1
|
Abstract
Amino acid dysregulation has emerged as an important driver of disease progression in various contexts. l-Serine lies at a central node of metabolism, linking carbohydrate metabolism, transamination, glycine, and folate-mediated one-carbon metabolism to protein synthesis and various downstream bioenergetic and biosynthetic pathways. l-Serine is produced locally in the brain but is sourced predominantly from glycine and one-carbon metabolism in peripheral tissues via liver and kidney metabolism. Compromised regulation or activity of l-serine synthesis and disposal occurs in the context of genetic diseases as well as chronic disease states, leading to low circulating l-serine levels and pathogenesis in the nervous system, retina, heart, and aging muscle. Dietary interventions in preclinical models modulate sensory neuropathy, retinopathy, tumor growth, and muscle regeneration. A serine tolerance test may provide a quantitative readout of l-serine homeostasis that identifies patients who may be susceptible to neuropathy or responsive to therapy.
Collapse
Affiliation(s)
- Michal K Handzlik
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA; ,
| | - Christian M Metallo
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA; ,
| |
Collapse
|
2
|
Metabolic remodeling of pyrimidine synthesis pathway and serine synthesis pathway in human glioblastoma. Sci Rep 2022; 12:16277. [PMID: 36175487 PMCID: PMC9522918 DOI: 10.1038/s41598-022-20613-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/15/2022] [Indexed: 12/02/2022] Open
Abstract
Glioblastoma is the most common brain tumor with dismal outcomes in adults. Metabolic remodeling is now widely acknowledged as a hallmark of cancer cells, but glioblastoma-specific metabolic pathways remain unclear. Here we show, using a large-scale targeted proteomics platform and integrated molecular pathway-level analysis tool, that the de novo pyrimidine synthesis pathway and serine synthesis pathway (SSP) are the major enriched pathways in vivo for patients with glioblastoma. Among the enzymes associated with nucleotide synthesis, RRM1 and NME1 are significantly upregulated in glioblastoma. In the SSP, SHMT2 and PSPH are upregulated but the upstream enzyme PSAT1 is downregulated in glioblastoma. Kaplan–Meier curves of overall survival for the GSE16011 and The Cancer Genome Atlas datasets revealed that high SSP activity correlated with poor outcome. Enzymes relating to the pyrimidine synthesis pathway and SSP might offer therapeutic targets for new glioblastoma treatments.
Collapse
|
3
|
Proteomic, Transcriptomic, Mutational, and Functional Assays Reveal the Involvement of Both THF and PLP Sites at the GmSHMT08 in Resistance to Soybean Cyst Nematode. Int J Mol Sci 2022; 23:ijms231911278. [PMID: 36232579 PMCID: PMC9570156 DOI: 10.3390/ijms231911278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/27/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
The serine hydroxymethyltransferase (SHMT; E.C. 2.1.2.1) is involved in the interconversion of serine/glycine and tetrahydrofolate (THF)/5,10-methylene THF, playing a key role in one-carbon metabolism, the de novo purine pathway, cellular methylation reactions, redox homeostasis maintenance, and methionine and thymidylate synthesis. GmSHMT08 is the soybean gene underlying soybean cyst nematode (SCN) resistance at the Rhg4 locus. GmSHMT08 protein contains four tetrahydrofolate (THF) cofactor binding sites (L129, L135, F284, N374) and six pyridoxal phosphate (PLP) cofactor binding/catalysis sites (Y59, G106, G107, H134, S190A, H218). In the current study, proteomic analysis of a data set of protein complex immunoprecipitated using GmSHMT08 antibodies under SCN infected soybean roots reveals the presence of enriched pathways that mainly use glycine/serine as a substrate (glyoxylate cycle, redox homeostasis, glycolysis, and heme biosynthesis). Root and leaf transcriptomic analysis of differentially expressed genes under SCN infection supported the proteomic data, pointing directly to the involvement of the interconversion reaction carried out by the serine hydroxymethyltransferase enzyme. Direct site mutagenesis revealed that all mutated THF and PLP sites at the GmSHMT08 resulted in increased SCN resistance. We have shown the involvement of PLP sites in SCN resistance. Specially, the effect of the two Y59 and S190 PLP sites was more drastic than the tested THF sites. This unprecedented finding will help us to identify the biological outcomes of THF and PLP residues at the GmSHMT08 and to understand SCN resistance mechanisms.
Collapse
|
4
|
Savizi ISP, Maghsoudi N, Motamedian E, Lewis NE, Shojaosadati SA. Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells. Appl Microbiol Biotechnol 2022; 106:1113-1126. [PMID: 35044498 DOI: 10.1007/s00253-021-11755-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/21/2021] [Accepted: 12/27/2021] [Indexed: 11/02/2022]
Abstract
Ammonia is a toxic byproduct of CHO cell metabolism, which inhibits cell growth, reduces cell viability, alters glycosylation, and decreases recombinant protein productivity. In an attempt to minimize the ammonium accumulation in cell culture media, different amino acids were added individually to the culture medium before the production phase to alleviate the negative effects of ammonium on cell culture performance. Among all the amino acids examined in this study, valine showed the most positive impact on CHO cell culture performance. When the cultured CHO cells were fed with 5 mM valine, EPO titer was increased by 25% compared to the control medium, and ammonium and lactate production were decreased by 23 and 26%, respectively, relative to the control culture. Moreover, the sialic acid content of the EPO protein in valine-fed culture was higher than in the control culture, most likely because of the lower ammonium concentration. Flux balance analysis (FBA) results demonstrated that the citric acid cycle was enriched by valine feeding. The measurement of TCA cycle activity supported this finding. The analysis revealed that there might be a link between promoting tricarboxylic acid (TCA) cycle metabolism in valine-fed culture and reduction in lactate and ammonia accumulation. Furthermore, in valine-fed culture, FBA outcomes showed that alanine was excreted into the medium as the primary mechanism for reducing ammonium concentration. It was predicted that the elevated TCA cycle metabolism was concurrent with an increment in recombinant protein production. Taken together, our data demonstrate that valine addition could be an effective strategy for mitigating the negative impacts of ammonium and enhancing glycoprotein production in both quality and quantity. KEY POINTS: • Valine feeding can mitigate the negative impacts of ammonia on CHO cell growth. • Valine addition assists the ammonia removal mechanism by enriching the TCA cycle. • Ammonia is removed from the media through alanine excretion in valine-fed culture.
Collapse
Affiliation(s)
- Iman Shahidi Pour Savizi
- Biotechnology Department, Faculty of Chemical Engineering, Tarbiat Modares University, P.O. Box 14155-4838, Tehran, Iran
| | - Nader Maghsoudi
- Neuroscience Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Ehsan Motamedian
- Biotechnology Department, Faculty of Chemical Engineering, Tarbiat Modares University, P.O. Box 14155-4838, Tehran, Iran
| | - Nathan E Lewis
- Department of Bioengineering, University of California, La Jolla, San Diego, CA, USA.,School of Medicine, Novo Nordisk Foundation Center for Biosustainability at the University of California, La Jolla, San Diego, CA, USA.,Department of Pediatrics, School of Medicine, University of California, La Jolla, San Diego, CA, USA
| | - Seyed Abbas Shojaosadati
- Biotechnology Department, Faculty of Chemical Engineering, Tarbiat Modares University, P.O. Box 14155-4838, Tehran, Iran.
| |
Collapse
|
5
|
Björkblom B, Wibom C, Eriksson M, Bergenheim AT, Sjöberg RL, Jonsson P, Brännström T, Antti H, Sandström M, Melin B. OUP accepted manuscript. Neuro Oncol 2022; 24:1454-1468. [PMID: 35157758 PMCID: PMC9435506 DOI: 10.1093/neuonc/noac042] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Benny Björkblom
- Corresponding Author: Dr. Benny Björkblom, PhD, Department of Chemistry, Umeå University, Linnaeus väg 10, SE-901 87 Umeå, Sweden ()
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Maria Eriksson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - A Tommy Bergenheim
- Department of Clinical Science, Neuroscience, Umeå University, Umeå, Sweden
| | - Rickard L Sjöberg
- Department of Clinical Science, Neuroscience, Umeå University, Umeå, Sweden
| | - Pär Jonsson
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Henrik Antti
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Maria Sandström
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Beatrice Melin
- Corresponding Author: Professor Beatrice Melin, MD, PhD, Department of Radiation Sciences, Oncology, Umeå University, SE-901 87 Umeå, Sweden ()
| |
Collapse
|
6
|
Rish AJ, Drennen JK, Anderson CA. Metabolic trends of Chinese hamster ovary cells in biopharmaceutical production under batch and fed-batch conditions. Biotechnol Prog 2021; 38:e3220. [PMID: 34676699 DOI: 10.1002/btpr.3220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/07/2022]
Abstract
Extensive knowledge of Chinese hamster ovary (CHO) cell metabolism is required to improve process productivity and culture performance in biopharmaceutical manufacturing. However, CHO cells show a dynamic metabolism during culturing in batch and fed-batch bioreactors. CHO cell metabolism is generally described as taking place in three stages: exponential growth phase, stationary phase, and death phase. This review aims to summarize the trends of central metabolism for CHO cells during each stage. Additional insights into how culture conditions are related to phase transitions and force metabolic rewiring are provided. Understanding of CHO cell metabolism lends itself to improving culture qualities by, for example, identifying sources of toxic byproducts and pathways for cellular engineering. In summary, this review describes the changes in CHO cell central metabolism over the course of the culture.
Collapse
Affiliation(s)
- Adam J Rish
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
7
|
Tan YL, Sou NL, Tang FY, Ko HA, Yeh WT, Peng JH, Chiang EPI. Tracing Metabolic Fate of Mitochondrial Glycine Cleavage System Derived Formate In Vitro and In Vivo. Int J Mol Sci 2020; 21:ijms21228808. [PMID: 33233834 PMCID: PMC7699879 DOI: 10.3390/ijms21228808] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Folate-mediated one-carbon (1C) metabolism is a major target of many therapies in human diseases. Studies have focused on the metabolism of serine 3-carbon as it serves as a major source for 1C units. The serine 3-carbon enters the mitochondria transferred by folate cofactors and eventually converted to formate and serves as a major building block for cytosolic 1C metabolism. Abnormal glycine metabolism has been reported in many human pathological conditions. The mitochondrial glycine cleavage system (GCS) catalyzes glycine degradation to CO2 and ammonium, while tetrahydrofolate (THF) is converted into 5,10-methylene-THF. GCS accounts for a substantial proportion of whole-body glycine flux in humans, yet the particular metabolic route of glycine 2-carbon recycled from GCS during mitochondria glycine decarboxylation in hepatic or bone marrow 1C metabolism is not fully investigated, due to the limited accessibility of human tissues. Labeled glycine at 2-carbon was given to humans and primary cells in previous studies for investigating its incorporations into purines, its interconversion with serine, or the CO2 production in the mitochondria. Less is known on the metabolic fate of the glycine 2-carbon recycled from the GCS; hence, a model system tracing its metabolic fate would help in this regard. We took the direct approach of isotopic labeling to further explore the in vitro and in vivo metabolic fate of the 2-carbon from [2-13C]glycine and [2-13C]serine. As the 2-carbon of glycine and serine is decarboxylated and catabolized via the GCS, the original 13C-labeled 2-carbon is transferred to THF and yield methyleneTHF in the mitochondria. In human hepatoma cell-lines, 2-carbon from glycine was found to be incorporated into deoxythymidine (dTMP, dT + 1), M + 3 species of purines (deoxyadenine, dA and deoxyguanine, dG), and methionine (Met + 1). In healthy mice, incorporation of GCS-derived formate from glycine 2-carbon was found in serine (Ser + 2 via cytosolic serine hydroxy methyl transferase), methionine, dTMP, and methylcytosine (mC + 1) in bone marrow DNA. In these experiments, labeled glycine 2-carbon directly incorporates into Ser + 1, A + 2, and G + 2 (at C2 and C8 of purine) in the cytosol. It is noteworthy that since the serine 3-carbon is unlabeled in these experiments, the isotopic enrichments in dT + 1, Ser + 2, dA + 3, dG + 3, and Met + 1 solely come from the 2-carbon of glycine/serine recycled from GCS, re-enters the cytosolic 1C metabolism as formate, and then being used for cytosolic syntheses of serine, dTMP, purine (M + 3) and methionine. Taken together, we established model systems and successfully traced the metabolic fate of mitochondrial GCS-derived formate from glycine 2-carbon in vitro and in vivo. Nutritional supply significantly alters formate generation from GCS. More GCS-derived formate was used in hepatic serine and methionine syntheses, whereas more GCS-derived formate was used in dTMP synthesis in the bone marrow, indicating that the utilization and partitioning of GCS-derived 1C unit are tissue-specific. These approaches enable better understanding concerning the utilization of 1C moiety generated from mitochondrial GCS that can help to further elucidate the role of GCS in human disease development and progression in future applications. More studies on GCS using these approaches are underway.
Collapse
Affiliation(s)
- Yee-Ling Tan
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
| | - Nga-Lai Sou
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University (NCHU), Taichung 402, Taiwan
| | - Feng-Yao Tang
- Department of Nutrition, China Medical University, Taichung 402, Taiwan;
| | - Hsin-An Ko
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
| | - Wei-Ting Yeh
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
| | - Jian-Hau Peng
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University (NCHU), Taichung 402, Taiwan
- Microbial Genomics Ph.D. Graduate Program, National Chung Hsing University (NCHU), Taichung 402, Taiwan
| | - En-Pei Isabel Chiang
- Food Science and Biotechnology, National Chung Hsing University (NCHU), Taichung 402, Taiwan; (Y.-L.T.); (N.-L.S.); (H.-A.K.); (W.-T.Y.); (J.-H.P.)
- Department of Nutrition, China Medical University, Taichung 402, Taiwan;
- Microbial Genomics Ph.D. Graduate Program, National Chung Hsing University (NCHU), Taichung 402, Taiwan
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Correspondence: ; Tel.: +886-4-22853049; Fax: +886-4-22876211
| |
Collapse
|
8
|
Lakhssassi N, Piya S, Knizia D, El Baze A, Cullen MA, Meksem J, Lakhssassi A, Hewezi T, Meksem K. Mutations at the Serine Hydroxymethyltransferase Impact its Interaction with a Soluble NSF Attachment Protein and a Pathogenesis-Related Protein in Soybean. Vaccines (Basel) 2020; 8:vaccines8030349. [PMID: 32629961 PMCID: PMC7563484 DOI: 10.3390/vaccines8030349] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/01/2023] Open
Abstract
Resistance to soybean cyst nematodes (SCN) in “Peking-type” resistance is bigenic, requiring Rhg4-a and rhg1-a. Rhg4-a encodes a serine hydroxymethyltransferase (GmSHMT08) and rhg1-a encodes a soluble NSF attachment protein (GmSNAP18). Recently, it has been shown that a pathogenesis-related protein, GmPR08-Bet VI, potentiates the interaction between GmSHMT08 and GmSNAP18. Mutational analysis using spontaneously occurring and ethyl methanesulfonate (EMS)-induced mutations was carried out to increase our knowledge of the interacting GmSHMT08/GmSNAP18/GmPR08-Bet VI multi-protein complex. Mutations affecting the GmSHMT08 protein structure (dimerization and tetramerization) and interaction sites with GmSNAP18 and GmPR08-Bet VI proteins were found to impact the multi-protein complex. Interestingly, mutations affecting the PLP/THF substrate binding and catalysis did not affect the multi-protein complex, although they resulted in increased susceptibility to SCN. Most importantly, GmSHMT08 and GmSNAP18 from PI88788 were shown to interact within the cell, being potentiated in the presence of GmPR08-Bet VI. In addition, we have shown the presence of incompatibility between the GmSNAP18 (rhg1-b) of PI88788 and GmSHMT08 (Rhg4-a) from Peking. Components of the reactive oxygen species (ROS) pathway were shown to be induced in the SCN incompatible reaction and were mapped to QTLs for resistance to SCN using different mapping populations.
Collapse
Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (S.P.); (T.H.)
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Mallory A. Cullen
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA;
| | - Aicha Lakhssassi
- Faculty of Sciences and Technologies, University of Lorraine, 54000 Nancy, France;
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (S.P.); (T.H.)
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
- Correspondence: ; Tel.: +1-618-453-3103
| |
Collapse
|
9
|
Engel AL, Lorenz NI, Klann K, Münch C, Depner C, Steinbach JP, Ronellenfitsch MW, Luger AL. Serine-dependent redox homeostasis regulates glioblastoma cell survival. Br J Cancer 2020; 122:1391-1398. [PMID: 32203214 PMCID: PMC7188854 DOI: 10.1038/s41416-020-0794-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 02/07/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022] Open
Abstract
Background The amino acid serine is an important substrate for biosynthesis and redox homeostasis. We investigated whether glioblastoma (GBM) cells are dependent on serine for survival under conditions of the tumour microenvironment. Methods Serine availability in GBM cells was modulated pharmacologically, genetically and by adjusting serine and glycine concentrations in the culture medium. Cells were investigated for regulation of serine metabolism, proliferation, sensitivity to hypoxia-induced cell death and redox homeostasis. Results Hypoxia-induced expression of phosphoglycerate dehydrogenase (PHGDH) and the mitochondrial serine hydroxymethyltransferase (SHMT2) was observed in three of five tested glioma cell lines. Nuclear factor erythroid 2-related factor (Nrf) 2 activation also induced PHGDH and SHMT2 expression in GBM cells. Low levels of endogenous PHGDH as well as PHGDH gene suppression resulted in serine dependency for cell growth. Pharmacological inhibition of PHGDH with CBR-5884 reduced proliferation and sensitised cells profoundly to hypoxia-induced cell death. This effect was accompanied by an increase in reactive oxygen species and a decrease in the NADPH/NADP+ ratio. Similarly, hypoxia-induced cell death was enhanced by PHGDH gene suppression and reduced by PHGDH overexpression. Conclusions Serine facilitates adaptation of GBM cells to conditions of the tumour microenvironment and its metabolism could be a plausible therapeutic target.
Collapse
Affiliation(s)
- Anna L Engel
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,University Cancer Center Frankfurt (UCT), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Nadja I Lorenz
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,University Cancer Center Frankfurt (UCT), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Kevin Klann
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany
| | - Christian Münch
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany.,Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany.,Cardio-Pulmonary Institute, Frankfurt am Main, Germany
| | - Cornelia Depner
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Joachim P Steinbach
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,University Cancer Center Frankfurt (UCT), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Michael W Ronellenfitsch
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany. .,University Cancer Center Frankfurt (UCT), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany. .,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany. .,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany.
| | - Anna-Luisa Luger
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,University Cancer Center Frankfurt (UCT), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| |
Collapse
|
10
|
Alptekin A, Ye B, Yu Y, Poole CJ, van Riggelen J, Zha Y, Ding HF. Glycine decarboxylase is a transcriptional target of MYCN required for neuroblastoma cell proliferation and tumorigenicity. Oncogene 2019; 38:7504-7520. [PMID: 31444411 PMCID: PMC6908766 DOI: 10.1038/s41388-019-0967-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/05/2019] [Accepted: 08/09/2019] [Indexed: 12/12/2022]
Abstract
Genomic amplification of the oncogene MYCN is a major driver in the development of high-risk neuroblastoma, a pediatric cancer with poor prognosis. Given the challenge in targeting MYCN directly for therapy, we sought to identify MYCN-dependent metabolic vulnerabilities that can be targeted therapeutically. Here, we report that the gene encoding glycine decarboxylase (GLDC), which catalyzes the first and rate-limiting step in glycine breakdown with the production of the one-carbon unit 5,10-methylene-tetrahydrofolate, is a direct transcriptional target of MYCN. As a result, GLDC expression is markedly elevated in MYCN-amplified neuroblastoma tumors and cell lines. This transcriptional upregulation of GLDC expression is of functional significance, as GLDC depletion by RNA interference inhibits the proliferation and tumorigenicity of MYCN-amplified neuroblastoma cell lines by inducing G1 arrest. Metabolomic profiling reveals that GLDC knockdown disrupts purine and central carbon metabolism and reduces citrate production, leading to a decrease in the steady-state levels of cholesterol and fatty acids. Moreover, blocking purine or cholesterol synthesis recapitulates the growth inhibitory effect of GLDC knockdown. These findings reveal a critical role of GLDC in sustaining the proliferation of neuroblastoma cells with high-level GLDC expression and suggest that MYCN amplification is a biomarker for GLDC-based therapeutic strategies against high-risk neuroblastoma.
Collapse
Affiliation(s)
- Ahmet Alptekin
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Bingwei Ye
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Yajie Yu
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, 443000, Yichang, China
| | - Candace J Poole
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Jan van Riggelen
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Yunhong Zha
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, 443000, Yichang, China
| | - Han-Fei Ding
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA. .,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA. .,Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
| |
Collapse
|
11
|
Asano K, Suzuki T, Saito A, Wei FY, Ikeuchi Y, Numata T, Tanaka R, Yamane Y, Yamamoto T, Goto T, Kishita Y, Murayama K, Ohtake A, Okazaki Y, Tomizawa K, Sakaguchi Y, Suzuki T. Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease. Nucleic Acids Res 2019; 46:1565-1583. [PMID: 29390138 PMCID: PMC5829720 DOI: 10.1093/nar/gky068] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/23/2018] [Indexed: 12/21/2022] Open
Abstract
Modified uridine containing taurine, 5-taurinomethyluridine (τm5U), is found at the anticodon first position of mitochondrial (mt-)transfer RNAs (tRNAs). Previously, we reported that τm5U is absent in mt-tRNAs with pathogenic mutations associated with mitochondrial diseases. However, biogenesis and physiological role of τm5U remained elusive. Here, we elucidated τm5U biogenesis by confirming that 5,10-methylene-tetrahydrofolate and taurine are metabolic substrates for τm5U formation catalyzed by MTO1 and GTPBP3. GTPBP3-knockout cells exhibited respiratory defects and reduced mitochondrial translation. Very little τm5U34 was detected in patient's cells with the GTPBP3 mutation, demonstrating that lack of τm5U results in pathological consequences. Taurine starvation resulted in downregulation of τm5U frequency in cultured cells and animal tissues (cat liver and flatfish). Strikingly, 5-carboxymethylaminomethyluridine (cmnm5U), in which the taurine moiety of τm5U is replaced with glycine, was detected in mt-tRNAs from taurine-depleted cells. These results indicate that tRNA modifications are dynamically regulated via sensing of intracellular metabolites under physiological condition.
Collapse
Affiliation(s)
- Kana Asano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ayaka Saito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | - Tomoyuki Numata
- Biological Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Ryou Tanaka
- Department of Veterinary Surgery, Tokyo University of Agriculture and Technology, Animal Medical Center, Fuchu, Tokyo 183-8509, Japan
| | - Yoshihisa Yamane
- Department of Veterinary Surgery, Tokyo University of Agriculture and Technology, Animal Medical Center, Fuchu, Tokyo 183-8509, Japan
| | - Takeshi Yamamoto
- Tamaki Laboratory, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Tamaki, Mie 519-0423, Japan
| | - Takanobu Goto
- Department of Chemistry & Biochemistry, National Institute of Technology, Numazu College, Numazu, Shizuoka 410-8501, Japan
| | - Yoshihito Kishita
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1240, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba 266-0007, Japan
| | - Akira Ohtake
- Department of Pediatrics, Saitama Medical University, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Yasushi Okazaki
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1240, Japan.,Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1240, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
12
|
Kory N, Wyant GA, Prakash G, Uit de Bos J, Bottanelli F, Pacold ME, Chan SH, Lewis CA, Wang T, Keys HR, Guo YE, Sabatini DM. SFXN1 is a mitochondrial serine transporter required for one-carbon metabolism. Science 2019; 362:362/6416/eaat9528. [PMID: 30442778 DOI: 10.1126/science.aat9528] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022]
Abstract
One-carbon metabolism generates the one-carbon units required to synthesize many critical metabolites, including nucleotides. The pathway has cytosolic and mitochondrial branches, and a key step is the entry, through an unknown mechanism, of serine into mitochondria, where it is converted into glycine and formate. In a CRISPR-based genetic screen in human cells for genes of the mitochondrial pathway, we found sideroflexin 1 (SFXN1), a multipass inner mitochondrial membrane protein of unclear function. Like cells missing mitochondrial components of one-carbon metabolism, those null for SFXN1 are defective in glycine and purine synthesis. Cells lacking SFXN1 and one of its four homologs, SFXN3, have more severe defects, including being auxotrophic for glycine. Purified SFXN1 transports serine in vitro. Thus, SFXN1 functions as a mitochondrial serine transporter in one-carbon metabolism.
Collapse
Affiliation(s)
- Nora Kory
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA
| | - Gregory A Wyant
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA
| | - Gyan Prakash
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Jelmi Uit de Bos
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Francesca Bottanelli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael E Pacold
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA.,Department of Radiation Oncology at NYU Langone Medical Center, New York, NY 10016, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Caroline A Lewis
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Tim Wang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA
| | - Heather R Keys
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Yang Eric Guo
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA. .,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA
| |
Collapse
|
13
|
Lakhssassi N, Patil G, Piya S, Zhou Z, Baharlouei A, Kassem MA, Lightfoot DA, Hewezi T, Barakat A, Nguyen HT, Meksem K. Genome reorganization of the GmSHMT gene family in soybean showed a lack of functional redundancy in resistance to soybean cyst nematode. Sci Rep 2019; 9:1506. [PMID: 30728404 PMCID: PMC6365578 DOI: 10.1038/s41598-018-37815-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022] Open
Abstract
In soybeans, eighteen members constitute the serine hydroxymethyltransferase (GmSHMT) gene family, of which the cytosolic-targeted GmSHMT08c member has been reported to mediate resistance to soybean cyst nematode (SCN). This work presents a comprehensive study of the SHMT gene family members, including synteny, phylogeny, subcellular localizations, haplotypes, protein homology modeling, mutational, and expression analyses. Phylogenetic analysis showed that SHMT genes are divided into four classes reflecting their subcellular distribution (cytosol, nucleus, mitochondrion, and chloroplast). Subcellular localization of selected GmSHMT members supports their in-silico predictions and phylogenetic distribution. Expression and functional analyses showed that GmSHMT genes display many overlapping, but some divergent responses during SCN infection. Furthermore, mutational analysis reveals that all isolated EMS mutants that lose their resistance to SCN carry missense and nonsense mutations at the GmSHMT08c, but none of the Gmshmt08c mutants carried mutations in the other GmSHMT genes. Haplotype clustering analysis using the whole genome resequencing data from a collection of 106 diverse soybean germplams (15X) was performed to identify allelic variants and haplotypes within the GmSHMT gene family. Interestingly, only the cytosolic-localized GmSHMT08c presented SNP clusters that were associated with SCN resistance, supporting our mutational analysis. Although eight GmSHMT members respond to the nematode infestation, functional and mutational analysis has shown the absence of functional redundancy in resistance to SCN. Structural analysis and protein homology modeling showed the presence of spontaneous mutations at important residues within the GmSHMT proteins, suggesting the presence of altered enzyme activities based on substrate affinities. Due to the accumulation of mutations during the evolution of the soybean genome, the other GmSHMT members have undergone neofunctionalization and subfunctionalization events.
Collapse
Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Gunvant Patil
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65201, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Azam Baharlouei
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - My Abdelmajid Kassem
- Department of Biological Sciences, Fayetteville State University, Fayetteville, NC, 28301, USA
| | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Abdelali Barakat
- Department of Biology, University of South Dakota, Vermillion, SD, 57069, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65201, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA.
| |
Collapse
|
14
|
Ritacco FV, Wu Y, Khetan A. Cell culture media for recombinant protein expression in Chinese hamster ovary (CHO) cells: History, key components, and optimization strategies. Biotechnol Prog 2018; 34:1407-1426. [DOI: 10.1002/btpr.2706] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Frank V. Ritacco
- Biologics Process DevelopmentBristol‐Myers Squibb Pennington New Jersey United States
| | - Yongqi Wu
- Biologics Process DevelopmentBristol‐Myers Squibb Pennington New Jersey United States
| | - Anurag Khetan
- Biologics Process DevelopmentBristol‐Myers Squibb Pennington New Jersey United States
| |
Collapse
|
15
|
Sweeny EA, Singh AB, Chakravarti R, Martinez-Guzman O, Saini A, Haque MM, Garee G, Dans PD, Hannibal L, Reddi AR, Stuehr DJ. Glyceraldehyde-3-phosphate dehydrogenase is a chaperone that allocates labile heme in cells. J Biol Chem 2018; 293:14557-14568. [PMID: 30012884 DOI: 10.1074/jbc.ra118.004169] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/05/2018] [Indexed: 11/06/2022] Open
Abstract
Cellular heme is thought to be distributed between a pool of sequestered heme that is tightly bound within hemeproteins and a labile heme pool required for signaling and transfer into proteins. A heme chaperone that can hold and allocate labile heme within cells has long been proposed but never been identified. Here, we show that the glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) fulfills this role by acting as an essential repository and allocator of bioavailable heme to downstream protein targets. We identified a conserved histidine in GAPDH that is needed for its robust heme binding both in vitro and in mammalian cells. Substitution of this histidine, and the consequent decreases in GAPDH heme binding, antagonized heme delivery to both cytosolic and nuclear hemeprotein targets, including inducible nitric-oxide synthase (iNOS) in murine macrophages and the nuclear transcription factor Hap1 in yeast, even though this GAPDH variant caused cellular levels of labile heme to rise dramatically. We conclude that by virtue of its heme-binding property, GAPDH binds and chaperones labile heme to create a heme pool that is bioavailable to downstream proteins. Our finding solves a fundamental question in cell biology and provides a new foundation for exploring heme homeostasis in health and disease.
Collapse
Affiliation(s)
- Elizabeth A Sweeny
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Anuradha Bharara Singh
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Ritu Chakravarti
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Osiris Martinez-Guzman
- the School of Chemistry and Biochemistry and Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Arushi Saini
- the School of Chemistry and Biochemistry and Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Mohammad Mahfuzul Haque
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Greer Garee
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195
| | - Pablo D Dans
- the Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Balidiri Reixac 10-12, Barcelona 08028, Spain, and
| | - Luciana Hannibal
- the Laboratory of Clinical Biochemistry and Metabolism, Center of Pediatrics, Medical Center, University of Freiburg, D-79106 Freiburg, Germany
| | - Amit R Reddi
- the School of Chemistry and Biochemistry and Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Dennis J Stuehr
- From the Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio 44195,
| |
Collapse
|
16
|
Svoboda LK, Teh SSK, Sud S, Kerk S, Zebolsky A, Treichel S, Thomas D, Halbrook CJ, Lee HJ, Kremer D, Zhang L, Klossowski S, Bankhead AR, Magnuson B, Ljungman M, Cierpicki T, Grembecka J, Lyssiotis CA, Lawlor ER. Menin regulates the serine biosynthetic pathway in Ewing sarcoma. J Pathol 2018; 245:324-336. [PMID: 29672864 DOI: 10.1002/path.5085] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/02/2018] [Accepted: 04/06/2018] [Indexed: 12/20/2022]
Abstract
Developmental transcription programs are epigenetically regulated by multi-protein complexes, including the menin- and MLL-containing trithorax (TrxG) complexes, which promote gene transcription by depositing the H3K4me3 activating mark at target gene promoters. We recently reported that in Ewing sarcoma, MLL1 (lysine methyltransferase 2A, KMT2A) and menin are overexpressed and function as oncogenes. Small molecule inhibition of the menin-MLL interaction leads to loss of menin and MLL1 protein expression, and to inhibition of growth and tumorigenicity. Here, we have investigated the mechanistic basis of menin-MLL-mediated oncogenic activity in Ewing sarcoma. Bromouridine sequencing (Bru-seq) was performed to identify changes in nascent gene transcription in Ewing sarcoma cells, following exposure to the menin-MLL interaction inhibitor MI-503. Menin-MLL inhibition resulted in early and widespread reprogramming of metabolic processes. In particular, the serine biosynthetic pathway (SSP) was the pathway most significantly affected by MI-503 treatment. Baseline expression of SSP genes and proteins (PHGDH, PSAT1, and PSPH), and metabolic flux through the SSP were confirmed to be high in Ewing sarcoma. In addition, inhibition of PHGDH resulted in reduced cell proliferation, viability, and tumor growth in vivo, revealing a key dependency of Ewing sarcoma on the SSP. Loss of function studies validated a mechanistic link between menin and the SSP. Specifically, inhibition of menin resulted in diminished expression of SSP genes, reduced H3K4me3 enrichment at the PHGDH promoter, and complete abrogation of de novo serine and glycine biosynthesis, as demonstrated by metabolic tracing studies with 13 C-labeled glucose. These data demonstrate that the SSP is highly active in Ewing sarcoma and that its oncogenic activation is maintained, at least in part, by menin-dependent epigenetic mechanisms involving trithorax complexes. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Laurie K Svoboda
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Selina Shiqing K Teh
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sudha Sud
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Samuel Kerk
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Aaron Zebolsky
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sydney Treichel
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Dafydd Thomas
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Christopher J Halbrook
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ho-Joon Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Daniel Kremer
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Szymon Klossowski
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Armand R Bankhead
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Brian Magnuson
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Elizabeth R Lawlor
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| |
Collapse
|
17
|
Chen C, Pérez de Nanclares M, Kurtz JF, Trudeau MP, Wang L, Yao D, Saqui-Salces M, Urriola PE, Mydland LT, Shurson GC, Overland M. Identification of redox imbalance as a prominent metabolic response elicited by rapeseed feeding in swine metabolome. J Anim Sci 2018; 96:1757-1768. [PMID: 29518202 PMCID: PMC6140949 DOI: 10.1093/jas/sky080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 03/02/2018] [Indexed: 11/13/2022] Open
Abstract
Rapeseed (RS) is an abundant and inexpensive source of energy and AA in diets for monogastrics and a sustainable alternative to soybean meal. It also contains diverse bioactive phytochemicals that could have antinutritional effects at high dose. When the RS-derived feed ingredients (RSF) are used in swine diets, the uptake of these nutrients and phytochemicals is expected to affect the metabolic system. In this study, 2 groups of young pigs (17.8 ± 2.7 kg initial BW) were equally fed a soybean meal-based control diet and an RSF-based diet, respectively, for 3 wk. Digesta, liver, and serum samples from these pigs were examined by liquid chromatography-mass spectrometry-based metabolomic analysis to determine the metabolic effects of the 2 diets. Analyses of digesta samples revealed that sinapine, sinapic acid, and gluconapin were robust exposure markers of RS. The distribution of free AA along the intestine of RSF pigs was consistent with the reduced apparent ileal digestibility of AA observed in these pigs. Despite its higher fiber content, the RSF diet did not affect microbial metabolites in the digesta, including short-chain fatty acids and secondary bile acids. Analyses of the liver and serum samples revealed that RSF altered the levels of AA metabolites involved in the urea cycle and 1-carbon metabolism. More importantly, RSF increased the levels of multiple oxidized metabolites and aldehydes while decreased the levels of ascorbic acid and docosahexaenoic acid-containing lipids in the liver and serum, suggesting that RSF could disrupt redox balance in young pigs. Overall, the results indicated that RSF elicited diverse metabolic events in young pigs through its influences on nutrient and antioxidant metabolism, which might affect the performance and health in long-term feeding and also provide the venues for nutritional and processing interventions to improve the utilization of RSF in pigs.
Collapse
Affiliation(s)
- C Chen
- Department of Food Science and Nutrition, University of Minnesota, St Paul, MN
| | - M Pérez de Nanclares
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Os, Norway
| | - J F Kurtz
- Department of Food Science and Nutrition, University of Minnesota, St Paul, MN
| | - M P Trudeau
- Department of Animal Science, University of Minnesota, St Paul, MN
| | - L Wang
- Department of Food Science and Nutrition, University of Minnesota, St Paul, MN
| | - D Yao
- Department of Food Science and Nutrition, University of Minnesota, St Paul, MN
| | - M Saqui-Salces
- Department of Animal Science, University of Minnesota, St Paul, MN
| | - P E Urriola
- Department of Animal Science, University of Minnesota, St Paul, MN
| | - L T Mydland
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Os, Norway
| | - G C Shurson
- Department of Animal Science, University of Minnesota, St Paul, MN
| | - M Overland
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Os, Norway
| |
Collapse
|
18
|
Woo CC, Chen WC, Teo XQ, Radda GK, Lee PTH. Downregulating serine hydroxymethyltransferase 2 (SHMT2) suppresses tumorigenesis in human hepatocellular carcinoma. Oncotarget 2018; 7:53005-53017. [PMID: 27391339 PMCID: PMC5288164 DOI: 10.18632/oncotarget.10415] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/29/2016] [Indexed: 12/29/2022] Open
Abstract
Serine-glycine biosynthetic pathway diverts the glycolytic intermediate 3-phosphoglycerate to synthesize serine and glycine, of which the latter was found to correlate with cancer cell proliferation. Increased de novo biosynthesis of glycine by serine hydroxymethyltransferase 2 (SHMT2) is the central mechanism to fuel one-carbon pools supporting tumorigenesis. However, the therapeutic potential in targeting SHMT2 in hepatocellular carcinoma (HCC) is unknown. In this study we showed that SHMT2 inhibition significantly suppressed liver tumorigenesis. In vitro, SHMT2-knockdown was found to reduce cell growth and tumorigenicity in Huh-7 and HepG2 liver cancer cells. Moreover SHMT2-knockdown Huh-7 cells failed to form tumor xenograft after subcutaneous inoculation into nude mice. Similarly, inducible SHMT2 inhibition, via doxycycline-added drinking water, was found to reduce tumor incidence and tumor growth in a human tumor xenograft mouse model. SHMT2-knockdown increased the susceptibility of Huh-7 cells to doxorubicin suggesting its potential in combination chemotherapy. Through isotopomer tracing of [2–13C] glycine metabolism, we demonstrated that SHMT2 activity is associated with cancer phenotype. However, overexpression of SHMT2 was insufficient to transform immortalized hepatic cells to malignancy, suggesting that SHMT2 is one of the building blocks in liver cancer metabolism but does not initiate malignant transformation. Moreover, our results suggest that glycine, but not 5,10-methylenetetrahydrofolate, from the SHMT2-mediated enzymatic reaction is instrumental in tumorigenesis. Indeed, we found that SHMT2-knockdown cells exhibited increased glycine uptake. Taken together, our data suggest that SHMT2 may be a potential target in the treatment of human HCC.
Collapse
|
19
|
Ben Yahia B, Gourevitch B, Malphettes L, Heinzle E. Segmented linear modeling of CHO fed-batch culture and its application to large scale production. Biotechnol Bioeng 2016; 114:785-797. [PMID: 27869296 PMCID: PMC5324675 DOI: 10.1002/bit.26214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 08/16/2016] [Accepted: 11/02/2016] [Indexed: 12/21/2022]
Abstract
We describe a systematic approach to model CHO metabolism during biopharmaceutical production across a wide range of cell culture conditions. To this end, we applied the metabolic steady state concept. We analyzed and modeled the production rates of metabolites as a function of the specific growth rate. First, the total number of metabolic steady state phases and the location of the breakpoints were determined by recursive partitioning. For this, the smoothed derivative of the metabolic rates with respect to the growth rate were used followed by hierarchical clustering of the obtained partition. We then applied a piecewise regression to the metabolic rates with the previously determined number of phases. This allowed identifying the growth rates at which the cells underwent a metabolic shift. The resulting model with piecewise linear relationships between metabolic rates and the growth rate did well describe cellular metabolism in the fed‐batch cultures. Using the model structure and parameter values from a small‐scale cell culture (2 L) training dataset, it was possible to predict metabolic rates of new fed‐batch cultures just using the experimental specific growth rates. Such prediction was successful both at the laboratory scale with 2 L bioreactors but also at the production scale of 2000 L. This type of modeling provides a flexible framework to set a solid foundation for metabolic flux analysis and mechanistic type of modeling. Biotechnol. Bioeng. 2017;114: 785–797. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Bassem Ben Yahia
- Biochemical Engineering InstituteSaarland UniversityCampus A1.5, D‐66123 SaarbrückenGermany
- Upstream Process Sciences Biotech SciencesUCB Pharma S.A.Avenue de l'Industrie, Braine l'Alleud B‐1420Belgium
| | - Boris Gourevitch
- Institut de NeuroScience Paris‐Saclay (NeuroPSI)UMR CNRS 9197
- Université Paris‐SudOrsay Cedex 91405France
| | - Laetitia Malphettes
- Upstream Process Sciences Biotech SciencesUCB Pharma S.A.Avenue de l'Industrie, Braine l'Alleud B‐1420Belgium
| | - Elmar Heinzle
- Biochemical Engineering InstituteSaarland UniversityCampus A1.5, D‐66123 SaarbrückenGermany
| |
Collapse
|
20
|
Calise SJ, Purich DL, Nguyen T, Saleem DA, Krueger C, Yin JD, Chan EKL. 'Rod and ring' formation from IMP dehydrogenase is regulated through the one-carbon metabolic pathway. J Cell Sci 2016; 129:3042-52. [PMID: 27343244 DOI: 10.1242/jcs.183400] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 06/21/2016] [Indexed: 12/29/2022] Open
Abstract
'Rods and rings' (RRs) are conserved, non-membrane-bound intracellular polymeric structures composed, in part, of inosine monophosphate dehydrogenase (IMPDH), a key enzyme leading to GMP and GTP biosynthesis. RR formation is induced by IMPDH inhibitors as well as glutamine deprivation. They also form upon treatment of cells with glutamine synthetase inhibitors. We now report that depriving cells of serine and glycine promotes RR formation, and we have traced these effects to dihydrofolate reductase (DHFR) and serine hydroxymethyltransferase-2 (SHMT2), pivotal enzymes in one-carbon metabolism and nucleotide biosynthesis. RR assembly is likewise induced upon DHFR inhibition by methotrexate or aminopterin as well as siRNA-mediated knockdown of DHFR or SHMT2. Because RR assembly occurs when guanine nucleotide biosynthesis is inhibited, and because RRs rapidly disassemble after the addition of guanine nucleotide precursors, RR formation might be an adaptive homeostatic mechanism, allowing IMPDH to sense changes in the one-carbon folate pathway.
Collapse
Affiliation(s)
- S John Calise
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Daniel L Purich
- Department of Biochemistry and Molecular Biology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610-0245, USA
| | - Thuy Nguyen
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Dania A Saleem
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Claire Krueger
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Joyce D Yin
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, 1395 Center Drive, Gainesville, FL 32610-0424, USA
| |
Collapse
|
21
|
Pacold ME, Brimacombe KR, Chan SH, Rohde JM, Lewis CA, Swier LJYM, Possemato R, Chen WW, Sullivan LB, Fiske BP, Cho S, Freinkman E, Birsoy K, Abu-Remaileh M, Shaul YD, Liu CM, Zhou M, Koh MJ, Chung H, Davidson SM, Luengo A, Wang AQ, Xu X, Yasgar A, Liu L, Rai G, Westover KD, Vander Heiden MG, Shen M, Gray NS, Boxer MB, Sabatini DM. A PHGDH inhibitor reveals coordination of serine synthesis and one-carbon unit fate. Nat Chem Biol 2016; 12:452-8. [PMID: 27110680 PMCID: PMC4871733 DOI: 10.1038/nchembio.2070] [Citation(s) in RCA: 345] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/24/2016] [Indexed: 01/07/2023]
Abstract
Serine is a both a proteinogenic amino acid and the source of one-carbon units essential for de novo purine and deoxythymidine synthesis. In the canonical glucose-derived serine synthesis pathway, Homo sapiens phosphoglycerate dehydrogenase (PHGDH) catalyzes the first, rate-limiting step. Genetic loss of PHGDH is toxic towards PHGDH-overexpressing breast cancer cell lines even in the presence of exogenous serine. Here, we use a quantitative high-throughput screen to identify small molecule PHGDH inhibitors. These compounds reduce the production of glucose-derived serine in cells and suppress the growth of PHGDH-dependent cancer cells in culture and in orthotopic xenograft tumors. Surprisingly, PHGDH inhibition reduced the incorporation into nucleotides of one-carbon units from glucose-derived and exogenous serine. We conclude that glycolytic serine synthesis coordinates the use of one-carbon units from endogenous and exogenous serine in nucleotide synthesis, and suggest that one-carbon unit wasting may contribute to the efficacy of PHGDH inhibitors in vitro and in vivo.
Collapse
Affiliation(s)
- Michael E Pacold
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Dana-Farber Cancer Institute, Longwood Center, Boston, Massachusetts, USA.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kyle R Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jason M Rohde
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Caroline A Lewis
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Lotteke J Y M Swier
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Walter W Chen
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lucas B Sullivan
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Brian P Fiske
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Steve Cho
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, New York, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yoav D Shaul
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Chieh Min Liu
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Minerva Zhou
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Min Jung Koh
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Haeyoon Chung
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shawn M Davidson
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Alba Luengo
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
| | - Amy Q Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Li Liu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | | | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Nathanael S Gray
- Dana-Farber Cancer Institute, Longwood Center, Boston, Massachusetts, USA
| | - Matthew B Boxer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
22
|
Nicolae A, Wahrheit J, Nonnenmacher Y, Weyler C, Heinzle E. Identification of active elementary flux modes in mitochondria using selectively permeabilized CHO cells. Metab Eng 2015; 32:95-105. [PMID: 26417715 DOI: 10.1016/j.ymben.2015.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 09/02/2015] [Accepted: 09/08/2015] [Indexed: 12/23/2022]
Abstract
Metabolic compartmentation is a key feature of mammalian cells. Mitochondria are the powerhouse of eukaryotic cells, responsible for respiration and the TCA cycle. We accessed the mitochondrial metabolism of the economically important Chinese hamster ovary (CHO) cells using selective permeabilization. We tested key substrates without and with addition of ADP. Based on quantified uptake and production rates, we could determine the contribution of different elementary flux modes to the metabolism of a substrate or substrate combination. ADP stimulated the uptake of most metabolites, directly by serving as substrate for the respiratory chain, thus removing the inhibitory effect of NADH, or as allosteric effector. Addition of ADP favored substrate metabolization to CO2 and did not enhance the production of other metabolites. The controlling effect of ADP was more pronounced when we supplied metabolites to the first part of the TCA cycle: pyruvate, citrate, α-ketoglutarate and glutamine. In the second part of the TCA cycle, the rates were primarily controlled by the concentrations of C4-dicarboxylates. Without ADP addition, the activity of the pyruvate carboxylase-malate dehydrogenase-malic enzyme cycle consumed the ATP produced by oxidative phosphorylation, preventing its accumulation and maintaining metabolic steady state conditions. Aspartate was taken up only in combination with pyruvate, whose uptake also increased, a fact explained by complex regulatory effects. Isocitrate dehydrogenase and α-ketoglutarate dehydrogenase were identified as the key regulators of the TCA cycle, confirming existent knowledge from other cells. We have shown that selectively permeabilized cells combined with elementary mode analysis allow in-depth studying of the mitochondrial metabolism and regulation.
Collapse
Affiliation(s)
- Averina Nicolae
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Judith Wahrheit
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Yannic Nonnenmacher
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Christian Weyler
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Elmar Heinzle
- Universität des Saarlandes, Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany.
| |
Collapse
|
23
|
Sellick CA, Croxford AS, Maqsood AR, Stephens GM, Westerhoff HV, Goodacre R, Dickson AJ. Metabolite profiling of CHO cells: Molecular reflections of bioprocessing effectiveness. Biotechnol J 2015. [DOI: 10.1002/biot.201400664] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
24
|
Kim D, Fiske BP, Birsoy K, Freinkman E, Kami K, Possemato RL, Chudnovsky Y, Pacold ME, Chen WW, Cantor JR, Shelton LM, Gui DY, Kwon M, Ramkissoon SH, Ligon KL, Kang SW, Snuderl M, Vander Heiden MG, Sabatini DM. SHMT2 drives glioma cell survival in ischaemia but imposes a dependence on glycine clearance. Nature 2015; 520:363-7. [PMID: 25855294 PMCID: PMC4533874 DOI: 10.1038/nature14363] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 03/03/2015] [Indexed: 12/15/2022]
Abstract
Cancer cells adapt their metabolic processes to support rapid proliferation, but less is known about how cancer cells alter metabolism to promote cell survival in a poorly vascularized tumor microenvironment1–3. Here, we identify a key role for serine and glycine metabolism in the survival of brain cancer cells within the ischemic zones of gliomas. In human glioblastoma multiforme (GBM), mitochondrial serine hydroxymethyltransferase (SHMT2) and glycine decarboxylase (GLDC) are highly expressed in the pseudopalisading cells that surround necrotic foci. We find that SHMT2 activity limits that of pyruvate kinase (PKM2) and reduces oxygen consumption, eliciting a metabolic state that confers a profound survival advantage to cells in poorly vascularized tumor regions. GLDC inhibition impairs cells with high SHMT2 levels as the excess glycine not metabolized by GLDC can be converted to the toxic molecules aminoacetone and methylglyoxal. Thus, SHMT2 is required for cancer cells to adapt to the tumor environment, but also renders these cells sensitive to glycine cleavage system inhibition.
Collapse
Affiliation(s)
- Dohoon Kim
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Brian P Fiske
- 1] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [2] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [3] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Kivanc Birsoy
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Elizaveta Freinkman
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Kenjiro Kami
- Human Metabolome Technologies, Inc., Tsuruoka 997-0052, Japan
| | - Richard L Possemato
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Yakov Chudnovsky
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Michael E Pacold
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA [6] Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Walter W Chen
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Jason R Cantor
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Laura M Shelton
- Human Metabolome Technologies America, Inc., Boston, Massachusetts 02134, USA
| | - Dan Y Gui
- 1] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [2] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [3] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Manjae Kwon
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Shakti H Ramkissoon
- 1] Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [3] Department of Pathology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Keith L Ligon
- 1] Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [3] Department of Pathology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Seong Woo Kang
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center and Medical School, New York, New York 10016, USA
| | - Matthew G Vander Heiden
- 1] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [2] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [3] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA [4] Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - David M Sabatini
- 1] Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA [4] Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA [5] Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| |
Collapse
|
25
|
Staszewska A, Kurowska E, Bal W. Ternary complex formation and competition quench fluorescence of ZnAF family zinc sensors. Metallomics 2014; 5:1483-90. [PMID: 23939683 DOI: 10.1039/c3mt00007a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Our current understanding of the intracellular thermodynamics and kinetics of Zn(ii) ions is largely based on the application of fluorescent sensor molecules, used to study and visualize the concentration, distribution and transport of Zn(ii) ions in real time. Such agents are designed for high selectivity for zinc in respect to other biological metal ions. However, the issue of their sensitivity to physiological levels of low molecular weight Zn(ii) ligands (LMWLs) has not been addressed. We followed the effects of eight such compounds on the fluorescence of ZnAF-1 and ZnAF-2F, two representatives of the ZnAF family of fluorescein-based zinc sensors containing the N,N-bis(2-pyridylmethyl)ethylenediamine chelating unit. Fluorescence titrations of equimolar Zn(ii)-ZnAF-1 and Zn(ii)-ZnAF-2F solutions with acetate, phosphate, citrate, glycine, glutamic acid, histidine, ATP and GSH demonstrated strong fluorescence quenching. These results are interpreted in terms of an interplay of the formation of the [ZnAF-Zn(ii)-LMWL] ternary complexes and the competition for Zn(ii) between ZnAF and LMWLs. UV-vis spectroscopic titrations revealed the existence of supramolecular interactions between the fluorescein moiety of ZnAF-1 and ATP and His, which, however, did not contribute to fluorescence quenching. Therefore, the obtained results show that the ZnAF sensors, other currently used zinc sensors containing the N,N-bis(2-pyridylmethyl)ethylenediamine unit, and, in general, all sensors that do not saturate the Zn(ii) coordination sphere may co-report cellular metabolites and Zn(ii) ions, leading to misrepresentations of the concentrations and fluxes of biological zinc.
Collapse
Affiliation(s)
- Anna Staszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a 02-106, Warsaw, Poland.
| | | | | |
Collapse
|
26
|
The histone H3 methyltransferase G9A epigenetically activates the serine-glycine synthesis pathway to sustain cancer cell survival and proliferation. Cell Metab 2013; 18:896-907. [PMID: 24315373 PMCID: PMC3878056 DOI: 10.1016/j.cmet.2013.11.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/30/2013] [Accepted: 10/16/2013] [Indexed: 12/13/2022]
Abstract
Increased activation of the serine-glycine biosynthetic pathway is an integral part of cancer metabolism that drives macromolecule synthesis needed for cell proliferation. Whether this pathway is under epigenetic control is unknown. Here we show that the histone H3 lysine 9 (H3K9) methyltransferase G9A is required for maintaining the pathway enzyme genes in an active state marked by H3K9 monomethylation and for the transcriptional activation of this pathway in response to serine deprivation. G9A inactivation depletes serine and its downstream metabolites, triggering cell death with autophagy in cancer cell lines of different tissue origins. Higher G9A expression, which is observed in various cancers and is associated with greater mortality in cancer patients, increases serine production and enhances the proliferation and tumorigenicity of cancer cells. These findings identify a G9A-dependent epigenetic program in the control of cancer metabolism, providing a rationale for G9A inhibition as a therapeutic strategy for cancer.
Collapse
|
27
|
Carinhas N, Duarte TM, Barreiro LC, Carrondo MJT, Alves PM, Teixeira AP. Metabolic signatures of GS-CHO cell clones associated with butyrate treatment and culture phase transition. Biotechnol Bioeng 2013; 110:3244-57. [DOI: 10.1002/bit.24983] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/26/2013] [Accepted: 06/12/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Nuno Carinhas
- iBET; Instituto de Biologia Experimental e Tecnológica; Apartado 12 2781-901 Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Av. da República 2780-157 Oeiras Portugal
| | - Tiago M. Duarte
- iBET; Instituto de Biologia Experimental e Tecnológica; Apartado 12 2781-901 Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Av. da República 2780-157 Oeiras Portugal
| | - Laura C. Barreiro
- iBET; Instituto de Biologia Experimental e Tecnológica; Apartado 12 2781-901 Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Av. da República 2780-157 Oeiras Portugal
| | - Manuel J. T. Carrondo
- iBET; Instituto de Biologia Experimental e Tecnológica; Apartado 12 2781-901 Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Av. da República 2780-157 Oeiras Portugal
- Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; 2829-516 Caparica Portugal
| | - Paula M. Alves
- iBET; Instituto de Biologia Experimental e Tecnológica; Apartado 12 2781-901 Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Av. da República 2780-157 Oeiras Portugal
| | - Ana P. Teixeira
- iBET; Instituto de Biologia Experimental e Tecnológica; Apartado 12 2781-901 Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Av. da República 2780-157 Oeiras Portugal
| |
Collapse
|
28
|
|
29
|
Tibbetts AS, Appling DR. Compartmentalization of Mammalian folate-mediated one-carbon metabolism. Annu Rev Nutr 2010; 30:57-81. [PMID: 20645850 DOI: 10.1146/annurev.nutr.012809.104810] [Citation(s) in RCA: 479] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The recognition that mitochondria participate in folate-mediated one-carbon metabolism grew out of pioneering work beginning in the 1950s from the laboratories of D.M. Greenberg, C.G. Mackenzie, and G. Kikuchi. These studies revealed mitochondria as the site of oxidation of one-carbon donors such as serine, glycine, sarcosine, and dimethylglycine. Subsequent work from these laboratories and others demonstrated the participation of folate coenzymes and folate-dependent enzymes in these mitochondrial processes. Biochemical and molecular genetic approaches in the 1980s and 1990s identified many of the enzymes involved and revealed an interdependence of cytoplasmic and mitochondrial one-carbon metabolism. These studies led to the development of a model of eukaryotic one-carbon metabolism that comprises parallel cytosolic and mitochondrial pathways, connected by one-carbon donors such as serine, glycine, and formate. Sequencing of the human and other mammalian genomes has facilitated identification of the enzymes that participate in this intercompartmental one-carbon metabolism, and animal models are beginning to clarify the roles of the cytoplasmic and mitochondrial isozymes of these enzymes. Identifying the mitochondrial transporters for the one-carbon donors and elucidating how flux through these pathways is controlled are two areas ripe for exploration.
Collapse
Affiliation(s)
- Anne S Tibbetts
- Department of Chemistry and Biochemistry, and the Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | | |
Collapse
|
30
|
Desler C, Lykke A, Rasmussen LJ. The effect of mitochondrial dysfunction on cytosolic nucleotide metabolism. J Nucleic Acids 2010; 2010. [PMID: 20862377 PMCID: PMC2938461 DOI: 10.4061/2010/701518] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/19/2010] [Indexed: 12/13/2022] Open
Abstract
Several enzymes of the metabolic pathways responsible for metabolism of cytosolic ribonucleotides and deoxyribonucleotides are located in mitochondria. Studies described in this paper suggest dysfunction of the mitochondria to affect these metabolic pathways and limit the available levels of cytosolic ribonucleotides and deoxyribonucleotides, which in turn can result in aberrant RNA and DNA synthesis. Mitochondrial dysfunction has been linked to genomic instability, and it is possible that the limiting effect of mitochondrial dysfunction on the levels of nucleotides and resulting aberrant RNA and DNA synthesis in part can be responsible for this link. This paper summarizes the parts of the metabolic pathways responsible for nucleotide metabolism that can be affected by mitochondrial dysfunction.
Collapse
Affiliation(s)
- Claus Desler
- Center for Healthy Aging, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | | |
Collapse
|
31
|
Du H, Vitiello D, Sarno JL, Taylor HS. 3-Phosphoglycerate dehydrogenase expression is regulated by HOXA10 in murine endometrium and human endometrial cells. Reproduction 2010; 139:237-45. [PMID: 19778996 DOI: 10.1530/rep-08-0376] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
3-Phosphoglycerate dehydrogenase (PHGDH, 3-PGDH) is an enzyme necessary for de novo l-serine biosynthesis. HOXA10 expression is required for endometrial receptivity; however, few target genes of HOXA10 regulation are known. Using a microarray we identified Phgdh as a target of HOXA10 regulation in murine endometrium and confirmed this regulatory relationship in human endometrial cells. PHGDH was downregulated 2.0-fold by HOXA10 and upregulated 4.4-fold by HOXA10 antisense in vivo. In human endometrial cells, real-time PCR results show that pcDNA3.1/HOXA10 transfection decreased PHGDH mRNA expression to 40% of pretreatment level (P<0.05), while PHGDH mRNA expression was increased 2.1-fold (P<0.05) by HOXA10 siRNA. Western blot results confirmed the regulatory relationship in both primary human endometrial stromal and epithelial cells, as well as in human endometrial stromal cells and Ishikawa cells. In human cycling endometrial tissue, immunohistochemical results showed that PHGDH expression is relatively high in the proliferative phase in glandular cells and lower in the secretory phase. Here we report novel expression and regulation of PHGDH in murine and human endometrium. PHGDH is expressed in both endometrial epithelial and stromal cells. HOXA10 represses endometrial PHGDH expression. PHGDH is necessary for serine biosynthesis, which serves as a substrate for protein synthesis. One mechanism by which HOXA10 regulates cellular differentiation may involve limiting protein synthesis in the secretary phase.
Collapse
Affiliation(s)
- Hongling Du
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University, PO Box 208063, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | | | | | | |
Collapse
|
32
|
Nijhout HF, Gregory JF, Fitzpatrick C, Cho E, Lamers KY, Ulrich CM, Reed MC. A mathematical model gives insights into the effects of vitamin B-6 deficiency on 1-carbon and glutathione metabolism. J Nutr 2009; 139:784-91. [PMID: 19244383 PMCID: PMC2666368 DOI: 10.3945/jn.109.104265] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We experimented with a mathematical model for 1-carbon metabolism and glutathione (GSH) synthesis to investigate the effects of vitamin B-6 deficiency on the reaction velocities and metabolite concentrations in this metabolic network. The mathematical model enabled us to independently alter the activities of each of the 5 vitamin B-6-dependent enzymes and thus determine which inhibitions were responsible for the experimentally observed consequences of a vitamin B-6 deficiency. The effect of vitamin B-6 deficiency on serine and glycine concentrations in tissues and plasma was almost entirely due to its effects on the activity of glycine decarboxylase. The effect of vitamin B-6 restriction on GSH concentrations appeared to be indirect, arising from the fact that vitamin B-6 restriction increases oxidative stress, which, in turn, affects several enzymes in 1-carbon metabolism as well as the GSH transporter. Vitamin B-6 restriction causes an abnormally high and prolonged homocysteine response to a methionine load test. This effect appeared to be mediated solely by its effects on cystathionine beta-synthase. Reduction of the enzymatic activity of serine hydroxymethyltransferase (SHMT) had negligible effects on most metabolite concentrations and reaction velocities. Reduction or total elimination of cytoplasmic SHMT had a surprisingly moderate effect on metabolite concentrations and reaction velocities. This corresponds to the experimental findings that a reduction in the enzymatic activity of SHMT has little effect on 1-carbon metabolism. Our simulations showed that the primary function of SHMT was to increase the rate by which the glycine-serine balance was reequilibrated after a perturbation.
Collapse
Affiliation(s)
- H. Frederik Nijhout
- Department of Biology, Duke University, Durham, NC 27708; Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611; Department of Mathematics, Duke University, Durham, NC 27708; Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and University of Washington, Department of Epidemiology and Interdisciplinary Graduate Program in the Nutrition Sciences, Seattle, WA 98195
| | - Jesse F. Gregory
- Department of Biology, Duke University, Durham, NC 27708; Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611; Department of Mathematics, Duke University, Durham, NC 27708; Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and University of Washington, Department of Epidemiology and Interdisciplinary Graduate Program in the Nutrition Sciences, Seattle, WA 98195
| | - Courtney Fitzpatrick
- Department of Biology, Duke University, Durham, NC 27708; Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611; Department of Mathematics, Duke University, Durham, NC 27708; Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and University of Washington, Department of Epidemiology and Interdisciplinary Graduate Program in the Nutrition Sciences, Seattle, WA 98195
| | - Eugenia Cho
- Department of Biology, Duke University, Durham, NC 27708; Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611; Department of Mathematics, Duke University, Durham, NC 27708; Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and University of Washington, Department of Epidemiology and Interdisciplinary Graduate Program in the Nutrition Sciences, Seattle, WA 98195
| | - K. Yvonne Lamers
- Department of Biology, Duke University, Durham, NC 27708; Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611; Department of Mathematics, Duke University, Durham, NC 27708; Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and University of Washington, Department of Epidemiology and Interdisciplinary Graduate Program in the Nutrition Sciences, Seattle, WA 98195
| | - Cornelia M. Ulrich
- Department of Biology, Duke University, Durham, NC 27708; Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611; Department of Mathematics, Duke University, Durham, NC 27708; Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and University of Washington, Department of Epidemiology and Interdisciplinary Graduate Program in the Nutrition Sciences, Seattle, WA 98195
| | - Michael C. Reed
- Department of Biology, Duke University, Durham, NC 27708; Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611; Department of Mathematics, Duke University, Durham, NC 27708; Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and University of Washington, Department of Epidemiology and Interdisciplinary Graduate Program in the Nutrition Sciences, Seattle, WA 98195
| |
Collapse
|
33
|
Deshpande R, Yang TH, Heinzle E. Towards a metabolic and isotopic steady state in CHO batch cultures for reliable isotope-based metabolic profiling. Biotechnol J 2009; 4:247-63. [DOI: 10.1002/biot.200800143] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
34
|
Chang WN, Tsai JN, Chen BH, Huang HS, Fu TF. Serine hydroxymethyltransferase isoforms are differentially inhibited by leucovorin: characterization and comparison of recombinant zebrafish serine hydroxymethyltransferases. Drug Metab Dispos 2007; 35:2127-37. [PMID: 17664250 DOI: 10.1124/dmd.107.016840] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Serine hydroxymethyltransferase (SHMT) provides activated one-carbon units required for the biosynthesis of nucleotides, protein, and methyl group by converting serine and tetrahydrofolate to glycine and N(5),N(10)-methylenetetrahydrofolate. It is postulated that SHMT activity is associated with the development of methotrexate resistance and the in vivo activity of SHMT is regulated by the binding of N(5)-CHO-THF, the rescue agent in high-dose methotrexate chemotherapy. The aim of this study is to advance our understanding of the folate-mediated one-carbon metabolism in zebrafish by characterizing zebrafish mitochondrial SHMT. The cDNA encoding zebrafish mitochondrial SHMT was cloned, overexpressed in Escherichia coli, and purified with a three-step purification protocol. Similarities in structural, physical, and kinetic properties were revealed between the recombinant zebrafish mitochondrial SHMT and its mammalian orthologs. Surprisingly, leucovorin significantly inhibits the aldol cleavage of serine catalyzed by zebrafish cytosolic SHMT but inhibits to a lesser extent the reaction catalyzed by the mitochondrial isozyme. This is, to our knowledge, the first report on zebrafish mitochondrial folate enzyme as well as the differential inhibition of leucovorin on these two SHMT isoforms. Western blot analysis revealed tissue-specific distribution with the highest enrichment present in liver for both cytosolic and mitochondrial SHMTs. Intracellular localization was confirmed by confocal microscopy for both mitochondrial and cytosolic SHMTs. Unexpectedly, the cytosolic isoform was observed in both nucleus and cytosol. Together with the previous report on zebrafish cytosolic SHMT, we suggest that zSHMTs can be used in in vitro assays for folate-related investigation and antifolate drug discovery.
Collapse
Affiliation(s)
- Wen-Ni Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan 701, Taiwan
| | | | | | | | | |
Collapse
|
35
|
Christensen KE, MacKenzie RE. Mitochondrial one-carbon metabolism is adapted to the specific needs of yeast, plants and mammals. Bioessays 2006; 28:595-605. [PMID: 16700064 DOI: 10.1002/bies.20420] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In eukaryotes, folate metabolism is compartmentalized between the cytoplasm and organelles. The folate pathways of mitochondria are adapted to serve the metabolism of the organism. In yeast, mitochondria support cytoplasmic purine synthesis through the generation of formate. This pathway is important but not essential for survival, consistent with the flexibility of yeast metabolism. In plants, the mitochondrial pathways support photorespiration by generating serine from glycine. This pathway is essential under photosynthetic conditions and the enzyme expression varies with photosynthetic activity. In mammals, the expression of the mitochondrial enzymes varies in tissues and during development. In embryos, mitochondria supply formate and glycine for purine synthesis, a process essential for survival; in adult tissues, flux through mitochondria can favor serine production. The differences in the folate pathways of mitochondria depending on species, tissues and developmental stages, profoundly alter the nature of their metabolic contribution.
Collapse
|
36
|
Dickson TM, Edison E, Brosnan JT, House JD. Hyperglycinemia due to folate deficiency in rats: evidence for the lack of involvement of the hepatic glycine cleavage system. J Nutr Biochem 2005; 16:736-42. [PMID: 16081265 DOI: 10.1016/j.jnutbio.2005.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Revised: 03/15/2005] [Accepted: 03/28/2005] [Indexed: 10/25/2022]
Abstract
In addition to a well-recognized hyperhomocysteinemic state, folate deficiency also leads to profound hyperglycinemia. To further characterize the latter observation, two trials were conducted using a folate-deficient rat model to (1) determine the sensitivity of plasma glycine to folate repletion and (2) test the hypothesis that hyperglycinemia results from a reduced flux through the folate-dependent glycine cleavage system (GCS). Weanling male Sprague-Dawley rats were used, and they consumed an amino acid-defined diet with either 0 (FD) or 1 (FA) mg/kg of crystalline folic acid. In Trial 1, 30 rats consumed the FD diet for 28 days. Rats then consumed diets containing 0.1, 0.2, 0.3 or 0.4 mg/kg of folic acid for 14 days before termination. In Trial 2, 16 rats were allocated to receive either the FA (n=8) or FD (n=8) diet for 30 days before termination. Liver mitochondria were isolated and flux through the GCS (measured as 14CO2 production from 1-14C-glycine) was determined. Plasma from blood collected at termination was analyzed for folate, homocysteine and glycine. In Trial 1, both homocysteine and glycine responded linearly to increased dietary folic acid (milligrams per kilogram) levels (P<.05). In Trial 2, plasma folate (FA=25.85 vs. FD=0.66; S.E.M.=1.4 microM), homocysteine (FA=11.1 vs. FD=55.3; S.E.M.=1.7 microM) and glycine (FA=564 vs. FD=1983; S.E.M.=114 microM) were significantly affected by folate deficiency (P<.0001). However, glycine flux through hepatic GCS was not affected by folate deficiency (P>.05). These results provide evidence that in a folate-deficient rat model, both homocysteine and glycine are sensitive to dietary folic acid levels; however, the observed hyperglycinemia does not appear to be related to a reduced flux through the hepatic GCS.
Collapse
Affiliation(s)
- Tyra M Dickson
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
| | | | | | | |
Collapse
|
37
|
Fu TF, Hunt S, Schirch V, Safo MK, Chen BH. Properties of human and rabbit cytosolic serine hydroxymethyltransferase are changed by single nucleotide polymorphic mutations. Arch Biochem Biophys 2005; 442:92-101. [PMID: 16137637 DOI: 10.1016/j.abb.2005.07.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 07/20/2005] [Accepted: 07/21/2005] [Indexed: 11/21/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) is a key enzyme in the formation and regulation of the folate one-carbon pool. Recent studies on human subjects have shown the existence of two single nucleotide polymorphisms that may be associated with several disease states. One of these mutations results in Ser394 being converted to an Asn (S394N) and the other in the change of Leu474 to a Phe (L474F). These mutations were introduced into the cDNA for both human and rabbit cytosolic SHMT and the mutant enzymes expressed and purified from an Escherichia coli expression system. The mutant enzymes show normal values for kcat and Km for serine. However, the S394N mutant enzyme has increased dissociation constant values for both glycine and tetrahydrofolate (tetrahydropteroylglutamate) and its pentaglutamate form compared to wild-type enzyme. The L474F mutant shows lowered affinity (increased dissociation constant) for only the pentaglutamate form of the folate ligand. Both mutations result in decreased rates of pyridoxal phosphate addition to the mutant apo enzymes to form the active holo enzymes. Neither mutation significantly affects the stability of SHMT or the rate at which it converts 5,10-methenyl tetrahydropteroyl pentaglutamate to 5-formyl tetrahydropteroyl pentaglutamate. Analysis of the structures of rabbit and human SHMT show how mutations at these two sites can result in the observed functional differences.
Collapse
Affiliation(s)
- Tzu-Fun Fu
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, College of Medicine, Tainan 701, Taiwan.
| | | | | | | | | |
Collapse
|
38
|
Scheer JB, Mackey AD, Gregory JF. Activities of hepatic cytosolic and mitochondrial forms of serine hydroxymethyltransferase and hepatic glycine concentration are affected by vitamin B-6 intake in rats. J Nutr 2005; 135:233-8. [PMID: 15671219 DOI: 10.1093/jn/135.2.233] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP)-dependent enzyme that exists as cytosolic and mitochondrial isozymes that catalyze the reversible interconversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methyleneTHF. SHMT is a major source of one-carbon units for cellular metabolism, but its sensitivity to various degrees of altered vitamin B-6 nutritional status has not been determined. In this study, cytosolic and mitochondrial SHMT activities were measured in liver from rats fed dietary pyridoxine (PN) ranging from adequate to deficient levels (2, 1, 0.5, 0.1, and 0 mg PN/kg diet; n = 10 per group). Both mitochondrial and cytosolic SHMT activities increased (P < 0.001) with increasing dietary PN over this range, and activities were a linear function of liver PLP concentration. Mitochondrial SHMT comprised approximately 70% of total activity. Assays conducted with and without in vitro addition of PLP indicated that total SHMT (apo- and holoenzyme forms) varied with dietary PN for each isoform, but that the proportion of each present as the apoenzyme was not affected by PN intake. This aspect of SHMT nutritional regulation differs from that of many other PLP-dependent enzymes. Hepatic glycine concentration was inversely related to vitamin B-6 intake (P < 0.05), which suggests a functional effect of altered SHMT activity. Overall these results demonstrate the potential for disruption of SHMT-mediated one-carbon metabolism by inadequate vitamin B-6 intake.
Collapse
Affiliation(s)
- Jennifer B Scheer
- Food Science and Human Nutrition Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | | | | |
Collapse
|
39
|
Hyndman ME, Manns BJ, Snyder FF, Bridge PJ, Scott-Douglas NW, Fung E, Parsons HG. Vitamin B12 decreases, but does not normalize, homocysteine and methylmalonic acid in end-stage renal disease: a link with glycine metabolism and possible explanation of hyperhomocysteinemia in end-stage renal disease. Metabolism 2003; 52:168-72. [PMID: 12601627 DOI: 10.1053/meta.2003.50022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The genetic and environmental factors influencing catabolism of homocysteine in end-stage renal disease (ESRD) patients remain poorly understood. This study investigated how genetic and nutritional influences affect the response to high-dose vitamin B(12) and folate treatment in ESRD patients with hyperhomocysteinemia. We studied 81 hemodialysis patients with hyperhomocysteinemia (> 16 micromol/L) on varied doses of a multivitamin containing 1 mg of folic acid per day. After screening blood work, all patients were switched to daily multivitamin therapy including 1 mg of folic acid for 4 weeks. Vitamin B(12), 1 mg/d, was added for an additional 4 weeks. Patients were then randomized to receive folic acid or placebo. The influence of the 3 methylenetetrahydrofolate reductase (MTHFR) 677 C-->T genotypes on the efficacy of vitamin therapy was assessed. In addition, we investigated how the metabolic complications of ESRD, including the relationship between methylmalonic acid (MMA) and circulating glycine, may contribute to hyperhomocysteinemia. There was no significant difference in total homocysteine (tHcy) levels between the MTHFR 677 C-->T genotypes during the screening phase of the trial. Treatment with a daily multivitamin containing 1 mg folate significantly lowered tHcy levels in all patients by 19.2%. Further supplementation with 1 mg vitamin B(12) resulted in greater tHcy reduction among subjects with the MTHFR 677 T/T genotype (P<.01, T/T v C/C or C/T) while lowering MMA equally in all MTHFR genotypes. There was a significant positive correlation between plasma glycine levels and MMA (P <.05). High-dose vitamin therapy significantly lowers, but does not normalize, MMA and tHcy levels. The MTHFR genotype, while influencing homocysteine levels, was not responsible for the majority of the elevation in plasma tHcy.
Collapse
Affiliation(s)
- Matthew Eric Hyndman
- Division of Nephrology, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | | | | | | | | | | |
Collapse
|
40
|
Narkewicz MR, Jones G, Thompson H, Kolhouse F, Fennessey PV. Folate cofactors regulate serine metabolism in fetal ovine hepatocytes. Pediatr Res 2002; 52:589-94. [PMID: 12357055 DOI: 10.1203/00006450-200210000-00020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The fetal liver is the primary site of fetal serine production. The regulation of this unique fetal hepatic serine production is unknown. We hypothesized that serine production would be responsive to folate cofactor supply or hormonal regulation. To test this hypothesis, we determined the effect of key folate cofactors and insulin and glucagon on serine and glycine metabolism in primary culture of fetal ovine hepatocytes. Hepatocytes were cultured in serum-free, low-folate media [5 nM 5-methyl-tetrahydrofolate (THF)] with or without 50 nM 5,10-methylene-THF (MTHF) or 5-formyl-THF (FTHF). Serine and glycine production (P) and utilization (U) were determined by stable isotope dilution with [1-(13)C]serine and [1-(13)C]glycine for 24 h. The effect of insulin (1 microM) or glucagon (1 micro M) was determined in a similar manner. Under basal conditions, serine P (43.2 +/- 5.1 micromol/mg DNA per 24 h) is greater than serine U (24.1 +/- 3.1 micromol/mg DNA per 24 h), whereas glycine U (27.3 +/- 3.0 micromol/mg DNA per 24 h) exceeds glycine P (16.7 +/- 1.9 micromol/mg DNA per 24 h). MTHF results in a significant decrease in serine U (16.0 +/- 2.7 micromol/mg DNA per 24 h; p = 0.02 versus low folate), with no change in serine P. FTHF reduces serine P (36.2 +/- 4.9 micromol/mg DNA per 24 h; p = 0.01), but does not alter serine U. There were no effects on glycine metabolism with 50 nM MTHF or FTHF. Serine P and U were inversely correlated whereas glycine P and U were directly correlated with the media concentration of MTHF or FTHF. Glucagon treatment increased serine U by 260 +/- 65% versus low folate (p = 0.0004) but did not change serine P. Insulin treatment led to parallel increases in both serine P and U. Both folate cofactor availability and hormone concentrations regulate serine metabolism in the fetal liver. We speculate that serine metabolism may be a marker of fetal hepatic folate cofactor supply.
Collapse
Affiliation(s)
- Michael R Narkewicz
- Department of Pediatrics, Section of Pediatric Gastroenterology, University of Colorado School of Medicine and The Children's Hospital, Denver, Colorado 80218, USA.
| | | | | | | | | |
Collapse
|
41
|
Pind S, Slominski E, Mauthe J, Pearlman K, Swoboda KJ, Wilkins JA, Sauder P, Natowicz MR. V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme. J Biol Chem 2002; 277:7136-43. [PMID: 11751922 DOI: 10.1074/jbc.m111419200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A deficiency of 3-phosphoglycerate dehydrogenase (PHGDH) is a disorder of serine biosynthesis identified in children with congenital microcephaly, seizures, and severe psychomotor retardation. We report here the identification of the 1468G-->A (V490M) mutation of this gene in two siblings of an Ashkenazi Jewish family, providing further evidence that the V490M mutation is a common, panethnic cause of this deficiency. Using a novel, DNA-based diagnostic test, the mutation was not detected in 400 non-Jewish controls; one heterozygote was found among 400 persons of Ashkenazi Jewish ethnicity. Extensive biochemical studies were undertaken to characterize the effect of this mutation on enzyme activity, turnover, and stability. The V490M PHGDH yielded less than 35% of the activity observed for the wild-type enzyme when overexpressed by transient transfection or when comparing the endogenous activity in fibroblast cells from the patients with controls. Immunoblotting studies showed a comparable reduction in the level of immunoreactive PHGDH in cells expressing the mutant enzyme. Pulse-chase experiments with metabolically labeled PHGDH indicated that this resulted from an increased rate of degradation of the mutant enzyme following its synthesis. Thermolability analyses of mutant and wild-type enzyme activity revealed no significant differences. While others have proposed that the V490M mutation decreases the V(max) of the enzyme, we conclude that this mutation impairs the folding and/or assembly of PHGDH but has minimal effects on the activity or stability of that portion of the V490M mutant that reaches a mature conformation.
Collapse
Affiliation(s)
- Steven Pind
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0W3, Canada.
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Shaheduzzaman S, Krishnan V, Petrovic A, Bittner M, Meltzer P, Trent J, Venkatesan S, Zeichner S. Effects of HIV-1 Nef on cellular gene expression profiles. J Biomed Sci 2002; 9:82-96. [PMID: 11810028 DOI: 10.1007/bf02256581] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The early human immunodeficiency virus (HIV) accessory protein Nef makes an important contribution to virulence, but the mechanisms by which Nef influences pathogenesis remain unclear. Many well-studied effects of Nef, like CD4 and class I MHC downregulation, occur posttranslationally. However, Nef has the potential to affect gene expression by interfering with cell signaling pathways and by virtue of structural features such as the Pro-X-X-Pro motif, which may interact with src homology region-3 domains of src-like kinases. We used a cDNA microarray screening strategy to identify cellular genes whose steady state transcriptional levels may be affected by Nef. We generated HeLa cell lines expressing wild-type or mutant HIV-1 nef protein sequences. Using cDNA microarray technology, we compared the patterns of cellular gene expression in the various cell lines to the pattern in non-Nef-expressing HeLa cells. By matching the patterns of cellular gene expression in HeLa cell lines expressing various Nefs with that of parental HeLa cells, we identified several cellular genes whose expression was modulated differentially by Nef and its mutants. We confirmed the differential expression of selected genes by RNA filter blotting. Genes expressed at higher levels included proteases, transcription factors, protein kinases, nuclear import/export proteins, adaptor molecules and cyclins, some of which have previously been implicated as being important for HIV replication and pathogenesis. The results indicate that Nef expression can alter the expression of cellular genes and suggest that this alteration in cellular gene expression may serve to optimize the cell to support the subsequent stages of viral replication.
Collapse
Affiliation(s)
- Syed Shaheduzzaman
- HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Cuskelly GJ, Stacpoole PW, Williamson J, Baumgartner TG, Gregory JF. Deficiencies of folate and vitamin B(6) exert distinct effects on homocysteine, serine, and methionine kinetics. Am J Physiol Endocrinol Metab 2001; 281:E1182-90. [PMID: 11701432 DOI: 10.1152/ajpendo.2001.281.6.e1182] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Folate and vitamin B(6) act in generating methyl groups for homocysteine remethylation, but the kinetic effects of folate or vitamin B(6) deficiency are not known. We used an intravenous primed, constant infusion of stable isotope-labeled serine, methionine, and leucine to investigate one-carbon metabolism in healthy control (n = 5), folate-deficient (n = 4), and vitamin B(6)-deficient (n = 5) human subjects. The plasma homocysteine concentration in folate-deficient subjects [15.9 +/- 2.1 (SD) micromol/l] was approximately two times that of control (7.4 +/- 1.7 micromol/l) and vitamin B(6)-deficient (7.7 +/- 2.1 micromol/l) subjects. The rate of methionine synthesis by homocysteine remethylation was depressed (P = 0.027) in folate deficiency but not in vitamin B(6) deficiency. For all subjects, the homocysteine remethylation rate was not significantly associated with plasma homocysteine concentration (r = -0.44, P = 0.12). The fractional synthesis rate of homocysteine from methionine was positively correlated with plasma homocysteine concentration (r = 0.60, P = 0.031), and a model incorporating both homocysteine remethylation and synthesis rates closely predicted plasma homocysteine levels (r = 0.85, P = 0.0015). Rates of homocysteine remethylation and serine synthesis were inversely correlated (r = -0.89, P < 0.001). These studies demonstrate distinctly different metabolic consequences of vitamin B(6) and folate deficiencies.
Collapse
Affiliation(s)
- G J Cuskelly
- Food Science and Human Nutrition Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611-0307, USA
| | | | | | | | | |
Collapse
|
44
|
Affiliation(s)
- Jesse F Gregory
- Food Science and Human Nutrition Department, PO Box 110370, Gainesville, FL 32611-0374
| | - Barry Shane
- Department of Nutritional Sciences, University of California, Berkeley, Berkeley, CA 94720-3104
| |
Collapse
|
45
|
Fu TF, Rife JP, Schirch V. The role of serine hydroxymethyltransferase isozymes in one-carbon metabolism in MCF-7 cells as determined by (13)C NMR. Arch Biochem Biophys 2001; 393:42-50. [PMID: 11516159 DOI: 10.1006/abbi.2001.2471] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The role of cytosolic and mitochondrial serine hydroxymethyltransferase in supplying one-carbon groups for purine and thymidylate biosynthesis in MCF-7 cells was investigated by observing folate-mediated one-carbon metabolism of l-[3-(13)C]serine, [2-(13)C]glycine, and [(13)C]formate. (13)C NMR was used to follow the incorporation of label into carbons 2 and 8 of purines and the methyl group attached to carbon 5 of thymidylate. The percentage enrichment of the (13)C label in purines was determined from the splitting patterns of the (1)H NMR spectra of C2 and C8 of adenine and C8 of guanine. The results show that formate is the major precursor in the cytosol of the one-carbon group in 10-formyltetrahydrofolate, which is used in purine biosynthesis, and the one-carbon group in 5,10-methylenetetrahydrofolate, which is used in thymidylate biosynthesis. Formate is formed in the mitochondria from carbon 3 of serine. The cleavage of serine to glycine and 5,10-methylenetetrahydrofolate by cytosolic serine hydroxymethyltransferase does not appear to be a major source of one-carbon groups for either purine or thymidylate biosynthesis. Carbon 3 of serine accounts for about 95% of the one-carbon pool, suggesting that other sources of one-carbon groups represent only minor pathways. [2-(13)C]Glycine is not a donor of one-carbons groups, confirming that MCF-7 cells lack a functional glycine cleavage system.
Collapse
Affiliation(s)
- T F Fu
- Department of Biochemistry, Institute for Structural Biology and Drug Discovery, 800 East Leigh Street, Suite 212, Richmond, Virginia 23219, USA
| | | | | |
Collapse
|
46
|
Thompson HR, Jones GM, Narkewicz MR. Ontogeny of hepatic enzymes involved in serine- and folate-dependent one-carbon metabolism in rabbits. Am J Physiol Gastrointest Liver Physiol 2001; 280:G873-8. [PMID: 11292595 DOI: 10.1152/ajpgi.2001.280.5.g873] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Serine occupies a central position in folate-dependent, one-carbon metabolism through 5,10-methylenetetrahydrofolate (MTHF) and 5-formyltetrahydrofolate (FTHF). We characterized the ontogeny of the specific activity of key enzymes involved in serine, 5,10-MTHF, and 5-FTHF metabolism: methenyltetrahydrofolate synthetase (MTHFS), MTHF reductase (MTHFR), the glycine cleavage system (GCS), methionine synthase (MS), and serine hydroxymethyltransferase (SHMT) in rabbit liver, placenta, brain, and kidney. In liver, MTHFS activity is low in the fetus (0.36 +/- 0.07 nmol. min(-1). mg protein(-1)), peaks at 3 wk (1.48 +/- 0.50 nmol. min(-1). mg protein(-1)), and then decreases to adult levels (1.13 +/- 0.32 nmol. min(-1). mg protein(-1)). MTHFR activity is highest early in gestation (24.9 +/- 2.4 nmol. h(-1). mg protein(-1)) and declines rapidly by birth (4.7 +/- 1.3 nmol. h(-1). mg protein(-1)). MS is highest during fetal life and declines after birth. Cytosolic SHMT activity does not vary during development, but mitochondrial SHMT peaks at 23 days. GCS activity is high in the fetus and the neonate, declining after weaning. In placenta and brain, all activities are low throughout gestation. Cytosolic and mitochondrial SHMT activities are low in kidney and rise after weaning, whereas MTHFS is low throughout development. These data suggest that the liver is the primary site of activity for these enzymes. Throughout development, there are multiple potential sources for production of 5,10-MTHF, but early in gestation high MTHFR activity and low MTHFS activity could reduce 5,10-MTHF availability.
Collapse
Affiliation(s)
- H R Thompson
- Department of Pediatrics, Section of Pediatric Gastroenterology, Hepatology, and Nutrition, University of Colorado School of Medicine, Denver, CO 80218, USA
| | | | | |
Collapse
|
47
|
Gregory JF, Cuskelly GJ, Shane B, Toth JP, Baumgartner TG, Stacpoole PW. Primed, constant infusion with [2H3]serine allows in vivo kinetic measurement of serine turnover, homocysteine remethylation, and transsulfuration processes in human one-carbon metabolism. Am J Clin Nutr 2000; 72:1535-41. [PMID: 11101483 DOI: 10.1093/ajcn/72.6.1535] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND One-carbon metabolism involves both mitochondrial and cytosolic forms of folate-dependent enzymes in mammalian cells, but few in vivo data exist to characterize the biochemical processes involved. OBJECTIVE We conducted a stable-isotopic investigation to determine the fates of exogenous serine and serine-derived one-carbon units in homocysteine remethylation in hepatic and whole-body metabolism. DESIGN A healthy man aged 23 y was administered [2,3,3-(2)H(3)]serine and [5,5,5-(2)H(3)]leucine by intravenous primed, constant infusion. Serial plasma samples were analyzed to determine the isotopic enrichment of free glycine, serine, leucine, methionine, and cystathionine. VLDL apolipoprotein B-100 served as an index of liver free amino acid labeling. RESULTS [(2)H(1)]Methionine and [(2)H(2)]methionine were labeled through homocysteine remethylation. We propose that [(2)H(2)]methionine occurs by remethylation with [(2)H(2)]methyl groups (as 5-methyltetrahydrofolate) formed only from cytosolic processing of [(2)H(3)]serine, whereas [(2)H(1)]methionine is formed with labeled one-carbon units from mitochondrial oxidation of C-3 serine to [(2)H(1)]formate to yield cytosolic [(2)H(1)]methyl groups. The labeling pattern of cystathionine formed from homocysteine and labeled serine suggests that cystathionine is derived mainly from a serine pool different from that used in apolipoprotein B-100 synthesis. CONCLUSIONS The appearance of both [(2)H(1)]- and [(2)H(2)]methionine forms indicates that both cytosolic and mitochondrial metabolism of exogenous serine generates carbon units in vivo for methyl group production and homocysteine remethylation. This study also showed the utility of serine infusion and indicated functional roles of cytosolic and mitochondrial compartments in one-carbon metabolism.
Collapse
Affiliation(s)
- J F Gregory
- Department of Nutritional Sciences, University of California Berkeley, Berkeley, CA, USA.
| | | | | | | | | | | |
Collapse
|
48
|
Cook RJ. Defining the steps of the folate one-carbon shuffle and homocysteine metabolism. Am J Clin Nutr 2000; 72:1419-20. [PMID: 11101465 DOI: 10.1093/ajcn/72.6.1419] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
49
|
Klomp LW, de Koning TJ, Malingré HE, van Beurden EA, Brink M, Opdam FL, Duran M, Jaeken J, Pineda M, Van Maldergem L, Poll-The BT, van den Berg IE, Berger R. Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency--a neurometabolic disorder associated with reduced L-serine biosynthesis. Am J Hum Genet 2000; 67:1389-99. [PMID: 11055895 PMCID: PMC1287916 DOI: 10.1086/316886] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2000] [Accepted: 10/12/2000] [Indexed: 01/24/2023] Open
Abstract
3-phosphoglycerate dehydrogenase (PHGDH) deficiency is a disorder of L-serine biosynthesis that is characterized by congenital microcephaly, psychomotor retardation, and seizures. To investigate the molecular basis for this disorder, the PHGDH mRNA sequence was characterized, and six patients from four families were analyzed for sequence variations. Five patients from three different families were homozygous for a single nucleotide substitution predicted to change valine at position 490 to methionine. The sixth patient was homozygous for a valine to methionine substitution at position 425; both mutations are located in the carboxyterminal part of PHGDH. In vitro expression of these mutant proteins resulted in significant reduction of PHGDH enzyme activities. RNA-blot analysis indicated abundant expression of PHGDH in adult and fetal brain tissue. Taken together with the severe neurological impairment in our patients, the data presented in this paper suggest an important role for PHGDH activity and L-serine biosynthesis in the metabolism, development, and function of the central nervous system.
Collapse
Affiliation(s)
- L W Klomp
- Department of Metabolic Diseases, University Medical Center Utrecht, 3584 AE Utrecht, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Snell K, Baumann U, Byrne PC, Chave KJ, Renwick SB, Sanders PG, Whitehouse SK. The genetic organization and protein crystallographic structure of human serine hydroxymethyltransferase. ADVANCES IN ENZYME REGULATION 2000; 40:353-403. [PMID: 10828359 DOI: 10.1016/s0065-2571(99)00035-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- K Snell
- Section of Structural Biology, Institute of Cancer Research, University of London, SW7 3RP, London, UK.
| | | | | | | | | | | | | |
Collapse
|