res2 (also pct1; product p73res2/Pct1) encodes a 657-residue sequence-specific DNA-binding subunit of the fission yeast MBF transcription factor (also called DSC1), the G1/S (Start) transcriptional regulator of Schizosaccharomyces pombe and, with its paralog Res1, the counterpart of the budding yeast Swi4 and Mbp1 subunits of SBF and MBF. Its N-terminal APSES/KilA-N helix-turn-helix domain (residues 8-115) carries the MCB-recognition and dimerization activity of the protein, a central block of two ankyrin repeats is shared with Res1 and Cdc10, and Res2 associates with the Swi6-like shared subunit Cdc10, which strongly enhances its otherwise weak DNA binding. Res2-Cdc10 (and the Res1-Res2-Cdc10 core of the vegetative complex) binds MluI cell-cycle box (MCB, ACGCGT) elements but not SCB or E2F sites, occupies the promoter chromatin of MCB-containing genes such as cdc22, cdc18, cdt1, cig2 and cnp1 throughout the cell cycle, and activates their RNA polymerase II transcription at Start. Res2 is the subunit of the promoter-bound complex through which the complex is switched off outside G1: the corepressor pair Nrm1/Yox1 and the S-phase cyclin Cig2, both themselves MBF targets, bind Res2 and repress MBF-dependent transcription in feedback loops, and res2 deletion derepresses most MBF-dependent transcripts in G2, so Res2 contributes to both activation and repression of the regulon. res2 deletion is viable in the mitotic cycle, where Res1-Cdc10 predominates, but res2 is highly induced during nitrogen starvation and conjugation, is required for the initiation of premeiotic DNA synthesis and for correct meiotic MCB-driven transcription of rec8, rec11, cdc18 and cdc22, and its loss causes a severe meiotic defect, so Res2-Cdc10 is the MBF form that predominates at the meiotic Start. Checkpoint control of the complex acts through Cdc10, Nrm1 and Yox1 rather than through Res2 itself, and DNA damage releases the Res1-Res2-Cdc10 core from chromatin.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000082 G1/S transition of mitotic cell cycle | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the APSES-family node PTN000917496 (Swi4, Mbp1 and Swi6 with their C. albicans and S. pombe counterparts), seeded by the budding yeast SBF/MBF subunits and the C. albicans orthologs. Every extant member of the node is a subunit of a G1/S transcription factor (SBF, MBF, pombe MBF), so the node placement is sound and Res2 is inside the clade that inherited the function. Reason: res2+ was isolated as a multicopy suppressor of a res1 null mutant and is required, redundantly with res1+, for the initiation of mitotic DNA synthesis (PMID:8168485); Res2-Cdc10 is one of the two parallel Start systems of fission yeast (PMID:7588609), and Res2 supplies MCB-binding activity to the MBF complex whose G1/S output (cdc18, cdt1, cdc22, cig2) is the Start switch. Core function, even though the mitotic role is redundant with Res1 and res2 deletion is viable. Supporting Evidence: PMID:8168485 res2+ is largely redundant in function with res1+ and is required for the initiation of mitotic and premeiotic DNA synthesis, but has an additional role in meiotic division. PMID:7588609 Fission yeast possess two such overlapping systems, Res1-Cdc10 and Res2-Cdc10, both of which act to start the mitotic and meiotic cycles. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | EXP PMID:30635289 Cell Cycle-Regulated Transcription of CENP-A by the MBF Comp... | ACCEPT | Summary: Aristizabal-Corrales, Yang and Li 2019 (full text cached): a visual screen for CENP-A (Cnp1) misregulation recovered nrm1, yox1 and res2 deletions; res2 deletion raises cnp1 mRNA and protein about twofold, abolishes the G1 peak of cnp1 expression, and Res2 is found by ChIP on the cnp1 promoter, whose MCB1 box is required for the MBF repressors to restrict cnp1 transcription to G1. nrm1 res2 and yox1 res2 double mutants are no worse than res2 alone, so Nrm1/Yox1 repress cnp1 through Res2. Reason: Direct evidence that Res2 is the promoter-bound MBF subunit through which the Nrm1/Yox1 corepressors restrict a Pol II target gene (cnp1) outside G1, consistent with the earlier finding that res2p switches off S-phase transcription in G2 (PMID:9303312). The repressive role is a core, Res2-specific function of the complex. Supporting Evidence: PMID:30635289 ChIP analysis showed that Nrm1, Yox1, and Res2 bind to the cnp1 promoter ( Figure 4B ). PMID:30635289 Deletion of nrm1 or yox1 resulted in a βΌ 5β6-fold increase in cnp1 mRNA levels, whereas res2 deletion led to a more modest twofold increase PMID:30635289 the nrm1 β res2 β and yox1 β res2 β double mutants display the same cnp1 mRNA level as the res2 β single mutant ( Figure 4C ), suggesting that Nrm1 and Yox1 suppress cnp1 levels by interacting with Res2. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IMP PMID:9303312 Control of S-phase periodic transcription in the fission yea... | ACCEPT | Summary: Baum, Wuarin and Nurse 1997 (abstract-only cache): analysis of cdc10p, res1p, res2p and rep2p in S-phase periodic transcription of the mitotic cycle defines a new role for res2p in switching off S-phase transcription during G2; the DSC1 bandshift activity requires res2p and correlates with inactive transcription. Reason: The founding evidence for the repressive role of Res2: in res2 mutants S-phase transcription is not shut off in G2. Later work explains the mechanism (Cig2, Nrm1 and Yox1 act on MBF through Res2; PMID:11781565, PMID:30635289) and genome-wide profiling confirms that most MBF-dependent transcripts are constitutively derepressed in res2 cells. Core function. Supporting Evidence: PMID:9303312 define a new role for res2p, previously demonstrated to be important in the meiotic cycle, in switching off S-phase transcription during G2 of the mitotic cycle PMID:9303312 We suggest that S-phase transcription is controlled by both activation and repression, and that res2p represses transcription in G2 of the cell cycle as a part of the DSC1 complex. file:SCHPO/res2/res2-deep-research-falcon.md Most MBF-dependent transcripts become constitutively derepressed in *res2Ξ*, supporting a major role in transcriptional shutoff, but **yox1, cig2, and mik1** can retain near-wild-type expression. |
| GO:0000785 chromatin | IDA PMID:17936710 Ctp1 is a cell-cycle-regulated protein that functions with M... | ACCEPT | Summary: Limbo et al. 2007 (abstract-only cache): the Ctp1 paper shows that ctp1+ transcription is periodic, with onset at the start of DNA replication, which is the MBF signature; the abstract does not describe the chromatin assay for Res2 (presumably ChIP of MBF subunits at the ctp1 promoter), so the specific evidence is deferred to the PomBase curator who read the full text. Reason: The claim is correct for the gene: Res2 acts on promoter chromatin as an MCB-binding subunit of MBF, and the same term is independently supported by Res2-HA ChIP on the cdc22 and cdc18 promoters (PMID:24006488) and on the cnp1 promoter (PMID:30635289). Abstract-only cache; full-text evidence is not second-guessed. Supporting Evidence: PMID:17936710 Transcription of ctp1(+) is periodic during the cell cycle, with the onset of its expression coinciding with the start of DNA replication. PMID:24006488 both Res1 and Res2 are released from chromatin after treatment with MMS |
| GO:0000785 chromatin | IDA PMID:24006488 The DNA damage and the DNA replication checkpoints converge ... | ACCEPT | Summary: Ivanova et al. 2013 (full text cached): ChIP of Res2-HA shows Res2 loaded on the cdc22 and cdc18 promoters in untreated cells and released from chromatin, together with Res1 and Cdc10, after MMS-induced DNA damage, while the Cdc10-Res2 interaction is preserved, so the MBF core leaves chromatin as a complex. Reason: Direct chromatin-occupancy evidence at MBF target promoters, which is where the DNA-binding subunit of MBF acts. Chromatin is the correct site-of-activity term for Res2's core function. Supporting Evidence: PMID:24006488 Loading of Res1 (left) or Res2 (right) on cdc22 and cdc18 promoters was measured by ChIP analysis of chromatin extracts isolated from untreated or MMS-treated PMID:24006488 both Res1 and Res2 are released from chromatin after treatment with MMS |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | HDA PMID:40015273 A comprehensive Schizosaccharomyces pombe atlas of physical ... | ACCEPT | Summary: Skribbe et al. 2025 (abstract-only cache): a library of 89 endogenously tagged S. pombe transcription factors profiled by IP-MS and ChIP-seq, defining binding sites across 2,027 genomic regions; Res2 is not named in the abstract and the row rests on the dataset. Reason: Genome-wide ChIP-seq occupancy of a sequence-specific transcription factor at promoter regions is appropriate HDA support for cis-regulatory region binding, and it agrees with the targeted evidence that the Res2-Cdc10 heteromer binds MCB elements in vitro and in vivo (PMID:7926774) and with earlier ChIP-chip of tagged Res2 at MBF target promoters. Core function. Supporting Evidence: PMID:40015273 We created a comprehensive library of 89 endogenously tagged S. pombe TFs, mapping their protein and chromatin interactions using immunoprecipitation-mass spectrometry and chromatin immunoprecipitation sequencing. file:SCHPO/res2/res2-deep-research-falcon.md Genome-wide ChIP-chip using chromosomally tagged Res2 placed it at MBF-associated promoter and intragenic sites. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the APSES-family node, seeded by the three S. pombe MBF subunits Res2 itself (SPAC22F3.09c), Cdc10 (SPBC336.12c) and Res1 (SPBC725.16). Res2 in its own WITH list is expected: its experimental MCB-binding annotation (PMID:7926774) is one of the descendant evidences used to place the IBD, so this row says that the function is inherited rather than lineage-specific. Reason: Res2 carries the APSES DNA-binding domain, its N-terminal region contains the DNA-binding activity of the MBF complex (PMID:24006488), and the Res2-Cdc10 heteromer binds MCB but not SCB or E2F sites (PMID:7926774). The contributes_to qualifier reflects that full-length Res2 alone binds DNA weakly and that in vivo the MCB-binding activity belongs to the Res1-Res2-Cdc10 complex, which is exactly the weaker claim being graded. Correct term and node. Supporting Evidence: PMID:7926774 The p73pct1/p85cdc10 complex binds both in vitro and in vivo to MCB but not SCB or E2F sites. PMID:24006488 Res2, which contains the DNA-binding activity of the MBF complex in its amino-terminal region file:SCHPO/res2/res2-deep-research-falcon.md Full-length Res2 binds DNA only weakly by itself; Cdc10 strongly enhances binding. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IDA PMID:30635289 Cell Cycle-Regulated Transcription of CENP-A by the MBF Comp... | ACCEPT | Summary: Aristizabal-Corrales, Yang and Li 2019 (full text cached): ChIP shows Res2 bound to the cnp1 (CENP-A) promoter, which contains two candidate MCB boxes; deletion or CG-to-TA mutation of the proximal MCB1 box derepresses cnp1 four- to fivefold and abolishes the res2-dependent repression, so the MCB1 element is the cis-regulatory site through which Res2-containing MBF acts. Reason: In vivo occupancy of a defined MCB cis-regulatory element in a Pol II promoter, coupled with element mutagenesis that removes the Res2-dependent effect, is direct evidence for sequence-specific cis-regulatory binding by Res2. Core function. Supporting Evidence: PMID:30635289 ChIP analysis showed that Nrm1, Yox1, and Res2 bind to the cnp1 promoter ( Figure 4B ). PMID:30635289 We identified the MCB (MluI cell cycle box) motif in the CENP-A promoter, and further showed that the MBF complex binds to the motif to restrict CENP-A transcription to G1. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IDA PMID:7926774 pct1+, which encodes a new DNA-binding partner of p85cdc10, ... | ACCEPT | Summary: Zhu, Takeda, Nasmyth and Jones 1994 (abstract-only cache): pct1+ (res2+) was cloned as a gene encoding a 73 kDa protein that interacts with p85cdc10 to form an MCB-binding heteromer; the p73pct1/p85cdc10 complex binds MCB elements in vitro and in vivo but not SCB or E2F sites, and p73pct1 carries an N-terminal domain similar to the Swi4/Mbp1 DNA-binding domains. Reason: The founding biochemical evidence that Res2 supplies MCB-specific DNA binding as part of a Cdc10-containing heteromer; contributes_to is the appropriate qualifier for the complex-level binding assayed here. Consistent with the later mapping of the DNA-binding activity to the Res2 N-terminal region (PMID:24006488). Supporting Evidence: PMID:7926774 We report the cloning of a new gene, pct1+, encoding a 73-kD protein that interacts with p85cdc10 to form an MCB-binding heteromer. PMID:7926774 The p73pct1/p85cdc10 complex binds both in vitro and in vivo to MCB but not SCB or E2F sites. PMID:7926774 p73pct1 has centrally located ankyrin repeats and a putative amino-terminal DNA-binding domain that has extensive sequence similarity to the DNA-binding domains of the Saccharomyces cerevisiae SWI4 and MBP1 proteins. |
| GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific | EXP PMID:9303312 Control of S-phase periodic transcription in the fission yea... | ACCEPT | Summary: Baum, Wuarin and Nurse 1997 (abstract-only cache): res2p is required to switch off S-phase transcription in G2 of the mitotic cycle, the DSC1 bandshift activity requires res2p and correlates with inactive transcription, and the authors conclude that res2p represses transcription in G2 as part of the DSC1 complex. Reason: Res2 is the DNA-binding subunit of the promoter-bound complex through which repression is exerted: it carries MCB-binding activity (PMID:7926774, PMID:24006488) and is the docking point for the Cig2 cyclin (PMID:11781565) and for the Nrm1/Yox1 corepressor pair (PMID:30635289) that shut MBF off outside G1. A DNA-binding repressor MF is the right representation of this Res2-specific role, alongside the activator MF for the G1/S and meiotic outputs; the dual activator/repressor nature of Res2 is explicitly recognised in the later literature. Supporting Evidence: PMID:9303312 We show that the presence of the in vitro bandshift activity DSC1, conventionally thought to represent the active complex, requires res2p and correlates with inactive transcription. PMID:30635289 Res2, a DNA-binding protein, together with Res1 and Cdc10, forms the core of the MBF complex, and is involved in both activation and repression of the transcriptional activity PMID:30635289 Nrm1 and Yox1 are known to form a dimer that suppresses the transcriptional activity of the MBF complex outside of G1 by interacting with Res2 |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | EXP PMID:14648198 DSC1-MCB regulation of meiotic transcription in Schizosaccha... | ACCEPT | Summary: Cunliffe, White and McInerny 2004 (abstract-only cache): MCB-containing genes (rec8, rec11, cdc18, cdc22) are co-ordinately transcribed during premeiotic S phase, synthetic and native MCB motifs confer meiosis-specific transcription on a reporter, a DSC1-like MCB-binding complex is present in meiotic cells, and cdc10+, res2+, rep1+ and rep2+ (but not res1+) are required for correct meiotic transcription. Reason: The MCB-binding subunit required for meiotic MCB-driven Pol II transcription is Res2, not Res1, so the activator MF is correctly placed on Res2 for the meiotic program; the same MF is supported for the mitotic cycle by the res2-dependent induction of the cig2 (cyc17) transcript (PMID:7909513) and by the requirement for res2+ in initiating mitotic and premeiotic DNA synthesis (PMID:8168485). Core function. Supporting Evidence: PMID:14648198 We found that cdc10+, res2+, rep1+ and rep2+ are required for correct meiotic transcription, while res1+ is not required for this process. PMID:14648198 Several genes, including rec8+, rec11+, cdc18+, and cdc22+, which contain MCB motifs in their promoter regions, are found to be co-ordinately regulated during pre-meiotic S-phase. |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the APSES-family node, seeded by Res2's own experimental activator rows (SPAC22F3.09c is the target itself, which is expected), by budding yeast Swi4 and by Mbp1. All donors are DNA-binding subunits of G1/S transcriptional activators. Reason: Res2 binds MCB elements and, as part of MBF, activates Pol II transcription of the S-phase regulon in the mitotic cycle and of rec8, rec11, cdc18 and cdc22 in premeiotic S phase (PMID:7909513, PMID:14648198). The activator MF is the correct term and Res2 in its own WITH list reflects experimental grounding on the target, not circularity. Supporting Evidence: PMID:11781565 The Mlu1-binding factor (MBF) from the fission yeast Schizosaccharomyces pombe contains the proteins Res1p and Res2p and binds to the Mlu1 cell-cycle box (MCB) element in DNA, activating the transcription of genes required for S phase. PMID:7909513 This induction is lost in res2- cells, whereas the poly(A)+ transcript is significantly reduced in res1- cells. |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learned rule assigning the Pol II activator MF; it reproduces the experimentally established function. Reason: Matches the EXP, IMP and IBA rows for the same term; correct level of specificity for an electronic annotation. Supporting Evidence: PMID:11781565 The Mlu1-binding factor (MBF) from the fission yeast Schizosaccharomyces pombe contains the proteins Res1p and Res2p and binds to the Mlu1 cell-cycle box (MCB) element in DNA, activating the transcription of genes required for S phase. |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IMP PMID:7909513 A B-type cyclin negatively regulates conjugation via interac... | ACCEPT | Summary: Obara-Ishihara and Okayama 1994 (abstract-only cache): the B-type cyclin cyc17 (cig2) is transcribed as a vegetative poly(A)+ RNA and a conjugation-induced poly(A)- RNA; the conjugation-specific induction is lost in res2 cells whereas the vegetative transcript is reduced in res1 cells, and the mating inhibition and pat1 rescue caused by res2+ overexpression require cyc17+. Reason: Loss of a specific MCB-promoter-driven Pol II transcript (cyc17/cig2) in res2 mutant cells, together with the dependence of res2+ overexpression phenotypes on that target, is IMP evidence for Res2 acting as a DNA-binding activator of the cig2 promoter, consistent with the MBF dependence of cig2 transcription (PMID:11781565). Core function. Supporting Evidence: PMID:7909513 This induction is lost in res2- cells, whereas the poly(A)+ transcript is significantly reduced in res1- cells. PMID:7909513 However, the mating inhibition as well as the ability to rescue the pat1 mutation by overexpression of res1+ and res2+ are totally abolished in cyc17- cells. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the APSES-type HTH DNA-binding domain superfamily (IPR036887), which is the Res2 N-terminal MCB-recognition domain (UniProt DOMAIN 8-115, H-T-H motif 39-60). Reason: Correct but generic; unlike Cdc10, Res2 genuinely carries the DNA-binding activity of MBF in its N-terminal region (PMID:24006488), so the domain-level inference is true. The specific activity (GO:0000978, sequence-specific binding of MCB cis-regulatory elements) is carried by the IDA, HDA and IBA rows. Acceptable as a domain-level electronic annotation. Supporting Evidence: PMID:24006488 Res2, which contains the DNA-binding activity of the MBF complex in its amino-terminal region |
| GO:0005515 protein binding | IPI PMID:11781565 Feedback regulation of the MBF transcription factor by cycli... | MODIFY | Summary: Interaction with the S-phase B-type cyclin Cig2 (PomBase:SPAPB2B4.03) from Ayte et al. 2001 (abstract-only cache): cig2 is an MBF target, deletion of its MCB elements perturbs other MBF-dependent genes, and Cig2p binds Res2p, promotes phosphorylation of Res1p and inhibits MBF-dependent transcription, closing a feedback-inhibition loop. Reason: Generic protein binding is uninformative. The abstract explicitly attributes the direct cyclin contact to Res2, and the Res2-Cig2 interaction is the mechanism by which Cig2-Cdc2 feeds back on MBF, so GO:0030332 cyclin binding is the evidence-backed informative MF. The functional consequence (repression of MBF-dependent transcription after G1/S) is captured by the GO:0000122 and GO:0001227 rows. Proposed replacements: cyclin binding Supporting Evidence: PMID:11781565 Cig2p can bind to Res2p, promote the phosphorylation of Res1p and inhibit MBF-dependent gene transcription. PMID:11781565 Cig2p thus forms an autoregulating feedback-inhibition loop with MBF which is important for normal regulation of the cell cycle. |
| GO:0005515 protein binding | IPI PMID:11781565 Feedback regulation of the MBF transcription factor by cycli... | MODIFY | Summary: Interaction with Cdc10 (PomBase:SPBC336.12c) from Ayte et al. 2001 (abstract-only cache), the paper establishing the Cig2 feedback loop on MBF. Res2 associates with the shared subunit Cdc10 to form the MCB-binding heteromer (PMID:7926774), and the Cdc10-Res2 interaction is stable even when the complex is evicted from chromatin (PMID:24006488). Reason: Generic protein binding is uninformative. The Res2-Cdc10 association is the obligate heterodimeric unit of active MBF (Cdc10 strongly enhances the otherwise weak DNA binding of Res2), so GO:0046982 protein heterodimerization activity is the informative MF term, following the treatment of the Res1-Cdc10, Mbp1-Swi6 and Swi4-Swi6 pairs in the res1, MBP1 and SWI4 reviews; complex membership is separately captured by the GO:0030907 rows. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:11781565 The Mlu1-binding factor (MBF) from the fission yeast Schizosaccharomyces pombe contains the proteins Res1p and Res2p and binds to the Mlu1 cell-cycle box (MCB) element in DNA, activating the transcription of genes required for S phase. PMID:7926774 We report the cloning of a new gene, pct1+, encoding a 73-kD protein that interacts with p85cdc10 to form an MCB-binding heteromer. PMID:24006488 As shown in Figure 2B, the interaction between Cdc10 and Res2 was well preserved, if not improved, after treating fission yeast cells with MMS. |
| GO:0005515 protein binding | IPI PMID:11781565 Feedback regulation of the MBF transcription factor by cycli... | MODIFY | Summary: Interaction with the paralogous DNA-binding subunit Res1 (PomBase:SPBC725.16) from Ayte et al. 2001 (abstract-only cache). Res1 and Res2 together form the heterodimeric DNA-binding domain of the vegetative MBF complex (PMID:24006488). Reason: Generic protein binding is uninformative. The Res1-Res2 association is the heterodimeric DNA-binding unit of MBF, so GO:0046982 protein heterodimerization activity is the informative MF, mirroring the reciprocal rows in the res1 review; complex membership is separately captured by the GO:0030907 rows. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:11781565 The Mlu1-binding factor (MBF) from the fission yeast Schizosaccharomyces pombe contains the proteins Res1p and Res2p and binds to the Mlu1 cell-cycle box (MCB) element in DNA, activating the transcription of genes required for S phase. PMID:24006488 Res1 and Res2, which form a heterodimeric DNA-binding domain |
| GO:0005515 protein binding | IPI PMID:11781565 Feedback regulation of the MBF transcription factor by cycli... | MODIFY | Summary: IntAct-derived duplicate of the Res2-Cdc10 interaction (UniProtKB:P01129 is Cdc10) from Ayte et al. 2001; same evidence as the PomBase:SPBC336.12c row. Reason: As for the PomBase-sourced row: the Res2-Cdc10 pair is the obligate heterodimeric unit of active MBF, so GO:0046982 protein heterodimerization activity is the informative replacement for generic protein binding; complex membership is captured by the GO:0030907 rows. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:7926774 We report the cloning of a new gene, pct1+, encoding a 73-kD protein that interacts with p85cdc10 to form an MCB-binding heteromer. file:SCHPO/res2/res2-deep-research-falcon.md Full-length Res2 binds DNA only weakly by itself; Cdc10 strongly enhances binding. |
| GO:0005515 protein binding | IPI PMID:11781565 Feedback regulation of the MBF transcription factor by cycli... | MODIFY | Summary: IntAct-derived duplicate of the Res2-Res1 interaction (UniProtKB:P33520 is Res1) from Ayte et al. 2001; same evidence as the PomBase:SPBC725.16 row. Reason: As for the PomBase-sourced row: Res1 and Res2 form the heterodimeric DNA-binding domain of MBF (PMID:24006488), so GO:0046982 protein heterodimerization activity is the informative replacement for generic protein binding. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:24006488 Res1 and Res2, which form a heterodimeric DNA-binding domain |
| GO:0005515 protein binding | IPI PMID:11781565 Feedback regulation of the MBF transcription factor by cycli... | MODIFY | Summary: IntAct-derived duplicate of the Res2-Cig2 interaction (UniProtKB:P36630 is the cyclin Cig2) from Ayte et al. 2001; same evidence as the PomBase:SPAPB2B4.03 row. Reason: As for the PomBase-sourced row: the abstract attributes direct cyclin binding to Res2, so GO:0030332 cyclin binding is the evidence-backed informative MF replacing generic protein binding. Proposed replacements: cyclin binding Supporting Evidence: PMID:11781565 Cig2p can bind to Res2p, promote the phosphorylation of Res1p and inhibit MBF-dependent gene transcription. |
| GO:0005515 protein binding | IPI PMID:18682565 DNA replication checkpoint promotes G1-S transcription by in... | MODIFY | Summary: Interaction with Nrm1 (UniProtKB:O42913) from de Bruin et al. 2008 (abstract and discussion cached): Nrm1 is the MBF-specific corepressor that represses MBF-dependent G1/S transcription at the end of G1 and is phosphorylated by Cds1 under replication stress, which releases it from MBF. The cached text does not describe the Res2-Nrm1 assay, so the specific evidence is deferred to the curator; that Nrm1/Yox1 repress MBF by interacting with Res2 is stated explicitly in later work (PMID:30635289). Reason: Generic protein binding is uninformative. Nrm1 is a transcription corepressor of MBF and Res2 is the subunit it docks on to switch the complex off, so GO:0001222 transcription corepressor binding is the informative MF; the functional output is captured by the GO:0000122 and GO:0001227 rows. Removal is not appropriate because the cited paper does support a specific function for this interaction. Proposed replacements: transcription corepressor binding Supporting Evidence: PMID:18682565 Nrm1, a corepressor of MBF dependent G 1 -S transcription, is a target of the DNA replication checkpoint kinase Cds1 PMID:30635289 Nrm1 and Yox1 are known to form a dimer that suppresses the transcriptional activity of the MBF complex outside of G1 by interacting with Res2 |
| GO:0005515 protein binding | IPI PMID:21132016 Yox1 links MBF-dependent transcription to completion of DNA ... | MODIFY | Summary: Interaction with Cdc10 (UniProtKB:P01129) from Gomez-Escoda et al. 2011 (full text cached): immunoprecipitation of chromosomally HA-tagged Cdc10 followed by iTRAQ LC-MS/MS recovers Cdc10, Res1 and Res2 as the most enriched proteins together with the repressor Yox1, whose binding to Cdc10 requires Res1 and Res2. Reason: Generic protein binding is uninformative. The recovered Res2-Cdc10 association is the obligate heterodimeric unit of MBF, so GO:0046982 protein heterodimerization activity is the informative MF, as for the other Res2-Cdc10 rows; complex membership is separately captured by the GO:0030907 rows. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:21132016 The most enriched proteins in the purification were Cdc10, Res1, Res2, as expected PMID:21132016 in the absence of Res1 or Res2, Yox1 was not able to bind to Cdc10 |
| GO:0005515 protein binding | IPI PMID:7588609 Fission yeast Rep2 is a putative transcriptional activator s... | MODIFY | Summary: Interaction with the zinc-finger protein Rep2 (PomBase:SPBC2F12.11c) from Nakashima et al. 1995 (abstract-only cache): rep2+ was isolated as a multicopy suppressor of a cdc10-ts mutant, Rep2 is an essential component of the active Res2-Cdc10 complex, and the data indicate that it is a transcriptional activator subunit that interacts with the MCB-binding subunit complex formed by Res2 and Cdc10. Reason: Generic protein binding is uninformative. The cited paper characterises Rep2 as the coactivator subunit recruited by the Res2-Cdc10 DNA-binding unit, so GO:0001223 transcription coactivator binding is the evidence-backed informative MF for Res2 in this interaction; the transcriptional output is captured by the GO:0001228 and GO:0045944 rows. Proposed replacements: transcription coactivator binding Supporting Evidence: PMID:7588609 Our data suggest that Rep2 is a transcriptional activator subunit which interacts with the MCB binding subunit complex formed by Res2 and Cdc10. PMID:7588609 Here we show that the Rep2 zinc finger protein is an essential component of the active Res2-Cdc10 transcriptional regulator complex and likely to play a role in the control of cell cycle 'start'. |
| GO:0005515 protein binding | IPI PMID:7588609 Fission yeast Rep2 is a putative transcriptional activator s... | MODIFY | Summary: Interaction with Cdc10 (PomBase:SPBC336.12c) from Nakashima et al. 1995 (abstract-only cache), which describes the MCB-binding subunit complex formed by Res2 and Cdc10 as the platform on which the activator subunit Rep2 acts. Reason: Generic protein binding is uninformative. The Res2-Cdc10 pair is the obligate heterodimeric MCB-binding unit of MBF, so GO:0046982 protein heterodimerization activity is the informative MF, as for the other Res2-Cdc10 rows. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:7588609 Our data suggest that Rep2 is a transcriptional activator subunit which interacts with the MCB binding subunit complex formed by Res2 and Cdc10. PMID:7926774 We report the cloning of a new gene, pct1+, encoding a 73-kD protein that interacts with p85cdc10 to form an MCB-binding heteromer. |
| GO:0005515 protein binding | IPI PMID:7926774 pct1+, which encodes a new DNA-binding partner of p85cdc10, ... | MODIFY | Summary: Interaction with Cdc10 (PomBase:SPBC336.12c) from Zhu, Takeda, Nasmyth and Jones 1994 (abstract-only cache): pct1+ (res2+) encodes a 73 kDa protein that interacts with p85cdc10 to form an MCB-binding heteromer, and pct1+ overexpression rescues the cdc10-129 ts mutant but not a cdc10 null. Reason: Generic protein binding is uninformative. This is the discovery of the Res2-Cdc10 heteromer, the obligate DNA-binding unit of the second MBF form, so GO:0046982 protein heterodimerization activity is the informative MF term; the inability of pct1+ to bypass a cdc10 null shows that the heterodimer, not Res2 alone, is the functional unit. Complex membership is separately captured by the GO:0030907 rows. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:7926774 We report the cloning of a new gene, pct1+, encoding a 73-kD protein that interacts with p85cdc10 to form an MCB-binding heteromer. PMID:7926774 Overexpression of pct1+ is sufficient to rescue the growth of the cdc10-129 temperature-sensitive mutant at the restrictive temperature, although it is unable to rescue a cdc10 null mutation. |
| GO:0005634 nucleus | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: Matsuyama et al. 2006 (abstract-only cache): ORFeome-wide localization of 4,431 YFP-tagged fission yeast proteins; Res2 is not named in the abstract and the nucleus row rests on the dataset. Reason: Consistent with the site of the core function: Res2 occupies the promoter chromatin of cdc22, cdc18 and cnp1 by ChIP (PMID:24006488, PMID:30635289) and genome-wide ChIP-chip places tagged Res2 at MBF-associated loci. The nucleus is where the transcription function is exerted. Supporting Evidence: PMID:16823372 Next, we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome, by tagging each ORF with the yellow fluorescent protein. file:SCHPO/res2/res2-deep-research-falcon.md Res2 acts primarily in the **nucleus on chromatin**, in complexes containing Cdc10 and Res1 during vegetative growth and a Res2βCdc10-centered complex during meiotic differentiation. |
| GO:0005737 cytoplasm | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | KEEP AS NON CORE | Summary: Matsuyama et al. 2006 (abstract-only cache): proteome-wide localization of 4,431 C-terminally YFP-tagged ORFeome clones expressed from a plasmid; the Res2-YFP image was scored as including cytoplasmic signal. Reason: A single high-throughput observation from an over-expressed tagged construct. Res2 acts on promoter chromatin in the nucleus (PMID:24006488, PMID:30635289), MBF stays bound to its target promoters through the cell cycle so that its activity is regulated by corepressor loading rather than by relocalisation (PMID:21132016), and no regulated nucleocytoplasmic shuttling of the kind shown for budding yeast Swi6 has been reported for Res2. Retained as a non-core location, as for the equivalent Cdc10 row. Supporting Evidence: PMID:16823372 Next, we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome, by tagging each ORF with the yellow fluorescent protein. PMID:21132016 MBF is bound to its target promoters throughout the cell cycle ( Wuarin et al, 2002 ), suggesting that MBF activity is not due to modulation of its DNA-binding activity. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | REMOVE | Summary: PAINT inference of a cytoplasmic site of activity at the APSES-family node, seeded by a single donor, budding yeast Swi6 (SGD:S000004172). Swi6 genuinely cycles between nucleus and cytoplasm through cell-cycle-regulated nuclear import and export, but the DNA-binding subunits do not: Res2 acts on promoter chromatin (PMID:24006488, PMID:30635289), and no cytoplasmic activity of Res2 has been described. Reason: Over-propagated IBA argued against on target-specific grounds, exactly as for Res1, Cdc10, Swi4 and Mbp1 in the sibling reviews. The cytoplasmic localization is a Swi6-specific regulatory property of the shared activator subunit, not a property of the DNA-binding subunits, and even for Swi6 the cytoplasm is where the inactive, exported pool resides, so "is_active_in cytoplasm" is not the right claim at this node; for Res2 it is contradicted by its promoter occupancy through the cell cycle (PMID:21132016) and by the absence of any reported cytoplasmic function. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000917496 SUPPORTS SOURCE BUT NOT TARGET Family node grouping the DNA-binding subunits (Swi4, Mbp1, Res1, Res2) with the regulatory subunits (Swi6, Cdc10); the cytoplasm evidence belongs only to the Swi6 branch. SGD:S000004172 Β· SWI6 SUPPORTS SOURCE BUT NOT TARGET Swi6 is cytoplasmic in S/G2/M because of regulated nuclear transport; Res2 is chromatin-bound by ChIP and MBF stays promoter-bound through the cell cycle. Supporting Evidence: PMID:24006488 Loading of Res1 (left) or Res2 (right) on cdc22 and cdc18 promoters was measured by ChIP analysis of chromatin extracts isolated from untreated or MMS-treated PMID:21132016 MBF is bound to its target promoters throughout the cell cycle ( Wuarin et al, 2002 ), suggesting that MBF activity is not due to modulation of its DNA-binding activity. file:SCHPO/res2/res2-deep-research-falcon.md Res2 acts primarily in the **nucleus on chromatin**, in complexes containing Cdc10 and Res1 during vegetative growth and a Res2βCdc10-centered complex during meiotic differentiation. |
| GO:0005829 cytosol | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | KEEP AS NON CORE | Summary: Matsuyama et al. 2006 (abstract-only cache): the same ORFeome YFP-localization dataset as the cytoplasm and nucleus HDA rows, with the diffuse cytoplasmic signal of the over-expressed Res2-YFP fusion scored as cytosol. Reason: Same single high-throughput observation as the cytoplasm HDA row. Res2 functions on nuclear promoter chromatin as part of a complex that remains promoter-bound through the cell cycle (PMID:24006488, PMID:21132016); a cytosolic pool, if real, is not where the transcription function is exerted. Retained as a non-core location. Supporting Evidence: PMID:16823372 Next, we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome, by tagging each ORF with the yellow fluorescent protein. PMID:24006488 both Res1 and Res2 are released from chromatin after treatment with MMS |
| GO:0006357 regulation of transcription by RNA polymerase II | IDA PMID:8168485 res2+, a new member of the cdc10+/SWI4 family, controls the ... | MODIFY | Summary: Miyamoto, Tanaka and Okayama 1994 (abstract-only cache), the founding res2 paper: res2+ was cloned as a multicopy suppressor of a res1 null mutant, encodes a 73 kDa Swi/ankyrin-motif protein most similar to Res1, is largely redundant with res1+ and required for the initiation of mitotic and premeiotic DNA synthesis, is highly induced during conjugation, depends on cdc10+ for its activity, and with Cdc10 forms the second of two parallel Start systems that regulate S-phase-specific genes. Reason: The essence is sound but the term is too general. The direction of the effect established here and in the companion paper is positive: Res2-Cdc10 is a Start transcription system required to initiate DNA synthesis, and res2 loss abolishes the conjugation-specific induction of cig2 (PMID:7909513) and impairs meiotic MCB-driven transcription (PMID:14648198). GO:0045944 positive regulation of transcription by RNA polymerase II is the correct specific term for this evidence (the separate repressive role of Res2 in G2 is carried by the GO:0000122 rows from other papers). Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:8168485 They encode structurally related transcriptional complex proteins and regulate some S phase-specific genes. PMID:8168485 res2+ is largely redundant in function with res1+ and is required for the initiation of mitotic and premeiotic DNA synthesis, but has an additional role in meiotic division. PMID:7909513 This induction is lost in res2- cells, whereas the poly(A)+ transcript is significantly reduced in res1- cells. |
| GO:0030907 MBF transcription complex | EXP PMID:9303312 Control of S-phase periodic transcription in the fission yea... | ACCEPT | Summary: Baum, Wuarin and Nurse 1997 (abstract-only cache): res2p analysed as one of the components of the S-phase transcriptional machinery; the in vitro DSC1 (MBF) bandshift activity requires res2p, and res2p represses transcription in G2 as part of the DSC1 complex. Reason: Res2 is a core subunit of MBF/DSC1 together with Cdc10 and Res1 (PMID:11781565, PMID:21132016, PMID:24006488) and the DSC1 bandshift depends on it. Correct complex term; core function. Supporting Evidence: PMID:9303312 We show that the presence of the in vitro bandshift activity DSC1, conventionally thought to represent the active complex, requires res2p and correlates with inactive transcription. PMID:11781565 The Mlu1-binding factor (MBF) from the fission yeast Schizosaccharomyces pombe contains the proteins Res1p and Res2p and binds to the Mlu1 cell-cycle box (MCB) element in DNA, activating the transcription of genes required for S phase. |
| GO:0030907 MBF transcription complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the APSES-family node, seeded by the three S. pombe MBF subunits (including Res2 itself, SPAC22F3.09c, which is expected) and by budding yeast Mbp1 and Swi6. The node also propagates MBF membership to Swi4, which is a genuine problem for the budding yeast SBF subunit, but for Res2 the inference simply restates its own experimental complex membership. Reason: Res2 is an experimentally established core subunit of the fission yeast MBF complex (PMID:11781565, PMID:21132016, PMID:24006488); the target appearing in its own WITH list is expected and reflects experimental grounding on Res2 itself. Supporting Evidence: PMID:21132016 The most enriched proteins in the purification were Cdc10, Res1, Res2, as expected PMID:24006488 Res1 and Res2, which form a heterodimeric DNA-binding domain |
| GO:0030907 MBF transcription complex | IDA PMID:24006488 The DNA damage and the DNA replication checkpoints converge ... | ACCEPT | Summary: Ivanova et al. 2013 (full text cached): the MBF core is described as Cdc10 with Res1 and Res2 forming a heterodimeric DNA-binding domain; Res2 co-immunoprecipitates with Cdc10-HA before and after MMS treatment, and the Res1-Res2-Cdc10 core is released from chromatin as a complex when the DNA damage checkpoint is activated. Reason: Direct co-immunoprecipitation and co-behaviour evidence that Res2 is a stable component of the MBF complex. Correct complex term; core function. Supporting Evidence: PMID:24006488 As shown in Figure 2B, the interaction between Cdc10 and Res2 was well preserved, if not improved, after treating fission yeast cells with MMS. PMID:24006488 Res1 and Res2, which form a heterodimeric DNA-binding domain |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the APSES-family node, seeded by every experimentally characterised member of the family, including Res2 itself (SPAC22F3.09c, expected), the other pombe MBF subunits, the budding yeast SBF/MBF subunits, the C. albicans orthologs and the A. nidulans MbpA. All are subunits of G1/S transcriptional activators. Reason: Res2-containing MBF activates Pol II transcription of the S-phase regulon at Start and of the meiotic MCB genes in premeiotic S phase (PMID:7909513, PMID:14648198, PMID:11781565). Correct term and node; core function. Supporting Evidence: PMID:11781565 The Mlu1-binding factor (MBF) from the fission yeast Schizosaccharomyces pombe contains the proteins Res1p and Res2p and binds to the Mlu1 cell-cycle box (MCB) element in DNA, activating the transcription of genes required for S phase. PMID:14648198 We found that cdc10+, res2+, rep1+ and rep2+ are required for correct meiotic transcription, while res1+ is not required for this process. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:7909513 A B-type cyclin negatively regulates conjugation via interac... | ACCEPT | Summary: Obara-Ishihara and Okayama 1994 (abstract-only cache): the conjugation-induced poly(A)- cyc17 (cig2) transcript is lost in res2 mutant cells, and the mating inhibition and pat1 rescue produced by res2+ overexpression depend on cyc17+. Reason: Loss of induction of a specific Pol II target transcript in res2 cells is direct IMP evidence for positive regulation of Pol II transcription by Res2, matching the MBF dependence of cig2 (PMID:11781565). Core function. Supporting Evidence: PMID:7909513 This induction is lost in res2- cells, whereas the poly(A)+ transcript is significantly reduced in res1- cells. PMID:7909513 On the other hand, the poly(A)- transcript is highly induced during conjugation. |
| GO:0051445 regulation of meiotic cell cycle | IMP PMID:7926774 pct1+, which encodes a new DNA-binding partner of p85cdc10, ... | MODIFY | Summary: Zhu, Takeda, Nasmyth and Jones 1994 (abstract-only cache): deletion of pct1+ (res2+) is not lethal but results in a severe meiotic defect, leading the authors to propose that the two Cdc10-containing MCB-binding complexes play differential roles in mitotic division and meiosis. The companion paper shows res2+ is required for the initiation of premeiotic DNA synthesis and has an additional role in meiotic division (PMID:8168485), and later work shows Res2 (not Res1) is required for meiotic MCB-driven transcription (PMID:14648198). Reason: The essence is sound but the term is too general: the direction is clearly positive, since loss of res2 blocks premeiotic S phase and meiotic progression and res2+ is the MBF subunit that drives the premeiotic transcription of rec8, rec11, cdc18 and cdc22. GO:0051446 positive regulation of meiotic cell cycle is the correct specific term for this IMP evidence. Res2 does the work of this regulation as a transcription factor (activating the meiotic MCB regulon), so a regulation term rather than a meiosis-process term is appropriate. Proposed replacements: positive regulation of meiotic cell cycle Supporting Evidence: PMID:7926774 A deletion of pct1+ is not lethal but does result in a severe meiotic defect. PMID:8168485 res2+ is largely redundant in function with res1+ and is required for the initiation of mitotic and premeiotic DNA synthesis, but has an additional role in meiotic division. PMID:14648198 We found that cdc10+, res2+, rep1+ and rep2+ are required for correct meiotic transcription, while res1+ is not required for this process. |
| GO:0090575 RNA polymerase II transcription regulator complex | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA rule placing Res2 in a Pol II transcription regulator complex; GO:0030907 MBF transcription complex is a descendant, so the electronic annotation is a correct generalisation of the experimental complex rows. Reason: True and consistent with the MBF rows; a generic electronic parent of the specific complex term is acceptable. Supporting Evidence: PMID:21132016 The most enriched proteins in the purification were Cdc10, Res1, Res2, as expected |
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Download this section (compressed HTML)Q: Res2 carries both an activator MF (GO:0001228) and a repressor MF (GO:0001227), and genome-wide profiling shows that most MBF targets are derepressed in res2 cells while a few (yox1, cig2, mik1) are not. Is the repressive output of Res2 entirely the result of Nrm1/Yox1 and Cig2 docking on a DNA-bound activator, so that GO:0001227 overstates an intrinsic repressor activity, or does Res2 make a promoter-specific contribution (for example through its ankyrin/central region) that justifies keeping both MF terms?
Suggested experts: Jose Ayte, Robertus A. M. de Bruin
Q: The PAINT node PTN000917496 groups the DNA-binding subunits (Swi4, Mbp1, Res1, Res2) with the shared regulatory subunits (Swi6, Cdc10), so that Res2 receives "is_active_in cytoplasm" from Swi6 and its MCB-binding IBA carries the contributes_to qualifier while the activator IBA uses enables. Should the DNA-binding and regulatory branches be separated so that localization, DNA-binding and complex-identity terms are placed on the correct clade?
Suggested experts: Curt Wittenberg, Nick Rhind
Q: Res2-Cdc10 is required for premeiotic S-phase transcription of rec8, rec11, cdc18 and cdc22, and the older model links Res2 to mat1/mei3 induction upstream of Pat1 inactivation. Which of these meiotic outputs are direct Res2 targets by ChIP in meiotic cells, and should the meiotic role be represented as positive regulation of the meiotic cell cycle, as a meiotic G1/S (premeiotic DNA replication) transcription term, or both?
Suggested experts: Christopher J. McInerny, Hiroto Okayama
Experiment: Perform ChIP-seq of endogenously tagged Res2, Res1, Cdc10, Nrm1 and Yox1 in elutriated wild-type, res2, nrm1 yox1 and cig2 cells across G1, S and G2 combined with nascent transcription (4tU-seq), and map the Res2 surfaces required for Nrm1/Yox1 and Cig2 binding by alanine scanning of the ankyrin/central region. If separation-of-function alleles that lose corepressor or cyclin docking but retain MCB binding derepress the regulon in G2 exactly as res2 deletion does, the repressive role is a docking function and GO:0001227 should be reconsidered in favour of corepressor/cyclin-binding terms.
Hypothesis: Res2 and Res1 occupy overlapping but distinct MCB promoter sets, and the repressive behaviour of Res2 in G2 is entirely conferred by Nrm1/Yox1 and Cig2 docking rather than by an intrinsic repressor activity of the Res2 DNA-binding domain.
Type: ChIP-seq with separation-of-function alleles and nascent transcription readouts
Experiment: Express Res1 from the res2 promoter (and Res2 from the res1 promoter) and APSES domain-swap chimeras in res2 diploids induced to enter meiosis, and score premeiotic S-phase timing, rec8/rec11/cdc18 transcription by RT-qPCR, MCB occupancy by ChIP and spore viability. Rescue by Res1 expressed from the res2 promoter would place the specificity in expression timing; rescue only by chimeras carrying the Res2 APSES domain would place it in DNA recognition or dimerization.
Hypothesis: The meiotic specificity of Res2-Cdc10 is encoded in the Res2 APSES domain and its nitrogen-starvation-induced expression, not in a meiosis-specific partner.
Type: promoter-swap and domain-swap genetics with meiotic transcription and progression readouts
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