SLC25A19 (Q9HC21) review notes

Identity and family

• UniProt Q9HC21 (TPC_HUMAN), gene SLC25A19 (HGNC:14409). RecName "Mitochondrial thiamine pyrophosphate carrier"; short name MTPPT. Old synonyms DNC (deoxynucleotide carrier) and MUP1 (mitochondrial uncoupling protein 1) [file:human/SLC25A19/SLC25A19-uniprot.txt "RecName: Full=Mitochondrial thiamine pyrophosphate carrier"].
• Member of the mitochondrial carrier (SLC25) family, TC 2.A.29 [file:human/SLC25A19/SLC25A19-uniprot.txt "Belongs to the mitochondrial carrier (TC 2.A.29) family"]. 320 aa, ~35 kDa, three tandem Solcar repeats, six predicted transmembrane helices; N- and C-termini face the cytosol PMID:27188525.

Core function: mitochondrial thiamine pyrophosphate (TPP/ThPP/ThDP) carrier

• Physiological role: imports thiamine pyrophosphate (the activated cofactor form of vitamin B1) from cytosol into the mitochondrial matrix. Mammalian cells cannot make TPP inside mitochondria, so this uptake supplies the cofactor for matrix TPP-dependent enzymes (PDH, OGDH/α-ketoglutarate dehydrogenase, BCKDH) PMID:27188525.
• Transport is an exchange/antiport: TPP in, thiamine monophosphate out (yeast ortholog Tpc1p mechanism), and in vitro SLC25A19 catalyzes exchange not uniport PMID:17035501. UniProt encodes the Rhea reaction thiamine phosphate(out) + thiamine diphosphate(in) = thiamine phosphate(in) + thiamine diphosphate(out) (RHEA:73383).
• MF term: GO:0090422 thiamine pyrophosphate transmembrane transporter activity (verified current OLS label). BP: GO:0030974 thiamine pyrophosphate transmembrane transport. Location: GO:0005743 mitochondrial inner membrane.

Reclassification from "deoxynucleotide carrier" (DNC) — history

• Originally characterized as the human mitochondrial deoxynucleotide carrier: recombinant protein in proteoliposomes transported dNDPs (and less efficiently dNTPs) in exchange for dNDPs/ADP/ATP PMID:11226231. Km for dNTP uptake was millimolar — ~1000x higher than physiological — arguing against a physiological dNT role PMID:15539640.
• Lam et al. showed DNC/SLC25A19 knockdown/overexpression does not affect mtDNA depletion by dideoxynucleoside analogs or mitochondrial dNTP uptake PMID:15539640.
• Kang & Samuels (PMID:18280798, abstract-only, not cached in full) argued from the evidence that DNC is not the mitochondrial deoxyribonucleotide carrier (UniProt reference [7]).
• Slc25a19 knockout mouse: normal mitochondrial dNTP/rNTP pools, no mtDNA depletion, but undetectable mitochondrial ThPP; ThPP transport confirmed by reconstituted transport assay; loss causes embryonic lethality, open neural tube, anemia, elevated α-ketoglutarate from OGDH dysfunction [PMID:17035501 "We found that these animals have normal mitochondrial ribo- and deoxyribonucleoside triphosphate levels, suggesting that transport of these molecules is not the primary role of SLC25A19"; "We conclude that SLC25A19 transports ThPP"].
• UniProt CAUTION documents the reclassification [file:human/SLC25A19/SLC25A19-uniprot.txt "Previously identified as the mitochondrial deoxyribonucleotide carrier (PubMed:11226231). However other experiments later demonstrated that SLC25A19 is a thiamine diphosphate transporter"].
• Curation consequence: the old deoxynucleotide MF/BP annotations (GO:0030233, GO:0030302, GO:0015932) are historical/mis-assignments. GOA already carries explicit NOT annotations for GO:0030233 and GO:0030302 (PMID:15539640, PMID:17035501). The residual positive deoxynucleotide annotations (TAS/NAS from PMID:11226231; ARBA IEA nucleobase-containing MF) are superseded and handled as REMOVE (IEA) / MARK_AS_OVER_ANNOTATED (TAS/NAS author statements, which are not experimental).

Subcellular localization

• Mitochondrial inner membrane / mitochondrion, multipass membrane protein [file:human/SLC25A19/SLC25A19-uniprot.txt "SUBCELLULAR LOCATION: Mitochondrion membrane"; "Multi-pass membrane protein"]. Supported experimentally by PMID:15539640, PMID:27188525, PMID:31506564 (EXP mitochondrial membrane), by HPA IDA (mitochondrion), and by high-confidence mitochondrial proteomics PMID:34800366.
• A nucleus HDA annotation (GO:0005634, PMID:21630459) comes from a human sperm-nucleus proteome; sperm nuclei were purified "without any tail fragments, acrosome or mitochondria" PMID:21630459. For a mitochondrial inner-membrane carrier this is almost certainly a proteomics contaminant / not a functional nuclear localization; kept as non-core (HDA is high-throughput, not an experimental small-scale assignment to remove).

Structure-function

• Site-directed mutagenesis (TPP uptake by isolated mitochondria of HepG2 cells expressing WT vs mutant hMTPPT): Ile33, Ser34, Asp37, His137, Lys291 important for function; Thr29, Arg30, His82, Lys231, Phe298 dispensable PMID:27188525.

Disease

• Microcephaly, Amish type (MCPHA, MIM 607196): severe congenital microcephaly, 2-ketoglutaric (α-ketoglutaric) aciduria, death in first year; G177A hypomorph reduces TPP transport ~70% [file:human/SLC25A19/SLC25A19-uniprot.txt "characterized by severe congenital microcephaly and severe 2-\nketoglutaric aciduria"; PMID:12185364 variant].
• Thiamine metabolism dysfunction syndrome 4 (THMD4, MIM 613710): recurrent flaccid paralysis/encephalopathy, bilateral striatal necrosis, progressive polyneuropathy; variants G125S, S194P, Q192H reduce TPP uptake [PMID:19798730; PMID:31506564 "the mitochondrial TPP transporter (hMTPPT)"].
• Reactome R-HSA-8875838 "SLC25A19 transports ThDP from cytosol to mitochondrial matrix" and R-HSA-196819 "Vitamin B1 (thiamin) metabolism" describe the pathway context; ThDP is a cofactor for PDH, OGDH and BCKDH [reactome/R-HSA-8875838 "ThDP is a cofactor for the mitochondrial enzymes pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, and branched chain amino acid dehydrogenase"].

Annotation review summary (actions)

• Core: GO:0090422 (MF, transporter), GO:0030974 (BP, transport), GO:0005743 (CC, inner membrane) — ACCEPT the experimental/IBA supporting instances.
• GO:0005739 mitochondrion and GO:0031966 mitochondrial membrane — ACCEPT (correct, less precise parents of inner membrane); redundant precision handled by keeping inner-membrane as core.
• Deoxynucleotide terms: NOT annotations (GO:0030233, GO:0030302) ACCEPT (they correctly record the refuted function). Positive TAS/NAS deoxynucleotide (PMID:11226231) MARK_AS_OVER_ANNOTATED (superseded, author-statement not experimental). ARBA IEA GO:0015932 nucleobase-containing compound transmembrane transporter activity — REMOVE (wrong-substrate electronic prediction, contradicted by the physiological reclassification and by explicit NOT deoxynucleotide annotations).
• GO:0042723 thiamine-containing compound metabolic process (IEA/TAS) — KEEP_AS_NON_CORE (true but a broad parent of the specific transport function).
• GO:0009229 thiamine diphosphate biosynthetic process (from UniProt DR, Ensembl IEA) — not in GOA TSV; SLC25A19 is a transporter, not a biosynthetic enzyme; would be over-annotation if present (noted, not in review file).
• GO:0055085 transmembrane transport (InterPro IEA) — KEEP_AS_NON_CORE (correct broad parent).
• GO:0005634 nucleus (HDA, sperm nucleus proteome) — KEEP_AS_NON_CORE (likely contaminant; HDA not removed).