USP36 is a nucleolar ubiquitin-specific protease (peptidase C19 family, USP36/Ubp10 subfamily) with an N-terminal USP catalytic domain and a long, basic, low-complexity C-terminal region that targets it to nucleoli. It removes ubiquitin, including Lys-48-linked chains, from nucleolar ribosome-biogenesis factors such as nucleophosmin, fibrillarin, the RNA helicase DHX33 and the largest RNA polymerase I subunit, and from c-Myc in the nucleolus, protecting them from proteasomal degradation. Through these substrates it sustains rRNA synthesis and processing, nucleolar structure and ribosome production, and it is essential for cell and embryo viability in mammals. It also deubiquitinates monoubiquitinated histone H2B at target genes such as CDKN1A, has been reported to promote SUMOylation of nucleolar proteins such as EXOSC10, restrains p62-dependent selective autophagy, and a cytoplasmic pool modulates the E3 ligase NEDD4L. The donkey product A0A9L0JCH5 is the Ensembl-canonical transcript of the donkey gene; it is 78% identical to human USP36, retains the catalytic Cys and His residues, and differs from the other donkey splice forms only by a 33-residue insertion within the USP domain that is not found in horse, human, mouse or cattle USP36.
Summary: Cysteine-type deubiquitinase activity, from the combined IEA pipeline (InterPro USP domain, EC 3.4.19.12, PANTHER node PTN002549981 and human USP36). Human USP36 deubiquitinates nucleophosmin and fibrillarin, c-Myc in vitro and in cells, DHX33 and CEP63; the human gene also carries a PAINT IBA for this term.
Reason: Core activity of a USP-family deubiquitinase, transferred within PANTHER subfamily PTHR24006:SF653 (USP36), which contains donkey, human and mouse USP36. The donkey protein conserves the catalytic nucleophile Cys131 and proton acceptor His415 (human His382). The 33-residue insertion in this splice form lies between the catalytic boxes and its effect is untested, but the activity is accepted at the gene level.
USP36 deubiquitylated the nucleolar proteins nucleophosmin/B23 and fibrillarin, and stabilized them by counteracting ubiquitylation-mediated proteasomal degradation
Summary: Nucleus, from TreeGrafter PANTHER node PTN002549981 (the human counterpart is a PAINT IBA is_active_in nucleus). USP36 is a nuclear, predominantly nucleolar, protein.
Reason: Correct but less specific than the nucleolus, where USP36 localizes and acts; the gene already carries nucleolus (GO:0005730), so this is modified to it. USP36 also acts on chromatin (H2B), so the general nuclear location is not wrong.
Summary: Nucleolus, from the combined IEA pipeline (human USP36 experimental). USP36 localizes to nucleoli via its basic C-terminal region and was found in the HeLa nucleolar proteome.
Reason: Principal site of USP36 action; experimentally established in human cells.
Summary: Cytoplasm, by Ensembl Compara from the human experimental annotation (PMID:27445338).
Reason: A cytoplasmic pool of USP36 was seen by immunofluorescence and fractionation in rat PC12 cells, where USP36 binds NEDD4L; the characterized ribosome-biogenesis functions are nucleolar, so this location is kept as non-core.
Summary: Cytosol, from TreeGrafter PANTHER node PTN002549981 (human counterpart is a PAINT IBA is_active_in cytosol from a deep USP node). A cytoplasmic pool of USP36 has been reported.
Reason: A cytoplasmic pool of USP36 was seen by immunofluorescence and fractionation in rat PC12 cells, where USP36 binds NEDD4L; the characterized ribosome-biogenesis functions are nucleolar, so this location is kept as non-core.
Summary: Chromatin organization, by Ensembl Compara from human IMP (PMID:29274341, H2Bub1 deubiquitination at the p21/CDKN1A locus).
Reason: True but general: the evidence is histone H2B deubiquitination at specific loci, which the gene already carries as chromatin remodeling (GO:0006338, an is_a child of chromatin organization, inferred from the H2B deubiquitinase activity). Modified to that term, which is itself non-core relative to the nucleolar role.
Summary: Chromatin remodeling, inferred by GO_REF:0000108 from the histone H2B deubiquitinase activity annotation.
Reason: Follows from H2Bub1 deubiquitination by human USP36 in cells and in vitro and at the p21 locus; a secondary, locus-specific function relative to the nucleolar role, kept non-core.
depletion of USP36 increases H2Bub1 at the p21 locus, primarily within its gene body
GO:0006511 ubiquitin-dependent protein catabolic process
IEA GO_REF:0000104
MARK AS OVER ANNOTATED
Summary: Ubiquitin-dependent protein catabolic process, from a UniRule family rule. The characterized activity of USP36 is the opposite direction - it removes ubiquitin from nucleophosmin, fibrillarin, MYC and CEP63 and thereby protects them from proteasomal degradation.
Reason: A family-wide UniRule default for peptidase C19 members. The process describes the degradation of ubiquitinated proteins; no evidence shows USP36 performing a step of it (for example as a proteasome-associated DUB). Its documented role is the opposite, protecting substrates from proteasomal degradation, which is captured by protein stabilization.
USP36 deubiquitylated the nucleolar proteins nucleophosmin/B23 and fibrillarin, and stabilized them by counteracting ubiquitylation-mediated proteasomal degradation
Summary: Nucleolus organization, by Ensembl Compara from mouse Usp36. USP36 depletion causes a less-developed nucleolar morphology in human cells.
Reason: USP36 contributes to nucleolar organization by stabilizing nucleolar structural and biogenesis proteins, but the evidence is loss-of-function morphology (less-developed nucleoli after depletion, nucleolar defects in knockout embryos); kept as non-core.
Summary: Negative regulation of macroautophagy, by Ensembl Compara from human IMP (PMID:22622177). USP36 loss activates p62-dependent selective autophagy in Drosophila and human cells.
Reason: Supported by loss-of-function data in Drosophila and human cells (USP36 loss activates p62-dependent selective autophagy, dependent on the DUB activity); a regulatory consequence of the deubiquitinase activity on ubiquitinated proteins, not the central role, so non-core.
Summary: Nuclear speck, from the combined pipeline based on human high-throughput imaging (Human Protein Atlas, GO_REF:0000052).
Reason: Plausible additional nuclear location from imaging data only; not where USP36's characterized functions are executed. Kept as non-core; no independent publication supports it.
Summary: Regulation of protein stability, by Ensembl Compara from human experimental annotation (the human gene also has a PAINT IBA for this term).
Reason: Correct but general: every documented case is USP36 increasing the stability of a substrate by removing ubiquitin (nucleophosmin, fibrillarin, c-Myc, DHX33, CEP63, RNA Pol I). The gene already carries the more specific child protein stabilization (GO:0050821), so modified to it.
USP36 deubiquitylated the nucleolar proteins nucleophosmin/B23 and fibrillarin, and stabilized them by counteracting ubiquitylation-mediated proteasomal degradation
Summary: Regulation of apoptotic process, from TreeGrafter PANTHER node PTN002549981; the human IBA counterpart is placed at a deep USP node seeded by Drosophila and Arabidopsis members, not by USP36.
Reason: The deep-node assertion reflects regulators of apoptosis elsewhere in the USP family. For USP36 the only link is that knockdown in cancer cells induces apoptosis together with cell-cycle arrest, which the authors attribute to loss of DHX33 and ribosome biogenesis. That is an indirect consequence of nucleolar dysfunction, not regulation of the apoptotic machinery by USP36.
USP36 down-regulation alters cell proliferation in human cancer cells by inducing both apoptosis and cell cycle arrest, and that reducing DHX33 levels through short hairpin RNA interference has the same effect
USP36 deubiquitylated the nucleolar proteins nucleophosmin/B23 and fibrillarin, and stabilized them by counteracting ubiquitylation-mediated proteasomal degradation
Summary: Histone H2B deubiquitinase activity, by Ensembl Compara from human IMP (PMID:29274341). Human USP36 deubiquitinates H2Bub1 in cells and in vitro.
Reason: Experimentally reported for human USP36 (in vitro and in cells); the yeast relative Ubp10 is an H2B deubiquitinase too. It is a precise term but secondary to the nucleolar role, so kept as non-core.
Summary: K48-linked deubiquitinase activity, by Ensembl Compara from human IDA (PMID:35989368, CEP63).
Reason: Removal of Lys-48-linked chains is consistent with USP36's role in protecting substrates from proteasomal degradation; experimentally reported for human USP36.
Summary: Regulation of rRNA processing, from the combined pipeline (human and mouse USP36). USP36 depletion reduces rRNA transcription and processing.
Reason: USP36 deubiquitinates and stabilizes rRNA-synthesis and processing factors (fibrillarin, nucleophosmin, DHX33, the RNA Pol I large subunit), and human USP36 complements yeast ubp10 for pre-rRNA processing, so it regulates rRNA processing through its own activity on these factors.
USP36 reduces the ubiquitination levels and increases the stability of the DEAH-box RNA helicase DHX33
Core Functions
Nucleolar ubiquitin-specific protease that removes ubiquitin, including Lys-48-linked chains, from ribosome-biogenesis factors (nucleophosmin, fibrillarin, DHX33, RNA Pol I large subunit) and c-Myc, stabilizing them and sustaining rRNA synthesis and processing.
USP36 deubiquitylated the nucleolar proteins nucleophosmin/B23 and fibrillarin, and stabilized them by counteracting ubiquitylation-mediated proteasomal degradation
Q: Is the 33-residue Gly/Pro/Ala-rich insertion in the donkey Ensembl-canonical USP36 transcript (A0A9L0JCH5, residues 253-285; absent from the 1123-aa donkey splice form A0A9L0I9H9 and from horse, human, mouse and cattle USP36) a real donkey splice form, and does it change deubiquitinase activity or substrate choice?
Q: Is the SUMO ligase activity reported for human USP36 toward EXOSC10 and snoRNP proteins reproducible, and does it need the USP catalytic cysteine? If confirmed, should GO SUMO ligase activity be annotated to the USP36 subfamily?
Suggested Experiments
Experiment: RT-PCR across the donkey exon carrying residues 253-285 in several tissues to establish whether the 1156-aa splice form is expressed, followed by ubiquitin-AMC hydrolysis and Lys-48 versus Lys-63 di-ubiquitin cleavage of the catalytic domain with and without the insertion.
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
Assessment of 1 ProtNLM2 GO prediction for donkey USP36 (A0A9L0JCH5), judged against the donkey GOA record (cysteine-type deubiquitinase activity, protein deubiquitination, protein stabilization, regulation of rRNA processing, nucleolus and others), the human ortholog Q9P275 and cached USP36 studies (PMID:19208757, PMID:25775507), and a donkey-human alignment (78% identity, catalytic Cys/His conserved). Ubiquitin-dependent protein catabolic process is present in donkey GOA only through a family-level UniRule, which the gene review marks as over-annotated; the characterized activity of USP36 protects its substrates from proteasomal degradation rather than carrying out a step of it, so the prediction is refuted (NPI). Non-GO ProtNLM2 outputs, not scored: subcellular locations 'Cytoplasm' and 'Nucleus' (both consistent with human data, though they omit the principal nucleolar location) and function text 'Deubiquitinating enzyme that removes conjugated ubiquitin from specific proteins to regulate different cellular processes', which is a correct but generic USP-family statement.
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
GO:0006511 ubiquitin-dependent protein catabolic processGO_BP
NPI β Nonparalog incorrect Review score: 0/2
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-10-14
FREQUENCY BIAS
Review rationale: The term is already in donkey GOA, but only via a family-wide UniRule (GO_REF:0000104) applied to peptidase C19 members, so the overlap does not establish correctness and the prediction is not novel. Donkey USP36 sits in PANTHER subfamily PTHR24006:SF653 (ubiquitin carboxyl-terminal hydrolase 36) with its catalytic Cys/His conserved, so the human ortholog's characterized activity transfers. That activity runs against the predicted process. Human USP36 deubiquitinates nucleophosmin, fibrillarin and c-Myc and thereby stabilizes them against proteasomal degradation (PMID:19208757, PMID:25775507), and PubMed searches for USP36 with degradation or proteasome return substrate-stabilization reports only, with no report of USP36 acting in a step of ubiquitin-dependent catabolism such as proteasome-associated chain trimming. The re-reviewed gene review marks the GOA row for this term as over-annotated on these grounds, which refute the prediction. ProtNLM2 repeats the generic DUB-family process label rather than the protein's substrate-protective role (protein stabilization).
Supporting Evidence:
PMID:19208757: "USP36 deubiquitylated the nucleolar proteins nucleophosmin/B23 and fibrillarin, and stabilized them by counteracting ubiquitylation-mediated proteasomal degradation"
PMID:25775507: "USP36 interacts with and deubiquitinates c-Myc in cells and in vitro, leading to the stabilization of c-Myc"
file:EQUAS/USP36/USP36-bioinformatics/RESULTS.md: "The catalytic nucleophile (donkey Cys131 = human Cys131) and proton acceptor (donkey His415 = human His382) of the USP domain are conserved."