Asr1 (SPCC126.07c) is a 571-residue fission-yeast protein with an N-terminal atypical RING finger (residues 18-79) followed by a PHD finger (residues 122-170) and a long, partly disordered C-terminal region. It belongs to the PHRF1-related PHD/RING family (PANTHER PTHR12618:SF20), which also contains human PHRF1 and Komagataella phaffii Atg35. It is predicted to act as a RING-type E3 ubiquitin ligase, by orthology to budding-yeast Asr1, a RING/PHD ubiquitin ligase that binds the phosphorylated CTD of RNA polymerase II and ubiquitylates Rpb1 and Rpb2. A proteome-wide GFP-fusion screen placed the protein in both the nucleus and the cytosol. Its substrates, E2 partner and biological process in fission yeast have not been studied.
Summary: ARBA rule assigning chromatin location; plausible but not established for the fission-yeast protein.
Reason: This is an ARBA machine-learning assertion with no fission-yeast chromatin evidence behind it; the only target localization data (an ORFeome GFP screen) report nucleus and cytosol, not chromatin. It is nevertheless plausible, because the budding-yeast protein that PomBase treats as the ortholog is recruited to RNA polymerase II through phosphorylated CTD and acts in subtelomeric silencing. That orthology is not supported by PANTHER, which puts budding-yeast Asr1 in a different family (see RESULTS.md), and the CTD recognition is a property of Asr1 rather than of the shared RING module. Without a chromatin immunoprecipitation or chromatin-fraction experiment on the fission-yeast protein the term can be neither accepted nor rejected.
Ser7 is essential for the recruitment of Asr1 to RNAPII-CTD, potentially playing a role in the silencing of a subset of subtelomeric genes in budding yeast
file:SCHPO/asr1/asr1-bioinformatics/RESULTS.md
S. cerevisiae Asr1 Q06834: PTHR45798:SF97 (family RING-H2 FINGER PROTEIN ATL61-RELATED-RELATED), a different PANTHER family
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
ACCEPT
Summary: Nuclear localization from the S. pombe ORFeome GFP-fusion localization screen.
Reason: The genome-wide localization study of tagged fission-yeast ORFs, curated by PomBase and cited by UniProt, places the protein in both the nucleus and the cytoplasm. Nuclear and cytoplasmic distribution is also reported for the budding-yeast protein, which shuttles between the two. The term is as specific as a high-throughput screen allows.
Supporting Evidence:
file:SCHPO/asr1/asr1-uniprot.txt
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16823372}. Nucleus CC {ECO:0000269|PubMed:16823372}.
Summary: UniProt subcellular-location mapping; the UniProt note itself rests on the ORFeome localization study.
Reason: The UniProt subcellular-location statement mapped here is tied to PMID:16823372 by an experimental evidence code, so this electronic row restates the same nuclear localization as the HDA row and is accepted with it.
Supporting Evidence:
file:SCHPO/asr1/asr1-uniprot.txt
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16823372}. Nucleus CC {ECO:0000269|PubMed:16823372}.
Summary: Correct but general; the same study supports the more specific cytosol term the gene already carries.
Reason: The UniProt cytoplasm statement derives from the ORFeome localization study, which PomBase curated more specifically as cytosol (GO:0005829, HDA). Cytoplasm is true, but the gene already carries the more specific part_of descendant from the same evidence, so the replacement is cytosol.
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
ACCEPT
Summary: Cytosolic localization from the S. pombe ORFeome GFP-fusion localization screen.
Reason: PomBase curated cytosol from the genome-wide localization screen, together with nucleus. The dual distribution matches the nucleocytoplasmic shuttling reported for budding-yeast Asr1, which accumulates in the nucleus only under alcohol stress.
Summary: No biological process has been established for the fission-yeast protein; the ND annotation is correct.
Reason: There are no fission-yeast studies of asr1 beyond the localization screen. The Falcon literature search found none, and a search for the budding-yeast relative found only budding-yeast papers. The budding-yeast processes (RNA polymerase II subunit ejection, subtelomeric silencing, alcohol tolerance, a septin phenotype seen on overexpression) are tied to Asr1-specific features or phenotypes. PomBase transferred only the molecular function by orthology and kept ND for process, and that choice should stand. The orthology is also not supported by PANTHER placement. The gene's literature search record (Falcon deep research) finds no study of this protein in S. pombe that identifies a biological process.
Supporting Evidence:
file:SCHPO/asr1/asr1-bioinformatics/RESULTS.md
Only properties of the shared RING module (E3 ubiquitin ligase activity) are safe to transfer; Asr1-specific features such as Ser5P/Ser7P CTD recognition are not.
file:SCHPO/asr1/asr1-deep-research-falcon.md
No pathway assignment specific to O94400 could be substantiated.
Summary: ARBA assignment of the root complex term; no complex is known for this protein.
Reason: This ARBA prediction names only the uninformative root of the complex branch. No stable complex containing the fission-yeast protein has been described. Its budding-yeast relative binds RNA polymerase II transiently as an E3 enzyme and does not act as a polymerase subunit, so a part_of complex claim is not supported even by analogy.
ISO PMID:19064926 Modulation of RNA polymerase II subunit composition by ubiqu...
ACCEPT
Summary: E3 ubiquitin ligase activity transferred by PomBase from budding-yeast Asr1; the RING module that carries the activity is conserved.
Reason: Budding-yeast Asr1 is a RING-finger ubiquitin ligase that ubiquitylates Rpb1 and Rpb2 and works with the E2 Ubc2. The fission-yeast protein keeps the RING and PHD fingers in the same order at the N-terminus, and its RING module aligns with Asr1 (z = 14) and still more closely with PHRF1 and Atg35 in its own PANTHER subfamily (z = 28 and 23). Ubiquitin ligase activity is a property of that shared RING module, so the general MF term transfers, although PANTHER does not support the one-to-one orthology (Asr1 is classified in PTHR45798). The Rpb1/Rpb2 substrates, CTD phospho-recognition and E2 identity are Asr1-specific and are not transferred. Activity has not been tested on the fission-yeast protein.
Here, we report that the Saccharomyces cerevisiae protein Asr1 is a RING finger ubiquitin-ligase that binds directly to RNA polymerase II via the carboxyl-terminal domain (CTD) of the largest subunit of the enzyme.
Finally, we show that Ubc2 is an E2 of Asr1 for its ubiquitination properties.
file:SCHPO/asr1/asr1-uniprot.txt
DR Pfam; PF00628; PHD; 1. DR Pfam; PF13639; zf-RING_2; 1.
file:SCHPO/asr1/asr1-bioinformatics/RESULTS.md
All four proteins share a homologous N-terminal RING + PHD module (all z > 13).
Core Functions
Predicted RING-type E3 ubiquitin ligase acting in the nucleus and cytosol, inferred from the conserved N-terminal RING/PHD module shared with budding-yeast Asr1 and the PHRF1 subfamily. Substrates and E2 partner in fission yeast are unknown.
Here, we report that the Saccharomyces cerevisiae protein Asr1 is a RING finger ubiquitin-ligase that binds directly to RNA polymerase II via the carboxyl-terminal domain (CTD) of the largest subunit of the enzyme.
file:SCHPO/asr1/asr1-bioinformatics/RESULTS.md
All four proteins share a homologous N-terminal RING + PHD module (all z > 13).
Q: Which endogenous proteins does Asr1 ubiquitylate in fission yeast, and does it bind the phosphorylated CTD of RNA polymerase II as budding-yeast Asr1 does?
Q: Is budding-yeast Asr1 the true ortholog of the PHRF1/Atg35 lineage (PTHR12618:SF20)? If so, its PANTHER placement in the plant ATL RING-H2 family (PTHR45798) and the IBA it receives from that family's node should be revisited.
Suggested Experiments
Experiment: Purify recombinant Asr1 RING/PHD region and test E2-dependent autoubiquitination in vitro, with RING zinc-ligand cysteine mutants as controls; then test binding to Ser5P/Ser7P CTD peptides.
Experiment: Tag endogenous asr1 and perform ChIP and ubiquitin-remnant proteomics in wild-type and asr1 deletion cells to identify chromatin occupancy and substrates.
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.
The single ProtNLM2 prediction, metal ion binding, is a correct novel prediction. It is supported by the target's zinc-finger architecture, a PHD finger with an intact Cys4-His-Cys3 ligand set plus an atypical RING finger, and the gene's GOA set carries no metal- or zinc-binding term.
Review rationale: Metal ion binding is supported by the target's zinc-finger architecture. The reviewed sequence record identifies a PHD finger at residues 122-170 (PROSITE-ProRule PRU00146) and an atypical RING finger at residues 18-79 (PRU00175). The PHD sequence retains the full Cys4-His-Cys3 zinc-ligand pattern (C124, C126, C141, C144, H149, C152, C165, C168), so zinc coordination by this domain is a diagnostic structural inference. No direct zinc-binding assay exists for the fission-yeast protein, and PubMed searches for the gene and the PHRF1 family returned no metal-binding experiment. The gene's GOA annotations contain no metal-ion or zinc-ion binding term (only ubiquitin protein ligase activity, which is not an is_a ancestor or descendant of metal ion binding), so the prediction is novel. The ProtNLM2 output was hydrated from GO:0008270 zinc ion binding, which would be the more precise term.