id: Q7T347
gene_symbol: ufsp2
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:7955
  label: Danio rerio
description: ufsp2 encodes a UFM1-specific cysteine protease (peptidase C78 family)
  that functions as the primary deUFMylase in the UFM1 conjugation pathway. The enzyme
  cleaves UFM1 from conjugated substrates (deconjugation) and processes UFM1 precursors
  to expose the C-terminal glycine required for conjugation (maturation). Its principal
  substrate is UFMylated RPL26 on ER-bound 60S ribosomal subunits, where deUFMylation
  by ufsp2 is required for ribosome recycling during ER-associated ribosome quality
  control. All annotations for zebrafish ufsp2 are inferred from mammalian orthologs
  (human UFSP2 and mouse Ufsp2) by sequence similarity.
references:
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: PMID:15071506
  title: A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier
  findings:
  - statement: UFM1 was identified as a novel ubiquitin-fold modifier with a dedicated
      conjugation system involving E1 (UBA5) and E2 (UFC1) enzymes, conserved in metazoa
      and plants but not yeast.
    supporting_text: Ufm1, Uba5, and Ufc1 are all conserved in metazoa and plants
      but not in yeast
- id: PMID:17182609
  title: Two novel ubiquitin-fold modifier 1 (Ufm1)-specific proteases, UfSP1 and
    UfSP2
  findings:
  - statement: UfSP1 and UfSP2 were identified as cysteine proteases specific for
      UFM1, with UfSP2 conserved across multicellular organisms.
    supporting_text: UfSP2 is present in most, if not all, of multicellular organisms
  - statement: UfSP1/2 are strictly specific for UFM1 and do not cleave ubiquitin,
      SUMO-1, or ISG15.
    supporting_text: cleaved the C-terminal extension of Ufm1 but not that of ubiquitin
  - statement: The catalytic cysteine is essential for protease activity.
    supporting_text: replacement of the conserved Cys residue by Ser resulted in a
      complete loss of the UfSP1 and UfSP2 activities
- id: PMID:21228277
  title: Structure of ubiquitin-fold modifier 1-specific protease UfSP2
  findings:
  - statement: Crystal structure of mouse UfSP2 reveals a two-domain architecture
      with an unconventional catalytic triad (Cys294, Asp418, His420).
    supporting_text: The C-terminal catalytic domain is similar to UfSP1 with Cys(294),
      Asp(418), His(420), Tyr(282), and a regulatory loop participating in catalysis
  - statement: The N-terminal domain of UfSP2 mediates substrate recognition and ER
      recruitment via interaction with DDRGK1 (C20orf116).
    supporting_text: The novel N-terminal domain shows a unique structure and plays a
      role in the recognition of its cellular substrate C20orf116 and thus in the
      recruitment of UfSP2 to the endoplasmic reticulum
- id: PMID:30626644
  title: Ribosomal protein RPL26 is the principal target of UFMylation
  findings:
  - statement: RPL26 is the primary cellular UFMylation target, modified at K132/K134
      on ER-bound 60S subunits. UFSP2 reverses this modification.
    supporting_text: a largely uncharacterized ribosomal protein, RPL26, is the principal
      target of UFM1 conjugation
  - statement: RPL26 UFMylation and deUFMylation occur at the ER surface via
      tethered enzyme complexes.
    supporting_text: RPL26 UFMylation and de-UFMylation is catalyzed by enzyme complexes
      tethered to the cytoplasmic surface of the ER
  - statement: UFMylated RPL26 is enriched on ER-associated ribosomes.
    supporting_text: UFMylated RPL26 is highly enriched on ER membrane-bound ribosomes
      and polysomes
- id: PMID:37036982
  title: RPL26/uL24 UFMylation is essential for ribosome-associated quality control
    at the endoplasmic reticulum
  findings:
  - statement: RPL26 UFMylation is required for degradation of stalled nascent chains
      at the ER via RQC and the ubiquitin-proteasome system.
    supporting_text: UFMylation of translocon-bound 60S subunits modulates the RTJ
      to promote access of proteasomes and RQC machinery to ER-APs
- id: PMID:26428751
  title: Identification of a mutation in the ubiquitin-fold modifier 1-specific peptidase
    2 gene, UFSP2, in an extended South African family with Beukes hip dysplasia
  findings:
  - statement: A Y290H mutation in UFSP2 abolishes deUFMylase activity and causes
      autosomal dominant Beukes hip dysplasia.
    supporting_text: the BHD mutation abolishes UFSP2-mediated C-terminal cleavage
      of its substrate, Ufm1
- id: PMID:33473208
  title: A pathogenic UFSP2 variant in an autosomal recessive form of pediatric neurodevelopmental
    anomalies and epilepsy
  findings:
  - statement: A homozygous V115E variant in the N-terminal domain of UFSP2 causes
      neurodevelopmental delay and epilepsy by impairing deUFMylation.
    supporting_text: the variant more prominently affects de-UFMylation rather than
      UFMylation
- id: PMID:38383785
  title: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER
  findings:
  - statement: UFMylation of uL24/RPL26 on ER-associated 60S ribosomal subunits
      facilitates rescue and recycling of the large subunit after ribosome-associated
      quality control splits stalled ribosomes during co-translational translocation
      at the ER.
    supporting_text: UFM1 conjugation (UFMylation) facilitates the rescue of 60S
      ribosomal subunits (60S) that are released after ribosome-associated
      quality-control-mediated splitting of ribosomes that stall during
      co-translational translocation of secretory proteins into the ER.
- id: file:DANRE/ufsp2/ufsp2-deep-research-bioreason-sft.md
  title: BioReason SFT functional summary for ufsp2 (Danio rerio)
  findings:
  - statement: BioReason SFT correctly identifies ufsp2 as a cytoplasmic cysteine
      protease specializing in UFM1 processing and deconjugation, with a two-domain
      architecture supporting ER-proximal protein quality control.
- id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
  title: Falcon deep research report on ufsp2 (Danio rerio)
  findings:
  - statement: |
      Zebrafish ufsp2 (UniProt Q7T347) is the Ufm1-specific protease 2, a peptidase
      C78 family cysteine protease in the UFMylation system that acts as a UFM1-directed
      deconjugating enzyme and pro-UFM1 maturase, typically positioned at the
      endoplasmic reticulum through interaction with ODR4. No direct zebrafish primary
      studies were recovered, so function is inferred from conserved cross-species
      (human/mouse) mechanistic studies.
    reference_section_type: OTHER
    supporting_text: |-
      The UniProt accession **Q7T347** corresponds to **Danio rerio ufsp2**, annotated as **Ufm1-specific protease 2 (UfSP2)**, a cysteine protease in the UFMylation (UFM1 conjugation) system. In the retrieved literature corpus, “UFSP2/Ufsp2” consistently refers to the **UFM1-specific protease 2** (not an unrelated gene), functioning as a UFM1-directed deconjugating enzyme and pro-UFM1 maturase, typically positioned at the **endoplasmic reticulum (ER)** through interaction with **ODR4**.
  - statement: |
      UFSP2 is a UFM1-specific cysteine protease/isopeptidase whose activity depends
      on a catalytic cysteine and a conserved Cys-Asp-His catalytic triad; activity is
      abolished by thiol-reactive reagents such as N-ethylmaleimide or by mutation of
      the catalytic cysteine.
    reference_section_type: OTHER
    supporting_text: |-
      UFSP2 is described as a UFM1-specific **cysteine protease/isopeptidase**, with activity dependent on a catalytic cysteine and a conserved **Cys–Asp–His** catalytic triad (often discussed alongside an additional conserved Tyr typical of cysteine-based Ub/UBL proteases). UFSP activity can be inhibited by thiol-reactive reagents such as **N-ethylmaleimide (NEM)** or by mutation of the catalytic cysteine.
  - statement: |
      UFSP2 catalyzes two reactions: proteolytic maturation of pro-UFM1 to mature UFM1
      required for UFMylation, and hydrolysis of isopeptide bonds linking UFM1 to
      substrate proteins (de-UFMylation). pro-UFM1 activation requires removal of a
      Ser84-Cys85 dipeptide to expose the conjugatable UFM1 C-terminus.
    reference_section_type: OTHER
    supporting_text: |-
      Cross-species evidence supports that UFSP2 catalyzes:
      - **Proteolytic maturation of pro-UFM1** to mature UFM1 required for UFMylation, and
      - **Hydrolysis of isopeptide bonds** linking UFM1 to substrate proteins (de-UFMylation).
  - statement: |
      A functional division of labor is described: UFSP2 is the major de-UFMylase for
      ER-associated substrates, efficiently removing UFM1 from ribosomal protein RPL26
      (uL24); UFSP2 knockout causes drastic accumulation of UFMylated proteins. UFSP1
      is more efficient for pro-UFM1 maturation and de-UFMylation of UFC1 at Lys122.
    reference_section_type: OTHER
    supporting_text: |-
      - **UFSP2**: a major **de-UFMylase** for ER-associated substrates, particularly efficiently removing UFM1 from the ribosomal protein **RPL26 (uL24)**; UFSP2 knockout causes a **drastic accumulation of UFMylated proteins** in cell systems summarized in reviews.
  - statement: |
      UFSP2 can also reverse UFMylation on model substrates such as DDRGK1/UFBP1 and
      ASC1 in vitro and in cell studies, in addition to RPL26/uL24.
    reference_section_type: OTHER
    supporting_text: |-
      UFSP2 can also reverse UFMylation on model substrates such as **DDRGK1/UFBP1** and **ASC1** in vitro/cell studies.
  - statement: |
      UFSP2 is positioned at the endoplasmic reticulum via interaction with the
      ER membrane protein ODR4, tethering it spatially to major UFMylation events on
      ER-associated ribosomes and thus to ER proteostasis and ribosome quality control.
      Reviews also list nucleus/cytoplasm/ER localization, but ER tethering is the
      strongest mechanistic conclusion.
    reference_section_type: OTHER
    supporting_text: |-
      In the current pathway-centric view, this ER tethering spatially matches UFSP2 to major UFMylation events on **ER-associated ribosomes**, and thus to ER proteostasis/ribosome quality control processes.
  - statement: |
      A 2024 Nature study frames UFSP2 as an ER-tethered UFM1-specific hydrolase in a
      model where the UFMylation machinery promotes recycling of 60S ribosomal subunits
      from the ER, consistent with UFSP2's role in ribosome disassembly/recycling
      during ER-associated quality control.
    reference_section_type: OTHER
    supporting_text: |-
      A 2024 Nature study (“UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER”) provides primary, high-authority support for a model in which UFMylation machinery promotes **recycling of 60S ribosomal subunits** from ER-associated states, and it explicitly frames UFSP2 as an **ER-tethered UFM1-specific hydrolase** in this functional context.
existing_annotations:
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Correct. UFSP2 is recruited to the ER via its N-terminal domain interaction
      with DDRGK1, and acts on UFMylated RPL26 on ER-bound ribosomes. This is a functionally
      important localization site.
    action: ACCEPT
    reason: The ER localization is well supported by structural studies showing the
      N-terminal domain recruits UFSP2 to the ER via DDRGK1, and functional studies
      demonstrating its role in deUFMylation of ER-associated ribosomal subunits.
    supported_by:
    - reference_id: PMID:21228277
      supporting_text: plays a role in the recognition of its cellular substrate C20orf116
        and thus in the recruitment of UfSP2 to the endoplasmic reticulum
    - reference_id: PMID:30626644
      supporting_text: RPL26 UFMylation and de-UFMylation is catalyzed by enzyme complexes
        tethered to the cytoplasmic surface of the ER
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        In the current pathway-centric view, this ER tethering spatially matches UFSP2 to major UFMylation events on **ER-associated ribosomes**, and thus to ER proteostasis/ribosome quality control processes.
- term:
    id: GO:0071567
    label: deUFMylase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Correct. deUFMylase activity is the core molecular function of UFSP2.
      The enzyme cleaves UFM1 from conjugated substrates with strict specificity,
      using a catalytic cysteine-dependent mechanism.
    action: ACCEPT
    reason: This is the defining molecular function of UFSP2, supported by direct
      biochemical evidence from the mammalian orthologs showing specific cleavage
      of UFM1 conjugates, loss of activity upon Cys-to-Ser mutation, and accumulation
      of UFMylated RPL26 when UFSP2 is disrupted.
    supported_by:
    - reference_id: PMID:17182609
      supporting_text: cleaved the C-terminal extension of Ufm1 but not that of ubiquitin
    - reference_id: PMID:17182609
      supporting_text: replacement of the conserved Cys residue by Ser resulted in
        a complete loss of the UfSP1 and UfSP2 activities
    - reference_id: PMID:30626644
      supporting_text: RPL26, is the principal target of UFM1 conjugation...UFMylated
        RPL26 is highly enriched on ER membrane-bound ribosomes and polysomes
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-bioreason-sft.md
      supporting_text: A cytoplasmic cysteine protease that specializes in processing
        the ubiquitin-like modifier UFM1
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        UFSP2 is described as a UFM1-specific **cysteine protease/isopeptidase**, with activity dependent on a catalytic cysteine and a conserved **Cys–Asp–His** catalytic triad (often discussed alongside an additional conserved Tyr typical of cysteine-based Ub/UBL proteases). UFSP activity can be inhibited by thiol-reactive reagents such as **N-ethylmaleimide (NEM)** or by mutation of the catalytic cysteine.
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        - **UFSP2**: a major **de-UFMylase** for ER-associated substrates, particularly efficiently removing UFM1 from the ribosomal protein **RPL26 (uL24)**; UFSP2 knockout causes a **drastic accumulation of UFMylated proteins** in cell systems summarized in reviews.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Likely correct but non-core. Nuclear localization of UFSP2 has been reported
      for the mammalian ortholog, and UFSP2 has been observed to be recruited to DNA
      double-strand breaks. However, the primary functional site is the ER.
    action: KEEP_AS_NON_CORE
    reason: Nuclear localization is reported for the mammalian ortholog and there
      is evidence for UFSP2 function at DNA damage sites, but the core function of
      UFSP2 is at the ER where it deUFMylates RPL26 on ribosomal subunits. Falcon
      deep research notes that reviews list nucleus/cytoplasm/ER localization, but
      ER tethering is the strongest mechanistic conclusion, consistent with retaining
      nucleus as non-core.
    supported_by:
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        Some reviews also list nucleus/cytoplasm/ER localization, but ER tethering is the strongest mechanistic conclusion.
- term:
    id: GO:0006508
    label: proteolysis
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Correct but too general. UFSP2 performs a highly specific form of proteolysis
      -- it cleaves the isopeptide bond between UFM1 and its conjugated substrates.
      The term proteolysis does not capture this specificity.
    action: MODIFY
    reason: While proteolysis is technically accurate, it is overly broad for this
      specialized isopeptidase. The specific process is removal of the ubiquitin-like
      modifier UFM1 from substrate proteins (deUFMylation). No dedicated GO term for
      protein deUFMylation exists, so the closest correct existing BP term is
      GO:0070646 protein modification by small protein removal, whose definition
      explicitly covers removal of ubiquitin-like proteins (a sibling of protein
      deneddylation and protein desumoylation). A dedicated protein deUFMylation term
      is requested in proposed_new_terms.
    proposed_replacement_terms:
    - id: GO:0070646
      label: protein modification by small protein removal
      description: Closest correct existing BP term for UFM1 deconjugation; its
        definition explicitly includes removal of ubiquitin-like proteins. Unlike
        GO:0016579 (protein deubiquitination), it is not ubiquitin-specific and is
        the direct parent of the analogous protein desumoylation (GO:0016926) and
        protein deneddylation (GO:0000338) terms.
    supported_by:
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        Cross-species evidence supports that UFSP2 catalyzes:
        - **Proteolytic maturation of pro-UFM1** to mature UFM1 required for UFMylation, and
        - **Hydrolysis of isopeptide bonds** linking UFM1 to substrate proteins (de-UFMylation).
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: Redundant with the IBA annotation for nucleus. Consistent with subcellular
      localization data from the mammalian ortholog.
    action: KEEP_AS_NON_CORE
    reason: Redundant with the IBA-supported nucleus annotation. Retained as non-core
      since the primary functional site is the ER.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: Correct. UFSP2 is a soluble enzyme that resides in the cytoplasm and
      is recruited to the ER membrane surface where it acts on UFMylated substrates.
    action: KEEP_AS_NON_CORE
    reason: Cytoplasm is listed in UniProt subcellular location data and is consistent
      with UFSP2 being a soluble protease. However, the mechanistic picture points to
      constitutive ER tethering via the N-terminal domain interaction with DDRGK1/ODR4
      rather than dynamic recruitment, so cytoplasm is retained as a non-core
      localization.
    supported_by:
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        Some reviews also list nucleus/cytoplasm/ER localization, but ER tethering is the strongest mechanistic conclusion.
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: Redundant with the IBA annotation for ER. Correct and consistent with
      the role of UFSP2 at the ER membrane surface.
    action: ACCEPT
    reason: Redundant with the IBA-supported ER annotation, but independently correct
      based on UniProt subcellular location data from the mammalian ortholog.
    supported_by:
    - reference_id: PMID:21228277
      supporting_text: plays a role in the recognition of its cellular substrate C20orf116
        and thus in the recruitment of UfSP2 to the endoplasmic reticulum
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        The UniProt accession **Q7T347** corresponds to **Danio rerio ufsp2**, annotated as **Ufm1-specific protease 2 (UfSP2)**, a cysteine protease in the UFMylation (UFM1 conjugation) system. In the retrieved literature corpus, “UFSP2/Ufsp2” consistently refers to the **UFM1-specific protease 2** (not an unrelated gene), functioning as a UFM1-directed deconjugating enzyme and pro-UFM1 maturase, typically positioned at the **endoplasmic reticulum (ER)** through interaction with **ODR4**.
- term:
    id: GO:0071567
    label: deUFMylase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: Redundant with the IBA annotation for deUFMylase activity. Correct annotation
      from ARBA machine learning models.
    action: ACCEPT
    reason: Redundant with the IBA-supported annotation but independently correct.
      deUFMylase activity is the core molecular function.
    supported_by:
    - reference_id: PMID:17182609
      supporting_text: cleaved the C-terminal extension of Ufm1 but not that of ubiquitin
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        - **UFSP2**: a major **de-UFMylase** for ER-associated substrates, particularly efficiently removing UFM1 from the ribosomal protein **RPL26 (uL24)**; UFSP2 knockout causes a **drastic accumulation of UFMylated proteins** in cell systems summarized in reviews.
- term:
    id: GO:0032790
    label: ribosome disassembly
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Correct. UFSP2-mediated deUFMylation of RPL26 is a required step in the
      recycling of 60S ribosomal subunits from the ER. UFMylation marks stalled ribosomes
      for quality control, and UFSP2 removes UFM1 to enable ribosome recycling.
    action: ACCEPT
    reason: Supported by studies showing that RPL26 UFMylation at the ER triggers
      ribosome quality control and that UFSP2-mediated deUFMylation is needed for
      60S subunit recycling.
    supported_by:
    - reference_id: PMID:30626644
      supporting_text: RPL26, is the principal target of UFM1 conjugation...UFMylated
        RPL26 is highly enriched on ER membrane-bound ribosomes and polysomes
    - reference_id: PMID:37036982
      supporting_text: UFMylation of translocon-bound 60S subunits modulates the RTJ
        to promote access of proteasomes and RQC machinery to ER-APs
    - reference_id: PMID:38383785
      supporting_text: UFM1 conjugation (UFMylation) facilitates the rescue of 60S
        ribosomal subunits (60S) that are released after ribosome-associated
        quality-control-mediated splitting of ribosomes that stall during
        co-translational translocation of secretory proteins into the ER.
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        A 2024 Nature study (“UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER”) provides primary, high-authority support for a model in which UFMylation machinery promotes **recycling of 60S ribosomal subunits** from ER-associated states, and it explicitly frames UFSP2 as an **ER-tethered UFM1-specific hydrolase** in this functional context.
- term:
    id: GO:0006508
    label: proteolysis
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Correct but too general. Same issue as the IBA proteolysis annotation.
      UFSP2 performs specific isopeptide bond cleavage of UFM1 conjugates, not general
      proteolysis.
    action: MODIFY
    reason: Overly broad for this specialized isopeptidase. Should be replaced with
      a more specific term capturing UFM1 removal. As for the IBA proteolysis
      annotation, no dedicated protein deUFMylation BP term exists, so the closest
      correct existing term is GO:0070646 protein modification by small protein
      removal (a sibling of protein desumoylation and protein deneddylation). A
      dedicated protein deUFMylation term is requested in proposed_new_terms.
    proposed_replacement_terms:
    - id: GO:0070646
      label: protein modification by small protein removal
      description: Closest correct existing BP term for UFM1 deconjugation; not
        ubiquitin-specific (unlike GO:0016579), with a definition that explicitly
        covers removal of ubiquitin-like proteins.
    supported_by:
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        - **Hydrolysis of isopeptide bonds** linking UFM1 to substrate proteins (de-UFMylation).
- term:
    id: GO:0071567
    label: deUFMylase activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Redundant with IBA and IEA annotations for deUFMylase activity. Correct
      and well-supported by direct experimental data from the human ortholog.
    action: ACCEPT
    reason: Core molecular function, well supported by ISS from human UFSP2 (Q9NUQ7).
      Consistent with all other evidence lines.
    supported_by:
    - reference_id: PMID:17182609
      supporting_text: replacement of the conserved Cys residue by Ser resulted in
        a complete loss of the UfSP1 and UfSP2 activities
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        UFSP2 can also reverse UFMylation on model substrates such as **DDRGK1/UFBP1** and **ASC1** in vitro/cell studies.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Redundant with IBA and IEA nucleus annotations. Non-core localization.
    action: KEEP_AS_NON_CORE
    reason: Nucleus is a secondary localization site. The primary functional site
      is the ER.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Redundant with IEA cytoplasm annotation. Correct default localization
      for this soluble protease.
    action: KEEP_AS_NON_CORE
    reason: Cytoplasm is listed in UniProt subcellular location data for this soluble
      enzyme, but the mechanistic picture points to constitutive ER tethering via
      DDRGK1/ODR4 rather than dynamic recruitment. Non-core localization.
    supported_by:
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        Some reviews also list nucleus/cytoplasm/ER localization, but ER tethering is the strongest mechanistic conclusion.
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Redundant with IBA and IEA ER annotations. Correct and core localization
      for UFSP2 function.
    action: ACCEPT
    reason: ER is the primary functional site where UFSP2 deUFMylates RPL26 on ribosomal
      subunits. Well supported by structural and functional studies.
    supported_by:
    - reference_id: PMID:21228277
      supporting_text: plays a role in the recognition of its cellular substrate C20orf116
        and thus in the recruitment of UfSP2 to the endoplasmic reticulum
    - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
      supporting_text: |-
        In the current pathway-centric view, this ER tethering spatially matches UFSP2 to major UFMylation events on **ER-associated ribosomes**, and thus to ER proteostasis/ribosome quality control processes.
core_functions:
- description: UFSP2 functions as a thiol-dependent isopeptidase that cleaves UFM1
    from conjugated substrates (deUFMylation) and processes UFM1 precursors to their
    mature form. Its principal substrate is UFMylated RPL26 on ER-bound 60S ribosomal
    subunits, where deUFMylation is required for ribosome recycling during ER-associated
    quality control.
  molecular_function:
    id: GO:0071567
    label: deUFMylase activity
  directly_involved_in:
  - id: GO:0032790
    label: ribosome disassembly
  locations:
  - id: GO:0005783
    label: endoplasmic reticulum
  substrates:
  - id: UniProtKB:Q7SXA1
    label: UFMylated Rpl26 (60S ribosomal protein, zebrafish ortholog)
  supported_by:
  - reference_id: PMID:30626644
    supporting_text: a largely uncharacterized ribosomal protein, RPL26, is the principal
      target of UFM1 conjugation
  - reference_id: PMID:17182609
    supporting_text: cleaved the C-terminal extension of Ufm1 but not that of ubiquitin
  - reference_id: PMID:37036982
    supporting_text: UFMylation of translocon-bound 60S subunits modulates the RTJ
      to promote access of proteasomes and RQC machinery to ER-APs
  - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
    supporting_text: |-
      - **UFSP2**: a major **de-UFMylase** for ER-associated substrates, particularly efficiently removing UFM1 from the ribosomal protein **RPL26 (uL24)**; UFSP2 knockout causes a **drastic accumulation of UFMylated proteins** in cell systems summarized in reviews.
proposed_new_terms:
- proposed_name: protein deUFMylation
  proposed_definition: The process in which the ubiquitin-fold modifier UFM1 is
    cleaved from its target protein, removing one or more covalently attached UFM1
    groups from a substrate. This is the deconjugation arm of the UFMylation cycle,
    catalyzed by UFM1-specific proteases (e.g. UFSP2).
  justification: GO provides a molecular function term for deUFMylase activity
    (GO:0071567) and a biological process term for the forward reaction, protein
    ufmylation (GO:0071569), but lacks a corresponding biological process term for
    the reverse (deconjugation) reaction. Analogous deconjugation processes exist
    for other ubiquitin-like modifiers as children of GO:0070646 protein
    modification by small protein removal, namely protein deubiquitination
    (GO:0016579), protein desumoylation (GO:0016926), and protein deneddylation
    (GO:0000338). A protein deUFMylation term would complete this set and allow
    UFSP2 deconjugation activity to be annotated to an appropriately specific BP.
  proposed_parent:
    id: GO:0070646
    label: protein modification by small protein removal
  supported_by:
  - reference_id: file:DANRE/ufsp2/ufsp2-deep-research-falcon.md
    supporting_text: |-
      Cross-species evidence supports that UFSP2 catalyzes:
      - **Proteolytic maturation of pro-UFM1** to mature UFM1 required for UFMylation, and
      - **Hydrolysis of isopeptide bonds** linking UFM1 to substrate proteins (de-UFMylation).
suggested_questions:
- question: Has ufsp2 function been directly tested in zebrafish using morpholino
    knockdown or CRISPR knockout? Are there any zebrafish-specific phenotypes?
  experts: []
- question: Does zebrafish ufsp2 play a role in erythropoiesis or hematopoietic development,
    as suggested by the UFMylation pathway's role in erythroid differentiation in
    mammals?
  experts: []
suggested_experiments:
- description: Generate ufsp2 CRISPR knockout zebrafish and characterize phenotypes
    including skeletal development, neurological function, and ER stress markers to
    determine if the mammalian disease phenotypes are conserved.
  hypothesis: Loss of ufsp2 in zebrafish will cause ER stress-related phenotypes and
    potentially skeletal or neurological defects analogous to human UFSP2 mutations.
- description: Perform immunofluorescence microscopy in zebrafish embryos to confirm
    subcellular localization of ufsp2 at the ER, cytoplasm, and nucleus.
  hypothesis: Zebrafish ufsp2 will show predominantly ER and cytoplasmic localization,
    consistent with mammalian orthologs.