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An allosteric mechanism for switching between parallel tracks in mammalian sulfur metabolism. PLoS Comput Biol 2008; 4:e1000076. [PMID: 18451990 PMCID: PMC2346559 DOI: 10.1371/journal.pcbi.1000076] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 03/31/2008] [Indexed: 01/05/2023] Open
Abstract
Methionine (Met) is an essential amino acid that is needed for the synthesis of S-adenosylmethionine (AdoMet), the major biological methylating agent. Methionine used for AdoMet synthesis can be replenished via remethylation of homocysteine. Alternatively, homocysteine can be converted to cysteine via the transsulfuration pathway. Aberrations in methionine metabolism are associated with a number of complex diseases, including cancer, anemia, and neurodegenerative diseases. The concentration of methionine in blood and in organs is tightly regulated. Liver plays a key role in buffering blood methionine levels, and an interesting feature of its metabolism is that parallel tracks exist for the synthesis and utilization of AdoMet. To elucidate the molecular mechanism that controls metabolic fluxes in liver methionine metabolism, we have studied the dependencies of AdoMet concentration and methionine consumption rate on methionine concentration in native murine hepatocytes at physiologically relevant concentrations (40–400 µM). We find that both [AdoMet] and methionine consumption rates do not change gradually with an increase in [Met] but rise sharply (∼10-fold) in the narrow Met interval from 50 to 100 µM. Analysis of our experimental data using a mathematical model reveals that the sharp increase in [AdoMet] and the methionine consumption rate observed within the trigger zone are associated with metabolic switching from methionine conservation to disposal, regulated allosterically by switching between parallel pathways. This regulatory switch is triggered by [Met] and provides a mechanism for stabilization of methionine levels in blood over wide variations in dietary methionine intake. Methionine is an essential amino acid that is highly toxic at elevated levels, and the liver is primarily responsible for buffering its concentration in circulation. Intracellularly, methionine is needed for the synthesis of S-adenosylmethionine (AdoMet), the major biological methylating agent. Methionine used for AdoMet synthesis can be replenished via remethylation of homocysteine. Alternatively, homocysteine can be converted to cysteine via the transsulfuration pathway. A specific feature of liver methionine metabolism is the existence of twin pathways for AdoMet synthesis and degradation. In this study, we analyzed the dependence of methionine metabolism on methionine concentration in liver cells using a combined experimental and theoretical approach. We find a sharp transition in rat hepatocyte metabolism from methionine conservation to a disposal mode with an increase in methionine concentration above its physiological range. Mathematical modeling reveals that this transition is afforded by an allosteric mechanism for switching between parallel metabolic pathways. This study demonstrates a novel mechanism of trigger behavior in biological systems by which the substrate for the metabolic network switches metabolic flux between parallel tracks for sustaining two different metabolic modes.
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Reed MC, Thomas RL, Pavisic J, James SJ, Ulrich CM, Nijhout HF. A mathematical model of glutathione metabolism. Theor Biol Med Model 2008; 5:8. [PMID: 18442411 PMCID: PMC2391141 DOI: 10.1186/1742-4682-5-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 04/28/2008] [Indexed: 12/04/2022] Open
Abstract
Background Glutathione (GSH) plays an important role in anti-oxidant defense and detoxification reactions. It is primarily synthesized in the liver by the transsulfuration pathway and exported to provide precursors for in situ GSH synthesis by other tissues. Deficits in glutathione have been implicated in aging and a host of diseases including Alzheimer's disease, Parkinson's disease, cardiovascular disease, cancer, Down syndrome and autism. Approach We explore the properties of glutathione metabolism in the liver by experimenting with a mathematical model of one-carbon metabolism, the transsulfuration pathway, and glutathione synthesis, transport, and breakdown. The model is based on known properties of the enzymes and the regulation of those enzymes by oxidative stress. We explore the half-life of glutathione, the regulation of glutathione synthesis, and its sensitivity to fluctuations in amino acid input. We use the model to simulate the metabolic profiles previously observed in Down syndrome and autism and compare the model results to clinical data. Conclusion We show that the glutathione pools in hepatic cells and in the blood are quite insensitive to fluctuations in amino acid input and offer an explanation based on model predictions. In contrast, we show that hepatic glutathione pools are highly sensitive to the level of oxidative stress. The model shows that overexpression of genes on chromosome 21 and an increase in oxidative stress can explain the metabolic profile of Down syndrome. The model also correctly simulates the metabolic profile of autism when oxidative stress is substantially increased and the adenosine concentration is raised. Finally, we discuss how individual variation arises and its consequences for one-carbon and glutathione metabolism.
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Affiliation(s)
- Michael C Reed
- Department of Mathematics, Duke University, Durham, NC 27708, USA.
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53
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Piazza M, Feng XJ, Rabinowitz JD, Rabitz H. Diverse metabolic model parameters generate similar methionine cycle dynamics. J Theor Biol 2008; 251:628-39. [PMID: 18313076 PMCID: PMC2386584 DOI: 10.1016/j.jtbi.2007.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 12/12/2007] [Accepted: 12/17/2007] [Indexed: 12/13/2022]
Abstract
Parameter estimation constitutes a major challenge in dynamic modeling of metabolic networks. Here we examine, via computational simulations, the influence of system nonlinearity and the nature of available data on the distribution and predictive capability of identified model parameters. Simulated methionine cycle metabolite concentration data (both with and without corresponding flux data) was inverted to identify model parameters consistent with it. Thousands of diverse parameter families were found to be consistent with the data to within moderate error, with most of the parameter values spanning over 1000-fold ranges irrespective of whether flux data was included. Due to strong correlations within the extracted parameter families, model predictions were generally reliable despite the broad ranges found for individual parameters. Inclusion of flux data, by strengthening these correlations, resulted in substantially more reliable flux predictions. These findings suggest that, despite the difficulty of extracting biochemically accurate model parameters from system level data, such data may nevertheless prove adequate for driving the development of predictive dynamic metabolic models.
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Affiliation(s)
- Matthew Piazza
- Department of Chemistry, Princeton University, Princeton NJ, 08544
| | - Xiao-Jiang Feng
- Department of Chemistry, Princeton University, Princeton NJ, 08544
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton NJ, 08544
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Herschel Rabitz
- Department of Chemistry, Princeton University, Princeton NJ, 08544
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Abstract
Folate-mediated one-carbon metabolism is an unusually complex metabolic network, consisting of several interlocking cycles, and compartmentation between cytosol and mitochondria. The cycles have diverse functions, the primary being thymidylate synthesis (the rate limiting step in DNA synthesis), the initial steps in purine synthesis, glutathione synthesis, and a host of methyl transfer reactions that include DNA and histone methylation. Regulation within the network is accomplished by numerous allosteric interactions in which metabolites in one part of the network affect the activity of enzymes elsewhere in the network. Although a large body of experimental work has elucidated the details of the mechanisms in every part of the network, the multitude of complex and non-linear interactions within the network makes it difficult to deduce how the network as a whole operates. Understanding the operation of this network is further complicated by the fact that human populations maintain functional polymorphisms for several enzymes in the network, and that the network is subject to continual short and long-term fluctuations in its inputs as well as in demands on its various outputs. Understanding how such a complex system operates is possible only by means of mathematical models that take account of all the reactions and interactions. Simulations with such models can be used as an adjunct to laboratory experimentation to test ideas and alternative hypotheses and interpretations quickly and inexpensively. A number of mathematical models have been developed over the years, largely motivated by the need to understand the complex mechanisms by which anticancer drugs like methotrexate inhibit nucleotide synthesis and thus limit the ability of cells to divide. More recently, mathematical models have been used to investigate the regulatory and homeostatic mechanisms that allow the system to accommodate large fluctuations in one part of the network without affecting critical functions elsewhere in the network.
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Thomas DC. Multistage sampling for latent variable models. LIFETIME DATA ANALYSIS 2007; 13:565-581. [PMID: 17943440 DOI: 10.1007/s10985-007-9061-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Accepted: 09/12/2007] [Indexed: 05/25/2023]
Abstract
I consider the design of multistage sampling schemes for epidemiologic studies involving latent variable models, with surrogate measurements of the latent variables on a subset of subjects. Such models arise in various situations: when detailed exposure measurements are combined with variables that can be used to assign exposures to unmeasured subjects; when biomarkers are obtained to assess an unobserved pathophysiologic process; or when additional information is to be obtained on confounding or modifying variables. In such situations, it may be possible to stratify the subsample on data available for all subjects in the main study, such as outcomes, exposure predictors, or geographic locations. Three circumstances where analytic calculations of the optimal design are possible are considered: (i) when all variables are binary; (ii) when all are normally distributed; and (iii) when the latent variable and its measurement are normally distributed, but the outcome is binary. In each of these cases, it is often possible to considerably improve the cost efficiency of the design by appropriate selection of the sampling fractions. More complex situations arise when the data are spatially distributed: the spatial correlation can be exploited to improve exposure assignment for unmeasured locations using available measurements on neighboring locations; some approaches for informative selection of the measurement sample using location and/or exposure predictor data are considered.
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Affiliation(s)
- Duncan C Thomas
- Department of Preventive Medicine, University of Southern California, 1540 Alcazar St., CHP-220, Los Angeles, CA 90089-9011, USA.
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56
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Ji C, Shinohara M, Kuhlenkamp J, Chan C, Kaplowitz N. Mechanisms of protection by the betaine-homocysteine methyltransferase/betaine system in HepG2 cells and primary mouse hepatocytes. Hepatology 2007; 46:1586-96. [PMID: 17705221 PMCID: PMC2642650 DOI: 10.1002/hep.21854] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
UNLABELLED Betaine-homocysteine methyltransferase (BHMT) regulates homocysteine levels in the liver. We previously reported that the alteration of BHMT is associated with alcoholic liver steatosis and injury. In this study, we tested whether BHMT protects hepatocytes from homocysteine-induced injury and lipid accumulation. Both BHMT transfectants of HepG2 cells and primary mouse hepatocytes with suppressed BHMT were generated. Comparisons were made between the cell models with respect to their response to homocysteine treatments. Homocysteine metabolism was impaired in HepG2 cells, and the expression of BHMT in HepG2 cells ameliorated the impairment and stabilized the levels of intracellular homocysteine after the addition of exogenous homocysteine. BHMT expression inhibited homocysteine-induced glucose-regulated protein 78 (GRP78) and C/EBP-homologous protein (CHOP) and homocysteine-induced cell death. A betaine treatment protected primary mouse hepatocytes from a homocysteine-induced increase in GRP78 and cell death but not a tunicamycin-induced increase. Homocysteine induced greater CHOP expression (2.7-fold) in BHMT small interfering RNA (siRNA)-transfected cells than in a control (1.9-fold). Homocysteine-induced cell death was increased by 40% in the siRNA-treated cells in comparison with the control. Apolipoprotein B (apoB) expression was higher and triglycerides and cholesterol were lower in HepG2 expressing BHMT. In primary mouse hepatocytes, homocysteine induced the accumulation of triglycerides and cholesterol, which was reduced in the presence of betaine. Betaine partially reduced homocysteine-induced sterol regulatory element binding protein 1 expression in HepG2 cells and increased S-adenosylmethionine in primary mouse hepatocytes. CONCLUSION The BHMT/betaine system directly protects hepatocytes from homocysteine-induced injury but not tunicamycin-induced injury, including an endoplasmic reticulum stress response, lipid accumulation, and cell death. This system also exhibits a more generalized effect on liver lipids by inducing ApoB expression and increasing S-adenosylmethionine/S-adenosylhomocysteine.
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Affiliation(s)
- Cheng Ji
- University of Southern California Research Center for Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
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57
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Montañez R, Rodríguez-Caso C, Sánchez-Jiménez F, Medina MA. In silico analysis of arginine catabolism as a source of nitric oxide or polyamines in endothelial cells. Amino Acids 2007; 34:223-9. [PMID: 17520329 DOI: 10.1007/s00726-007-0502-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Accepted: 01/31/2007] [Indexed: 11/25/2022]
Abstract
We use a modeling and simulation approach to carry out an in silico analysis of the metabolic pathways involving arginine as a precursor of nitric oxide or polyamines in aorta endothelial cells. Our model predicts conditions of physiological steady state, as well as the response of the system to changes in the control parameter, external arginine concentration. Metabolic flux control analysis allowed us to predict the values of flux control coefficients for all the transporters and enzymes included in the model. This analysis fulfills the flux control coefficient summation theorem and shows that both the low affinity transporter and arginase share the control of the fluxes through these metabolic pathways.
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Affiliation(s)
- R Montañez
- Procel Group, Department of Molecular Biology and Biochemistry, University of Málaga, and CIBERER, Málaga, Spain
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58
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Anderson DF, Mattingly JC, Nijhout HF, Reed MC. Propagation of Fluctuations in Biochemical Systems, I: Linear SSC Networks. Bull Math Biol 2007; 69:1791-813. [PMID: 17457656 DOI: 10.1007/s11538-007-9192-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Accepted: 12/21/2006] [Indexed: 10/23/2022]
Abstract
We investigate the propagation of random fluctuations through biochemical networks in which the number of molecules of each species is large enough so that the concentrations are well modeled by differential equations. We study the effect of network topology on the emergent properties of the reaction system by characterizing the behavior of variance as fluctuations propagate down chains and studying the effect of side chains and feedback loops. We also investigate the asymptotic behavior of the system as one reaction becomes fast relative to the others.
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Affiliation(s)
- David F Anderson
- Department of Mathematics, Duke University, Durham, NC 27708, USA
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59
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Nijhout HF, Reed MC, Lam SL, Shane B, Gregory JF, Ulrich CM. In silico experimentation with a model of hepatic mitochondrial folate metabolism. Theor Biol Med Model 2006; 3:40. [PMID: 17150100 PMCID: PMC1713227 DOI: 10.1186/1742-4682-3-40] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 12/06/2006] [Indexed: 12/20/2022] Open
Abstract
Background In eukaryotes, folate metabolism is compartmentalized and occurs in both the cytosol and the mitochondria. The function of this compartmentalization and the great changes that occur in the mitochondrial compartment during embryonic development and in rapidly growing cancer cells are gradually becoming understood, though many aspects remain puzzling and controversial. Approach We explore the properties of cytosolic and mitochondrial folate metabolism by experimenting with a mathematical model of hepatic one-carbon metabolism. The model is based on known biochemical properties of mitochondrial and cytosolic enzymes. We use the model to study questions about the relative roles of the cytosolic and mitochondrial folate cycles posed in the experimental literature. We investigate: the control of the direction of the mitochondrial and cytosolic serine hydroxymethyltransferase (SHMT) reactions, the role of the mitochondrial bifunctional enzyme, the role of the glycine cleavage system, the effects of variations in serine and glycine inputs, and the effects of methionine and protein loading. Conclusion The model reproduces many experimental findings and gives new insights into the underlying properties of mitochondrial folate metabolism. Particularly interesting is the remarkable stability of formate production in the mitochondria in the face of large changes in serine and glycine input. The model shows that in the presence of the bifunctional enzyme (as in embryonic tissues and cancer cells), the mitochondria primarily support cytosolic purine and pyrimidine synthesis via the export of formate, while in adult tissues the mitochondria produce serine for gluconeogenesis.
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Affiliation(s)
| | - Michael C Reed
- Department of Mathematics, Duke University, Durham, NC 27708, USA
| | - Shi-Ling Lam
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Barry Shane
- Department of Nutrition Sciences and Toxicology, University of California, Berkeley, CA 94720-3104, USA
| | - Jesse F Gregory
- Department of Food Science and Human Nutrition, University of Florida, 32611-0370, USA
| | - Cornelia M Ulrich
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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60
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Reed MC, Nijhout HF, Neuhouser ML, Gregory JF, Shane B, James SJ, Boynton A, Ulrich CM. A mathematical model gives insights into nutritional and genetic aspects of folate-mediated one-carbon metabolism. J Nutr 2006; 136:2653-61. [PMID: 16988141 DOI: 10.1093/jn/136.10.2653] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Impaired folate-mediated 1-carbon metabolism has been linked to multiple disease outcomes. A better understanding of the nutritional and genetic influences on this complex biochemical pathway is needed to comprehend their impact on human health. To this end, we created a mathematical model of folate-mediated 1-carbon metabolism. The model uses published data on folate enzyme kinetics and regulatory mechanisms to simulate the impact of genetic and nutritional variation on critical aspects of the pathway. We found that the model predictions match experimental data, while providing novel insights into pathway kinetics. Our primary observations were as follows: 1) the inverse association between folate and homocysteine is strongest at very low folate concentrations, but there is no association at high folate concentrations; 2) the DNA methylation reaction rate is relatively insensitive to changes in folate pool size; and 3) as folate concentrations become very high, enzyme velocities decrease. With regard to polymorphisms in 5,10-methylenetetrahydrofolate reductase (MTHFR), the modeling predicts that decrease MTHFR activity reduces concentrations of S-adenosylmethionine and 5-methyltetrahydrofolate, as well as DNA methylation, while modestly increasing S-adenosylhomocysteine and homocysteine concentrations and thymidine or purine synthesis. Decreased folate together with a simulated vitamin B-12 deficiency results in decreases in DNA methylation and purine and thymidine synthesis. Decreased MTHFR activity superimposed on the B-12 deficiency appears to reverse the declines in purine and thymidine synthesis. These mathematical simulations of folate-mediated 1-carbon metabolism provide a cost-efficient approach to in silico experimentation that can complement and help guide laboratory studies.
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Affiliation(s)
- Michael C Reed
- Department of Mathematics, Duke University, Durham, NC 27708, USA
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61
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Boyles AL, Billups AV, Deak KL, Siegel DG, Mehltretter L, Slifer SH, Bassuk AG, Kessler JA, Reed MC, Nijhout HF, George TM, Enterline DS, Gilbert JR, Speer MC. Neural tube defects and folate pathway genes: family-based association tests of gene-gene and gene-environment interactions. ENVIRONMENTAL HEALTH PERSPECTIVES 2006; 114:1547-52. [PMID: 17035141 PMCID: PMC1626421 DOI: 10.1289/ehp.9166] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
BACKGROUND Folate metabolism pathway genes have been examined for association with neural tube defects (NTDs) because folic acid supplementation reduces the risk of this debilitating birth defect. Most studies addressed these genes individually, often with different populations providing conflicting results. OBJECTIVES Our study evaluates several folate pathway genes for association with human NTDs, incorporating an environmental cofactor: maternal folate supplementation. METHODS In 304 Caucasian American NTD families with myelomeningocele or anencephaly, we examined 28 polymorphisms in 11 genes: folate receptor 1, folate receptor 2, solute carrier family 19 member 1, transcobalamin II, methylenetetrahydrofolate dehydrogenase 1, serine hydroxymethyl-transferase 1, 5,10-methylenetetrahydrofolate reductase (MTHFR), 5-methyltetrahydrofolate-homo-cysteine methyltransferase, 5-methyltetrahydrofolate-homocysteine methyltransferase reductase, betaine-homocysteine methyltransferase (BHMT), and cystathionine-beta-synthase. RESULTS Only single nucleotide polymorphisms (SNPs) in BHMT were significantly associated in the overall data set; this significance was strongest when mothers took folate-containing nutritional supplements before conception. The BHMT SNP rs3733890 was more significant when the data were stratified by preferential transmission of the MTHFR rs1801133 thermolabile T allele from parent to offspring. Other SNPs in folate pathway genes were marginally significant in some analyses when stratified by maternal supplementation, MTHFR, or BHMT allele transmission. CONCLUSIONS BHMT rs3733890 is significantly associated in our data set, whereas MTHFR rs1801133 is not a major risk factor. Further investigation of folate and methionine cycle genes will require extensive SNP genotyping and/or resequencing to identify novel variants, inclusion of environmental factors, and investigation of gene-gene interactions in large data sets.
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Affiliation(s)
- Abee L. Boyles
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Ashley V. Billups
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Kristen L. Deak
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Deborah G. Siegel
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Lorraine Mehltretter
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Susan H. Slifer
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Alexander G. Bassuk
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - John A. Kessler
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | | | | | - David S. Enterline
- Department of Radiology, Duke University Medical Center, Durham, North Carolina, USA
| | - John R. Gilbert
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Marcy C. Speer
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA
- Address correspondence to M.C. Speer, Duke University Medical Center, Box 3445, Durham, NC 27710 USA. Telephone: (919) 684-2702. Fax: (919) 684-0917. E-mail:
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Rodríguez-Caso C, Montañez R, Cascante M, Sánchez-Jiménez F, Medina MA. Mathematical modeling of polyamine metabolism in mammals. J Biol Chem 2006; 281:21799-21812. [PMID: 16709566 DOI: 10.1074/jbc.m602756200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Polyamines are considered as essential compounds in living cells, since they are involved in cell proliferation, transcription, and translation processes. Furthermore, polyamine homeostasis is necessary to cell survival, and its deregulation is involved in relevant processes, such as cancer and neurodegenerative disorders. Great efforts have been made to elucidate the nature of polyamine homeostasis, giving rise to relevant information concerning the behavior of the different components of polyamine metabolism, and a great amount of information has been generated. However, a complex regulation at transcriptional, translational, and metabolic levels as well as the strong relationship between polyamines and essential cell processes make it difficult to discriminate the role of polyamine regulation itself from the whole cell response when an experimental approach is given in vivo. To overcome this limitation, a bottom-up approach to model mathematically metabolic pathways could allow us to elucidate the systemic behavior from individual kinetic and molecular properties. In this paper, we propose a mathematical model of polyamine metabolism from kinetic constants and both metabolite and enzyme levels extracted from bibliographic sources. This model captures the tendencies observed in transgenic mice for the so-called key enzymes of polyamine metabolism, ornithine decarboxylase, S-adenosylmethionine decarboxylase and spermine spermidine N-acetyl transferase. Furthermore, the model shows a relevant role of S-adenosylmethionine and acetyl-CoA availability in polyamine homeostasis, which are not usually considered in systemic experimental studies.
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Affiliation(s)
- Carlos Rodríguez-Caso
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga E-29071, Spain
| | - Raúl Montañez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga E-29071, Spain
| | - Marta Cascante
- Departamento de Bioquímica, Facultad de Química, Universidad de Barcelona, Barcelona E-08028, Spain
| | - Francisca Sánchez-Jiménez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga E-29071, Spain
| | - Miguel A Medina
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Málaga E-29071, Spain.
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Ulrich CM, Nijhout HF, Reed MC. Mathematical Modeling: Epidemiology Meets Systems Biology. Cancer Epidemiol Biomarkers Prev 2006; 15:827-9. [PMID: 16702357 DOI: 10.1158/1055-9965.epi-06-0252] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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64
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Medina MA, Correa-Fiz F, Rodríguez-Caso C, Sánchez-Jiménez F. A comprehensive view of polyamine and histamine metabolism to the light of new technologies. J Cell Mol Med 2006; 9:854-64. [PMID: 16364195 DOI: 10.1111/j.1582-4934.2005.tb00384.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Polyamines and histamine are biogenic amines with multiple biological roles. In spite of the evidence for the involvement of both polyamines and histamine metabolism impairment in several highly prevalent pathological conditions, multiple questions concerning the molecular processes behind these effects remain to be elucidated. More comprehensive and systemic studies integrating molecular biology, biophysical and bioinformatics tools could contribute to accelerate the advances in this research area. This review is designed to underscore the main questions to be answered in polyamine and histamine research and how these new systemic approaches could help to find these answers.
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Affiliation(s)
- Miguel Angel Medina
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Málaga, Spain.
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65
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Prudova A, Martinov MV, Vitvitsky VM, Ataullakhanov FI, Banerjee R. Analysis of pathological defects in methionine metabolism using a simple mathematical model. Biochim Biophys Acta Mol Basis Dis 2006; 1741:331-8. [PMID: 15963701 DOI: 10.1016/j.bbadis.2005.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Accepted: 04/29/2005] [Indexed: 01/27/2023]
Abstract
Derangements in methionine metabolism are a hallmark of cancers and homocystinuria, an inborn error of metabolism. In this study, the metabolic consequences of the pathological changes associated with the key pathway enzymes, methionine adenosyl transferase (MAT), glycine N-methyl transferase (GNMT) and cystathionine beta-synthase (CBS) as well as an activation of polyamine metabolism, were analyzed using a simple mathematical model describing methionine metabolism in liver. The model predicts that the mere loss of allosteric regulation of CBS by adenosylmethionine (AdoMet) leads to an increase in homocysteine concentration. This is consistent with the experimental data on the corresponding genetic defects, which specifically impair allosteric activation but not basal enzyme activity. Application of the characteristics of transformed hepatocytes to our model, i.e., substitution of the MAT I/III isozyme by MAT II, loss of GNMT activity and activation of polyamine biosynthesis, leads to the prediction of a significantly different dependence of methionine metabolism on methionine concentrations. The theoretical predictions were found to be in good agreement with experimental data obtained with the human hepatoma cell line, HepG2.
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Affiliation(s)
- Anna Prudova
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664, USA
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66
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Ulrich CM, Curtin K, Potter JD, Bigler J, Caan B, Slattery ML. Polymorphisms in the reduced folate carrier, thymidylate synthase, or methionine synthase and risk of colon cancer. Cancer Epidemiol Biomarkers Prev 2006; 14:2509-16. [PMID: 16284371 DOI: 10.1158/1055-9965.epi-05-0261] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Folate metabolism supports the synthesis of nucleotides as well as the transfer of methyl groups. Polymorphisms in folate-metabolizing enzymes have been shown to affect risk of colorectal neoplasia and other malignancies. Using data from a population-based incident case-control study (1,600 cases and 1,962 controls), we investigated associations between genetic variants in the reduced folate carrier (RFC), thymidylate synthase (TS), methionine synthase (MTR), and 5,10-methylenetetrahydrofolate reductase (MTHFR) and colon cancer risk. The TS enhancer region (TSER) variant was associated with a reduced risk among men [2rpt/2rpt versus 3rpt/3rpt wild-type; odds ratio (OR), 0.7; 95% confidence interval, 0.6-0.98] but not women. When combined genotypes for both TS polymorphisms (TSER and 3'-untranslated region 1494delTTAAAG) were evaluated, ORs for variant genotypes were generally below 1.0, with statistically significantly reduced risks among women. Neither MTR D919G nor RFC 80G>A polymorphisms were associated with altered colon cancer risk. Because folate metabolism is characterized by interrelated reactions, we evaluated gene-gene interactions. Genotypes resulting in reduced MTHFR activity in conjunction with low TS expression were associated with a reduced risk of colon cancer. When dietary intakes were taken into account, individuals with at least one variant TSER allele (3rpt/2rpt or 2rpt/2rpt) were at reduced risk in the presence of a low folate intake. This study supports findings from adenoma studies indicating that purine synthesis may be a relevant biological mechanism linking folate metabolism to colon cancer risk. A pathway-based approach to data analysis is needed to help discern the independent and combined effects of dietary intakes and genetic variability in folate metabolism.
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Affiliation(s)
- Cornelia M Ulrich
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, M4-B402 Seattle, WA 98109-1024, USA.
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Ueland PM, Holm PI, Hustad S. Betaine: a key modulator of one-carbon metabolism and homocysteine status. Clin Chem Lab Med 2005; 43:1069-75. [PMID: 16197300 DOI: 10.1515/cclm.2005.187] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Betaine serves as a methyl donor in a reaction converting homocysteine to methionine, catalysed by the enzyme betaine-homocysteine methyltransferase. It has been used for years to lower the concentration of plasma total homocysteine (tHcy) in patients with homocystinuria, and has recently been shown to reduce fasting and in particular post-methionine load (PML) tHcy in healthy subjects. Betaine exists in plasma at concentrations of about 30 micromol/L; it varies 10-fold (from 9 to 90 micromol/L) between individuals, but the intra-individual variability is small. Major determinants are choline, dimethylglycine and folate in plasma, folic acid intake and gender. Recent studies have demonstrated that plasma betaine is a stronger determinant of PML tHcy than are vitamin B6 and folate. The betaine-PML tHcy relationship is attenuated after supplementation with B-vitamins, and is most pronounced in subjects with low folate. Betaine shows a weaker association with fasting tHcy (than with PML tHcy), and also this association is most pronounced in subjects with low folate. In pregnancy, plasma betaine declines until gestational week 20, and thereafter remains constant. From gestational week 20 onwards, fasting tHcy shows a strong inverse association with plasma betaine, and betaine becomes a stronger predictor than folate of fasting tHcy. To conclude, betaine status is a component of an individual's biochemical make-up with ramifications to one-carbon metabolism. Betaine status should be investigated in pathologies related to altered metabolism of homocysteine and folate, including cardiovascular disease, cancer and neural tube defects.
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Affiliation(s)
- Per Magne Ueland
- LOCUS for Homocysteine and Related Vitamins, Institute of Medicine, University of Bergen, Bergen, Norway.
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Abstract
Mild hyperhomocysteinemia is a risk factor for many diseases, including cardiovascular disease. We determined the effects of insulin resistance and of type 2 diabetes on homocysteine (Hcy) metabolism using Zucker diabetic fatty rats (ZDF/Gmi fa/fa and ZDF/Gmi fa/?). Plasma total Hcy was reduced in ZDF fa/fa rats by 24% in the pre-diabetic insulin-resistant stage, while in the frank diabetic stage there was a 59% reduction. Hepatic activities of several enzymes that play a role in the removal of Hcy:cystathionine beta-synthase (CBS), cystathionine gamma-lyase, and betaine:Hcy methyltransferase (BHMT) were increased as was methionine adenosyltransferase. CBS and BHMT mRNA levels and the hepatic level of S-adenosylmethionine were also increased in the ZDF fa/fa rats. Studies with primary hepatocytes showed that Hcy export and the transsulfuration flux in cells from ZDF fa/fa rats were particularly sensitive to betaine. Interestingly, liver betaine concentration was found to be significantly lower in the ZDf fa/fa rats at both 5 and 11 weeks. These results emphasize the importance of betaine metabolism in determining plasma Hcy levels in type 2 diabetes.
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Affiliation(s)
- Enoka P. Wijekoon
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Beatrice Hall
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Shobhitha Ratnam
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Margaret E. Brosnan
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Steven H. Zeisel
- Department of Nutrition, University of North Carolina, Chapel Hill, North Carolina
| | - John T. Brosnan
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
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70
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Ulrey CL, Liu L, Andrews LG, Tollefsbol TO. The impact of metabolism on DNA methylation. Hum Mol Genet 2005; 14 Spec No 1:R139-47. [PMID: 15809266 DOI: 10.1093/hmg/ddi100] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Methylation of genomic cytosines is one of the best characterized epigenetic mechanisms, and investigation of its relationship with other biochemical pathways represents a critical stage in the elucidation of biological information processing. The field also has immense potential for the development of medical treatments for any number of conditions ranging from aging to neurological disorders. The DNA methylation status of genes is responsible for many heritable traits and varies more or less independently of the genetic code. This variation is often a result of cellular environmental factors including metabolism. A key metabolite in this regard is homocysteine. Knowledge of homocysteine metabolism continues to be amassed, yet the part played by aberrant DNA methylation in homocysteine-related pathologies is often, at best, conjectural. In this analysis, we will review recent insights and attempt to speculate meaningfully concerning the dynamics of the methionine cycle in relation to DNA methylation and disease.
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Affiliation(s)
- Clayton L Ulrey
- Department of Biology, University of Alabama at Birmingham, 35294, USA
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71
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Davis SR, Quinlivan EP, Shelnutt KP, Ghandour H, Capdevila A, Coats BS, Wagner C, Shane B, Selhub J, Bailey LB, Shuster JJ, Stacpoole PW, Gregory JF. Homocysteine synthesis is elevated but total remethylation is unchanged by the methylenetetrahydrofolate reductase 677C->T polymorphism and by dietary folate restriction in young women. J Nutr 2005; 135:1045-50. [PMID: 15867279 DOI: 10.1093/jn/135.5.1045] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effects of folate status and the methylenetetrahydrofolate reductase (MTHFR) 677C-->T polymorphism on the kinetics of homocysteine metabolism are unclear. We measured the effects of dietary folate restriction on the kinetics of homocysteine remethylation and synthesis in healthy women (20-30 y old) with the MTHFR 677 C/C or T/T genotypes (n = 9/genotype) using i.v. primed, constant infusions of [(13)C(5)]methionine, [3-(13)C]serine, and [(2)H(3)]leucine before and after 7 wk of dietary folate restriction (115 mug dietary folate equivalents/d). Dietary folate restriction significantly reduced folate status ( approximately 65% reduction in serum folate) in both genotypes. Total remethylation flux was not affected by dietary folate restriction, the MTHFR 677C-->T polymorphism, or their combination. However, the percentage of remethylation from serine was reduced approximately 15% (P = 0.031) by folate restriction in C/C subjects. Further, homocysteine synthesis rates of T/T subjects and folate-restricted C/C subjects were twice that of C/C subjects at baseline. In conclusion, elevated homocysteine synthesis is a cause of mild hyperhomocysteinemia in women with marginal folate status, particularly those with the MTHFR 677 T/T genotype.
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Affiliation(s)
- Steven R Davis
- Food Science & Human Nutrition Department, Institute of Food and Agricultural Sciences, College of Medicine, University of Florida, Gainesville 32611-0370, USA
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Chillemi R, Zappacosta B, Simporè J, Persichilli S, Musumeci M, Musumeci S. Hyperhomocysteinemia in acute Plasmodium falciparum malaria: an effect of host-parasite interaction. Clin Chim Acta 2005; 348:113-20. [PMID: 15369744 DOI: 10.1016/j.cccn.2004.05.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 05/04/2004] [Accepted: 05/05/2004] [Indexed: 11/21/2022]
Abstract
BACKGROUND Plasmodium falciparum utilises the polyamine pathway, essential in proliferation and differentiation, and imposes an oxidative stress on host cell, enhancing the loss of glutathione. METHODS Standard hematological parameters were determined in 40 black African subjects with acute P. falciparum malaria, 30 aged 5-24 months, 5 aged 4-10 years and 5 aged 19-35 years. Plasma homocysteine, cysteine, glutathione and cysteinylglycine levels were measured by HPLC method. Twenty-eight healthy black children (15 aged 6-24 months and 13 aged 3-10 years) and 20 healthy black adults (aged 20-40 years) were also included as controls. RESULTS Plasma homocysteine levels were higher in all subjects with P. falciparum malaria and correlated positively with the disease severity and number of parasites, but negatively with Hb levels and patient ages. Cysteine level was found higher in all patients and markedly higher in 4-10 year old patients. Cysteinylglycine level was found lower particularly in 19-35 year old patients. Glutathione level was significantly lower in all patients. CONCLUSIONS The elevated level of homocysteine during acute P. falciparum infection suggests an imbalance in the folate cycle, which could be a consequence of the reduced availability of NADPH and Vit B12, caused by increased oxidative stress. This may suggest a selection for the C677T MTHFR allele, driven by P. falciparum in sub-Saharan regions. Hence Hcy level could be useful as a predictive parameter of severity, as well as of treatment efficacy.
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Affiliation(s)
- R Chillemi
- Department of Chemical Sciences, University of Catania, Catania, Italy
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Girard CL, Lapierre H, Matte JJ, Lobley GE. Effects of dietary supplements of folic acid and rumen-protected methionine on lactational performance and folate metabolism of dairy cows. J Dairy Sci 2005; 88:660-70. [PMID: 15653533 DOI: 10.3168/jds.s0022-0302(05)72730-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The present experiment was undertaken to determine the interactions between dietary supplements of folic acid and rumen-protected methionine on lactational performance and on indicators of folate metabolism during one lactation. Fifty-four multiparous Holstein cows were assigned to 9 blocks of 6 cows each according to their previous milk production. Within each block, 3 cows were fed a diet calculated to supply methionine as 1.75% metabolizable protein, equivalent to 70% of methionine requirement, whereas the 3 other cows were fed the same diet supplemented with 18 g of a rumen-protected methionine supplement. Within each diet, the cows received 0, 3, or 6 mg/d of folic acid per kg of body weight. Rumen-protected methionine increased milk total solid concentration but not yield. Supplementary folic acid increased crude protein and casein concentrations in milk of cows fed no supplementary methionine and the effect increased as lactation progressed; it also decreased milk lactose concentration. Folic acid supplements had the opposite effects on milk crude protein, casein, and lactose concentrations in cows fed rumen-protected methionine. Milk and milk component yields and dry matter intake were unchanged. Folic acid supplementation increased serum folates and this response was greater at 8 wk of lactation. It decreased serum cysteine in cows fed rumen-protected methionine, whereas it had no effect in cows fed no supplementary methionine. The highest serum concentrations of cysteine but the lowest of vitamin B(12) were observed at 8 wk of lactation. Serum clearance of folic acid following an i.v. injection of folic acid was slower at 8 wk of lactation. During this period, the high concentrations of serum folates and cysteine, the low serum concentrations of vitamin B(12) and methionine, and the slow serum clearance of folates strongly suggest that the vitamin B(12) supply was inadequate and interfered with folate use. It could explain the limited lactational response to supplementary folic acid observed in the present experiment.
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Affiliation(s)
- C L Girard
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Lennoxville, QC, Canada J1M 1Z3.
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Holm PI, Ueland PM, Vollset SE, Midttun Ø, Blom HJ, Keijzer MBAJ, den Heijer M. Betaine and Folate Status as Cooperative Determinants of Plasma Homocysteine in Humans. Arterioscler Thromb Vasc Biol 2005; 25:379-85. [PMID: 15550695 DOI: 10.1161/01.atv.0000151283.33976.e6] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Two published studies have demonstrated that betaine in the circulation is a determinant of plasma total homocysteine, but none had sufficient power to investigate the possible effect modification by folate status. METHODS AND RESULTS We measured homocysteine, betaine, folate, vitamin B(6), and related compounds in serum/plasma from 500 healthy men and women aged 34 to 69 years before (fasting levels) and 6 hours after a standard methionine loading test. Choline, dimethylglycine, and folate were determinants of plasma betaine in a multiple regression model adjusting for age and sex. The increase in homocysteine after loading showed a strong inverse association with plasma betaine and a weaker inverse association with folate and vitamin B(6). Fasting homocysteine showed a strong inverse relation to folate, a weak relation to plasma betaine, and no relation to vitamin B(6). Notably, adjusted (for age and sex) dose-response curves for the postmethionine increase in homocysteine or fasting homocysteine versus betaine showed that the inverse associations were most pronounced at low serum folate, an observation that was confirmed by analyses of interaction. CONCLUSIONS Collectively, these results show that plasma betaine is a strong determinant of increase in homocysteine after methionine loading, particularly in subjects with low folate status. In 500 healthy subjects, postmethionine load increase in tHcy showed a stronger inverse relation to betaine than to folate and vitamin B6, whereas for fasting tHcy, betaine was a weaker determinant than folate. For both tHcy modalities, the association with betaine was most pronounced in subjects with low folate status.
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Affiliation(s)
- Pål I Holm
- Locus for Homocysteine and Related Vitamins, University of Bergen, Norway
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Nijhout HF, Reed MC, Budu P, Ulrich CM. A mathematical model of the folate cycle: new insights into folate homeostasis. J Biol Chem 2004; 279:55008-16. [PMID: 15496403 DOI: 10.1074/jbc.m410818200] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A mathematical model is developed for the folate cycle based on standard biochemical kinetics. We use the model to provide new insights into several different mechanisms of folate homeostasis. The model reproduces the known pool sizes of folate substrates and the fluxes through each of the loops of the folate cycle and has the qualitative behavior observed in a variety of experimental studies. Vitamin B(12) deficiency, modeled as a reduction in the V(max) of the methionine synthase reaction, results in a secondary folate deficiency via the accumulation of folate as 5-methyltetrahydrofolate (the "methyl trap"). One form of homeostasis is revealed by the fact that a 100-fold up-regulation of thymidylate synthase and dihydrofolate reductase (known to occur at the G(1)/S transition) dramatically increases pyrimidine production without affecting the other reactions of the folate cycle. The model also predicts that an almost total inhibition of dihydrofolate reductase is required to significantly inhibit the thymidylate synthase reaction, consistent with experimental and clinical studies on the effects of methotrexate. Sensitivity to variation in enzymatic parameters tends to be local in the cycle and inversely proportional to the number of reactions that interconvert two folate substrates. Another form of homeostasis is a consequence of the nonenzymatic binding of folate substrates to folate enzymes. Without folate binding, the velocities of the reactions decrease approximately linearly as total folate is decreased. In the presence of folate binding and allosteric inhibition, the velocities show a remarkable constancy as total folate is decreased.
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Affiliation(s)
- H Frederik Nijhout
- Departments of Biology and Mathematics, Duke University, Durham, NC 27708, USA.
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