Ulp2 (SPAC17A5.07c) is a 638-residue SUMO-specific cysteine protease of the peptidase C48 (Ulp/SENP) family. Its C-terminal catalytic domain carries the conserved His-Asp-Cys triad (His440, Asp494, Cys544). By PANTHER classification it belongs to the SENP6/SENP7 family (PTHR46896), not to the family containing budding-yeast Ulp2/Smt4. Purified Ulp2 removes SUMO (Pmt3) from high-molecular-weight SUMO conjugates in an N-ethylmaleimide-sensitive manner, but processes the SUMO precursor much less efficiently than Ulp1; its main role is deconjugation and dismantling of poly-SUMO species, not SUMO maturation. Ulp2 sits mainly in intranuclear foci that often coincide with SUMO, with a small cytoplasmic pool and little signal at the nuclear periphery, which distinguishes it from the nuclear-pore-associated Ulp1. It is found in at least two large complexes and co-purifies with RNA-processing, ribosome-biogenesis and translation proteins, including the sumoylated translation initiation factor eIF4G. Deletion mutants accumulate high-molecular-weight SUMO species and are sensitive to hydroxyurea, cycloheximide and osmotic stress. Genetically, these defects depend on SUMO-chain formation and on SUMO-targeted ubiquitin ligase (STUbL) activity.
IPI PMID:24818994 The S. pombe translation initiation factor eIF4G is Sumoylat...
REMOVE
Summary: Ulp2 co-purifies and co-elutes with eIF4G (tif471, SPAC17C9.03) in large complexes; the interaction is real but generic protein binding conveys no functional information.
Reason: Following the protein-binding policy, the bare GO:0005515 term is uninformative and is removed; removal does not mean the eIF4G association is false. The paper shows co-purification and gel-filtration co-elution, not a characterised direct binding mode, so no more informative MF (for example a SUMO-modified-protein binding term) is supported. The informative molecular function of Ulp2 is deSUMOylase activity, captured elsewhere in this review.
Gel filtration analysis of whole cell extracts from cells containing Ulp2-myc and either eIF4G-HA or eIF3h-HA indicates that the majority of eIF4G co-elutes with Ulp2 (Figure 2B).
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
ACCEPT
Summary: The genome-wide YFP-tagging screen localised Ulp2 to the nucleus, and independent immunofluorescence of genomically tagged Ulp2 shows predominantly nuclear foci.
Reason: The ORFeome localisation screen (abstract only in cache) is the source of the curated UniProt nuclear location. The result agrees with the targeted study, which found Ulp2 mainly in intranuclear foci that often co-localise with SUMO. The nucleus is where Ulp2 carries out its main deconjugating function.
Summary: The PAINT node PTN002930416 spans SENP6, SENP7, their Drosophila relatives and pombe Ulp2. Nuclear activity is inherited from this node and is confirmed experimentally for Ulp2.
Reason: Ulp2 falls inside the PTHR46896 (SENP6/SENP7) clade that carries this IBD, and its own localisation data agree, so the inference holds. This is the same claim as the HDA and IEA nucleus rows.
Summary: SubCell mapping of the curated UniProt nuclear location, consistent with the direct imaging data.
Reason: The mapping comes from an experimentally supported UniProt location (PMID:16823372) and agrees with the targeted immunofluorescence. It is the same claim as the HDA and IBA nucleus rows.
Summary: Ulp2 has a small cytoplasmic pool, and Ulp2 itself (PomBase:SPAC17A5.07c) is one of the donors for this IBD.
Reason: Immunofluorescence detects a minor cytoplasmic fraction of Ulp2, so the inherited cytoplasm term is correct. Ulp2 appearing in its own WITH/FROM list shows experimental grounding on the target, not circularity. The cytoplasmic pool is minor; the main deconjugating activity is nuclear, so this location is kept as non-core. It is not a broad term awaiting refinement, because no more specific cytoplasmic structure is established for Ulp2 (see the stress granule row).
Summary: The Peptidase_C48 InterPro2GO mapping gives generic proteolysis. The process that Ulp2 has been shown to perform is cleavage of SUMO from conjugates.
Reason: Ulp2 hydrolyses the isopeptide bond joining SUMO to target lysines or to other SUMO moieties. That is protein desumoylation (GO:0016926), a protein-modification process, not bulk degradation of a substrate polypeptide. Desumoylation is not an is_a descendant of proteolysis, so this is a lateral correction to the specific, experimentally supported process term the gene already carries (IBA).
These results confirm that like S. cerevisiae Ulp2, S. pombe Ulp2 is a cysteine protease whose main function is in deconjugating SUMO from target proteins.
Summary: The term is correct (the C48 domain, His-Asp-Cys triad and NEM-sensitive activity) but general; deSUMOylase activity is an is_a descendant that the gene already carries by IDA.
Reason: GO:0016929 deSUMOylase activity is_a GO:0008234 cysteine-type peptidase activity (OLS ancestors checked). The direct assay supports the more specific term, so the general one is refined to it.
These results confirm that like S. cerevisiae Ulp2, S. pombe Ulp2 is a cysteine protease whose main function is in deconjugating SUMO from target proteins.
IDA PMID:24818994 The S. pombe translation initiation factor eIF4G is Sumoylat...
UNDECIDED
Summary: The cited paper shows eIF4G and SUMO in cytoplasmic granules under 1 M KCl stress. In the main-text figures, Ulp2 is imaged only under unstressed conditions, as nuclear foci with a minor cytoplasmic pool.
Reason: I read the full text and every Ulp2 localisation statement in it. None places Ulp2 itself in KCl-induced stress granules; the granule experiments use eIF4G-HA, SUMO and PABP-RFP. The PomBase curator may have used a supplementary panel that is not in the cached text, so the row is left undecided rather than removed. Ulp2 co-purifies with known stress-granule proteins (eIF4G, PABP), which makes the annotation plausible but does not demonstrate it.
Exposure of cells to conditions that lead to the formation of stress granules, results in increased sumoylation of eIF4G, and partial co-localisation of eIF4G and SUMO in the cytoplasm.
Summary: Inherited from the SENP6/SENP7 PAINT node (donors human SENP6 and mouse Senp6). Ulp2 sits inside that clade and has its own direct deconjugation evidence.
Reason: Ulp2 is a PTHR46896 member (subfamily SF3) under node PTN002930416 and retains the catalytic triad. Purified Ulp2 removes SUMO from high-molecular-weight conjugates in an NEM-dependent way, so the inherited process is confirmed on the target. This is the core biological process.
These results confirm that like S. cerevisiae Ulp2, S. pombe Ulp2 is a cysteine protease whose main function is in deconjugating SUMO from target proteins.
Comparison of SUMO-containing species in ulp1-d and ulp2-d cells (Figure 1C, lanes 3 and 4) supports the notion that the main function of Ulp2 is in the removal or dismantling of high Mr SUMO-containing species, rather than in processing precursor SUMO.
IDA PMID:24818994 The S. pombe translation initiation factor eIF4G is Sumoylat...
ACCEPT
Summary: Purified recombinant Ulp2 deconjugates SUMO from high-molecular-weight species in pombe extracts, and NEM blocks the activity.
Reason: Direct biochemical evidence of the core molecular function, with a cysteine-protease mechanism. It agrees with the family-level inheritance from the SENP6/SENP7 node.
These results confirm that like S. cerevisiae Ulp2, S. pombe Ulp2 is a cysteine protease whose main function is in deconjugating SUMO from target proteins.
Using assays we described previously [13], we demonstrate that Ulp2 is significantly less able than Ulp1 to process SUMO to the mature form (Figure 1A, lane 2 (Ulp1) and lane 3 (Ulp2)), but is capable of deconjugating SUMO from high Mr species in an N-ethylmaleimide- (NEM)-dependent manner (Figure 1B).
GO:0019783 ubiquitin-like protein peptidase activity
IEA GO_REF:0000117
MODIFY
Summary: The term is correct but general (SUMO is a ubiquitin-like modifier); deSUMOylase activity is an is_a descendant that the gene already carries by IDA.
Reason: GO:0016929 deSUMOylase activity is_a GO:0019783 ubiquitin-like protein peptidase activity (OLS ancestors checked). The ARBA rule is not itself evidence; the direct assay supports refining the term to the SUMO-specific deconjugase activity. Nothing suggests that Ulp2 acts on ubiquitin or other ubiquitin-like modifiers.
These results confirm that like S. cerevisiae Ulp2, S. pombe Ulp2 is a cysteine protease whose main function is in deconjugating SUMO from target proteins.
Summary: The term (cleavage within SUMO, i.e. precursor maturation) is inherited from the SENP6/7 node. Ulp2 does process precursor SUMO, but much less efficiently than Ulp1.
Reason: GO:0070139 is defined as hydrolysis of peptide bonds within SUMO, which is the precursor-maturation reaction. It is not an ancestor or descendant of GO:0016929. The direct comparison shows that Ulp2 can process the precursor but is much poorer at it than Ulp1, and the ulp1/ulp2 deletion comparison indicates that maturation is not its main physiological role. The PAINT inheritance is not contradicted; Ulp2 is inside the clade and keeps the catalytic triad. So the activity is retained as a real but minor capacity.
Using assays we described previously [13], we demonstrate that Ulp2 is significantly less able than Ulp1 to process SUMO to the mature form (Figure 1A, lane 2 (Ulp1) and lane 3 (Ulp2)), but is capable of deconjugating SUMO from high Mr species in an N-ethylmaleimide- (NEM)-dependent manner (Figure 1B).
EXP PMID:24818994 The S. pombe translation initiation factor eIF4G is Sumoylat...
MARK AS OVER ANNOTATED
Summary: The paper shows that Ulp2 co-purifies with translation factors, that eIF4G is sumoylated (more so under KCl stress), and that ulp2 deletion mutants are cycloheximide-sensitive. It does not measure translation in ulp2 mutants or show Ulp2-dependent deSUMOylation of eIF4G.
Reason: The full text is available. Its evidence is association (co-purification and co-elution with eIF4G and eIF3 subunits) plus a pleiotropic drug-sensitivity phenotype shared with sensitivity to hydroxyurea and KCl. No assay of translation rate, polysome profile or eIF4G activity in ulp2 mutants is reported. The authors themselves leave the role of eIF4G sumoylation open, and Ulp2 stays in large complexes after EDTA disrupts polysomes. Regulation of cytoplasmic translation therefore goes beyond what was shown; it is a hypothesis rather than an established process for Ulp2.
They are also sensitive to the protein synthesis inhibitor, cycloheximide (CHX, 10 and 20 µg/ml) and KCl (1 M) indicating that Ulp2 likely has roles in numerous cellular processes.
These data suggest that sumoylation of eIF4G may be associated with stress granule formation and/or proteolysis of the translation initiation factor.
Core Functions
SUMO-deconjugating (deSUMOylase) cysteine protease of the C48/SENP6-7 family. It mainly dismantles high-molecular-weight and poly-SUMO conjugates and acts mostly in intranuclear foci.
These results confirm that like S. cerevisiae Ulp2, S. pombe Ulp2 is a cysteine protease whose main function is in deconjugating SUMO from target proteins.
Using assays we described previously [13], we demonstrate that Ulp2 is significantly less able than Ulp1 to process SUMO to the mature form (Figure 1A, lane 2 (Ulp1) and lane 3 (Ulp2)), but is capable of deconjugating SUMO from high Mr species in an N-ethylmaleimide- (NEM)-dependent manner (Figure 1B).
Q: Is eIF4G a direct physiological Ulp2 substrate, and does its deSUMOylation control translation initiation or stress-granule recruitment?
Q: Does S. pombe Ulp2, like its PTHR46896 relatives SENP6 and SENP7, preferentially edit poly-SUMO chains? Which lineage-specific targeting regions direct it to intranuclear foci?
Q: Given that PANTHER places S. pombe Ulp2 with SENP6/SENP7 and S. cerevisiae Ulp2 in a separate family (PTHR46915), which budding-yeast Ulp2 substrates (for example centromeric or nucleolar factors) can be transferred to fission yeast at all?
Suggested Experiments
Experiment: Compare eIF4G sumoylation in wild-type and ulp2-deletion cells with and without 1 M KCl stress. Test whether purified Ulp2 deconjugates SUMO from immunopurified eIF4G, and measure polysome profiles in ulp2-deletion cells.
Type: biochemistry and polysome profiling
Experiment: Image genomically tagged Ulp2 together with an established stress-granule marker (for example Pabp-RFP) under 1 M KCl or heat stress, to test directly whether Ulp2 enters cytoplasmic stress granules.
Type: live-cell fluorescence microscopy
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.
Review rationale: Purified fission-yeast Ulp2 directly deconjugates SUMO from high-molecular-weight species, and the study identifies it as a cysteine protease. SUMO is a ubiquitin-like modifier, so the broad ubiquitin-like protein peptidase term is biologically correct. The more specific deSUMOylase activity GO:0016929 is experimentally established and already annotated; the XML records hydration from that term. This prediction loses substrate specificity and is therefore LSP. It does not imply a demonstrated ability to remove ubiquitin itself.
Supporting Evidence:
PMID:24818994: "These results confirm that like S. cerevisiae Ulp2, S. pombe Ulp2 is a cysteine protease whose main function is in deconjugating SUMO from target proteins."
Review rationale: Direct biochemical experiments establish Ulp2 as a SUMO-deconjugating cysteine protease, including sensitivity to N-ethylmaleimide. The conserved C48 catalytic domain is consistent with that mechanism. Cysteine-type peptidase activity is true but less precise than the already annotated deSUMOylase activity and its SUMO substrate specificity.
Supporting Evidence:
PMID:24818994: "These results confirm that like S. cerevisiae Ulp2, S. pombe Ulp2 is a cysteine protease whose main function is in deconjugating SUMO from target proteins."