Affinage

BHMT

Betaine--homocysteine S-methyltransferase 1 · UniProt Q93088

Length
406 aa
Mass
45.0 kDa
Annotated
2026-06-09
37 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

BHMT is a cytosolic hepatic enzyme that catalyzes betaine-dependent remethylation of homocysteine to methionine, thereby controlling the supply of S-adenosylmethionine and the cell's transmethylation capacity (PMID:28179424, PMID:27320863). Loss of BHMT in liver elevates S-adenosylhomocysteine, alters CpG methylation to repress loci including Iqgap2 and F2rl2, and drives preneoplastic foci, establishing that BHMT activity is required to maintain normal DNA methylation in hepatocytes (PMID:28179424). Beyond its housekeeping methyl-metabolism role, BHMT acts directly in epigenetic regulation: in oligodendrocytes it localizes to the nucleus, associates with chromatin and DNMT3a, and is required for betaine-induced histone and DNA methyltransferase activity (PMID:33975330), and in renal cells it raises SAM to enhance DNMT-mediated methylation of the NOX4 promoter, suppressing NOX4 and limiting ROS-driven apoptosis (PMID:41643883). BHMT loss links methyl metabolism to broader physiology, triggering homocysteine-induced ER stress, CREBH activation, and FGF21-mediated adipose browning (PMID:36755585), while its expression is required for betaine-dependent AMPK pathway activation and anti-lipogenic effects (PMID:27320863). Independently of catalysis, full-length BHMT is cleaved by the asparaginyl proteinase legumain in amphisomes in an autophagy-dependent manner, making it a reporter of autophagic flux (PMID:21610319), and in irradiated glioblastoma cells it is recognized on autophagosomes within an SDC1-TGM2-FLOT1 complex to promote autophagosome-lysosome fusion (PMID:37441590). In zebrafish, Bhmt acts upstream of Sonic Hedgehog signaling to control endoderm-derived organ and β-cell development (PMID:21952238).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2008 Medium

    Establishing that BHMT sequence variants alter substrate binding and that BHMT physically interacts with its paralog BHMT2 clarified the enzyme's functional determinants and quaternary context.

    Evidence COS-1 expression of variant allozymes with activity/Km assays and co-IP with BHMT2

    PMID:18457970

    Open questions at the time
    • No structural model of the BHMT-BHMT2 complex
    • Physiological consequence of altered Km not assessed in vivo
  2. 2011 High

    The discovery that BHMT is cleaved by legumain in amphisomes during autophagy revealed an unexpected, catalysis-independent role for BHMT as a proteolytic substrate and a tool for monitoring autophagic flux.

    Evidence Isolated rat hepatocytes with 3-MA, legumain inhibitor AJN-230, and MS identification of the p10 fragment

    PMID:21610319

    Open questions at the time
    • Functional consequence of cleavage for methionine metabolism unknown
    • Whether p10 fragment has activity not established
  3. 2011 High

    A frameshifting splice variant abolishing BHMT expression in hepatocellular carcinoma defined a loss-of-function event tied to liver tumor tissue.

    Evidence Exon junction sequencing, Western blot, IHC, and activity assays in HepG2 cells and tumors

    PMID:22138536

    Open questions at the time
    • Causal role of BHMT loss in tumorigenesis not tested
    • Mechanism driving aberrant splicing unknown
  4. 2011 High

    Genetic epistasis in zebrafish placed Bhmt upstream of Sonic Hedgehog in a developmental pathway controlling endodermal organ and β-cell formation, extending BHMT's relevance beyond metabolism.

    Evidence Morpholino knockdown with syu (shh-null) epistasis and qRT-PCR for shh

    PMID:21952238

    Open questions at the time
    • Molecular link between BHMT metabolism and shh transcription unresolved
    • Relevance to mammalian development not shown
  5. 2015 High

    Dissecting GST-BHMT reporter processing distinguished proteasome-inhibition-induced autophagy (requiring SQSTM1/NBR1, ERN1/IRE1, JNK, and the multimerization domain) from starvation-induced autophagy, refining BHMT's use as a pathway-specific flux reporter.

    Evidence GST-BHMT fragmentation assay with siRNA knockdowns and domain-deletion mutagenesis

    PMID:25984893

    Open questions at the time
    • Whether endogenous BHMT follows the same route not confirmed
    • Significance of multimerization for native BHMT function unclear
  6. 2016 Medium

    Comparing BHMT-expressing and BHMT-deficient hepatocyte lines showed BHMT is required for betaine-driven AMPK pathway activation, linking its remethylation activity to anti-lipogenic signaling.

    Evidence MCD-diet rat model plus H4IIE vs HepG2 cell comparison with phospho-signaling Western blots

    PMID:27320863

    Open questions at the time
    • Direct mechanism connecting SAM/homocysteine to LKB1/AMPK not defined
    • Confound from other cell-line differences besides BHMT
  7. 2017 High

    The Bhmt-null mouse demonstrated that BHMT activity is required to sustain hepatic DNA methylation, with its loss raising S-adenosylhomocysteine and causing locus-specific hypomethylation and preneoplastic foci.

    Evidence Bhmt-null mice with whole-genome bisulfite sequencing, transcriptomics, metabolomics, and histology

    PMID:28179424

    Open questions at the time
    • Causal chain from Iqgap2/F2rl2 repression to neoplasia not established
    • Which methyltransferases are limited by SAH not pinpointed
  8. 2021 Medium

    Detection of nuclear, chromatin-associated BHMT interacting with DNMT3a in oligodendrocytes proposed a direct role for BHMT in epigenetic regulation beyond cytosolic methyl supply.

    Evidence Immunocytochemistry, chromatin fractionation, co-IP with DNMT3a, and siRNA-dependent methyltransferase activity assays

    PMID:33975330

    Open questions at the time
    • Co-IP lacks reciprocal and structural validation
    • Mechanism of BHMT nuclear import unknown
  9. 2023 Medium

    Identifying BHMT as the autophagosomal partner recognized by TGM2 within an SDC1-TGM2-FLOT1 complex assigned BHMT a structural role in autophagosome-lysosome fusion underlying glioblastoma radioresistance.

    Evidence Co-IP, immunofluorescence, mRFP-GFP-LC3 reporter, and functional autophagy assays in radioresistant GBM cells

    PMID:37441590

    Open questions at the time
    • Direct BHMT-TGM2 binding interface not mapped
    • Whether catalytic activity is required for fusion role unknown
  10. 2023 Medium

    Tracing the Bhmt-KO phenotype to homocysteine-induced ER stress, CREBH activation, and FGF21 release defined a liver-to-adipose signaling axis arising from BHMT loss.

    Evidence Bhmt-KO mice with histology, expression profiling, and hormone/metabolite measurements

    PMID:36755585

    Open questions at the time
    • Direct trigger of CREBH by homocysteine not biochemically resolved
    • Contribution of other one-carbon perturbations not excluded
  11. 2026 Medium

    Rescue experiments established a BHMT→SAM→DNMT→NOX4-promoter-methylation axis by which BHMT overexpression suppresses NOX4 and protects renal cells from oxidative apoptosis.

    Evidence BHMT overexpression and NOX4 rescue assays with promoter methylation analysis in vitro and an IRI model

    PMID:41643883

    Open questions at the time
    • Which DNMT methylates the NOX4 promoter not specified
    • Generality beyond renal context untested
  12. 2026 Medium

    Combinatorial knockdown linked BHMT to BRCA1's control of choline metabolism and DNA double-strand-break susceptibility, positioning BHMT as a mediator of BRCA1-dependent genome maintenance.

    Evidence snRNA-seq, dual BRCA1/BHMT knockdown with DSB assays, and metabolomics in Brca1-deficient mice

    PMID:41781465

    Open questions at the time
    • Mechanism by which BRCA1 suppresses Bhmt expression unknown
    • Direct contribution of choline metabolism to DSB repair not demonstrated

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unresolved how BHMT's cytosolic remethylation activity is mechanistically coupled to its proposed nuclear chromatin and autophagosomal-fusion roles, and whether these moonlighting functions require its catalytic activity.
  • No structural basis for nuclear or autophagosomal localization
  • Catalysis-dependence of moonlighting functions untested
  • Trafficking signals directing BHMT to different compartments unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016740 transferase activity 2 GO:0140096 catalytic activity, acting on a protein 1
Localization
GO:0005634 nucleus 1 GO:0005694 chromosome 1 GO:0005829 cytosol 1
Pathway
R-HSA-4839726 Chromatin organization 3 R-HSA-9612973 Autophagy 3 R-HSA-1430728 Metabolism 2
Complex memberships
SDC1-TGM2-FLOT1-BHMT autophagosomal complex

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2008 BHMT variant allozymes expressed in COS-1 cells showed no significant differences from wild type in enzyme activity or immunoreactive protein levels, but had statistically significant differences in apparent Km values, indicating altered substrate binding. BHMT2 protein could not be functionally expressed alone but was stabilized by co-transfection with BHMT and co-precipitated with BHMT, indicating a direct physical interaction between the two paralogs. COS-1 cell expression of variant allozymes, enzyme activity assays, immunoreactive protein quantification, Km determination, co-transfection and co-immunoprecipitation Molecular genetics and metabolism Medium 18457970
2011 Full-length endogenous BHMT (45 kDa cytosolic enzyme) is cleaved in an autophagy-dependent (3-methyladenine-sensitive) manner in isolated rat hepatocytes, generating a novel N-terminal 10-kDa fragment (p10). The cleavage is performed by the asparaginyl proteinase legumain (inhibitable by AJN-230) and occurs primarily in amphisomes rather than lysosomes. This makes BHMT a useful probe/reporter for autophagic flux. Isolated rat hepatocytes, 3-methyladenine inhibition, specific legumain inhibitor (AJN-230), mass spectrometry identification of p10 fragment, leupeptin protection, asparagine inhibition of amphisome-lysosome fusion Autophagy High 21610319
2011 A splicing variant of BHMT exon 4 generates a frameshift with a premature termination codon in exon 5, resulting in complete loss of BHMT enzymatic activity and undetectable protein expression in HepG2 hepatocellular carcinoma cells and 5 of 6 tumor samples; this variant is absent from normal adult and fetal liver. RT-qPCR, exon junction analysis and sequencing, Western blot, immunohistochemistry, enzyme activity assay in HepG2 cells and tumor tissue The international journal of biochemistry & cell biology High 22138536
2011 Depletion of Bhmt in zebrafish morphants causes hypoplasia of liver, exocrine pancreas, and intestine, but paradoxically increases β-cell number. Genetic epistasis experiments showed that Bhmt depletion elevates sonic hedgehog (shh) transcript levels, and Bhmt depletion in Shh-deficient (syu) mutants failed to rescue the isletless phenotype, placing Shh downstream of Bhmt in the pathway controlling β-cell development. Antisense morpholino knockdown in zebrafish, genetic epistasis with syu (shh-null) mutant, qRT-PCR for shh transcripts, histological analysis of organ development Endocrinology High 21952238
2015 The GST-BHMT fusion reporter is cleaved in lysosomes in an autophagy-dependent manner. Under nutrient-rich conditions, proteasome inhibition induces GST-BHMT processing through a mechanism distinct from starvation-induced autophagy: it does not require MTOR or PRKAA/AMPK, but requires cargo receptors SQSTM1/p62 and NBR1, and depends on ER stress signaling via ERN1/IRE1 and MAPK8/JNK1 (but not XBP1), regulating BCL2-BECN1 dissociation. Additionally, the multimerization domain of GST-BHMT is required for proteasome inhibition-induced processing but is dispensable for starvation-induced processing. GST-BHMT reporter fragmentation assay, pharmacological and genetic proteasome inhibition, siRNA knockdown of MTOR, AMPK, SQSTM1, NBR1, ERN1, MAPK8, XBP1, domain deletion mutagenesis Autophagy High 25984893
2017 Bhmt-null mice develop elevated S-adenosylhomocysteine concentrations and preneoplastic foci in the liver (increased placental GST and CK8-18 activity starting at 12 weeks). Whole-genome methylation analysis identified differentially methylated CpGs leading to repression of Iqgap2 and F2rl2 genes, indicating that BHMT activity is required to maintain adequate DNA methylation and normal expression of these loci in liver. Bhmt-null mouse model, whole-genome bisulfite sequencing, RNA expression profiling, immunohistochemistry for preneoplastic markers, metabolite measurement (S-adenosylhomocysteine) FASEB journal High 28179424
2021 BHMT is present in the nucleus of oligodendrocytes (confirmed by immunocytochemistry in human MO3.13 cell line, primary rat oligodendrocytes, and MS postmortem tissue). BHMT expression is increased ~2-fold after oxidative insult. Chromatin fractionation showed direct interaction of BHMT on chromatin, and co-IP demonstrated interaction between BHMT and DNMT3a. Betaine administration increased both histone methyltransferase and DNA methyltransferase activity, and this effect was dependent on BHMT expression (abolished by siRNA knockdown), establishing BHMT as a chromatin-associated regulator of epigenetic marks in oligodendrocytes. Immunocytochemistry, chromatin fractionation, co-immunoprecipitation, qRT-PCR, siRNA knockdown, histone and DNA methyltransferase activity assays PloS one Medium 33975330
2023 After irradiation, SDC1 transports TGM2 from the cell membrane into the cytoplasm and to lysosomes via binding to FLOT1; TGM2 then recognizes BHMT on autophagosomes to coordinate the encounter between autophagosomes and lysosomes. This SDC1-TGM2-FLOT1-BHMT complex maintains autophagic flux in irradiated GBM cells and enhances radioresistance. Co-IP, immunofluorescence, mRFP-GFP-LC3 reporter, transmission electron microscopy, flow cytometry, colony formation, Western blot, qPCR in radioresistant GBM cells Theranostics Medium 37441590
2023 In a monkey hydroxynonenal-injection model of hepatocyte injury, BHMT protein was carbonylated (~2-fold increase by proteomics) and showed increased cleavage without upregulation. Impaired rough ER caused deficient BHMT synthesis, contributing to hepatic steatosis consistent with BHMT's role in phosphatidylcholine metabolism via choline pathway. Proteomics (DIA), Western blot, immunohistochemistry, electron microscopy in monkey liver model Nutrients Low 37111122
2024 Betaine upregulates BHMT expression, leading to increased NADPH production. Elevated NADPH in turn upregulates FTO expression. FTO then reduces m6A methylation in the CDS of Ppargc1α (PGC1α) mRNA, increasing PGC1α expression and inhibiting hepatic lipid accumulation, placing BHMT upstream in a betaine→BHMT→NADPH→FTO→m6A-PGC1α axis. Cell-based assays, siRNA knockdown, Western blot, m6A methylation quantification, gene expression analysis in NAFLD models The Journal of nutritional biochemistry Low 39154792
2026 BHMT overexpression in renal cells reduces ROS production and apoptosis under hypoxia/reoxygenation by enhancing SAM synthesis, which increases DNMT activity, leading to methylation of the NOX4 promoter and suppression of NOX4 transcription and expression. Rescue assays confirmed BHMT-mediated protection is dependent on NOX4 downregulation. RT-qPCR, Western blot, MTT assay, flow cytometry, ROS assays, promoter methylation analysis, BHMT overexpression and rescue experiments in vitro and in vivo IRI model Archives of biochemistry and biophysics Medium 41643883
2026 In murine hepatocytes, BRCA1 deficiency suppresses Bhmt expression. Concomitant knockdown of BRCA1 and BHMT in human hepatoma cells produced additive accumulation of DNA double-strand breaks and increased cell death susceptibility. BHMT repression under BRCA1-deficiency was associated with downregulation of choline metabolism (confirmed by metabolomics), identifying BHMT as a mediator of BRCA1's effects on choline metabolism and DNA damage response. Single nuclear RNA sequencing, siRNA knockdown in human hepatoma cells, DNA damage assays (DSBs), metabolomics in Brca1-deficient mice Scientific reports Medium 41781465
2016 Betaine supplementation in MCD diet-fed rats reversed the reduction of methionine and SAM and elevation of homocysteine by inducing BHMT and MAT expression. In H4IIE cells (which express BHMT), betaine prevented homocysteine-induced reduction of pAMPK/pACC/pSREBP-1c/pLKB1, but not in HepG2 cells (which lack BHMT), demonstrating that BHMT expression is required for the betaine-mediated activation of the AMPK pathway and anti-lipogenic effect. Rat dietary model, cell-based assays in H4IIE and HepG2 cells, Western blot for phosphorylated signaling proteins, BHMT and MAT protein expression, homocysteine and SAM measurement Biochemical and biophysical research communications Medium 27320863
2023 In Bhmt-KO mice, deletion of BHMT in the liver leads to homocysteine-induced ER stress, activation of hepatic transcription factor CREBH, and increased hepatic and plasma FGF21, which in turn promotes adipose browning and atrophy. This establishes a liver-to-adipose signaling axis downstream of BHMT loss. Bhmt-KO mouse model (C57Bl6/J background), histological analysis, gene expression profiling, metabolite/hormone measurements (Hcy, FGF21), ER stress marker analysis Heliyon Medium 36755585

Source papers

Stage 0 corpus · 37 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2003 Investigations of a common genetic variant in betaine-homocysteine methyltransferase (BHMT) in coronary artery disease. Atherosclerosis 67 12818402
2000 Betaine-homocysteine methyltransferase (BHMT): genomic sequencing and relevance to hyperhomocysteinemia and vascular disease in humans. Molecular genetics and metabolism 60 11073719
2008 Human betaine-homocysteine methyltransferase (BHMT) and BHMT2: common gene sequence variation and functional characterization. Molecular genetics and metabolism 59 18457970
2003 Common variant in betaine-homocysteine methyltransferase (BHMT) and risk for spina bifida. American journal of medical genetics. Part A 58 12749058
2023 SDC1-TGM2-FLOT1-BHMT complex determines radiosensitivity of glioblastoma by influencing the fusion of autophagosomes with lysosomes. Theranostics 32 37441590
2011 A splicing variant leads to complete loss of function of betaine-homocysteine methyltransferase (BHMT) gene in hepatocellular carcinoma. The international journal of biochemistry & cell biology 28 22138536
2011 Depletion of Bhmt elevates sonic hedgehog transcript level and increases β-cell number in zebrafish. Endocrinology 25 21952238
2013 Betaine homocysteine methyltransferase (BHMT)-dependent remethylation pathway in human healthy and tumoral liver. Clinical chemistry and laboratory medicine 23 23449526
2021 The BHMT-betaine methylation pathway epigenetically modulates oligodendrocyte maturation. PloS one 22 33975330
2011 Autophagic activity measured in whole rat hepatocytes as the accumulation of a novel BHMT fragment (p10), generated in amphisomes by the asparaginyl proteinase, legumain. Autophagy 21 21610319
2010 Polymorphisms located in the region containing BHMT and BHMT2 genes as maternal protective factors for orofacial clefts. European journal of oral sciences 21 20662904
2016 Association between BHMT gene rs3733890 polymorphism and cancer risk: evidence from a meta-analysis. OncoTargets and therapy 20 27578989
2016 Alleviation of hepatic fat accumulation by betaine involves reduction of homocysteine via up-regulation of betaine-homocysteine methyltransferase (BHMT). Biochemical and biophysical research communications 17 27320863
2024 Betaine alleviates nonalcoholic fatty liver disease (NAFLD) via a manner involving BHMT/FTO/m6A/ PGC1α signaling. The Journal of nutritional biochemistry 16 39154792
2017 Altered methylation of specific DNA loci in the liver of Bhmt-null mice results in repression of Iqgap2 and F2rl2 and is associated with development of preneoplastic foci. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 16 28179424
2011 MTHFD1 G1958A, BHMT G742A, TC2 C776G and TC2 A67G polymorphisms and head and neck squamous cell carcinoma risk. Molecular biology reports 16 21630102
2023 Homocysteine-induced endoplasmic reticulum stress activates FGF21 and is associated with browning and atrophy of white adipose tissue in Bhmt knockout mice. Heliyon 15 36755585
2019 Long non-coding RNA Bhmt-AS attenuates hepatic gluconeogenesis via modulation of Bhmt expression. Biochemical and biophysical research communications 15 31208716
2015 Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes. PloS one 14 26213999
2015 Downregulation of hepatic betaine:homocysteine methyltransferase (BHMT) expression in taurine-deficient mice is reversed by taurine supplementation in vivo. Amino acids 14 26481005
2015 The GST-BHMT assay reveals a distinct mechanism underlying proteasome inhibition-induced macroautophagy in mammalian cells. Autophagy 13 25984893
2011 BHMT gene polymorphisms as risk factors for cleft lip and cleft palate in a Chinese population. Biomedical and environmental sciences : BES 12 21565678
2019 Alleviation of paraquat-induced oxidative lung injury by betaine via regulation of sulfur-containing amino acid metabolism despite the lack of betaine-homocysteine methyltransferase (BHMT) in the lung. Food & function 10 30746538
2019 Association between BHMT and CBS gene promoter methylation with the efficacy of folic acid therapy in patients with hyperhomocysteinemia. Journal of human genetics 9 31558761
2019 Genetic and epigenetic regulation of BHMT is associated with folate therapy efficacy in hyperhomocysteinaemia. Asia Pacific journal of clinical nutrition 8 31826386
2016 Maternal Folate Status and the BHMT c.716G>A Polymorphism Affect the Betaine Dimethylglycine Pathway during Pregnancy. Nutrients 8 27735840
2012 Folate gene polymorphisms MTR A2756G, MTRR A66G, and BHMT G742A and risk for coronary artery disease: a meta-analysis. Genetic testing and molecular biomarkers 8 22339686
2022 Association and Interaction Effect of BHMT Gene Polymorphisms and Maternal Dietary Habits with Ventricular Septal Defect in Offspring. Nutrients 7 35956270
2022 Association of Maternal Betaine-Homocysteine Methyltransferase (BHMT) and BHMT2 Genes Polymorphisms with Congenital Heart Disease in Offspring. Reproductive sciences (Thousand Oaks, Calif.) 6 35835902
2011 [Effects of salinity and betaine on BHMT mRNA expression in Lateolabrax japonicus]. Dong wu xue yan jiu = Zoological research 6 21698793
2023 Vegetable Oil-Peroxidation Product 'Hydroxynonenal' Causes Hepatocyte Injury and Steatosis via Hsp70.1 and BHMT Disorders in the Monkey Liver. Nutrients 4 37111122
2019 Association between the BHMT gene rs3733890 polymorphism and the efficacy of oral folate therapy in patients with hyperhomocysteinemia. Annals of human genetics 3 31111486
2017 Acute lymphoblastic leukemia and genetic variations in BHMT gene: Case-control study and computational characterization. Cancer biomarkers : section A of Disease markers 2 28582843
2026 BHMT Prevents renal ischemia/reperfusion injury via suppressing ROS-induced apoptosis by targeting NOX4. Archives of biochemistry and biophysics 0 41643883
2026 Paradoxical oncogenic effects of hepatic Brca1 through modulating Bhmt. Scientific reports 0 41781465
2026 Targeting metabolic dysregulation in HCC: Development and validation of a dual-biomarker diagnostic model integrating ADH1C and BHMT. Clinics and research in hepatology and gastroenterology 0 41895659
2023 BHMT polymorphism and susceptibility to PTE in Chinese patients. European review for medical and pharmacological sciences 0 37203835

Missed literature

Know a paper Affinage missed for BHMT? Flag it for the maintainers and the community.

No submissions yet.