yml6

UniProt ID: O74801
Organism: Schizosaccharomyces pombe 972h-
Review Status: COMPLETE
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Gene Description

Yml6 (SPBC2D10.08c) is the nuclear-encoded mitochondrial large-subunit ribosomal protein uL4m of fission yeast, a 261-residue precursor with a predicted N-terminal mitochondrial transit peptide (residues 1-35) followed by the conserved ribosomal uL4 domain. It is imported into mitochondria and assembled into the 54S large subunit of the mitoribosome, the machine that synthesizes the mitochondrially encoded, largely membrane-embedded subunits of the respiratory chain and ATP synthase. It sits in the same PANTHER subfamily (PTHR10746:SF6) as budding-yeast Yml6 and human MRPL4. In the budding-yeast mitoribosome structure, uL4m, together with uL22m, forms the constriction of the nascent-polypeptide exit tunnel, a conserved structural feature of uL4 proteins. No enzymatic activity is attributed to the protein. Its molecular role is structural, binding rRNA and organizing the large-subunit architecture. In S. pombe, Yml6 has been recovered at low levels with the mitochondrial translational activator Ppr10.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003735 structural constituent of ribosome
IBA
GO_REF:0000033 		ACCEPT
Summary: Structural constituent of ribosome, inherited across the uL4 family; this is the core molecular function of Yml6.
Reason: The PAINT node PTN000078778 sits at the root of the uL4 family. Yml6 belongs to the same PANTHER subfamily (PTHR10746:SF6) as the experimental donor, S. cerevisiae Yml6 (SGD:S000004487, P51998), which is a resolved protein of the yeast mitoribosome large subunit (PMID:24675956). The structural role in the ribosome is the universally conserved property of uL4 proteins, so the inheritance is sound. The S. pombe protein is also recovered with mitoribosomal proteins in Ppr10 pulldowns (PMID:34119521).
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
Belongs to the universal ribosomal protein uL4 family.
file:SCHPO/yml6/yml6-uniprot.txt
DR PANTHER; PTHR10746:SF6; LARGE RIBOSOMAL SUBUNIT PROTEIN UL4M; 1.
PMID:24675956
Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4.
GO:0003735 structural constituent of ribosome
IEA
GO_REF:0000002 		ACCEPT
Summary: The InterPro2GO mapping makes the same structural-constituent claim as the IBA row and agrees with it.
Reason: Yml6 has the full Ribosomal_uL4 (IPR002136) and uL4 domain superfamily (IPR023574) signatures. This is a correct domain-to-function mapping, consistent with the IBA row for the same term.
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
DR InterPro; IPR002136; Ribosomal_uL4.
file:SCHPO/yml6/yml6-uniprot.txt
Belongs to the universal ribosomal protein uL4 family.
GO:0005739 mitochondrion
HDA
PMID:16823372
ORFeome cloning and global analysis of protein localization ... 		ACCEPT
Summary: Mitochondrial localization comes from the S. pombe genome-wide GFP-fusion screen.
Reason: UniProt records the mitochondrial location as experimental evidence from this screen (ECO:0000269, PubMed:16823372). It agrees with the predicted N-terminal transit peptide (residues 1-35) and with the protein's identity as a mitoribosome subunit. The cached paper is abstract-only, so I am deferring to the PomBase curators on the individual image. The term is broader than mitochondrial large ribosomal subunit, which is captured separately, but it is an accurate statement of where the protein is observed.
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:16823372}.
GO:0005739 mitochondrion
IEA
GO_REF:0000044 		ACCEPT
Summary: The UniProt subcellular-location mapping comes from the same curated observation as the HDA row.
Reason: This row is consistent with the HDA row for the same term, and it rests on the experimentally sourced UniProt subcellular-location statement.
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:16823372}.
GO:0005762 mitochondrial large ribosomal subunit
IBA
GO_REF:0000033 		ACCEPT
Summary: Yml6 is part of the mitochondrial large ribosomal subunit, inherited from the mitochondrial uL4m clade.
Reason: PTN000078780 is the eukaryotic mitochondrial uL4m node. Its donors are S. cerevisiae Yml6, human MRPL4 (Q9BYD3, also in PTHR10746:SF6) and a trypanosome mitoribosomal uL4 (Q385G8). Yml6 is inside this clade, as shown by the shared subfamily, its mitochondrial transit peptide and its observed mitochondrial location. In the budding-yeast mitoribosome, uL4m is a resolved component of the large subunit (PMID:24675956). S. pombe Yml6 copurifies with other mt-LSU proteins in Ppr10 preparations (PMID:34119521).
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
SUBUNIT: Component of the mitochondrial large ribosomal subunit (mt-
PMID:34119521
mt-LSU proteins (Aco2-Mrpl49, Mrpl7, and Yml6)
PMID:24675956
Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4.
GO:0005762 mitochondrial large ribosomal subunit
NAS
PMID:18245278
Bot1p is required for mitochondrial translation, respiratory... 		ACCEPT
Summary: The PomBase NAS statement makes the same claim as the IBA row and is correct.
Reason: The Bot1 paper (PMID:18245278) is about a small-subunit protein and does not mention Yml6 in its cached full text. The NAS presumably reflects the authors' or curators' list of S. pombe mitoribosomal proteins. The claim itself is well supported by subfamily membership, the PAINT mitochondrial uL4m node and the Ppr10 copurification (PMID:34119521), so I accept it on that independent support, not on the cited paper.
Supporting Evidence:
PMID:34119521
mt-LSU proteins (Aco2-Mrpl49, Mrpl7, and Yml6)
file:SCHPO/yml6/yml6-uniprot.txt
SUBUNIT: Component of the mitochondrial large ribosomal subunit (mt-
GO:0005840 ribosome
IBA
GO_REF:0000033 		MODIFY
Summary: Ribosome is correct but generic. For a mitochondrial uL4m, the specific location is the mitochondrial large ribosomal subunit.
Reason: The family-root node (PTN000078778) covers bacterial, plastid (AT1G07320) and mitochondrial uL4 proteins, so it can only assert the generic ribosome term. Yml6 is in the mitochondrial uL4m clade, and it already carries mitochondrial large ribosomal subunit (GO:0005762) from the PTN000078780 IBA and the PomBase NAS. That term is the precise version of this claim.
Propagation Review
Root cause: TERM SCOPING PROBLEM
Failure modes: GRANULARITY MISMATCH
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
SUBUNIT: Component of the mitochondrial large ribosomal subunit (mt-
PMID:34119521
mt-LSU proteins (Aco2-Mrpl49, Mrpl7, and Yml6)
GO:0005840 ribosome
IEA
GO_REF:0000002 		MODIFY
Summary: The InterPro2GO ribosome term is correct but generic. It is refined to mitochondrial large ribosomal subunit.
Reason: The domain mapping cannot tell organellar from cytosolic or bacterial ribosomes. Yml6 is a mitochondrial uL4m, as shown by its subfamily, transit peptide and observed location, and it already carries GO:0005762.
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
SUBUNIT: Component of the mitochondrial large ribosomal subunit (mt-
GO:0006412 translation
IEA
GO_REF:0000002 		MODIFY
Summary: Translation is correct but generic. Yml6 is a subunit of the mitoribosome, so the specific process is mitochondrial translation.
Reason: As a structural subunit of the ribosome, the protein does part of the work of translation. The ribosome it belongs to is the mitoribosome, and the gene already carries mitochondrial translation (GO:0032543) by ISS and NAS.
Proposed replacements: mitochondrial translation
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
dedicated translation machinery responsible for the synthesis of
GO:0006417 regulation of translation
IBA
GO_REF:0000033 		MARK AS OVER ANNOTATED
Summary: Regulation of translation was propagated from E. coli L4 (rplD, P60723). E. coli L4 represses its own S10 ribosomal-protein operon. There is no evidence for such regulation by a mitochondrial uL4m.
Reason: The only experimental donor is E. coli uL4 (P60723), and the term sits on the family-root node PTN000078778. The bacterial regulatory role is the autogenous feedback control of the S10 operon, in which free L4 acts on the operon's own leader mRNA. That mechanism depends on bacterial operon organization. The mitochondrial uL4m genes of fungi are single nuclear genes, not operons, and none of the eukaryotic donors at the mitochondrial node PTN000078780 (S. cerevisiae Yml6, human MRPL4, trypanosome uL4m) supplies a regulatory annotation. No study of Yml6 or its mitochondrial orthologs reports a translational-regulatory activity separate from its structural role in the ribosome. Being a subunit of the translating ribosome is not regulation of translation. The term is not absurd for a family that contains a known regulator, but for this mitochondrial member it is an over-propagation from a lineage-specific bacterial function.
Propagation Review
Root cause: PROPAGATION BAD
Failure modes: LINEAGE OR TAXON MISMATCH ROLE CONFLATION
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
FUNCTION: Component of the mitochondrial ribosome (mitoribosome), a
GO:0032543 mitochondrial translation
ISS
GO_REF:0000024 		ACCEPT
Summary: Mitochondrial translation, transferred from S. cerevisiae Yml6 (P51998), a same-subfamily ortholog. This is the core process.
Reason: P51998 and O74801 are both in PTHR10746:SF6 and both descend from the mitochondrial uL4m node PTN000078780, so this is an orthologous transfer of a conserved property. In the budding-yeast structure, uL4m is a component of the mitoribosome large subunit at the exit-tunnel constriction (PMID:24675956), where it does part of the work of protein synthesis. S. pombe Yml6 copurifies with the mitochondrial translational activator Ppr10 together with other mitoribosomal proteins (PMID:34119521).
Supporting Evidence:
file:SCHPO/yml6/yml6-uniprot.txt
dedicated translation machinery responsible for the synthesis of
PMID:24675956
Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4.
PMID:34119521
mt-LSU proteins (Aco2-Mrpl49, Mrpl7, and Yml6)
GO:0032543 mitochondrial translation
NAS
PMID:18245278
Bot1p is required for mitochondrial translation, respiratory... 		ACCEPT
Summary: The PomBase NAS statement makes the same claim as the ISS row and is accepted.
Reason: The cited Bot1 paper does not discuss Yml6 directly. The claim is the same as in the ISS row and is independently supported by orthology to S. cerevisiae Yml6 and by the S. pombe Ppr10 copurification data.
Supporting Evidence:
PMID:34119521
mt-LSU proteins (Aco2-Mrpl49, Mrpl7, and Yml6)

Core Functions

Structural constituent of the mitochondrial ribosome large (54S) subunit (uL4m). It organizes large-subunit rRNA architecture and forms part of the nascent-polypeptide exit-tunnel constriction, so it takes part in mitochondrial translation.

Molecular Function:
structural constituent of ribosome
Directly Involved In:
mitochondrial translation
Cellular Locations:
mitochondrion
In Complex:
mitochondrial large ribosomal subunit
Supporting Evidence:
  • file:SCHPO/yml6/yml6-uniprot.txt
    Belongs to the universal ribosomal protein uL4 family.
  • PMID:24675956
    Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4.
  • PMID:34119521
    mt-LSU proteins (Aco2-Mrpl49, Mrpl7, and Yml6)

References

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Suggested Questions for Experts

Q: Does the S. pombe mitoribosome contain Yml6 at the same exit-tunnel position as budding-yeast uL4m, and do fission-yeast-specific extensions of uL4m contact mitochondrion-specific rRNA expansion segments?

Q: Is there any evidence for a translational-regulatory (autogenous) function of eukaryotic mitochondrial uL4m that would justify inheriting GO:0006417 from E. coli L4 at the family-root PAINT node?

Suggested Experiments

Experiment: Deplete Yml6 or make a conditional allele (S. pombe is petite-negative) and assay mtLSU assembly by sucrose-gradient profiling, followed by mitochondrial translation by in vivo labeling of mitochondrially encoded proteins.

Type: genetic depletion with mitoribosome profiling

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 · yml6-protnlm-predictions-review.yaml · Review status: COMPLETE

ProtNLM2 emitted three broad GO terms for the mitochondrial uL4m ribosomal protein Yml6 (translation, ribonucleoprotein complex, ribosome). All are biologically correct, but each is an ancestor of a supported annotation the gene already carries (mitochondrial translation, GO:0032543; mitochondrial large ribosomal subunit, GO:0005762), so all three are less precise (LSP).

Source documents: genes/SCHPO/yml6/yml6-protnlm-source.xml · genes/SCHPO/yml6/yml6-protnlm-source.json · genes/SCHPO/yml6/yml6-uniprot.txt

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

GO:0006412 translation GO_BP
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: pre-release post-processed-2026_02_28k.xml · file:SCHPO/yml6/yml6-protnlm-source.xml
Review rationale: The target has the diagnostic uL4m family domain and mitochondrial localization. Target Yml6 also co-purifies at low levels with Ppr10 among mitoribosomal proteins (PMID:34119521). Characterized S. cerevisiae mitoribosome structures support transfer of the conserved mitochondrial ribosomal role. Translation is therefore supported, and the existing mitochondrial translation annotation (GO:0032543) is more specific within the biological-process aspect. The generic prediction is LSP.
Supporting Evidence:
  • file:SCHPO/yml6/yml6-uniprot.txt: "DR InterPro; IPR002136; Ribosomal_uL4."
  • PMID:24675956: "Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4."
  • PMID:34119521: "Mass spectrometry (MS) analysis of Ppr10-copurified proteins revealed that some proteins were specifically detected in the Ppr10-TAP preparation, albeit at low levels. These proteins included mt-SSU proteins (Nam9, Mrps28, Mrp4, and Mrps9), mt-LSU proteins (Aco2-Mrpl49, Mrpl7, and Yml6), SPAC750.08c (a putative NAD-dependent malic enzyme), SPBP4H10.18c (a Schizosaccharomyces specific protein of unknown function), and Anc1 (a mitochondrial ADP/ATP carrier)"
GO:1990904 ribonucleoprotein complex GO_CC
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: pre-release post-processed-2026_02_28k.xml · file:SCHPO/yml6/yml6-protnlm-source.xml
Review rationale: The target has the diagnostic uL4m family domain and mitochondrial localization. Target Yml6 also co-purifies at low levels with Ppr10 among mitoribosomal proteins (PMID:34119521). Characterized S. cerevisiae mitoribosome structures support transfer of the conserved mitochondrial ribosomal role. Membership in the mitochondrial large ribosomal subunit is a supported cellular-component annotation and is more specific than ribonucleoprotein complex. The predicted broad complex membership is LSP.
Supporting Evidence:
  • file:SCHPO/yml6/yml6-uniprot.txt: "DR InterPro; IPR002136; Ribosomal_uL4."
  • PMID:24675956: "Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4."
  • PMID:34119521: "Mass spectrometry (MS) analysis of Ppr10-copurified proteins revealed that some proteins were specifically detected in the Ppr10-TAP preparation, albeit at low levels. These proteins included mt-SSU proteins (Nam9, Mrps28, Mrp4, and Mrps9), mt-LSU proteins (Aco2-Mrpl49, Mrpl7, and Yml6), SPAC750.08c (a putative NAD-dependent malic enzyme), SPBP4H10.18c (a Schizosaccharomyces specific protein of unknown function), and Anc1 (a mitochondrial ADP/ATP carrier)"
GO:0005840 ribosome GO_CC
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: pre-release post-processed-2026_02_28k.xml · file:SCHPO/yml6/yml6-protnlm-source.xml
Review rationale: The target has the diagnostic uL4m family domain and mitochondrial localization. Target Yml6 also co-purifies at low levels with Ppr10 among mitoribosomal proteins (PMID:34119521). Characterized S. cerevisiae mitoribosome structures support transfer of the conserved mitochondrial ribosomal role. Membership in the mitochondrial large ribosomal subunit is a supported cellular-component annotation and is more specific than ribosome. The predicted broad complex membership is LSP.
Supporting Evidence:
  • file:SCHPO/yml6/yml6-uniprot.txt: "DR InterPro; IPR002136; Ribosomal_uL4."
  • PMID:24675956: "Beyond the entrance, the tunnel is lined by conserved elements (Fig. 6C), including the constriction site formed by uL22 and uL4."
  • PMID:34119521: "Mass spectrometry (MS) analysis of Ppr10-copurified proteins revealed that some proteins were specifically detected in the Ppr10-TAP preparation, albeit at low levels. These proteins included mt-SSU proteins (Nam9, Mrps28, Mrp4, and Mrps9), mt-LSU proteins (Aco2-Mrpl49, Mrpl7, and Yml6), SPAC750.08c (a putative NAD-dependent malic enzyme), SPBP4H10.18c (a Schizosaccharomyces specific protein of unknown function), and Anc1 (a mitochondrial ADP/ATP carrier)"

Deep Research

Falcon

(yml6-deep-research-falcon.md)

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📚 Additional Documentation

Notes

(yml6-notes.md)

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Protnlm Function Review

(yml6-protnlm-function-review.md)

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📄 View Raw YAML

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