EFM6 (YNL024C) is a cytoplasmic S-adenosyl-L-methionine-dependent protein-lysine N-methyltransferase of the seven-beta-strand (Class I) methyltransferase superfamily, specifically a member of methyltransferase family 16 (MTF16) within the METTL21 clade. It methylates the eukaryotic translation elongation factor 1A (eEF1A, encoded in S. cerevisiae by the paralogous genes TEF1 and TEF2) on lysine 390. EFM6 is one of a set of dedicated elongation-factor methyltransferases in budding yeast; the four known lysine methylations of eEF1A are each installed by a distinct enzyme, with EFM6 responsible for the Lys390 site. The enzyme is highly substrate-specific: despite being the closest yeast sequence homolog of the human Hsp70-specific methyltransferase METTL21A, it does not methylate yeast Hsp70 proteins. eEF1A-Lys390 methylation is a low-occupancy modification and is not conserved to mammalian eEF1A; the physiological consequence of the modification is not established.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008276 protein methyltransferase activity | IBA GO_REF:0000033 | MODIFY | Summary: Phylogenetically inferred protein methyltransferase activity. Correct but general: EFM6 is experimentally a protein-LYSINE N-methyltransferase acting on eEF1A-Lys390 (PMID:26115316), a specific child of this term. Retained as a valid parent; the specific molecular function is captured by GO:0016279. Reason: The essence (protein methyltransferase) is correct, but a more informative and experimentally supported term exists (GO:0016279 protein-lysine N-methyltransferase activity, already annotated by IEA and consistent with PMID:26115316). Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000378681 Β· METTL21/protein methyltransferase family node SUPPORTS TRANSFER The family-level protein methyltransferase activity is correct for EFM6, but the IBA term is a general parent; EFM6's experimentally established activity is the more specific protein-lysine N-methyltransferase activity (GO:0016279), so this is a granularity issue, not a bad transfer. Proposed replacements: protein-lysine N-methyltransferase activity Supporting Evidence: PMID:26115316 we here show that the YNL024C gene is required for methylation of eEF1A at Lys390, the only of these methylations for which the responsible MTase has not yet been identified. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic cytoplasmic-localization annotation (UniProt SubCell/UniRule). Consistent with the experimental HDA localization (PMID:14562095) and with a translation-associated cytoplasmic methyltransferase. |
| GO:0008757 S-adenosylmethionine-dependent methyltransferase activity | IEA GO_REF:0000117 | ACCEPT | Summary: Electronic (ARBA) SAM-dependent methyltransferase activity. Correct general parent term; the SAM-binding scaffold (motif I region, residues around 51/87-89/115) is intact in EFM6 and its SAM-dependent activity is experimentally established (PMID:26115316). More specific term GO:0016279 also annotated. |
| GO:0016279 protein-lysine N-methyltransferase activity | IEA GO_REF:0000104 | ACCEPT | Summary: Protein-lysine N-methyltransferase activity, the correct specific molecular function. This exactly matches the experimental demonstration that EFM6 methylates eEF1A on the epsilon-amino group of Lys390 (PMID:26115316). Core molecular function of EFM6. Supporting Evidence: PMID:26115316 over-expression of Ynl024c caused a dramatic increase in Lys390 methylation, with trimethylation becoming the predominant state. |
| GO:0008757 S-adenosylmethionine-dependent methyltransferase activity | ISS PMID:12872006 Automated identification of putative methyltransferases from... | ACCEPT | Summary: Sequence-similarity prediction of SAM-dependent methyltransferase activity from the genome-wide Katz/Clarke MTase catalog. A correct general parent term, later confirmed experimentally (PMID:26115316). Redundant with the ARBA IEA annotation to the same term. |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Experimental (high-throughput GFP) cytoplasmic localization from the global yeast localization study. Consistent with EFM6 acting on the abundant cytoplasmic translation factor eEF1A. Core cellular location. |
| GO:0008150 biological_process | ND GO_REF:0000015 | ACCEPT | Summary: Root biological_process with No Data. This honestly reflects the state of knowledge: although EFM6's molecular function (eEF1A-Lys390 methylation) is established, the downstream biological process served by this low-occupancy modification is unknown and described as an enigma (PMID:26115316). No specific BP should be invented. Reason: The biological role of EFM6-mediated eEF1A methylation is genuinely undetermined in the literature; ND is the appropriate state rather than an over-annotated process term. |
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Download this section (compressed HTML)Q: What is the physiological function of eEF1A-Lys390 methylation, and under what conditions (stress, sporulation, aging) is it regulated?
Suggested experts: Yeast translation and elongation-factor biologists, Protein methylation / post-translational modification biologists
Q: Does EFM6 act as a standalone methyltransferase on eEF1A, and does the GTP/GDP conformational state of eEF1A gate the modification?
Suggested experts: Methyltransferase enzymologists, eEF1A structural biologists
Experiment: Compare efm6Ξ and eEF1A-K390R strains to wild type across growth, translational fidelity, stress and sporulation conditions, and non-canonical eEF1A assays (actin bundling, nuclear export), including quantitative phenotyping and proteomics.
Hypothesis: eEF1A-Lys390 methylation modulates a specific (possibly non-canonical) eEF1A function or a stress/aging response rather than bulk translation.
Type: comparative phenotyping / functional assays
Experiment: Reconstitute methylation with purified active EFM6 and eEF1A in defined GTP- vs GDP-bound states and measure steady-state kinetics; if soluble EFM6 cannot be purified, use co-expression or on-substrate/extract-based quantitative assays.
Hypothesis: EFM6 is a self-sufficient methyltransferase whose activity depends on the eEF1A nucleotide state.
Type: in vitro enzymology
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The biological process served by EFM6-mediated methylation of eEF1A at Lys390 is undetermined. It is not known why this specific low-occupancy lysine methylation is installed, what phenotype (if any) it modulates, or which of eEF1A's canonical (translation) or non-canonical (e.g. actin bundling, nuclear export) activities it influences.
OPEN BIOLOGY BP_DARK
What is known: The molecular function is firmly established: EFM6 is a SAM-dependent protein-lysine N-methyltransferase that specifically and directly methylates eEF1A on Lys390 (deletion abolishes the modification, overexpression drives di/tri-methylation, and an EFM6-containing extract methylates eEF1A in vitro). What is unknown is the downstream consequence, not the activity or the substrate site.
Significance: eEF1A is one of the most abundant proteins in the cell and carries four distinct, enzyme-dedicated lysine methylations; understanding what the Lys390 mark does would clarify why the cell maintains a dedicated methyltransferase for a modification present on only a small fraction of eEF1A molecules, and whether it tunes a specific eEF1A subfunction or acts as a regulated switch.
What would resolve it: Determine a phenotype for efm6Ξ (and for eEF1A K390R) under stress/aging/sporulation and non-canonical eEF1A assays; test whether Lys390 methylation is regulated in response to physiological cues; identify any interacting demethylase; measure effects on translational fidelity and on eEF1A actin/nuclear functions.
Provenance (the field's own admissions):
Gap: Whether EFM6 is enzymatically active as an isolated, purified protein, and its steady-state kinetic parameters and possible cofactor/partner requirements on eEF1A, are not established.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Direct methylation was demonstrated only from crude E. coli extracts overexpressing EFM6 (and required GTP), because soluble recombinant EFM6 with activity could not be purified; genetic and in vivo evidence for EFM6-dependent Lys390 methylation is nonetheless unambiguous.
Significance: A reconstituted single-enzyme assay would confirm EFM6 acts alone (versus needing a partner or a particular eEF1A/GTP conformational state) and enable mechanistic and structural study of an otherwise well-defined activity.
What would resolve it: Obtain soluble active recombinant EFM6 (e.g. alternative tags/hosts, co-expression with eEF1A, or on-substrate assays) and measure kinetics against eEF1A in defined GTP/GDP-bound states.
Provenance (the field's own admissions):
Gap: Whether EFM6 has any substrate other than eEF1A-Lys390 is untested beyond the exclusion of yeast Hsp70 proteins.
OPEN BIOLOGY MF_DARK
What is known: EFM6 does not methylate yeast Hsp70 (Ssa1/Ssb1/Ssb2) despite being the closest yeast homolog of the Hsp70-specific human METTL21A, and it is highly specific for eEF1A; no unbiased, proteome-wide substrate screen for EFM6 has been reported.
Significance: Excluding or discovering additional substrates would define the full functional scope of the enzyme and rule out (or in) a broader role beyond eEF1A.
What would resolve it: Perform an activity-based, proteome-wide substrate screen (e.g. using EFM6 as enzyme source with a methyltransferase-deficient extract, or SILAC/heavy-methyl profiling of efm6Ξ vs WT).
Provenance (the field's own admissions):
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