id: A0A8B8L1Z3 gene_symbol: A0A8B8L1Z3 product_type: PROTEIN status: DRAFT taxon: id: NCBITaxon:3816 label: Abrus precatorius description: >- A0A8B8L1Z3 (LOC113860185) is a 474-amino-acid protein from Abrus precatorius (Indian licorice). It has an N-terminal J domain (residues 70-135) followed by long low-complexity and disordered regions. It belongs to the plant-specific PTHR45496 family, subfamily SF19. The only Arabidopsis thaliana member of SF19 is At5g64360, which is known as SDJ1, DNAJ1 or EIP9. The Abrus protein is most similar to SDJ1 among Arabidopsis proteins (about 46% identity over its length) and the two have similar lengths. The J domain lacks the His-Pro-Asp (HPD) motif needed to stimulate Hsp70 ATPase activity. SDJ1 also lacks this motif, which argues against a canonical Hsp70 cochaperone role. In Arabidopsis, SDJ1 and its paralogs SDJ2 and SDJ3 are nuclear proteins. They lack DNA-binding domains. The SU(VAR)3-9 homologs SUVH1 and SUVH3, which read DNA methylation, recruit them to methylated euchromatic sites near transposons. There they enhance transcription of nearby genes, counteracting the silencing effect of transposon methylation. By descent, A0A8B8L1Z3 is predicted to be a nuclear transcriptional coactivator of this SUVH-SDJ type. The Abrus protein itself has not been characterized experimentally. references: - id: PMID:31775284 title: "Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of Abrus precatorius" reference_review: relevance: LOW correctness: VERIFIED review_notes: >- Genome-sequencing paper that is the source of the Abrus precatorius gene model, as cited in the UniProt record. It contains no functional information about this protein. Kept as provenance for the sequence. - id: PMID:30523112 title: "A DNA methylation reader complex that enhances gene transcription." reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Harris et al. 2018 (full text cached). Shows that SUVH1 and SUVH3 recruit DNAJ1 (At5g64360, the Arabidopsis PTHR45496:SF19 member and the closest relative of A0A8B8L1Z3) and DNAJ2 to methylated DNA. Tethering DNAJ1 to DNA activated transcription in plants, yeast and mammals. Basis for the predicted coactivator function of A0A8B8L1Z3. - id: PMID:30589221 title: "A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes." reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Zhao et al. 2019 (abstract only in the cache). Defines the SUVH-SDJ complex (SDJ1, SDJ2, SDJ3), shows that its components have transcriptional activation activity, and that they are needed to express promoter-methylated genes. - id: PMID:21700722 title: "EMF1 interacts with EIP1, EIP6 or EIP9 involved in the regulation of flowering time in Arabidopsis." reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Park et al. 2011 (abstract only). EIP9 is the same gene as SDJ1 (At5g64360). The abstract places the EMF1-EIP9 heterodimer in the nucleus and reports altered flowering time in eip9 mutants. The flowering-time result is an organismal phenotype and is not transferred to Abrus. - id: PMID:34185870 title: "Roles of IDM3 and SDJ1/2/3 in Establishment and/or Maintenance of DNA Methylation in Arabidopsis." reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Miao et al. 2021 (abstract only). The sdj1/2/3 triple mutant has reduced DNA methylation at a subset of RdDM targets, and SDJ1 and SDJ3 interact with RDM1 and DMS3. This shows the SDJs are needed for methylation there, but not how they take part, so no RdDM process term is transferred. - id: file:ABRPR/A0A8B8L1Z3/A0A8B8L1Z3-bioinformatics/RESULTS-rereview.md title: "A0A8B8L1Z3 re-review: placement among PTHR45496 relatives" reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Reproducible re-review analysis. Covers PANTHER 19.0 subfamily membership, the PAINT node PTN002896004 seed set, global alignment identities to the Arabidopsis and Populus relatives, and the absence of the HPD motif. - id: file:ABRPR/A0A8B8L1Z3/A0A8B8L1Z3-deep-research-falcon.md title: "Deep research report (falcon) on LOC113860185" reference_review: relevance: LOW correctness: MISCITED review_notes: >- Generic summary of J-domain proteins. It assumes a canonical HPD-dependent Hsp70 cochaperone role and never identifies the SUVH-SDJ relatives. It is no longer used as support for the core function; kept for provenance. existing_annotations: - term: id: GO:0005634 label: nucleus evidence_type: ISS original_reference_id: file:ABRPR/A0A8B8L1Z3/A0A8B8L1Z3-bioinformatics/RESULTS-rereview.md review: summary: >- Proposed nuclear location, inherited from PAINT node PTN002896004 and supported by experimental nuclear localization of the closest Arabidopsis relative EIP9/SDJ1. action: NEW reason: >- GOA has no annotations for A0A8B8L1Z3. Abrus is not one of the PANTHER reference genomes, so it cannot receive IBA rows. PAINT placed nucleus (IBD) at PTN002896004, a flowering-plant node whose descendants include SDJ1 (SF19), SDJ2 (SF1), SDJ3 (SF10) and ADMETOS (SF32). A0A8B8L1Z3 is a flowering-plant SF19 member, so it descends from this node. EIP9/SDJ1 (At5g64360) has a direct nuclear localization result, and the SUVH-SDJ complex works on chromatin. supported_by: - reference_id: file:ABRPR/A0A8B8L1Z3/A0A8B8L1Z3-bioinformatics/RESULTS-rereview.md supporting_text: >- PAINT asserts nucleus (GO:0005634) and GO:0001228 "DNA-binding transcription activator - reference_id: PMID:21700722 supporting_text: >- EMF1-EIP1, EMF1-EIP6 and EMF1-EIP9 heterodimers were localized in the nucleus - term: id: GO:0003713 label: transcription coactivator activity evidence_type: ISS original_reference_id: file:ABRPR/A0A8B8L1Z3/A0A8B8L1Z3-bioinformatics/RESULTS-rereview.md review: summary: >- Proposed transcription coactivator activity, by descent from the SUVH-SDJ J-domain proteins. These proteins activate transcription when methyl-DNA readers recruit them to DNA. action: NEW reason: >- At PTN002896004, PAINT asserts that SDJ-family proteins activate transcription, using GO:0001228 (DNA-binding transcription activator activity, RNA polymerase II-specific). This review keeps that function but uses the coactivator term instead of the DNA-binding transcription factor term, because the evidence points to a recruited coregulator. SDJ1 and SDJ2 have no DNA-binding domain. SUVH1 and SUVH3, which bind methylated DNA, recruit them to DNA, and activation was shown by tethering DNAJ1 artificially to DNA. SDJ2 already carries a direct experimental GO:0003713 annotation (PMID:30589221). This is a refinement of the term that PAINT assigned, not a function that PAINT left out. A0A8B8L1Z3 shares the subfamily of SDJ1/DNAJ1, the protein whose recruitment-dependent activation Harris et al. demonstrated. Confidence is moderate: no Abrus experiment exists. supported_by: - reference_id: PMID:30523112 supporting_text: >- Ectopic recruitment of DNAJ1 enhanced gene transcription in plants, yeast, and mammals. - reference_id: PMID:30523112 supporting_text: >- DNAJ1 and DNAJ2 lack any discernible methyl-binding domain, but they are robustly associated with SUVH1 and SUVH3 - reference_id: PMID:30589221 supporting_text: >- We demonstrate that the SUVH-SDJ complex components have transcriptional activation activity. - reference_id: file:ABRPR/A0A8B8L1Z3/A0A8B8L1Z3-bioinformatics/RESULTS-rereview.md supporting_text: >- The only Arabidopsis thaliana member of PTHR45496:SF19 is Q9FMF3 (At5g64360) core_functions: - description: >- Predicted nuclear transcriptional coactivator of the SUVH-SDJ type. In Arabidopsis, the closest relative SDJ1/DNAJ1 (same PANTHER subfamily, SF19) has no DNA-binding domain. The methyl-DNA readers SUVH1 and SUVH3 recruit it to methylated euchromatin and transposon-proximal sites, where it enhances transcription of nearby genes. The J domain of A0A8B8L1Z3 lacks the HPD motif, so it may not act as a canonical Hsp70 cochaperone. How these proteins activate transcription is unknown. The earlier core function ("protein folding chaperone" in the cytoplasm) was based only on the generic J-domain signature and is withdrawn. molecular_function: id: GO:0003713 label: transcription coactivator activity locations: - id: GO:0005634 label: nucleus directly_involved_in: - id: GO:0045893 label: positive regulation of DNA-templated transcription supported_by: - reference_id: PMID:30523112 supporting_text: >- Thus, the SUVH proteins bind to methylated DNA and recruit the DNAJ proteins to enhance proximal gene expression, thereby counteracting the repressive effects of transposon insertion near genes. - reference_id: file:ABRPR/A0A8B8L1Z3/A0A8B8L1Z3-bioinformatics/RESULTS-rereview.md supporting_text: >- The query's J domain (residues 70-135) has no His-Pro-Asp tripeptide. suggested_questions: - question: >- The PAINT node PTN002896004 is annotated with GO:0001228 (DNA-binding transcription activator activity, RNA polymerase II-specific). SDJ proteins have no DNA-binding domain and are recruited by SUVH1 and SUVH3. Should the node term be transcription coactivator activity (GO:0003713) instead? - question: >- The J domain of SDJ1-type proteins has no HPD motif. Does it still bind any Hsp70? Or has it been repurposed to recruit transcriptional machinery? - question: >- Does the Abrus SF19 protein interact with Abrus SUVH1/SUVH3 orthologs, and does it localize to methylated promoters? suggested_experiments: - hypothesis: >- A0A8B8L1Z3 activates transcription when it is recruited to DNA. description: >- Fuse A0A8B8L1Z3 to the GAL4 DNA-binding domain or a programmable zinc finger, and measure reporter activation in yeast and in Nicotiana benthamiana leaves. Include J-domain deletions as controls. experiment_type: reporter assay - hypothesis: >- A0A8B8L1Z3 is nuclear and forms a complex with Abrus SUVH1/SUVH3 orthologs. description: >- Co-express GFP-tagged A0A8B8L1Z3 with tagged Abrus SUVH1/SUVH3 orthologs in N. benthamiana. Image the proteins by confocal microscopy with a nuclear marker, then perform co-immunoprecipitation. experiment_type: fluorescence microscopy and co-immunoprecipitation