Affinage

RCHY1

RING finger and CHY zinc finger domain-containing protein 1 · UniProt Q96PM5

Length
261 aa
Mass
30.1 kDa
Annotated
2026-06-10
30 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RCHY1 (PIRH2) is a RING-domain E3 ubiquitin ligase that controls the abundance of multiple substrate proteins and contributes to selective autophagy (PMID:27519799, PMID:38536750). Its best-defined catalytic output is the ubiquitination and degradation of p53: this activity is hijacked by coronaviruses, since the SARS-CoV SARS-unique domain (SUD) and the papain-like proteases (PLpro) of SARS-CoV, MERS-CoV and HCoV-NL63 physically bind and stabilize RCHY1, augmenting p53 degradation and thereby antagonizing p53-dependent antiviral innate immunity (PMID:27519799). Beyond p53, RCHY1 directly binds and downregulates HDAC2 in a RING-domain-dependent manner (PMID:31630802). In selective autophagy, RCHY1 catalyzes K63-linked ubiquitination of melanosomes to confer cargo selectivity upstream of the OPTN–TBK1 receptor axis, driving melanophagy (PMID:38536750), and it independently promotes autophagic flux by facilitating autophagosome–lysosome fusion, a function conserved from Drosophila to human cells (PMID:41986295). RCHY1 levels are themselves regulated: Hoxa2 drives its ubiquitin-independent proteasomal degradation through the 19S/20S proteasome, stabilizing p53 (PMID:24244684, PMID:26496426), while PHB2 upregulates RCHY1 to accelerate p53/p21 turnover and proliferation (PMID:36342357).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2013 Medium

    Established that RCHY1 abundance is itself controlled, by identifying Hoxa2 as a factor that degrades RCHY1 and thereby stabilizes p53.

    Evidence Co-IP, knockdown/overexpression with protein-level readout, ubiquitination and proteasome-inhibitor assays

    PMID:24244684

    Open questions at the time
    • Mechanism of ubiquitin-independent recognition by the proteasome not resolved
    • Physiological context where Hoxa2 controls RCHY1 not defined
  2. 2015 Medium

    Refined the Hoxa2-RCHY1 degradation mechanism, mapping it to the Hoxa2 homeodomain plus C-terminus and showing engagement of both 19S and 20S proteasome and conservation across vertebrates.

    Evidence Deletion mutagenesis, proteasome complex interaction assays, Co-IP across multiple Hox proteins, cross-species analysis

    PMID:26496426

    Open questions at the time
    • Why only a subset of Hox proteins induce degradation despite shared homeodomain binding is unexplained
    • No structural model of the RCHY1-proteasome interaction
  3. 2016 High

    Showed that coronaviruses exploit RCHY1 by stabilizing it through SUD and PLpro binding, redirecting its p53-degrading activity to suppress antiviral immunity.

    Evidence Reciprocal Co-IP with domain mapping, in vivo ubiquitination assays, p53 degradation assays across multiple coronavirus homologs

    PMID:27519799

    Open questions at the time
    • Mechanism by which binding increases RCHY1 stability not defined
    • Role of CAMK2D phosphorylation in physiological RCHY1 regulation left open
  4. 2019 Medium

    Expanded RCHY1's substrate repertoire beyond p53 by demonstrating RING-dependent degradation of HDAC2 independent of p53 status.

    Evidence Co-IP, RING-domain mutant analysis, gain/loss-of-function across p53 wild-type, mutant, and null cell lines

    PMID:31630802

    Open questions at the time
    • Direct ubiquitin-transfer to HDAC2 not shown by reconstitution
    • Cellular consequences of HDAC2 loss downstream of RCHY1 not characterized
  5. 2022 Medium

    Placed RCHY1 in a tumor-promoting circuit, showing PHB2 upregulates RCHY1 to accelerate p53/p21 turnover and proliferation.

    Evidence PHB2/RCHY1 overexpression and knockdown, ubiquitination assays, proliferation assays in vitro and in vivo

    PMID:36342357

    Open questions at the time
    • Mechanism by which PHB2 upregulates RCHY1 not defined
    • Whether p53 and p21 are direct RCHY1 substrates in this context not demonstrated
  6. 2024 High

    Defined a non-p53 role for RCHY1 in selective autophagy by showing it K63-ubiquitinates melanosomes to recruit the OPTN-TBK1 receptor axis for melanophagy.

    Evidence siRNA knockdown, K63-ubiquitination assay, OPTN translocation and TBK1 phosphorylation assays, melanosome degradation quantification in B16F10 cells

    PMID:38536750

    Open questions at the time
    • How RCHY1 is targeted specifically to melanosomes is unknown
    • Direct melanosomal substrate of ubiquitination not identified
  7. 2024 Medium

    Demonstrated a conserved RCHY1 function in autophagic flux at the autophagosome-lysosome fusion step, distinct from cargo ubiquitination.

    Evidence Drosophila genetic screen and loss-of-function, siRNA in HeLa, autophagosome-lysosome fusion and autophagy flux assays

    PMID:41986295

    Open questions at the time
    • Whether E3 ligase activity is required for fusion not established
    • Molecular partners at the fusion machinery not identified
  8. 2026 Low

    Linked RCHY1-mediated p53 ubiquitination to skin aging via a Gorab-dependent axis affecting HDAC2 and ECM proteins.

    Evidence Conditional knockout mouse, ubiquitination assay, Western blot for p53/HDAC2/histone acetylation, ECM analysis

    PMID:41869872

    Open questions at the time
    • RCHY1 role inferred from correlation rather than direct manipulation in this system
    • Mechanistic connection between Gorab and RCHY1 activity unresolved
  9. 2026 Low

    Proposed DJ-1 as a further RCHY1 substrate within a LINC00839/UPF1 mRNA-stability axis regulating ferroptosis.

    Evidence LINC00839/RCHY1 knockdown and overexpression, mRNA stability assays, DJ-1 ubiquitination assay, rescue epistasis, in vivo tumor growth

    PMID:42135459

    Open questions at the time
    • Direct E3 activity toward DJ-1 not demonstrated by reconstitution or RING mutagenesis
    • Whether DJ-1 ubiquitination is K48-linked or degradative not specified

Open questions

Synthesis pass · forward-looking unresolved questions
  • How a single RING E3 ligase coordinates its degradative substrate functions (p53, HDAC2, DJ-1) with its non-degradative autophagy roles (melanosome K63-ubiquitination, autophagosome-lysosome fusion), and what determines substrate and cargo selectivity, remains unresolved.
  • No structural basis for RCHY1 substrate/cargo discrimination
  • Regulation switching RCHY1 between proteasomal and autophagic outputs unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016874 ligase activity 3 GO:0140096 catalytic activity, acting on a protein 3
Pathway
R-HSA-392499 Metabolism of proteins 2 R-HSA-9612973 Autophagy 2

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2016 RCHY1 (PIRH2) physically interacts with the SARS-CoV SARS-unique domain (SUD) subdomains 389-652 (SUD-NM) via RCHY1 residues 95-144. Association with SUD increases the stability of RCHY1 and augments RCHY1-mediated ubiquitination and degradation of p53, thereby antagonizing p53-dependent antiviral innate immunity. Similarly, papain-like proteases (PLpro) from SARS-CoV, MERS-CoV, and HCoV-NL63 physically interact with and stabilize RCHY1, triggering degradation of endogenous p53. CAMK2D binds SUD and normally influences RCHY1 stability by phosphorylation, but SUD does not regulate RCHY1 phosphorylation via CAMK2D. Co-immunoprecipitation, domain-mapping deletion constructs, in vivo ubiquitination assay, p53 degradation assays, phosphorylation analysis Proceedings of the National Academy of Sciences of the United States of America High 27519799
2013 Hoxa2 interacts with RCHY1 (PIRH2) and promotes its proteasomal degradation in an ubiquitin-independent manner. Hoxa2 also interacts with 20S proteasome subunits. Hoxa2-mediated RCHY1 degradation alters RCHY1-mediated ubiquitination of p53, leading to p53 stabilization. Co-immunoprecipitation, ectopic expression/knockdown with protein level readout, ubiquitination assays, proteasome inhibitor experiments PloS one Medium 24244684
2015 The Hoxa2-mediated degradation of RCHY1 involves both the 19S and 20S proteasome complexes and requires the Hoxa2 homeodomain and C-terminal moiety. The homeodomain is necessary but not sufficient for RCHY1 degradation. All tested Hox proteins interact with RCHY1 via the homeodomain, but only a subset can induce RCHY1 degradation. This interaction and functional consequence is evolutionarily conserved among vertebrates. Deletion mutagenesis, proteasome complex interaction assays, co-immunoprecipitation with multiple Hox protein variants, cross-species conservation analysis PloS one Medium 26496426
2019 RCHY1 directly interacts with HDAC2 and negatively regulates HDAC2 protein levels via its E3 ubiquitin ligase RING domain activity. Ectopic expression of wild-type RCHY1 decreased HDAC2 levels in cancer cells regardless of p53 status, while RING-domain mutant RCHY1 did not, and RCHY1 knockdown increased HDAC2 levels. Co-immunoprecipitation, ectopic expression and knockdown, RING-domain mutant analysis, protein level measurement across p53 wild-type, mutant, and null cell lines Biochemical and biophysical research communications Medium 31630802
2024 RCHY1 acts as an E3 ubiquitin ligase required for K63-linked ubiquitination of melanosomes. RCHY1 knockdown inhibited melanosome ubiquitination, blocked OPTN translocation to melanosomes (which requires ubiquitin-binding), prevented TBK1 activation and TBK1-mediated S187 OPTN phosphorylation, and abolished melanosome degradation. RCHY1 thus confers cargo selectivity in melanophagy upstream of the OPTN-TBK1 autophagy receptor axis. siRNA knockdown, K63-linked ubiquitination assay, immunofluorescence localization of OPTN to melanosomes, TBK1 phosphorylation assay, melanosome degradation quantification in B16F10 cells Proceedings of the National Academy of Sciences of the United States of America High 38536750
2024 RCHY1 promotes autophagic flux by facilitating autophagosome-lysosome fusion. Loss of Rchy1 in Drosophila larval midgut cells impaired autophagosome-lysosome fusion and led to accumulation of amphisomes. Depletion of RCHY1 in human HeLa cells also disrupted autophagic flux and reduced autolysosome formation, demonstrating evolutionary conservation of this function. Genetic screen in Drosophila, loss-of-function (Rchy1 knockdown/knockout), siRNA in HeLa cells, autophagosome-lysosome fusion assay, autophagy flux assays Cell death discovery Medium 41986295
2022 PHB2 (prohibitin 2) upregulates RCHY1, which in turn mediates ubiquitination and degradation of p53 and p21 to promote cell proliferation. DHA downregulates PHB2 in a ubiquitylation-dependent manner and subsequently blocks PHB2-induced RCHY1 upregulation and p53/p21 downregulation. RCHY1 is required for PHB2 to exert its tumor-promoting role. Overexpression and knockdown of PHB2 and RCHY1, ubiquitination assays, in vitro and in vivo proliferation assays, protein level analysis Molecular carcinogenesis Medium 36342357
2026 Gorab knockout in mouse dermal fibroblasts impairs RCHY1-mediated ubiquitination of P53, leading to P53 accumulation, increased HDAC2 levels, reduced histone acetylation, and downregulation of extracellular matrix proteins, promoting accelerated skin aging. Conditional knockout mouse model, protein ubiquitination assay, Western blot for P53/P21/P16/HDAC2/histone acetylation, ECM protein analysis Animal models and experimental medicine Low 41869872
2026 LINC00839 destabilizes RCHY1 mRNA through recruitment of UPF1, consequently inhibiting RCHY1-mediated ubiquitination and degradation of DJ-1 protein. RCHY1 depletion neutralized the effect of LINC00839 knockdown on ferroptosis, placing RCHY1 downstream of the LINC00839/UPF1 axis as the E3 ligase responsible for DJ-1 ubiquitination and degradation. LINC00839 and RCHY1 knockdown/overexpression, mRNA stability assays, ubiquitination assay for DJ-1, epistasis by rescue experiments, in vivo tumor growth assay NPJ precision oncology Low 42135459

Source papers

Stage 0 corpus · 30 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2003 Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (New York, N.Y.) 467 14671302
2015 Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell 279 26365491
1992 A new inhibitor of metalloproteinases from chicken: ChIMP-3. A third member of the TIMP family. The Journal of biological chemistry 279 1512267
2016 p53 down-regulates SARS coronavirus replication and is targeted by the SARS-unique domain and PLpro via E3 ubiquitin ligase RCHY1. Proceedings of the National Academy of Sciences of the United States of America 188 27519799
2006 Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS computational biology 106 16683019
2008 The horse pseudoautosomal region (PAR): characterization and comparison with the human, chimp and mouse PARs. Cytogenetic and genome research 43 18544933
2013 Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets. Nucleic acids research 33 23625967
2013 The homeodomain transcription factor Hoxa2 interacts with and promotes the proteasomal degradation of the E3 ubiquitin protein ligase RCHY1. PloS one 17 24244684
2019 E3 ligase RCHY1 negatively regulates HDAC2. Biochemical and biophysical research communications 13 31630802
2015 Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split. Retrovirology 13 26088204
2022 Dihydroartemisinin synergistically enhances the cytotoxic effects of oxaliplatin in colon cancer by targeting the PHB2-RCHY1 mediated signaling pathway. Molecular carcinogenesis 11 36342357
2024 RCHY1 and OPTN are required for melanophagy, selective autophagy of melanosomes. Proceedings of the National Academy of Sciences of the United States of America 8 38536750
2009 Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission. Virology journal 8 19818146
2015 Molecular Analysis of the HOXA2-Dependent Degradation of RCHY1. PloS one 7 26496426
2021 A Z-Linked E3 Ubiquitin Ligase Cs-rchy1 Is Involved in Gametogenesis in Chinese Tongue Sole, Cynoglossus semilaevis. Animals : an open access journal from MDPI 6 34827998
2005 Chimp genome: branching out. Nature 6 16136102
2022 CAMML with the Integration of Marker Proteins (ChIMP). Bioinformatics (Oxford, England) 4 36214642
2024 RCHY1 and OPTN: an E3-ligase and an autophagy receptor required for melanophagy, respectively. Autophagy 3 38899611
2018 Detection of microRNA-Target Interactions by Chimera PCR (ChimP). Methods in molecular biology (Clifton, N.J.) 3 29959680
2007 A structural genomics approach to the regulation of apoptosis: chimp vs. human. Genome informatics. International Conference on Genome Informatics 3 18546471
2025 Apparent differences between human and chimp proteomes are reduced when considering human population: Human specific variants are enriched in disordered and compositionally biased regions. PloS one 2 40743127
2024 CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments. Acta crystallographica. Section D, Structural biology 2 39361357
2022 Engineered Sleeping Beauty Transposon as Efficient System to Optimize Chimp Adenoviral Production. International journal of molecular sciences 2 35886882
2024 Hybrid sine cosine and spotted Hyena based chimp optimization for PI controller tuning in microgrids. Scientific reports 1 39472456
2010 Re-examination of chimp protein kinases suggests "novel architectures" are gene prediction artifacts. BMC genomics 1 20105302
2026 Gorab deficiency in skin dermis accelerates aging and is associated with dysregulation of RCHY1-mediated P53 ubiquitination. Animal models and experimental medicine 0 41869872
2026 Ubiquitin ligase RCHY1 regulates autophagosome-lysosome fusion. Cell death discovery 0 41986295
2026 LINC00839 transcriptionally activated by ELK1 represses ferroptosis in nasopharyngeal carcinoma by regulating UPF1/RCHY1/DJ-1 axis. NPJ precision oncology 0 42135459
2024 Enhanced diagnosing patients suspected of sarcoidosis using a hybrid support vector regression model with bald eagle and chimp optimizers. PeerJ. Computer science 0 39896373
2007 Neanderthal, chimp and human genomes: hypotheses wanted for research into brain evolution. Medical hypotheses 0 17651909

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