Tmlh

UniProt ID: Q9VDM7
Organism: Drosophila melanogaster
Review Status: DRAFT
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Gene Description

Tmlh (CG4335, TMLHE) encodes the Drosophila melanogaster trimethyllysine dioxygenase, an Fe(II)- and 2-oxoglutarate-dependent dioxygenase of the gamma-BBH/TMLD family that is orthologous to human TMLHE. By homology it catalyses the first committed step of L-carnitine biosynthesis, the 3-hydroxylation of free N6,N6,N6-trimethyl-L-lysine (released by turnover of proteins carrying methylated lysines) to 3-hydroxy-N6,N6,N6-trimethyl-L-lysine, coupled to oxidative decarboxylation of 2-oxoglutarate, in the mitochondrial matrix. In the larval fat body Tmlh expression is required for carnitine production; it is transcriptionally repressed by NetrinB-Unc-5 signalling from Ras-transformed tissue, and fat-body knockdown of Tmlh aggravates tumour-induced organismal lethality, which is rescued by dietary carnitine or acetyl-CoA. The catalytic activity itself has not been assayed for the fly enzyme.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005506 iron ion binding
IEA
GO_REF:0000002 		MODIFY
Summary: Iron ion binding from the InterPro trimethyllysine dioxygenase signature (IPR012776).
Reason: Correct but too general. Like other members of the gamma-BBH/TMLD family, Tmlh is expected to use ferrous iron as its catalytic cofactor (UniProt cofactor Fe(2+)), so ferrous iron binding (GO:0008198) is the more specific term. This is a cofactor-binding statement, not the core function.
Proposed replacements: ferrous iron binding
Supporting Evidence:
file:DROME/Tmlh/Tmlh-uniprot.txt
Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
GO:0005739 mitochondrion
IBA
GO_REF:0000033 		MODIFY
Summary: Mitochondrial localization by phylogenetic inference (PTN001642737; experimental donors human TMLHE Q9NVH6, mouse MGI:2180203, rat RGD:620629).
Reason: Correct but less specific than warranted. Mammalian TMLHE is a mitochondrial matrix enzyme (human Q9NVH6 has IDA for mitochondrial matrix), and mitochondrial matrix (GO:0005759) is already annotated to Tmlh by ISS; that term should replace mitochondrion.
Propagation Review
Root cause: TERM SCOPING PROBLEM
Failure modes: GRANULARITY MISMATCH
Sources checked:
PANTHER:PTN001642737 SUPPORTS TRANSFER
TMLD node; mitochondrial location is correct, matrix is the more precise compartment.
Proposed replacements: mitochondrial matrix
GO:0005759 mitochondrial matrix
ISS
GO_REF:0000024 		ACCEPT
Summary: Mitochondrial matrix localization transferred from human TMLHE (Q9NVH6).
Reason: Human TMLHE is localized to the mitochondrial matrix experimentally (the ISS source). For the fly protein, two independent lines agree: the Drosophila carnitine review (PMID:33371457) reports that CG4335 carries a consensus mitochondrial-targeting sequence, and PANTHER places Tmlh in the mitochondrial trimethyllysine dioxygenase subfamily (PTHR10696:SF51), whose characterized members are matrix enzymes. The matrix compartment itself rests on the human ortholog; no fly localization study exists (the UniProt record has no experimental SUBCELLULAR LOCATION comment and no transit peptide feature). Accepted on orthology.
Supporting Evidence:
PMID:33371457
The coded protein shares a 55% of similarity with hTMLDE (trimethyllysine hydroxylase, epsilon) and has a consensus sequence for mitochondrion localization.
file:DROME/Tmlh/Tmlh-uniprot.txt
PANTHER; PTHR10696:SF51; TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL; 1.
GO:0016491 oxidoreductase activity
IEA
GO_REF:0000002 		MODIFY
Summary: Generic oxidoreductase activity from the TauD/TfdA-like domain (IPR003819).
Reason: Correct but uninformative; trimethyllysine dioxygenase activity (GO:0050353), already annotated to Tmlh, is the specific activity.
GO:0016706 2-oxoglutarate-dependent dioxygenase activity
IEA
GO_REF:0000117 		MODIFY
Summary: ARBA-derived 2-oxoglutarate-dependent dioxygenase activity.
Reason: Correct family-level activity, but the specific reaction is known by orthology and is already annotated: trimethyllysine dioxygenase activity (GO:0050353), a descendant of this term.
GO:0045329 carnitine biosynthetic process
IBA
GO_REF:0000033 		ACCEPT
Summary: Carnitine biosynthesis by phylogenetic inference (PTN000075473; donors include human TMLHE Q9NVH6 and BBOX1 O75936, their mouse and rat orthologs, and Candida albicans enzymes).
Reason: Tmlh is inside the TMLD clade and performs the first catalytic step of carnitine biosynthesis; fly genetic data support a role in carnitine production in the fat body.
Supporting Evidence:
PMID:37140455
TMLHE plays an important role in carnitine biosynthesis and hence acetyl‐CoA production from fatty acids (Fig 4A).
GO:0045329 carnitine biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: Carnitine biosynthesis from InterPro IPR012776 and UniPathway UPA00118.
Reason: Consistent with the IBA and TAS annotations for the same process; the gene performs a pathway step. Tmlh matches the NCBIfam carnitine-pathway TMLD model (TIGR02410) and the InterPro trimethyllysine dioxygenase family (IPR012776); membership in this family, whose members catalyse the first step of carnitine biosynthesis, supports the process. Fly in vivo evidence (PMID:37140455) links Tmlh expression to carnitine levels.
Supporting Evidence:
file:DROME/Tmlh/Tmlh-uniprot.txt
NCBIfam; TIGR02410; carnitine_TMLD; 1.
PMID:33371457
TML is first hydroxylated by TML Hydroxylase (TMLH) to produce 3-Hydroxy-TriMethylLysine (HTML)
PMID:37140455
TMLHE plays an important role in carnitine biosynthesis and hence acetyl‐CoA production from fatty acids (Fig 4A).
GO:0045329 carnitine biosynthetic process
TAS
PMID:37140455
Oncogenic stress-induced Netrin is a humoral signaling molec... 		ACCEPT
Summary: FlyBase traceable author statement from Okada et al. 2023, who showed that fat-body Tmlh expression is suppressed by tumour-derived NetrinB, reducing carnitine biosynthesis.
Reason: The paper states that TMLHE drives carnitine biosynthesis and shows that tumour-induced loss of fat-body TMLHE lowers carnitine, with dietary carnitine rescuing survival. This is the core biological process of the gene.
Supporting Evidence:
PMID:37140455
Ras‐induced dysplastic tissues secrete NetB, which humorally inhibits TMLHE expression in the fat body, leading to reduction of carnitine biosynthesis (Fig 5M).
GO:0050353 trimethyllysine dioxygenase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Trimethyllysine dioxygenase activity from InterPro, Rhea RHEA:14181 and EC 1.14.11.8 mappings.
Reason: The specific catalytic activity of this enzyme family; core MF. Tmlh matches the InterPro trimethyllysine dioxygenase family (IPR012776) and the NCBIfam TMLD model (TIGR02410); family membership is the support, as the enzyme has not been assayed in the fly. The reaction is that of the characterized TMLH orthologs (PMID:33371457).
Supporting Evidence:
file:DROME/Tmlh/Tmlh-uniprot.txt
InterPro; IPR012776; Trimethyllysine_dOase.
file:DROME/Tmlh/Tmlh-uniprot.txt
NCBIfam; TIGR02410; carnitine_TMLD; 1.
PMID:33371457
TMLH, which catalyzes the hydroxylation reaction of TML to yield 3-hydroxy-TML (HTML)
GO:0050353 trimethyllysine dioxygenase activity
ISS
GO_REF:0000024 		ACCEPT
Summary: Trimethyllysine dioxygenase activity transferred from human TMLHE isoform 1 (Q9NVH6-1).
Reason: Human TMLHE has direct enzymatic evidence for this activity; Tmlh is its single fly ortholog (PANTHER PTHR10696:SF51). Core MF, by orthology.
Supporting Evidence:
file:DROME/Tmlh/Tmlh-uniprot.txt
PANTHER; PTHR10696:SF51; TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL; 1.
PMID:33371457
Blast analysis indicates that in Drosophila, Dmel/CG4335 is the putative orthologous gene, which is an uncharacterized gene harbored on the right arm of chromosome 3.

Core Functions

Trimethyllysine dioxygenase activity: Fe(II)/2-oxoglutarate-dependent 3-hydroxylation of free N6,N6,N6-trimethyl-L-lysine, the first step of L-carnitine biosynthesis, in the mitochondrial matrix (activity by orthology to human TMLHE; role in fat-body carnitine production supported by fly genetics).

Molecular Function:
trimethyllysine dioxygenase activity
Directly Involved In:
carnitine biosynthetic process
Cellular Locations:
mitochondrial matrix
Supporting Evidence:
  • file:DROME/Tmlh/Tmlh-uniprot.txt
    Converts trimethyllysine (TML) into hydroxytrimethyllysine
  • PMID:37140455
    TMLHE plays an important role in carnitine biosynthesis and hence acetyl‐CoA production from fatty acids (Fig 4A).
  • PMID:33371457
    Blast analysis indicates that in Drosophila, Dmel/CG4335 is the putative orthologous gene, which is an uncharacterized gene harbored on the right arm of chromosome 3.

References

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Suggested Questions for Experts

Q: Is Tmlh the rate-limiting step of carnitine synthesis in the fly fat body, and is trimethyllysine supply (from protein turnover) or Tmlh expression the main control point?

Q: How does NetrinB-Unc-5 signalling repress Tmlh transcription, and is Tmlh regulated by nutrient state (insulin signalling) under normal conditions?

Suggested Experiments

Experiment: Assay recombinant Tmlh for 2-oxoglutarate-coupled hydroxylation of trimethyllysine and measure trimethyllysine, hydroxytrimethyllysine and carnitine in Tmlh null mutants by LC-MS/MS.

Hypothesis: Tmlh is the sole fly trimethyllysine dioxygenase; mutants accumulate trimethyllysine and lack endogenous carnitine synthesis.

Deep Research

Falcon

(Tmlh-deep-research-falcon.md)

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FlyBase

(Tmlh-deep-research-flybase.md)
FlyBase gene description for Tmlh (DROME) FlyBase

FlyBase gene description for Tmlh (DROME)

Trimethyllysine hydroxylase (Tmlh) encodes a mitochondrial enzyme that catalyzes the hydroxylation of trimethyl-L-lysine to generate 3-hydroxy-trimethyllysine, the first step of carnitine biosynthesis.

📚 Additional Documentation

Notes

(Tmlh-notes.md)

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