| Functional area | Key findings (1-2 sentences) | Substrate/partner | Assay/evidence type | Source (authors/year/journal) | URL | Citation ID |
|---|---|---|---|---|---|---|
| Molecular function / DUB complex | Ubp3 is a deubiquitinating enzyme in *S. cerevisiae* that acts in a stable complex with the cofactor Bre5. Bre5 is an essential positive regulator of Ubp3 activity rather than merely a passive binding factor. | Bre5 | Biochemical and genetic characterization; interaction studies | Cohen, Stutz & Dargemont 2003, *J. Biol. Chem.* | https://doi.org/10.1074/jbc.c300451200 | (pqac-00000004) |
| ER-to-Golgi anterograde trafficking | Ubp3 specifically deubiquitinates the COPII coat subunit Sec23, and this activity requires Bre5. This places Ubp3 directly in secretory-pathway control at the ER/COPII interface. | Sec23, Bre5 | Substrate identification, deubiquitination/interaction studies | Cohen, Stutz & Dargemont 2003, *J. Biol. Chem.*; Suresh, Pascoe & Andrews 2020, *Open Biology* | https://doi.org/10.1074/jbc.c300451200 ; https://doi.org/10.1098/rsob.200279 | (pqac-00000004, pqac-00000000) |
| Golgi-to-ER retrograde trafficking | Disruption of **BRE5** causes defects in Golgi-to-ER retrograde transport, and the Ubp3-Bre5 complex also targets a COPI subunit. Together these data indicate Ubp3 coordinates both forward and reverse ER-Golgi trafficking. | Bre5, COPI subunit β′-COP | Mutant phenotyping in trafficking assays; substrate assignment | Cohen, Stutz & Dargemont 2003, *J. Biol. Chem.* | https://doi.org/10.1074/jbc.c300451200 | (pqac-00000004) |
| Ribophagy / selective autophagy | Ubp3-Bre5 is required for starvation-induced ribophagy, acting on ubiquitinated 60S ribosomal components so ribosomes can be selectively delivered for autophagic degradation. Ribosome ubiquitylation antagonizes this pathway, implying Ubp3 removes an inhibitory ubiquitin signal. | Bre5, 60S ribosomal proteins; antagonistic E3 Ltn1 | Starvation/ribophagy genetics and pathway analysis | Ossareh-Nazari et al. 2014, *J. Cell Biol.*; Suresh, Pascoe & Andrews 2020, *Open Biology* | https://doi.org/10.1083/jcb.201308139 ; https://doi.org/10.1098/rsob.200279 | (pqac-00000003, pqac-00000000) |
| Mitophagy regulation | A genome-wide SQA screen showed that loss of Ubp3 or Bre5 increases rapamycin-induced mitophagy, identifying the Ubp3-Bre5 complex as a negative regulator of mitophagy. In the same study, the complex was linked positively to bulk autophagy, ribophagy, and the Cvt pathway. | Bre5; mitochondrial autophagy pathway components | Synthetic quantitative array screen; rapamycin-induced mitophagy assays | Müller et al. 2015, *Cell Reports* | https://doi.org/10.1016/j.celrep.2015.01.044 | (pqac-00000001) |
| DNA damage response / DSB repair | Ubp3-Bre5 contributes to the cellular response to DNA damage by promoting non-homologous end joining and resistance to the DSB-inducing drug phleomycin. Catalytic activity of Ubp3 is required, and genetic antagonism with the Rsp5/Bul1 ligase pathway was reported. | Bre5; antagonistic Bul1/Rsp5 pathway | HO endonuclease survival assays, plasmid-repair/NHEJ assays, phleomycin sensitivity, co-IP, microarrays | Bilsland et al. 2007, *DNA Repair* | https://doi.org/10.1016/j.dnarep.2007.04.010 | (pqac-00000019, pqac-00000020, pqac-00000021, pqac-00000023) |
| UPR / translational control | During ER stress, SCF^Grr1 promotes Ubp3 degradation, which increases monoubiquitinated eS7A and enables efficient translation of spliced **HAC1i** mRNA. In **grr1Δ**, HAC1 translational efficiency is ~4-fold lower, and Ubp3 degradation is slowed; CHX-chase estimates gave an Ubp3 half-life of ~80 min with stress versus ~120 min without. | eS7A, Bre5, Grr1, Not4, HAC1i mRNA | Ribosome profiling, RNA-seq, CHX chase, co-IP, western blotting, tunicamycin sensitivity assays | Inada et al. 2024, preprint | https://doi.org/10.21203/rs.3.rs-4865151/v1 | (pqac-00000015, pqac-00000016, pqac-00000018) |
| Glucose repression / mitochondrial metabolism | A DUB knockout screen identified Ubp3 as necessary for glucose-mediated mitochondrial repression. **ubp3Δ** cells show increased mitochondrial membrane potential, higher basal OCR, higher Cox2, and altered ATP partitioning; after azide treatment ATP remained ~60% of total in WT versus ~40% in **ubp3Δ**, indicating a larger mitochondrial ATP contribution in the mutant. | Glycolytic enzymes Pfk1, Tdh2/Tdh3; mitochondrial ETC component Cox2 | DUB knockout screen, OCR assays, ATP measurements, western blots, mitochondrial staining | Vengayil et al. 2024, *eLife* | https://doi.org/10.7554/elife.90293 | (pqac-00000006, pqac-00000011) |
| Phosphate budgeting mechanism | Ubp3 constrains mitochondrial activation by maintaining high glycolytic flux; loss of Ubp3 lowers Pfk1 and GAPDH/Tdh2-Tdh3, reroutes glucose toward trehalose synthesis and PPP, and increases cellular and mitochondrial inorganic phosphate. These experiments were typically reported with three biological replicates and significance thresholds of *p*<0.05, **p*<0.01, ***p*<0.001. | Pfk1, Tdh2/Tdh3, Tps2, Mir1 | Proteomics, ^13C pulse-labeling, Pi measurements, OCR, Mitotracker, growth assays across strain backgrounds | Vengayil et al. 2024, *eLife* | https://doi.org/10.7554/elife.90293 | (pqac-00000007, pqac-00000008, pqac-00000009, pqac-00000010, pqac-00000012, pqac-00000013) |
| Proteostasis / sterol homeostasis | Ubp3 has also been implicated in enhancing proteasomal degradation of key sterol-homeostasis enzymes, expanding its functional repertoire beyond trafficking and autophagy. Review/excerpted evidence further links Ubp3 to RNAPII deubiquitination, Rad4 proteasomal turnover, heat resistance, and replicative lifespan control. | Sterol-homeostasis enzymes; RNAPII; Rad4; Cdc48; Ufd3 | Quantitative proteomics/turnover assays; literature synthesis | Lan et al. 2021, *J. Biol. Chem.*; Suresh, Pascoe & Andrews 2020, *Open Biology* | https://doi.org/10.1016/j.jbc.2021.100348 ; https://doi.org/10.1098/rsob.200279 | (pqac-00000002, pqac-00000005, pqac-00000000) |
| Localization contexts | Experimental contexts place Ubp3 at COPII/ER-Golgi trafficking sites (via Sec23/COPI), in the cytoplasm on ribosomal substrates during ribophagy, and functionally in mitochondrial regulation and ER-stress translation control. These localization inferences come from validated substrates and pathway assays rather than a single dedicated localization study in the provided evidence. | Sec23/COPI, ribosomal proteins/eS7A, mitochondrial pathway factors | Localization inferred from substrate/pathway-specific experiments across studies | Cohen, Stutz & Dargemont 2003, *J. Biol. Chem.*; Müller et al. 2015, *Cell Reports*; Inada et al. 2024, preprint; Vengayil et al. 2024, *eLife* | https://doi.org/10.1074/jbc.c300451200 ; https://doi.org/10.1016/j.celrep.2015.01.044 ; https://doi.org/10.21203/rs.3.rs-4865151/v1 ; https://doi.org/10.7554/elife.90293 | (pqac-00000004, pqac-00000001, pqac-00000015, pqac-00000016, pqac-00000006, pqac-00000011) |


*Table: This table compiles experimentally supported functions, substrates, partners, pathways, and localization contexts for the yeast deubiquitinase Ubp3/YER151C. It is useful as a quick evidence map linking specific claims to the underlying primary literature and context IDs.*