One-Carbon Metabolism: Formaldehyde’s Role in S-Adenosylmethionine Biosynthesis and Disease

Formaldehyde (FA), a major one-carbon unit, originates from both environmental exposure and endogenous sources. Its swift scavenging in cells through enzymatic oxidation forms the cornerstone of detoxification. FA’s role extends beyond a mere metabolic byproduct; it acts as a critical intermediary in the folate cycle, linking with the biosynthesis of S-adenosylmethionine (SAM), the primary cellular methyl donor. This intersection of FA with the folate cycle and SAM biosynthesis is crucial in maintaining cellular one-carbon balance. One-carbon metabolism is a fundamental cellular process that detoxifies reactive carbon species and channels them into biosynthetic pathways. This complex system balances detoxification and biosynthesis, impacting essential cellular functions and influencing disease states. One-carbon metabolism plays a crucial role in various cellular processes, including DNA synthesis and repair, methylation reactions, and amino acid metabolism. Dysregulation in this pathway can contribute to the development or progression of several diseases, for instance, alterations in one-carbon metabolism can affect DNA synthesis and repair mechanisms, potentially leading to genomic instability and carcinogenesis. Specific cancers, like colorectal, breast, and pancreatic cancers, have been linked to disruptions in this pathway. Moreover, abnormalities in one-carbon metabolism can lead to elevated homocysteine levels, a risk factor for cardiovascular diseases, including coronary artery disease, stroke, and peripheral vascular disease. Furthermore, impaired one-carbon metabolism can affect neurological functions due to its role in neurotransmitter synthesis and myelin sheath maintenance. It’s associated with conditions like Alzheimer’s disease, Parkinson’s disease, and cognitive impairments. Proper one-additionally, carbon metabolism is essential for fetal development. Deficiencies in folate metabolism can lead to neural tube defects such as spina bifida and anencephaly. Alterations in methylation processes, crucial for brain function and neurotransmitter synthesis, can contribute to psychiatric conditions like depression, bipolar disorder, and schizophrenia. Abnormal SAM and homocysteine levels, resulting from one-carbon metabolism dysregulation, are linked to liver diseases, including nonalcoholic fatty liver disease (NAFLD) and cirrhosis. One-carbon metabolism is also vital for bone health. Its dysregulation can contribute to osteoporosis and other bone-related disorders. These associations underscore the importance of one-carbon metabolism in a wide range of physiological and pathological processes, highlighting the need for further research into therapeutic strategies targeting this pathway.

Given FA’s electrophilic nature, the researchers hypothesized that it might selectively target cysteine residues across the proteome, impacting posttranslational modifications and thus influencing cellular processes. This hypothesis was tested through a proteome-wide profiling study aimed at understanding FA’s global reactivity and its regulatory roles in one-carbon metabolism.

In a new study published in Science Journal led by Professor Christopher J. Chang  from the University of California Berkeley and conducted by Dr. Vanha Pham, Kevin Bruemmer, Joel W. Toh, Eva Ge, Logan Tenney, Carl Ward, Felix Dingler, Christopher Millington, Dr. Carlos Garcia-Prieto, Dr. Mia Pulos-Holmes, Dr. Nicholas Ingolia, Dr. Lucas Pontel, Dr. Manel Esteller, Dr. Ketan Patel, and Dr. Daniel Nomura, the researchers conducted a series of innovative experiments to explore the role of FA in one-carbon metabolism, focusing on its interaction with cysteine residues and its influence on the biosynthesis of SAM.

To identify FA-sensitive cysteine sites across the proteome, the team used the isoTOP-ABPP platform, applying it to mouse liver lysates treated with FA. They used an activity-based probe to tag cysteine residues and then identified these tagged peptides using mass spectrometry, they identified numerous FA-reactive cysteine sites, particularly in proteins involved in one-carbon metabolism, challenging the view of FA as a non-selective electrophile. They treated purified MAT1A protein with FA, followed by peptide digestion and mass spectrometry analysis to pinpoint FA-induced modifications to identify direct sites of FA modification on MAT1A, a key enzyme in SAM biosynthesis and found specific cysteine residues on MAT1A as targets of FA modification.

The authors incubated purified MAT1A and MAT2A enzymes with varying concentrations of FA, and their activity in catalyzing SAM production was measured to study the effect of FA on the activity of MAT1A and its isoform MAT2A.  FA inhibited MAT1A activity in a dose-dependent manner but did not affect MAT2A, indicating isoform-specific inhibition.  To observe the impact of FA on cellular SAM levels, they used CRISPR-Cas9 technology to create HepG2 cell lines exclusively expressing either MAT1A or MAT2A. These cells were then treated with FA, and SAM levels were measured. In cells expressing MAT1A, FA treatment led to decreased SAM levels, affirming the inhibitory effect of FA on MAT1A at the cellular level.

To investigate the physiological effects of chronic FA elevation on SAM production and methylation processes in vivo. The team studied Adh5–/– mice, which exhibit elevated FA levels, analyzing metabolites, DNA, mRNA, and histone methylation. These mice showed a decrease in SAM levels and alterations in histone methylation, confirming the impact of elevated FA on one-carbon metabolism in a living organism.  Analysis of MAT1A and MAT2A expression, along with epigenetic changes in their promoters, was conducted in both the mouse model and cellular systems to understand how cells respond to FA-induced SAM deficiency. They observed an increase in MAT1A expression, likely as a compensatory mechanism to maintain SAM levels, regulated through both genetic and epigenetic mechanisms. To identify transcription factors involved in FA-induced regulation of MAT1A, Luciferase assays and transcription factor knockdown experiments were conducted to understand the regulation of MAT1A expression under FA stress and specific transcription factors were identified as key players in the regulation of MAT1A in response to elevated FA levels.

These experiments collectively provided a comprehensive understanding of how FA, as a one-carbon unit, contributes to the regulation of one-carbon metabolism, particularly impacting SAM biosynthesis and related methylation processes. The new study unveils a nuanced view of FA’s role in one-carbon metabolism. Contrary to its traditional perception as a toxic byproduct, FA emerges as a selective regulatory molecule, capable of influencing crucial metabolic pathways. Its interaction with MAT1A and the subsequent impact on SAM biosynthesis and epigenetic regulation underscore a sophisticated feedback mechanism in cellular metabolism. These findings pave the way for further exploration of the implications of FA in one-carbon metabolism and its broader connection to human health and disease. Understanding this intricate balance between FA and SAM biosynthesis could lead to novel insights into metabolic regulation and the development of therapeutic strategies for conditions where one-carbon balance is disrupted.