GO:0006730 one-carbon metabolic process: Folate and Methionine Cycle Pathway, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0006730 one-carbon metabolic process describes the chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
• One-carbon metabolism is compartmentalized between the cytosol and mitochondria, with the mitochondrial serine catabolism pathway feeding one-carbon units into the folate cycle.
• Serine, glycine, and folate are central substrates that supply one-carbon units for nucleotide synthesis, amino acid homeostasis, and methylation reactions.
• One-carbon metabolism supports S-adenosylmethionine (SAM) production, which is required for histone methylation and inflammatory macrophage function.
• Dysregulation of one-carbon metabolism is implicated in cancer, inflammatory diseases, and alcohol-associated carcinogenesis.
• Key genes include SHMT2, MTHFD2, MTHFR, MTR, and SFXN1, which are frequently studied using CRISPR knockout, point mutation, and overexpression models.
Description
One-carbon metabolic process (GO:0006730) encompasses the network of biochemical reactions that transfer one-carbon units in various oxidation states, serving as a hub for nucleotide biosynthesis, amino acid metabolism, and methylation reactions. This process is essential for cell proliferation and survival, as it provides the building blocks for DNA and RNA synthesis and supports epigenetic regulation through S-adenosylmethionine (SAM). The pathway is compartmentalized between the cytosol and mitochondria, with serine and glycine serving as major carbon donors. In recent years, one-carbon metabolism has emerged as a critical target in cancer research, given its role in supporting rapid tumor growth and its association with metabolic reprogramming. Furthermore, alcohol consumption and inflammatory conditions can perturb one-carbon metabolism, linking it to carcinogenesis and immune responses. Understanding the molecular players and regulatory mechanisms of this pathway is therefore of broad biomedical importance.
one-carbon metabolic process At A Glance
| GO ID | GO:0006730 |
|---|---|
| GO term | one-carbon metabolic process |
| Ontology | biological_process |
| Synonym | one carbon metabolic process, one carbon metabolism, one-carbon metabolism, one-carbon transfer metabolic process, one-carbon transfer metabolism |
| Major function | Transfer of one-carbon units in various oxidation states for nucleotide synthesis, amino acid metabolism, and methylation |
| Key substrates | Serine, glycine, folate, methionine, S-adenosylmethionine (SAM) |
| Subcellular locations | Cytosol, mitochondria |
| Related pathways | Folate cycle, methionine cycle, transsulfuration, serine synthesis |
What Is GO:0006730?
The one-carbon metabolic process (GO:0006730) is defined as the chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states. This includes the folate cycle, methionine cycle, and transsulfuration pathways, which collectively facilitate the donation and acceptance of methyl groups, formyl groups, and other one-carbon moieties for biosynthetic and methylation reactions.
Why Is one-carbon metabolic process Important in Cell Biology?
One-carbon metabolism is fundamental to cell proliferation and survival because it supplies one-carbon units for de novo purine and thymidylate synthesis, and it generates SAM for methylation of DNA, histones, and other biomolecules. Its dysregulation is a hallmark of many cancers, where increased flux supports tumor growth and metabolic adaptation. Additionally, one-carbon metabolism is implicated in inflammatory diseases, neurodegeneration, and alcohol-related pathologies, making it a prime target for therapeutic intervention and biomarker discovery.
• Supports nucleotide biosynthesis for DNA replication and repair.
• Provides methyl groups for epigenetic regulation via SAM.
• Links serine and glycine metabolism to cancer cell proliferation.
• Mitochondrial one-carbon metabolism is essential for redox homeostasis and formate production.
• Dysregulation contributes to alcohol-associated carcinogenesis.
• SAM scarcity sensed by RIPK1 can trigger cell death and inflammation.
• Tumor glycolysis intersects with one-carbon metabolism to fuel growth.
• Targeted by antifolate drugs in cancer and autoimmune diseases.
• Plays a role in immune cell activation and inflammatory responses.
• Potential biomarker for metabolic disorders and cancer diagnostics.
What Happens During one-carbon metabolic process?
Serine and Glycine Interconversion
In simple terms: Serine and glycine can be converted into each other, and this conversion releases one-carbon units.
Serine hydroxymethyltransferases (SHMT1 in cytosol, SHMT2 in mitochondria) catalyze the reversible conversion of serine to glycine, transferring a one-carbon unit to tetrahydrofolate (THF) to form 5,10-methylene-THF. This reaction is a major entry point for one-carbon units into the folate cycle. Mitochondrial SHMT2 is particularly important for providing one-carbon units for formate production, which can then be used in the cytosol for purine synthesis.
Folate Cycle and One-Carbon Interconversion
In simple terms: The folate cycle shuffles one-carbon units between different forms to support various biosynthetic reactions.
The folate cycle involves the interconversion of THF derivatives, including 5,10-methylene-THF, 5,10-methenyl-THF, and 10-formyl-THF. MTHFD2, a mitochondrial enzyme, catalyzes the conversion of 5,10-methylene-THF to 10-formyl-THF, which can be oxidized to formate. In the cytosol, MTHFD1 and MTHFD2L support similar reactions. These one-carbon units are used for de novo purine synthesis (via 10-formyl-THF) and thymidylate synthesis (via 5,10-methylene-THF).
Methionine Cycle and SAM Generation
In simple terms: The methionine cycle produces SAM, the main methyl donor for many cellular reactions.
Methionine synthase (MTR) regenerates methionine from homocysteine using 5-methyl-THF as a methyl donor, linking the folate cycle to the methionine cycle. Methionine is then converted to S-adenosylmethionine (SAM) by methionine adenosyltransferase (MAT). SAM serves as the universal methyl donor for methylation of DNA, RNA, proteins, and lipids. After methyl transfer, SAM becomes S-adenosylhomocysteine (SAH), which is hydrolyzed to homocysteine, completing the cycle.
Transsulfuration Pathway
In simple terms: Homocysteine can be diverted to produce cysteine and antioxidants.
Homocysteine can irreversibly enter the transsulfuration pathway, where cystathionine beta-synthase (CBS) and cystathionine gamma-lyase (CTH) convert it to cysteine. This pathway is important for glutathione synthesis and redox balance. It also provides an alternative fate for homocysteine when methionine cycle flux is altered.
Mitochondrial One-Carbon Metabolism and Formate Production
In simple terms: Mitochondria generate formate, which is exported to the cytosol for nucleotide synthesis.
Mitochondrial one-carbon metabolism is a major source of formate, which is produced from serine via the activity of SHMT2, MTHFD2, and MTHFD1L. Formate is then transported to the cytosol, where it contributes to purine and thymidylate synthesis. The mitochondrial serine transporter SFXN1 is required for this process, as it imports serine into mitochondria for catabolism.
Key Genes Involved in GO:0006730 one-carbon metabolic process
The following genes and proteins are central to one-carbon metabolic process and are frequently studied in research settings.
| Gene | Major Role | Research Relevance |
|---|---|---|
| SHMT2 | Serine hydroxymethyltransferase, mitochondrial; converts serine to glycine and generates 5,10-methylene-THF | Key target in cancer metabolism; knockout reduces tumor growth |
| MTHFD2 | Mitochondrial methylenetetrahydrofolate dehydrogenase; produces formate for nucleotide synthesis | Overexpressed in many cancers; linked to poor prognosis |
| MTHFR | Methylenetetrahydrofolate reductase; converts 5,10-methylene-THF to 5-methyl-THF | Polymorphisms affect folate metabolism and disease risk |
| MTR | Methionine synthase; regenerates methionine from homocysteine | Defects cause hyperhomocysteinemia; target for metabolic studies |
| SFXN1 | Mitochondrial serine transporter; imports serine for one-carbon metabolism | Essential for mitochondrial one-carbon flux; knockout impairs proliferation |
| MTHFD1 | Cytosolic methylenetetrahydrofolate dehydrogenase; supports folate cycle | Involved in purine synthesis and methylation |
| MTHFD1L | Mitochondrial 10-formyl-THF synthetase; produces formate | Required for mitochondrial formate production |
| MAT2A | Methionine adenosyltransferase; synthesizes SAM from methionine | Regulates methylation capacity; target in cancer |
| CBS | Cystathionine beta-synthase; initiates transsulfuration | Links one-carbon metabolism to redox balance |
| CTH | Cystathionine gamma-lyase; produces cysteine | Involved in glutathione synthesis |
| GART | Phosphoribosylglycinamide formyltransferase; uses 10-formyl-THF for purine synthesis | Direct consumer of one-carbon units |
| TYMS | Thymidylate synthase; uses 5,10-methylene-THF for dTMP synthesis | Target of 5-fluorouracil in cancer |
| DHFR | Dihydrofolate reductase; regenerates THF | Target of methotrexate |
| ATIC | AICAR transformylase; uses 10-formyl-THF in purine synthesis | Involved in purine biosynthesis |
| SLC25A32 | Mitochondrial folate transporter | Required for mitochondrial folate uptake |
| MTHFS | Methenyltetrahydrofolate synthetase; interconverts folate forms | Regulates folate cycle flux |
How Is one-carbon metabolic process Regulated?
One-carbon metabolism is regulated at multiple levels, including transcriptional control by nutrient-sensing pathways and post-translational modifications. The mTOR pathway promotes serine synthesis and one-carbon flux to support cell growth. The integrated stress response (ISR) can modulate expression of genes involved in serine and folate metabolism under amino acid deprivation. Additionally, SAM levels are sensed by RIPK1, which can trigger cell death and inflammation when SAM is scarce. This feedback regulation ensures that one-carbon units are allocated appropriately under varying metabolic conditions.
one-carbon metabolic process and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| SHMT2 | Cancer (e.g., glioma, breast cancer) | Knockout in cancer cell lines; xenograft models |
| MTHFD2 | Cancer (e.g., leukemia, melanoma) | CRISPR knockout; overexpression in cancer cells |
| MTHFR | Cardiovascular disease, neural tube defects | Point mutation knock-in in mice |
| MTR | Hyperhomocysteinemia, cancer | Knockout in cell lines; patient-derived mutations |
| SFXN1 | Cancer, metabolic disorders | Knockout in cancer cells; mitochondrial function assays |
One-Carbon Metabolism in Cancer
Cancer cells frequently upregulate one-carbon metabolism to meet the demands of rapid proliferation. Serine and glycine metabolism supports nucleotide synthesis and methylation reactions, and enzymes such as SHMT2 and MTHFD2 are often overexpressed in tumors. Targeting these enzymes with inhibitors or genetic knockdown can reduce tumor growth in preclinical models. Tumor glycolysis also intersects with one-carbon metabolism, providing carbon sources for biosynthetic pathways.
Alcohol-Associated Carcinogenesis and One-Carbon Metabolism
Alcohol consumption perturbs one-carbon metabolism by interfering with folate absorption and methionine synthesis, leading to altered methylation patterns and increased cancer risk. Chronic alcohol exposure can reduce SAM levels and impair DNA methylation, contributing to carcinogenesis in the liver, colon, and breast.
Inflammation and SAM Scarcity
One-carbon metabolism supports SAM production, which is required for histone methylation in inflammatory macrophages. When SAM is scarce, RIPK1 senses this deficiency and drives cell death and inflammation, linking one-carbon metabolism to inflammatory diseases. This pathway may be relevant in conditions such as colitis and sepsis.
From one-carbon metabolic process-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does knockout of SHMT2 reduce tumor growth? | SHMT2 knockout cancer cell lines and xenografts |
| How does MTHFD2 overexpression affect nucleotide synthesis? | MTHFD2 overexpression in cancer cells |
| What is the effect of MTHFR point mutations on folate metabolism? | MTHFR point mutation knock-in cell lines |
| Can SFXN1 knockout impair mitochondrial one-carbon flux? | SFXN1 knockout cells with serine tracing |
| Does SAM scarcity activate RIPK1? | RIPK1 knockout and SAM depletion models |
| How does alcohol exposure alter one-carbon metabolism? | Alcohol-treated cell lines and animal models |
How to Study the one-carbon metabolic process Process
| Method | What It Measures | Typical Application |
|---|---|---|
| 13C-serine tracing | Flux through one-carbon metabolism | Quantify formate and nucleotide synthesis |
| RNA-seq | Gene expression changes | Identify transcriptional regulation of one-carbon genes |
| CRISPR knockout screens | Essential genes for proliferation | Discover one-carbon metabolism dependencies |
| Metabolomics (LC-MS) | Levels of SAM, SAH, folate species | Assess methylation capacity and cycle activity |
| Proteomics | Protein abundance and modifications | Validate enzyme expression in models |
| Live-cell imaging | Mitochondrial serine import | Study SFXN1 function |
| Cell proliferation assay | Growth rate | Evaluate impact of gene knockout |
| Histone methylation Western blot | Epigenetic marks | Link one-carbon metabolism to methylation |
Metabolic Flux Analysis
Stable isotope tracing with 13C-serine or 13C-glycine followed by mass spectrometry can quantify one-carbon flux through the folate and methionine cycles. This method reveals how genetic perturbations affect metabolic rewiring.
Genomic and Transcriptomic Profiling
RNA-seq and CRISPR screens can identify genes essential for one-carbon metabolism and their transcriptional regulation. Bioinformatics analysis of public datasets can reveal expression patterns in cancer versus normal tissues.
Proteomics and Metabolomics
Mass spectrometry-based proteomics and metabolomics can measure enzyme abundance and metabolite levels, such as SAM, SAH, and folate species. These approaches are useful for validating knockout or overexpression models.
Imaging and Functional Assays
Fluorescence microscopy with targeted biosensors can monitor mitochondrial serine import and one-carbon flux in live cells. Cell proliferation and colony formation assays assess the functional consequences of metabolic perturbations.
How CRISPR Can Be Used to Study GO:0006730 one-carbon metabolic process
Knockout
CRISPR knockout of one-carbon metabolism genes such as SHMT2, MTHFD2, or SFXN1 can reveal their essentiality for cell proliferation and survival. Knockout cell lines are valuable for metabolic tracing and drug sensitivity studies.
Point Mutation
Point mutations in genes like MTHFR or MTR can be introduced using CRISPR base editing or homology-directed repair to model human polymorphisms and assess their impact on enzyme activity and disease risk.
Knock-in
Knock-in of tagged versions of one-carbon enzymes (e.g., FLAG-SHMT2) allows for immunoprecipitation and localization studies. Knock-in of reporter genes can enable live-cell imaging of metabolic flux.
Overexpression
CRISPR activation or lentiviral overexpression of MTHFD2 or SHMT2 can model the elevated one-carbon metabolism observed in cancer cells, facilitating studies on tumor growth and drug resistance.
How EDITGENE Supports one-carbon metabolic process Research
Researchers studying one-carbon metabolic process-related genes often need to determine whether a candidate gene is causally involved in metabolic regulation, disease progression, or therapeutic response. Generating precise genetic models is essential to validate hypotheses and uncover mechanistic insights.
Contact EDITGENE today to design your custom CRISPR model for one-carbon metabolic process research.
Frequently Asked Questions About one-carbon metabolic process
What is one-carbon metabolic process?
One-carbon metabolic process (GO:0006730) is the set of biochemical reactions that transfer one-carbon units in various oxidation states, supporting nucleotide synthesis, amino acid metabolism, and methylation.
What genes are involved in one-carbon metabolism?
Key genes include SHMT2, MTHFD2, MTHFR, MTR, SFXN1, MAT2A, and CBS, among others.
How is one-carbon metabolism regulated?
It is regulated by nutrient-sensing pathways like mTOR, the integrated stress response, and feedback from SAM levels sensed by RIPK1.
Why is one-carbon metabolism important in cancer?
Cancer cells upregulate one-carbon metabolism to support rapid proliferation, nucleotide synthesis, and methylation, making it a therapeutic target.
What is the role of serine in one-carbon metabolism?
Serine is a major one-carbon donor; it is converted to glycine by SHMT enzymes, generating 5,10-methylene-THF for the folate cycle.
How does alcohol affect one-carbon metabolism?
Alcohol interferes with folate absorption and methionine synthesis, leading to altered methylation and increased cancer risk.
What is SAM and why is it important?
S-adenosylmethionine (SAM) is the universal methyl donor produced in the methionine cycle; it is required for histone and DNA methylation.
What diseases are linked to one-carbon metabolism?
Cancer, cardiovascular disease, neural tube defects, and inflammatory conditions are associated with dysregulated one-carbon metabolism.
How can I study one-carbon metabolism in the lab?
Use stable isotope tracing, metabolomics, CRISPR knockout models, and proliferation assays to assess pathway activity and gene function.
What CRISPR models are available for one-carbon metabolism research?
EDITGENE offers knockout, point mutation, knock-in, and overexpression models for genes like SHMT2, MTHFD2, and MTHFR, plus library screening and bioinformatics services.
Conclusion
One-carbon metabolic process (GO:0006730) is a central metabolic hub that integrates serine, glycine, folate, and methionine metabolism to support nucleotide synthesis, methylation, and redox balance. Its dysregulation is implicated in cancer, inflammatory diseases, and alcohol-associated pathologies, making it a high-priority research area. Advances in CRISPR-based models and metabolic profiling continue to uncover new therapeutic opportunities targeting this pathway.
References
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- 2. Rumgay H et al.. 2021. Alcohol and Cancer: Epidemiology and Biological Mechanisms.. Nutrients 13(9) PMID: 34579050
- 3. Yu W et al.. 2019. One-Carbon Metabolism Supports S-Adenosylmethionine and Histone Methylation to Drive Inflammatory Macrophages.. Mol Cell 75(6):1147-1160.e5 PMID: 31420217
- 4. Locasale JW. 2013. Serine, glycine and one-carbon units: cancer metabolism in full circle.. Nat Rev Cancer 13(8):572-83 PMID: 23822983
- 5. Amelio I et al.. 2014. Serine and glycine metabolism in cancer.. Trends Biochem Sci 39(4):191-8 PMID: 24657017
- 6. Kory N et al.. 2018. SFXN1 is a mitochondrial serine transporter required for one-carbon metabolism.. Science 362(6416) PMID: 30442778
- 7. Chen Z et al.. 2025. RIPK1 senses S-adenosylmethionine scarcity to drive cell death and inflammation.. Cell Metab 37(8):1732-1749.e9 PMID: 40570842
- 8. Paul S et al.. 2022. Tumor glycolysis, an essential sweet tooth of tumor cells.. Semin Cancer Biol 86(Pt 3):1216-1230 PMID: 36330953
