation and tumorigenesis in vitro and in ASPS and RCC mouse models, underscoring VCPs potential as a novel therapeutic target.

cancer biology↗

bioRxiv2023

C. elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA

Abstract/SummaryInvertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, C. elegans Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1s helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways.

biochemistry↗

bioRxiv2023

Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway

The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase cassettes, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of structures of Cdc48 affinity purified from lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data reveal new elements of Shp1-Cdc48 binding and support a "hand-over-hand" mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by D2 in substrate translocation/unfolding.

biochemistry↗

bioRxiv2023

Visualizing the chaperone-mediated folding trajectory of the G protein β5 β-propeller

The cytosolic Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with {beta}- propeller domains. Here, we determined structures of CCT in complex with its accessory co chaperone, phosducin-like protein 1 (PhLP1), in the process of folding G{beta}5, a component of Regulator of G protein Signaling (RGS) complexes. Cryo-EM and image processing revealed an ensemble of distinct snapshots that represent the folding trajectory of G{beta}5 from an unfolded molten globule to a fully folded {beta}-propeller. These structures reveal the mechanism by which CCT directs G{beta}5 folding through initiating specific intermolecular contacts that facilitate the sequential folding of individual {beta}-sheets until the propeller closes into its native structure. This work directly visualizes chaperone-mediated protein folding and establishes that CCT directs folding by stabilizing intermediates through interactions with surface residues that permit the hydrophobic core to coalesce into its folded state.

biochemistry↗

bioRxiv2018

Vms1p is a release factor for the Ribosome-associated Quality control Complex

Eukaryotic cells employ the Ribosome-associated Quality control Complex (RQC) to maintain homeostasis despite defects that cause ribosomes to stall. The RQC comprises the E3 ubiquitin ligase Ltn1p, the ATPase Cdc48p, and the novel proteins Rqc1p and Rqc2p1-3. Following recognition and subunit splitting of stalled ribosomes, the RQC detects and assembles on 60S subunits that hold incomplete polypeptides linked to a tRNA (60S:peptidyl-tRNA)4-8. Ltn1p cooperates with Rqc1p to facilitate ubiquitination of the incomplete nascent chain, marking it for degradation7,9,10. Rqc2p stabilizes Ltn1p on the 60S3-5,8 and recruits charged tRNAs to the 60S to catalyze elongation of the nascent protein with Carboxy-terminal Alanine and Threonine extensions, or CAT tails, via a mechanism that is distinct from canonical translation4,10. CAT-tailing mobilizes and exposes lysine residues in the nascent chain, especially those stalled within the exit tunnel, thereby supporting efficient ubiquitination10,11. If the ubiquitin-proteasome system is overwhelmed or unavailable, CAT-tailed nascent chains aggregate in the cytosol or within organelles like the mitochondria12-14. Here we identify Vms1p as the tRNA hydrolase that releases nascent polypeptides for extraction and degradation in the RQC pathway.

biochemistry↗