Serine chirality guides metabolic flow between one-carbon metabolism and neuromodulator synthesis

Suzuki, M.; Adachi, K.; Wiriyasermukul, P.; Fukumura, M.; Tamura, R.; Hirano, Y.; Aizawa, Y.; Miyamoto, T.; Taniguchi, S.; Toda, M.; Homma, H.; Kanekura, K.; Yasuoka, K.; Kanai, T.; Sugimoto, M.; Nagamori, S.; Yasui, M.; Sasabe, J.

doi:10.1101/2024.09.03.610855

bioRxiv · 10.1101/2024.09.03.610855

Serine chirality guides metabolic flow between one-carbon metabolism and neuromodulator synthesis

Suzuki, M.·Adachi, K.·Wiriyasermukul, P.·Fukumura, M.·Tamura, R.·Hirano, Y.·Aizawa, Y.·Miyamoto, T.·Taniguchi, S.·Toda, M.·Homma, H.·Kanekura, K.·Yasuoka, K.·Kanai, T.·Sugimoto, M.·Nagamori, S.·Yasui, M.·Sasabe, J.

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Abstract

O_SCPLOWLC_SCPLOW-serine serves as a central metabolic node that integrates glycolytic flux, lipid metabolism, and one-carbon metabolism. In the mature central nervous system, O_SCPLOWLC_SCPLOW-serine is actively stereo-converted to O_SCPLOWDC_SCPLOW-serine, which functions as a neurotransmitter. However, the role of O_SCPLOWDC_SCPLOW-serine in cellular metabolism remains unclear. Here, we show that O_SCPLOWDC_SCPLOW-serine competes with mitochondrial O_SCPLOWLC_SCPLOW-serine transport, thereby suppressing one-carbon metabolism. Metabolomic analysis revealed that O_SCPLOWDC_SCPLOW-serine reduces intracellular glycine and formate levels, indicating inhibition of the initial step of the one-carbon pathway. Molecular dynamics simulations and enzymatic assays revealed that O_SCPLOWDC_SCPLOW-serine has low affinity for serine hydroxymethyltransferase 2 (Shmt2), which catalyzes the first step in mitochondrial one-carbon metabolism, and does not directly inhibit its activity. Instead, membrane transport assays demonstrated that O_SCPLOWDC_SCPLOW-serine competes with mitochondrial O_SCPLOWLC_SCPLOW-serine transport, depleting the substrate of Shmt2. Functionally, under O_SCPLOWLC_SCPLOW-serine poor conditions in vitro and ex vivo, O_SCPLOWDC_SCPLOW-serine inhibited the proliferation of immature and undifferentiated neural cells including glioblastoma stem cells, which depend highly on one-carbon metabolism. Notably, endogenous O_SCPLOWDC_SCPLOW-serine levels were low during early neurodevelopment, but increased with maturation, coinciding with a shift in the transcriptional profiles of serine metabolic enzymes at the cellular level. Given that O_SCPLOWLC_SCPLOW-serine supports neurodevelopment and O_SCPLOWDC_SCPLOW-serine modulates neurotransmission, this developmental shift in serine enantiomer metabolism appears to align with the functional transitions of the maturing nervous system. Thus, our findings reveal that serine chirality can influence mitochondrial substrate availability and one-carbon flux, offering previously unappreciated insight into the stereoselective regulation of cellular metabolism.

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Suzuki, M., Adachi, K., Wiriyasermukul, P., Fukumura, M., Tamura, R., Hirano, Y., Aizawa, Y., Miyamoto, T., Taniguchi, S., Toda, M., Homma, H., Kanekura, K., Yasuoka, K., Kanai, T., Sugimoto, M., Nagamori, S., Yasui, M., Sasabe, J.. 2024-09-06. Serine chirality guides metabolic flow between one-carbon metabolism and neuromodulator synthesis. https://doi.org/10.1101/2024.09.03.610855

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