PUS7

PUS7 is an RNA pseudouridine synthase that deposits pseudouridine (Ψ) across multiple RNA classes to control translation, transcription, and stress adaptation (PMID:35121864, PMID:41168165, PMID:41040199). Its crystal structure reveals two subdomains beyond the bacterial homolog and a substrate-screening mechanism in which all structural elements of tRNA—not merely the consensus sequence—are required for productive modification, with low product affinity favoring dissociation (PMID:34718722). Through tRNA pseudouridylation PUS7 controls codon-specific translation: in glioblastoma stem cells it tunes translation of regulators including suppression of TYK2 and the interferon-STAT1 pathway to drive tumorigenesis (PMID:35121864), and loss of PUS7-dependent ΨtRNA decreases tRNA-Asp levels, slowing Aspartate decoding and activating the integrated stress response with a metabolic shift toward glycolysis [PMID:bio_10.1101_2025.05.12.653498]. On mRNA, PUS7 pseudouridylates specific targets such as ALKBH3 at U696 to enhance translation efficiency (PMID:39175405), and stress drives its cytoplasmic relocalization to reshape the mRNA pseudouridylome enriched for metal-metabolism and ROS-response transcripts, increasing fitness under oxidative and metal stress (PMID:41040199). PUS7 also pseudouridylates 7SK snRNA, retaining P-TEFb in the inactive 7SK complex to limit RNA Pol II CTD Ser2 phosphorylation and suppress transcription elongation (PMID:41168165). Beyond catalysis, PUS7 engages catalysis-independent protein interactions—stabilized as an HSP90 client and binding SIRT1 and ANLN—to influence cancer-relevant signaling (PMID:31451225, PMID:33990203, PMID:36222184). Biallelic loss-of-function variants in PUS7 cause an intellectual-disability disorder, with truncating and missense variants abolishing pseudouridylation of tRNA and mRNA, reducing Ψ13 in tRNA, and producing neuronal and behavioral defects in model organisms (PMID:30526862, PMID:30778726).

1. 2018 High

   Established PUS7 as a disease-relevant pseudouridine synthase by showing that human truncating variants abolish its enzymatic activity and that its loss disrupts neuronal function, linking RNA pseudouridylation to a heritable neurodevelopmental phenotype.

   Evidence In vitro pseudouridylation assays on tRNA and mRNA with disease variants plus Drosophila knockout behavioral analysis

   PMID:30526862

   Open questions at the time

   • Did not identify the specific tRNA/mRNA targets whose loss drives neuronal dysfunction
   • Mechanistic link between Ψ loss and behavioral defect not resolved
2. 2019 High

   Refined the disease mechanism by tying patient variants to reduced tRNA Ψ13 and placing PUS7 genetically in a tRNA-modification pathway shared with TRM8.

   Evidence Ψ13 quantification in patient material and yeast pus7Δ trm8Δ complementation/epistasis

   PMID:30778726

   Open questions at the time

   • Functional consequence of Ψ13 loss on translation not directly shown
   • TRM8 epistasis mechanism in humans not established
3. 2019 Medium

   First identified a catalysis-independent protein partner, showing PUS7 forms a stable complex with SIRT1 via its N-terminal region.

   Evidence Pull-down, surface plasmon resonance, and truncation analysis

   PMID:31451225

   Open questions at the time

   • No functional consequence of the interaction established in this study
   • Whether binding affects catalysis untested
4. 2021 High

   Defined the structural basis of substrate selection, revealing metazoan-specific subdomains and a screening mechanism requiring intact tRNA architecture with product release driven by low affinity.

   Evidence 2.26 Å X-ray crystallography with in vitro activity and binding affinity assays

   PMID:34718722

   Open questions at the time

   • Structure of PUS7 bound to mRNA or 7SK not resolved
   • Basis of mRNA versus tRNA target discrimination unclear
5. 2021 High

   Connected PUS7 tRNA pseudouridylation to codon-specific translational control of oncogenic programs, demonstrating it sustains glioblastoma stem cell tumorigenesis and is druggable.

   Evidence Ψ-seq, shRNA/inhibitor loss-of-function, translational profiling, and mouse xenografts

   PMID:35121864

   Open questions at the time

   • Full set of codon-affected transcripts beyond TYK2 not enumerated
   • Selectivity of chemical inhibitors not characterized in detail
6. 2021 Medium

   Revealed a catalysis-independent oncogenic axis in which HSP90 stabilizes PUS7 protein and PUS7 regulates LASP1 to promote metastasis.

   Evidence Reciprocal Co-IP with MS, RNA-seq/proteomics, and in vivo metastasis assays with catalytic-independence shown

   PMID:33990203

   Open questions at the time

   • Mechanism by which PUS7 regulates LASP1 levels not defined
   • Single lab; reciprocal validation of LASP1 regulation limited
7. 2022 Medium

   Demonstrated PUS7 as a regulator of global translation rates, with deficiency elevating total protein synthesis and MYC.

   Evidence Patient fibroblast protein synthesis assays and western blotting

   PMID:35144859

   Open questions at the time

   • Molecular link between Ψ loss and increased translation not established
   • Single patient-derived system
8. 2022 Medium

   Extended the SIRT1 interaction to a functional cancer context, showing PUS7-SIRT1 binding activates Wnt/β-catenin signaling to drive colorectal cancer proliferation.

   Evidence Co-IP, RNA-seq, knockdown/overexpression, and in vitro/in vivo proliferation assays

   PMID:36222184

   Open questions at the time

   • Whether the effect depends on PUS7 catalytic activity not resolved
   • Direct mechanistic link to Wnt pathway components inferred from transcriptomics
9. 2024 High

   Provided site-resolved evidence for mRNA pseudouridylation as a translational enhancer, with PUS7 modifying ALKBH3 mRNA at U696 to boost its translation and suppress gastric cancer.

   Evidence Locus-specific Ψ detection, polysome profiling, and catalytic mutant analysis with xenografts

   PMID:39175405

   Open questions at the time

   • How U696 Ψ mechanistically enhances ribosome loading not defined
   • Generality across other mRNA targets not addressed
10. 2025 High

    Established a transcriptional role distinct from translation, showing PUS7 pseudouridylates 7SK snRNA to retain P-TEFb and suppress Pol II elongation, with loss promoting apoptosis and 5-FU sensitivity.

    Evidence 7SK Ψ-seq, P-TEFb/7SK Co-IP, Ser2P Pol II ChIP-seq, and dCas13b-guided site-specific pseudouridylation

    PMID:41168165

    Open questions at the time

    • How 7SK Ψ structurally affects P-TEFb retention not resolved
    • Breadth of elongation-controlled genes not fully mapped
11. 2025 Medium

    Connected PUS7-dependent tRNA-Asp depletion to the integrated stress response and a glycolytic metabolic shift, defining a tRNA-Asp–ISR–glycolysis axis that explains the neuronal phenotype.

    Evidence tRNA quantification, ribosome profiling for codon decoding, metabolic flux, and genetic/pharmacological rescue in Drosophila (preprint)

    PMID:bio_10.1101_2025.05.12.653498

    Open questions at the time

    • Preprint not yet peer-reviewed
    • Why tRNA-Asp is selectively sensitive to PUS7 loss unclear
12. 2025 Medium

    Showed stress-induced cytoplasmic relocalization reprograms the mRNA pseudouridylome toward metal/ROS-response transcripts, conferring fitness under oxidative and metal stress independently of tRNA sites.

    Evidence Live-cell imaging/fractionation, nanopore direct RNA Ψ-seq, engineered cytoplasmic PUS7, stress fitness assays, and TMT proteomics (preprint)

    PMID:41040199

    Open questions at the time

    • Preprint not yet peer-reviewed
    • Signal triggering relocalization not identified
13. 2025 Medium

    Implicated PUS7 in learning-dependent neuronal gene regulation, showing fear extinction drives PUS7-mediated exonic pseudouridylation of synaptogenic transcripts required for extinction memory.

    Evidence Stereotaxic knockdown, fear conditioning/extinction behavior, and transcriptome-wide Ψ profiling in mouse ILPFC

    PMID:41094471

    Open questions at the time

    • Specific Ψ targets driving memory not pinpointed
    • Whether effect requires catalytic activity not tested
14. 2025 Medium

    Identified PUS7 as a SARS-CoV-2 RNA-binding protein recognizing consensus motifs at viral terminal regions, raising a host-modification interface with viral RNA.

    Evidence RaPID coupled with mass spectrometry and nanopore direct RNA sequencing

    PMID:38028201

    Open questions at the time

    • Functional consequence of binding for viral replication not established
    • Whether PUS7 actually pseudouridylates viral RNA not demonstrated

• It remains unresolved how PUS7's catalytic (Ψ deposition on tRNA, mRNA, 7SK) and catalysis-independent (HSP90/SIRT1/ANLN scaffolding) activities are partitioned and coordinated across cell types and stress states.
• No unified model distinguishing when PUS7 acts as enzyme versus scaffold
• Regulation of nuclear-cytoplasmic partitioning incompletely defined
• Direct mRNA target rules for productive pseudouridylation in vivo not established