A0A1S3Y076

UniProt ID: A0A1S3Y076
Organism: Nicotiana tabacum
Review Status: DRAFT
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Gene Description

A0A1S3Y076 encodes a proteinaceous RNase P (PRORP) in Nicotiana tabacum (common tobacco). PRORP enzymes are single-subunit, protein-only ribonuclease P endonucleases that catalyze the removal of 5-prime leader sequences from precursor tRNAs (EC 3.1.26.5). The protein belongs to the pentatricopeptide repeat (PPR) family, P subfamily, and contains an N-terminal PPR domain for RNA substrate recognition, a central zinc-binding domain, and a C-terminal NYN metallonuclease domain that houses the catalytic active site. Catalysis requires Mg2+ as a cofactor. In the model plant Arabidopsis thaliana, three PRORP paralogs show differential localization: PRORP1 is dual-targeted to chloroplasts and mitochondria, while PRORP2 and PRORP3 localize to the nucleus. Based on domain architecture and phylogenetic placement, this tobacco protein is an ortholog of the Arabidopsis PRORP family. PRORP-mediated tRNA 5-prime maturation is essential for organellar and nuclear translation, and loss of organellar PRORP1 in Arabidopsis causes embryonic lethality. Plants are unique among eukaryotes in having completely replaced the ancestral ribonucleoprotein RNase P with protein-only PRORP enzymes across all cellular compartments.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004526 ribonuclease P activity
IBA
GO_REF:0000033 		ACCEPT
Summary: IBA annotation based on phylogenetic inference from characterized PRORP orthologs including Arabidopsis PRORP1 (AT2G16650), PRORP2 (AT2G32230), PRORP3 (AT4G21900), Drosophila FBgn0029858, and human KIAA0391 (O15091). The tobacco protein has the canonical PRORP domain architecture (PPR + NYN metallonuclease) and belongs to the same PANTHER family (PTHR13547). PRORP proteins have been experimentally demonstrated to catalyze RNase P activity in vitro, cleaving pre-tRNAs at the correct position. This is the core molecular function of the protein.
Reason: Ribonuclease P activity is the defining molecular function of PRORP enzymes. The phylogenetic inference is well supported by the conserved domain architecture and extensive biochemical characterization of plant PRORP orthologs in Arabidopsis, which demonstrated authentic RNase P cleavage activity with Michaelis-Menten parameters comparable to ribonucleoprotein RNase P.
Supporting Evidence:
file:TOBAC/A0A1S3Y076/A0A1S3Y076-deep-research-falcon.md
[Gutmann et al. 2012 demonstrated that] Arabidopsis PRORP proteins support RNase P activity in both organelles and the nucleus
GO_REF:0000033
[IBA with/from includes] AGI_LocusCode:AT2G16650, AT2G32230, AT4G21900, FB:FBgn0029858, UniProtKB:O15091
GO:0001682 tRNA 5'-leader removal
IBA
GO_REF:0000033 		ACCEPT
Summary: IBA annotation for tRNA 5-prime leader removal, the biological process directly catalyzed by RNase P. This is the essential first step in tRNA maturation, producing mature 5-prime ends required for functional tRNA molecules. The phylogenetic inference is based on Arabidopsis PRORP1/2/3 orthologs, all of which have been experimentally shown to cleave pre-tRNAs at the canonical RNase P site.
Reason: tRNA 5-prime leader removal is the direct biological process carried out by RNase P enzymes. This is well established for all characterized PRORP proteins in plants and is the core biological process annotation for this gene product. The IBA inference from Arabidopsis PRORP orthologs is reliable.
Supporting Evidence:
file:TOBAC/A0A1S3Y076/A0A1S3Y076-deep-research-falcon.md
[PRORP] catalyzes the essential endonucleolytic removal of 5-prime leader sequences from precursor transfer RNAs (pre-tRNAs)
GO_REF:0000033
[IBA with/from includes] AGI_LocusCode:AT2G16650, AT2G32230, AT4G21900
GO:0001682 tRNA 5'-leader removal
IEA
GO_REF:0000120 		ACCEPT
Summary: IEA annotation for tRNA 5-prime leader removal from the UniProt automatic annotation pipeline (ARBA + PANTHER). This is redundant with the IBA annotation above but derived independently through automated methods. The annotation is correct and consistent with the known function of PRORP enzymes.
Reason: Correct automated annotation that is consistent with and independently supports the IBA annotation. tRNA 5-prime leader removal is the core biological process of PRORP enzymes. The ARBA rule and PANTHER family assignment both correctly identify this function.
GO:0004526 ribonuclease P activity
IEA
GO_REF:0000120 		ACCEPT
Summary: IEA annotation for ribonuclease P activity from the UniProt automatic annotation pipeline, based on ARBA rules, the EC number assignment (EC 3.1.26.5), and PANTHER family membership. Redundant with the IBA annotation above but derived independently. The annotation is correct.
Reason: Correct automated annotation that is consistent with and independently supports the IBA annotation. Ribonuclease P activity is the defining molecular function of PRORP enzymes, and the EC number 3.1.26.5 is correctly assigned.

Core Functions

A0A1S3Y076 is a protein-only RNase P (PRORP) that catalyzes the endonucleolytic cleavage of 5-prime leader sequences from precursor tRNAs. The catalytic activity resides in the C-terminal NYN metallonuclease domain and requires Mg2+ as a cofactor. The N-terminal PPR domain mediates substrate recognition by binding the tRNA elbow region. This is the core and sole known molecular function of the protein.

Molecular Function:
ribonuclease P activity
Directly Involved In:
tRNA 5'-leader removal
Supporting Evidence:
  • file:TOBAC/A0A1S3Y076/A0A1S3Y076-deep-research-falcon.md
    [PRORP] catalyzes the essential endonucleolytic removal of 5-prime leader sequences from precursor transfer RNAs (pre-tRNAs)

References

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Suggested Questions for Experts

Q: Which specific cellular compartment(s) does A0A1S3Y076 localize to in tobacco? Arabidopsis has three PRORP paralogs with distinct localizations (PRORP1 to organelles, PRORP2/3 to nucleus). The deep research suggests this tobacco protein may be organellar based on domain architecture, but the GOA annotations from IBA include with/from evidence from all three Arabidopsis PRORPs. Direct localization data in tobacco would clarify the annotation.

Suggested Experiments

Experiment: GFP fusion localization of A0A1S3Y076 in tobacco cells to determine whether the protein targets to chloroplasts, mitochondria, the nucleus, or multiple compartments. This would enable appropriate cellular component annotations.

Hypothesis: Based on domain architecture comparisons to Arabidopsis PRORP1, A0A1S3Y076 may localize to chloroplasts and/or mitochondria, but this has not been experimentally verified in tobacco.

Experiment: In vitro RNase P activity assay with recombinant A0A1S3Y076 protein using tobacco organellar or nuclear pre-tRNA substrates to confirm catalytic activity and determine substrate preferences.

Hypothesis: Recombinant A0A1S3Y076 will cleave pre-tRNA substrates at the canonical RNase P site in a Mg2+-dependent manner, consistent with characterized Arabidopsis PRORP orthologs.

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 · A0A1S3Y076-protnlm-predictions-review.yaml · Review status: COMPLETE

The PRORP architecture supports tRNA maturation, already represented by the more specific tRNA 5-prime-leader-removal annotation.

Source documents: genes/TOBAC/A0A1S3Y076/A0A1S3Y076-uniprot.txt · genes/TOBAC/A0A1S3Y076/A0A1S3Y076-goa.tsv · publications/PMID_22549728.md

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

GO:0008033 tRNA processing GO_BP
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target combines PPR repeats with the PRORP catalytic region and has curated IBAs for RNase P activity and tRNA 5-prime-leader removal. Experiments on Arabidopsis PRORPs establish this cleavage step in plant tRNA maturation (PMID:22549728), supporting transfer to the tobacco homolog. The predicted tRNA processing term is broader than the existing leader-removal process. It is biologically supported but less precise.
Supporting Evidence:
  • file:TOBAC/A0A1S3Y076/A0A1S3Y076-uniprot.txt: "ID A0A1S3Y076_TOBAC Unreviewed; 540 AA. ... DR GO; GO:0004526; F:ribonuclease P activity; IBA:GO_Central. ... DR GO; GO:0001682; P:tRNA 5'-leader removal; IBA:GO_Central. ... DR InterPro; IPR031595; PRORP_C. ... DR PANTHER; PTHR13547:SF13; PROTEINACEOUS RNASE P 2; 1. ... FT DOMAIN 4..208 ... FT /note="PROP1-like PPR" ... FT DOMAIN 251..476 ... FT /note="PRORP""
  • PMID:22549728: "cleaves the 5' leader sequence of tRNA precursors"

Deep Research

Falcon

(A0A1S3Y076-deep-research-falcon.md)

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