A0A8B6BFL6

UniProt ID: A0A8B6BFL6
Organism: Mytilus galloprovincialis
Review Status: DRAFT
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Gene Description

A0A8B6BFL6 (ORF MGAL_10B073878) is a predicted 612-residue protein of the Mediterranean mussel Mytilus galloprovincialis encoded by a DIRS-type (tyrosine recombinase) retrotransposon. It consists of a reverse transcriptase (RT) domain (residues ~174-349, with an intact YLDD polymerase motif C) followed by a DIRS1-type RNase H domain, preceded by an N-terminal region of unknown function. It belongs to PANTHER subfamily PTHR33050:SF7, together with the RT-RNase H protein encoded by ORF2 of the Dictyostelium DIRS-1 element, which it aligns with across both domains. It also shares more distant similarity with the hepadnavirus polymerases in the same subfamily. In DIRS elements, cDNA synthesis is carried out by the RT-RNase H protein, while integration is carried out by a separately encoded tyrosine recombinase. This protein contains no recombinase domain. Its expected role is therefore reverse transcription of the element RNA (RNA-directed DNA polymerase activity with associated RNase H degradation of the RNA template) during retrotransposition. No experimental characterisation of the mussel protein exists, and it is unknown whether the encoding element is intact or mobile.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003964 RNA-directed DNA polymerase activity
ISS NEW
Summary: NEW: GOA has no annotations for this accession. RT activity is the defining function of the DIRS-type RT-RNase H protein.
Reason: The Pfam RVT_1 domain (174-349) retains the YLDD polymerase motif C. The protein is in PTHR33050:SF7 with the Dictyostelium DIRS-1 ORF2 RT-RNase H and aligns with it across both domains (z=51.7 vs shuffled controls). The DIRS-1 RT is shown genetically to supply cDNA synthesis in trans. Inferred by sequence similarity (ISS) only, with no direct assay.
Supporting Evidence:
file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md
RT motif C (Y-x-D-D): `YLDD` at 300-303, inside the Pfam RVT_1 domain (174-349).
PMID:32170321
indicated that the endogenous DIRS-1 reverse transcriptase can act in trans
GO:0032197 retrotransposition
ISS NEW
Summary: NEW: the RT-RNase H protein performs the cDNA-synthesis step of the element's retrotransposition cycle.
Reason: This is participation, not necessity: the protein catalyses reverse transcription of the element RNA, which is a step of retrotransposition. DNA integration and DNA recombination are deliberately not proposed. In DIRS elements those steps are performed by the separately encoded tyrosine recombinase, and this protein has no similarity to it.
Supporting Evidence:
PMID:32170321
indicated that the endogenous DIRS-1 reverse transcriptase can act in trans
file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md
The target aligns with DIRS-1 ORF2 continuously across both the RT and the RNase H regions

Core Functions

Reverse transcription of the DIRS-type element RNA. The RT domain (with intact YLDD motif C) synthesises cDNA on an RNA template, which is the copying step of the element's retrotransposition cycle. The function is inferred from domain architecture, an intact polymerase motif, and membership of PTHR33050:SF7 alongside the Dictyostelium DIRS-1 ORF2 RT, which element-level genetics shows supplies the RT activity for DIRS-1 mobility. Integration is not assigned to this protein, because DIRS elements perform it with a separately encoded tyrosine recombinase.

Molecular Function:
RNA-directed DNA polymerase activity
Directly Involved In:
retrotransposition
Supporting Evidence:
  • file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-uniprot.txt
    Pfam; PF00078; RVT_1; 1.
  • file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md
    RT motif C (Y-x-D-D): `YLDD` at 300-303, inside the Pfam RVT_1 domain (174-349).
  • PMID:32170321
    indicated that the endogenous DIRS-1 reverse transcriptase can act in trans

RNase H degradation of the RNA strand of the RNA-DNA hybrids formed during reverse transcription. This is inferred from the DIRS1-type RNase H domain (CDD cd09275), which aligns with the RNase H region of DIRS-1 ORF2 and has a candidate first catalytic carboxylate. It is weaker than the RT inference, because the catalytic DEDD set has not been mapped residue by residue.

Molecular Function:
RNA-DNA hybrid ribonuclease activity
Directly Involved In:
retrotransposition
Supporting Evidence:
  • file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-uniprot.txt
    CDD; cd09275; RNase_HI_RT_DIRS1; 1.
  • PMID:32170321
    These comprise, next to the name-giving YR, a putative GAG protein (GAG), a reverse transcriptase (RT) and an RNase H (RH).

References

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Suggested Questions for Experts

Q: Is this protein encoded by an intact DIRS-type element (with GAG and tyrosine recombinase ORFs and inverted terminal repeats at the locus), or by a degraded copy?

Q: Should DIRS-type RT-RNase H proteins be separated from hepadnavirus polymerases at the subfamily level in PANTHER, given that PTHR33050:SF7 currently groups them together?

Q: Is there evidence of recent retrotransposition activity for this element in the M. galloprovincialis population, such as polymorphic insertions?

Suggested Experiments

Experiment: Express and purify the RT-RNase H region and test RNA-dependent DNA polymerase and RNase H activities in vitro (primer extension on an RNA template; cleavage of a labelled RNA-DNA hybrid), with a YLDD-to-YLAA mutant as a control.

Experiment: Perform RNA-seq across tissues and developmental stages to determine whether the encoding retrotransposon is transcriptionally active.

Experiment: Annotate the genomic locus to test for companion GAG and tyrosine recombinase ORFs, and build a phylogeny of the RT domain with classified DIRS, PAT, Ngaro and VIPER elements.

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.

ProtNLM2 External predictions

View prediction review YAML · A0A8B6BFL6-protnlm-predictions-review.yaml · Review status: COMPLETE

A0A8B6BFL6 is the RT-RNase H protein of a DIRS-type (tyrosine recombinase) retrotransposon in Mytilus galloprovincialis. It has a reverse-transcriptase domain (174-349) with an intact YLDD motif C and a DIRS1-type RNase H domain, and it aligns with the Dictyostelium DIRS-1 ORF2 RT-RNase H in PANTHER PTHR33050:SF7. GOA carries no annotations for this accession. The DNA binding prediction is a correct but broad consequence of reverse transcription on a DNA primer (COR). The DNA recombination and DNA integration predictions are unresolved (UNC): in DIRS elements the strand-exchange step that integrates the cDNA is attributed to the separately encoded tyrosine recombinase, and this protein has no recombinase or integrase domain and no similarity to the DIRS-1 recombinase, but an accessory role of the RT-RNase H protein in preparing or delivering the integration substrate is neither shown nor excluded. Its established process role is reverse transcription within retrotransposition.

Source documents: genes/MYTGA/A0A8B6BFL6/A0A8B6BFL6-uniprot.txt · genes/MYTGA/A0A8B6BFL6/A0A8B6BFL6-goa.tsv · genes/MYTGA/A0A8B6BFL6/A0A8B6BFL6-ai-review.yaml · genes/MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md · interpro/panther/PTHR33050/PTHR33050-review.yaml · publications/PMID_32170321.md · publications/PMID_26104693.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0003677 DNA binding GO_MF
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: GOA has no annotations for this accession, so the term is novel. The protein has a Pfam RVT_1 reverse-transcriptase domain (174-349) with an intact YLDD motif C and aligns continuously with the Dictyostelium DIRS-1 ORF2 RT-RNase H in the same PANTHER subfamily (PTHR33050:SF7), whose RT is shown genetically to supply cDNA synthesis for DIRS-1 retrotransposition. RNA-directed DNA polymerase activity extends a DNA primer strand on an RNA template, so DNA engagement is an inherent part of the inferred catalysis. GO:0003677 is not an ancestor of GO:0003964 RNA-directed DNA polymerase activity (OLS4), so LSP does not apply, although DNA binding is a minimally informative description of an enzyme whose DNA contact is with its own substrate. The support is a family transfer with an intact motif, not an assay of the mussel protein.
Supporting Evidence:
GO:0006310 DNA recombination GO_BP
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: GOA has no annotations for this accession. The recombination step of DIRS-type elements is the site-specific recombination by which the element-encoded tyrosine recombinase (YR) integrates the circular cDNA intermediate. In DIRS-1 the YR is a separate ORF from the RT-RNase H protein, and A0A8B6BFL6 has no recombinase domain and no detectable similarity to the DIRS-1 YR (z = -0.7 against shuffled controls), so it cannot perform the strand-exchange chemistry. That does not refute participation in the process: the protein makes the cDNA that is recombined, the enzyme that converts the single-stranded circle to the double-stranded recombination substrate has not been identified, and a scaffolding or binding contribution to a YR-containing complex has neither been shown nor excluded. With no positive refutation and no evidence of participation, the prediction is uncertain. The gene review assigns this protein to reverse transcription within retrotransposition and does not annotate DNA recombination.
Supporting Evidence:
  • PMID:26104693: "Site-specific recombination is believed to integrate the circle without creating duplications of the target sites."
  • PMID:32170321: "These comprise, next to the name-giving YR, a putative GAG protein (GAG), a reverse transcriptase (RT) and an RNase H (RH)."
  • PMID:32170321: "The resulting single-stranded circular DNA would then be converted to a double-stranded circular DNA, which would be ready to be incorporated into the genome by means of the DIRS-1-encoded YR activity."
  • file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md: "The target has no detectable similarity to the DIRS-1 tyrosine recombinase."
GO:0015074 DNA integration GO_BP
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: GOA has no annotations for this accession. DIRS-type elements are defined by a tyrosine recombinase in place of an integrase or endonuclease, and that recombinase mediates genomic integration of the element. A0A8B6BFL6 is the RT-RNase H protein: it has no integrase or recombinase domain and does not align with the DIRS-1 tyrosine recombinase, so it does not catalyse the joining step. The RT generates the cDNA that is integrated, which establishes necessity rather than participation. An accessory role, such as completing the double-stranded circular substrate or acting in a pre-integration complex with the recombinase, has not been tested in any DIRS element and is not excluded by the sequence. The prediction therefore rests on missing evidence rather than refutation and is uncertain. The gene review assigns this protein to retrotransposition through reverse transcription and does not annotate DNA integration.
Supporting Evidence:
  • PMID:32170321: "As this name suggests, the group is characterized by the presence of tyrosine recombinases instead of an integrase (INT) or endonuclease (13,14). Usually, these enzymes mediate site-specific genomic integration of retrotransposons (15)."
  • PMID:32170321: "The resulting single-stranded circular DNA would then be converted to a double-stranded circular DNA, which would be ready to be incorporated into the genome by means of the DIRS-1-encoded YR activity."
  • file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md: "Because DIRS elements encode the YR as a separate ORF, this protein is not expected to carry recombinase or integration activity itself."

Deep Research

Falcon

(A0A8B6BFL6-deep-research-falcon.md)

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📚 Additional Documentation

Notes

(A0A8B6BFL6-notes.md)

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📄 View Raw YAML

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