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Pan T, Jin H, Zhou C, Yan M. Rice Serine Hydroxymethyltransferases: Evolution, Subcellular Localization, Function and Perspectives. PLANTS (BASEL, SWITZERLAND) 2024; 13:1116. [PMID: 38674525 PMCID: PMC11053755 DOI: 10.3390/plants13081116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
In rice, there is a lack of comprehensive research on the functional aspects of the members of the serine hydroxymethyltransferase (SHMT) gene family. This study provides a comprehensive investigation of the SHMT gene family, covering phylogeny, gene structure, promoter analysis, expression analysis, subcellular localization, and protein interaction. Remarkably, we discovered a specific gene loss event occurred in the chloroplast-localized group IIa SHMTs in monocotyledons. However, OsSHMT3, which originally classified within cytoplasmic-localized group Ib, was found to be situated within chloroplasts in rice protoplasts. All five OsSHMTs are capable of forming homodimers, with OsSHMT3 being the only one able to form dimers with other OsSHMTs, except for OsSHMT1. It is proposed that OsSHMT3 functions as a mobile protein, collaborating with other OsSHMT proteins. Furthermore, the results of cis-acting element prediction and expression analysis suggested that members of the OsSHMT family could be involved in diverse stress responses and hormone regulation. Our study aims to provide novel insights for the future exploration of SHMTs.
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Affiliation(s)
| | | | | | - Mengyuan Yan
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China; (H.J.); (C.Z.)
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2
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Scaletti ER, Gustafsson Westergren R, Andersson Y, Wiita E, Henriksson M, Homan EJ, Jemth A, Helleday T, Stenmark P. The First Structure of Human MTHFD2L and Its Implications for the Development of Isoform-Selective Inhibitors. ChemMedChem 2022; 17:e202200274. [PMID: 35712863 PMCID: PMC9796130 DOI: 10.1002/cmdc.202200274] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/15/2022] [Indexed: 01/01/2023]
Abstract
Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is a mitochondrial 1-carbon metabolism enzyme, which is an attractive anticancer drug target as it is highly upregulated in cancer but is not expressed in healthy adult cells. Selective MTHFD2 inhibitors could therefore offer reduced side-effects during treatment, which are common with antifolate drugs that target other 1C-metabolism enzymes. This task is challenging however, as MTHFD2 shares high sequence identity with the constitutively expressed isozymes cytosolic MTHFD1 and mitochondrial MTHFD2L. In fact, one of the most potent MTHFD2 inhibitors reported to date, TH7299, is actually more active against MTHFD1 and MTHFD2L. While structures of MTHFD2 and MTHFD1 exist, no MTHFD2L structures are available. We determined the first structure of MTHFD2L and its complex with TH7299, which reveals the structural basis for its highly potent MTHFD2L inhibition. Detailed analysis of the MTHFD2L structure presented here clearly highlights the challenges associated with developing truly isoform-selective MTHFD2 inhibitors.
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Affiliation(s)
- Emma R. Scaletti
- Department of Biochemistry and BiophysicsStockholm UniversitySvante Arrhenius väg 16 CStockholm106 91Sweden
| | | | - Yasmin Andersson
- Drug Discovery and Development Platform, Science for Life Laboratory School of BiotechnologyRoyal Institute of TechnologyTomtebodavägen 23aStockholm17165Sweden
| | - Elisee Wiita
- Science for Life LaboratoryDepartment of Oncology-PathologyKarolinska InstituteTomtebodavägen 23aStockholm171 65Sweden
| | - Martin Henriksson
- Science for Life LaboratoryDepartment of Oncology-PathologyKarolinska InstituteTomtebodavägen 23aStockholm171 65Sweden
| | - Evert J. Homan
- Science for Life LaboratoryDepartment of Oncology-PathologyKarolinska InstituteTomtebodavägen 23aStockholm171 65Sweden
| | - Ann‐Sofie Jemth
- Science for Life LaboratoryDepartment of Oncology-PathologyKarolinska InstituteTomtebodavägen 23aStockholm171 65Sweden
| | - Thomas Helleday
- Science for Life LaboratoryDepartment of Oncology-PathologyKarolinska InstituteTomtebodavägen 23aStockholm171 65Sweden,Department of Oncology and MetabolismThe University of SheffieldBeech Hill RoadSheffieldS10 2RXUK
| | - Pål Stenmark
- Department of Biochemistry and BiophysicsStockholm UniversitySvante Arrhenius väg 16 CStockholm106 91Sweden
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3
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Mühlenhoff U, Weiler BD, Nadler F, Millar R, Kothe I, Freibert SA, Altegoer F, Bange G, Lill R. The iron-sulfur cluster assembly (ISC) protein Iba57 executes a tetrahydrofolate-independent function in mitochondrial [4Fe-4S] protein maturation. J Biol Chem 2022; 298:102465. [PMID: 36075292 PMCID: PMC9551070 DOI: 10.1016/j.jbc.2022.102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 10/25/2022] Open
Abstract
Mitochondria harbor the bacteria-inherited iron-sulfur cluster assembly (ISC) machinery to generate [2Fe-2S] and [4Fe-4S] proteins. In yeast, assembly of [4Fe-4S] proteins specifically involves the ISC proteins Isa1, Isa2, Iba57, Bol3, and Nfu1. Functional defects in their human equivalents cause the multiple mitochondrial dysfunction syndromes (MMDS), severe disorders with a broad clinical spectrum. The bacterial Iba57 ancestor YgfZ was described to require tetrahydrofolate (THF) for its function in the maturation of selected [4Fe-4S] proteins. Both YgfZ and Iba57 are structurally related to an enzyme family catalyzing THF-dependent one-carbon transfer reactions including GcvT of the glycine cleavage system. On this basis, a universally conserved folate requirement in ISC-dependent [4Fe-4S] protein biogenesis was proposed. To test this idea for mitochondrial Iba57, we performed genetic and biochemical studies in S. cerevisiae, and we solved the crystal structure of Iba57 from the thermophilic fungus Chaetomium thermophilum. We provide three lines of evidence for the THF independence of the Iba57-catalyzed [4Fe-4S] protein assembly pathway. First, yeast mutants lacking folate show no defect in mitochondrial [4Fe-4S] protein maturation. Second, the 3D structure of Iba57 lacks many of the side chain contacts to THF as defined in GcvT, and the THF binding pocket is constricted. Third, mutations in conserved Iba57 residues that are essential for THF-dependent catalysis in GcvT do not impair Iba57 function in vivo, in contrast to an exchange of the invariant, surface-exposed cysteine residue. We conclude that mitochondrial Iba57, despite structural similarities to both YgfZ and THF-binding proteins, does not utilize folate for its function.
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Affiliation(s)
- Ulrich Mühlenhoff
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany.
| | - Benjamin Dennis Weiler
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany
| | - Franziska Nadler
- Present address: University Medical Center Göttingen, Department of Cellular Biochemistry Humboldtallee 23, 37073 Göttingen, Germany
| | - Robert Millar
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Present address: Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Isabell Kothe
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany
| | - Sven-Andreas Freibert
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany
| | - Florian Altegoer
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Fachbereich Chemie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Present address: Heinrich-Heine Universität Du¨sseldorf, Institut für Mikrobiologie, Universitätsstraße 1, 40225 Du¨sseldorf, Germany
| | - Gert Bange
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Fachbereich Chemie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany; Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032 Marburg, Germany.
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4
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Pöhner I, Quotadamo A, Panecka-Hofman J, Luciani R, Santucci M, Linciano P, Landi G, Di Pisa F, Dello Iacono L, Pozzi C, Mangani S, Gul S, Witt G, Ellinger B, Kuzikov M, Santarem N, Cordeiro-da-Silva A, Costi MP, Venturelli A, Wade RC. Multitarget, Selective Compound Design Yields Potent Inhibitors of a Kinetoplastid Pteridine Reductase 1. J Med Chem 2022; 65:9011-9033. [PMID: 35675511 PMCID: PMC9289884 DOI: 10.1021/acs.jmedchem.2c00232] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
The optimization
of compounds with multiple targets is a difficult
multidimensional problem in the drug discovery cycle. Here, we present
a systematic, multidisciplinary approach to the development of selective
antiparasitic compounds. Computational fragment-based design of novel
pteridine derivatives along with iterations of crystallographic structure
determination allowed for the derivation of a structure–activity
relationship for multitarget inhibition. The approach yielded compounds
showing apparent picomolar inhibition of T. brucei pteridine reductase 1 (PTR1), nanomolar inhibition of L.
major PTR1, and selective submicromolar inhibition of parasite
dihydrofolate reductase (DHFR) versus human DHFR. Moreover, by combining
design for polypharmacology with a property-based on-parasite optimization,
we found three compounds that exhibited micromolar EC50 values against T. brucei brucei while retaining
their target inhibition. Our results provide a basis for the further
development of pteridine-based compounds, and we expect our multitarget
approach to be generally applicable to the design and optimization
of anti-infective agents.
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Affiliation(s)
- Ina Pöhner
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), D-69118 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, D-69120 Heidelberg, Germany
| | - Antonio Quotadamo
- Tydock Pharma srl, Strada Gherbella 294/B, 41126 Modena, Italy.,Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Joanna Panecka-Hofman
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), D-69118 Heidelberg, Germany.,Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Rosaria Luciani
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Flavio Di Pisa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Lucia Dello Iacono
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Gesa Witt
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Nuno Santarem
- Instituto de Investigação e Inovação em Saúde, Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
| | - Anabela Cordeiro-da-Silva
- Instituto de Investigação e Inovação em Saúde, Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal.,Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Maria P Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Alberto Venturelli
- Tydock Pharma srl, Strada Gherbella 294/B, 41126 Modena, Italy.,Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), D-69118 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, D-69120 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, D-69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, D-69120 Heidelberg, Germany
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5
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Aliyu H, Gorte O, Neumann A, Ochsenreither K. Global Transcriptome Profile of the Oleaginous Yeast Saitozyma podzolica DSM 27192 Cultivated in Glucose and Xylose. J Fungi (Basel) 2021; 7:758. [PMID: 34575796 PMCID: PMC8466774 DOI: 10.3390/jof7090758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/08/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022] Open
Abstract
Unlike conventional yeasts, several oleaginous yeasts, including Saitozyma podzolica DSM 27192, possess the innate ability to grow and produce biochemicals from plant-derived lignocellulosic components such as hexose and pentose sugars. To elucidate the genetic basis of S. podzolica growth and lipid production on glucose and xylose, we performed comparative temporal transcriptome analysis using RNA-seq method. Approximately 3.4 and 22.2% of the 10,670 expressed genes were differentially (FDR < 0.05, and log2FC > 1.5) expressed under batch and fed batch modes, respectively. Our analysis revealed that a higher number of sugar transporter genes were significantly overrepresented in xylose relative to glucose-grown cultures. Given the low homology between proteins encoded by most of these genes and those of the well-characterised transporters, it is plausible to conclude that S. podzolica possesses a cache of putatively novel sugar transporters. The analysis also suggests that S. podzolica potentially channels carbon flux from xylose via both the non-oxidative pentose phosphate and potentially via the first steps of the Weimberg pathways to yield xylonic acid. However, only the ATP citrate lyase (ACL) gene showed significant upregulation among the essential oleaginous pathway genes under nitrogen limitation in xylose compared to glucose cultivation. Combined, these findings pave the way toward the design of strategies or the engineering of efficient biomass hydrolysate utilization in S. podzolica for the production of various biochemicals.
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Affiliation(s)
- Habibu Aliyu
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (O.G.); (A.N.)
| | | | | | - Katrin Ochsenreither
- Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (O.G.); (A.N.)
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6
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Watanabe M, Chiba Y, Hirai MY. Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:643403. [PMID: 34025692 PMCID: PMC8137854 DOI: 10.3389/fpls.2021.643403] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/17/2021] [Indexed: 05/19/2023]
Abstract
The metabolism of an organism is closely related to both its internal and external environments. Metabolites can act as signal molecules that regulate the functions of genes and proteins, reflecting the status of these environments. This review discusses the metabolism and regulatory functions of O-acetylserine (OAS), S-adenosylmethionine (AdoMet), homocysteine (Hcy), and serine (Ser), which are key metabolites related to sulfur (S)-containing amino acids in plant metabolic networks, in comparison to microbial and animal metabolism. Plants are photosynthetic auxotrophs that have evolved a specific metabolic network different from those in other living organisms. Although amino acids are the building blocks of proteins and common metabolites in all living organisms, their metabolism and regulation in plants have specific features that differ from those in animals and bacteria. In plants, cysteine (Cys), an S-containing amino acid, is synthesized from sulfide and OAS derived from Ser. Methionine (Met), another S-containing amino acid, is also closely related to Ser metabolism because of its thiomethyl moiety. Its S atom is derived from Cys and its methyl group from folates, which are involved in one-carbon metabolism with Ser. One-carbon metabolism is also involved in the biosynthesis of AdoMet, which serves as a methyl donor in the methylation reactions of various biomolecules. Ser is synthesized in three pathways: the phosphorylated pathway found in all organisms and the glycolate and the glycerate pathways, which are specific to plants. Ser metabolism is not only important in Ser supply but also involved in many other functions. Among the metabolites in this network, OAS is known to function as a signal molecule to regulate the expression of OAS gene clusters in response to environmental factors. AdoMet regulates amino acid metabolism at enzymatic and translational levels and regulates gene expression as methyl donor in the DNA and histone methylation or after conversion into bioactive molecules such as polyamine and ethylene. Hcy is involved in Met-AdoMet metabolism and can regulate Ser biosynthesis at an enzymatic level. Ser metabolism is involved in development and stress responses. This review aims to summarize the metabolism and regulatory functions of OAS, AdoMet, Hcy, and Ser and compare the available knowledge for plants with that for animals and bacteria and propose a future perspective on plant research.
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Affiliation(s)
- Mutsumi Watanabe
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yukako Chiba
- Graduate School of Life Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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7
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Liao Y, Wang F, Zhang Y, Cai H, Song F, Hou J. Silencing SHMT2 inhibits the progression of tongue squamous cell carcinoma through cell cycle regulation. Cancer Cell Int 2021; 21:220. [PMID: 33863325 PMCID: PMC8052717 DOI: 10.1186/s12935-021-01880-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background Serine hydroxymethyltransferase 2 (SHMT2) is a vital metabolic enzyme in one carbon metabolism catalyzing the conversion of serine to glycine, which has been reported to play a crucial role in the progression of tumors. However, its function in tongue squamous cell carcinoma (TSCC) remains unclear. Methods SHMT2 expression was analyzed using samples in online databases, and was assessed through immunohistochemistry staining of collected clinical specimens. The correlation between SHMT2 expression and the cell cycle was predicted through bioinformatic analysis, including weighted gene co-expression network analysis (WGCNA) and gene set enrichment analysis (GSEA). After transfection with siRNA, CCK8 assay, Edu staining, flow cytometry, trans-well assay, and wound healing experiments were performed to verify the functional role of SHMT2 in vitro. A stable cell line with SHMT2 silencing was established to detect the oncogenic function of SHMT2 in vivo. Results The expression of SHMT2 was up-regulated in TSCC tissues and cell lines compared with normal groups, and highly expressed SHMT2 significantly indicated a poorer clinical outcome for TSCC patients. Bioinformatic analysis found that high expression of SHMT2 was closely related with biologic process including cell cycle and cell cycle G1/S transition. Down regulating of SHMT2 significantly suppressed the proliferation, invasive and migrative ability of TSCC cells, and induced the prolongation of the G1 phase of the cell cycle in vitro. Furthermore, western blot showed that cell cycle-related regulators such as cyclin-dependent kinase 4 (CDK4) and cyclinD1 expression levels were decreased, while the expression levels of the cyclin-dependent kinase inhibitors p21Cip1 and p27Kip1 were increased after SHMT2 knockdown. Silencing SHMT2 in the HN6 cell line using short hairpin RNA also impeded tumor growth in vivo. Conclusions Overexpression of SHMT2 in TSCC indicated low survival rates, and was associated with aggressive behaviors of TSCC. It was also found to be involved in cell cycle regulation of TSCC cells. SHMT2 may serve as a novel prognostic indicator of TSCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01880-5.
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Affiliation(s)
- Yan Liao
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China
| | - Fang Wang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China
| | - Yadong Zhang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China
| | - Hongshi Cai
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China
| | - Fan Song
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China
| | - Jinsong Hou
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China. .,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, Guangdong, China.
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8
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Song X, Liu Y, Wang T, Zhang S, Sun M, Shu J, Wei J, Diao J, Li J, Li Y, Chen L, Zhu P, Qin J. Association of Maternal Dietary Habits and MTHFD1 Gene Polymorphisms With Ventricular Septal Defects in Offspring: A Case-Control Study. Front Pediatr 2021; 9:785440. [PMID: 35186819 PMCID: PMC8847777 DOI: 10.3389/fped.2021.785440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES This study aimed at assessing the association between maternal methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) gene polymorphisms, maternal dietary habits, and their interactions with the risk of ventricular septal defects (VSD) in offspring. METHODS From November 2017 to March 2019, a case-control study comprising 360 mothers of VSD cases and 504 mothers of healthy infants was conducted in Han Chinese populations. The main exposures of interest were maternal dietary habits in early pregnancy and MTHFD1 gene polymorphisms. Logistic regression models were used to estimate the main effects and interaction effects. RESULTS It was observed that maternal excessive intake of pickled vegetables (aOR = 1.85, 95%CI: 1.45-2.37), smoked foods (aOR = 1.93, 95%CI: 1.48-2.51), barbecued foods (aOR = 1.74, 95%CI: 1.28-2.36), and fried foods (aOR = 1.68, 95%CI: 1.30-2.17) were associated with a higher risk of VSD in offspring, whereas maternal excessive intake of fresh meat (aOR = 0.61, 95%CI: 0.47-0.79), fish and shrimp (aOR = 0.29, 95%CI: 0.23-0.38), fresh eggs (aOR = 0.54, 95%CI: 0.42-0.70), fresh fruits or vegetables (aOR = 0.44, 95%CI: 0.33-0.60), soy foods (aOR = 0.65, 95%CI: 0.53-0.80), and milk products (aOR = 0.49, 95%CI: 0.40-0.59) could contribute significantly to a lower risk of VSD in offspring. Furthermore, the genetic polymorphisms of maternal MTHFD1 gene at rs1950902 (GA vs. GG: aOR = 0.67, 95%CI: 0.50-0.90) and rs2236222 (GG vs. AA: aOR = 2.75, 95%CI: 1.57-4.83) were significantly associated with the risk of VSD in offspring. In addition, there was a significant interaction effect between maternal dietary habits and MTHFD1 gene polymorphisms on the risk of VSD. CONCLUSIONS Maternal dietary factors, MTHFD1 genetic polymorphisms, and their interactions were all associated with the risk of VSD in offspring. However, further research in diverse ethnic populations and with a larger sample size is warranted to corroborate our findings. TRIAL REGISTRATION Registered in Chinese Clinical Trial Registry Center; registration number, ChiCTR1800016635; registration date, 06/14/2018 (Retrospectively registered); URL of trial registry record, https://www.chictr.org.cn/showproj.aspx?proj=28300.
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Affiliation(s)
- Xinli Song
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Yiping Liu
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Tingting Wang
- National Health Committee Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Senmao Zhang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Mengting Sun
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jing Shu
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jianhui Wei
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jingyi Diao
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jinqi Li
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Yihuan Li
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Letao Chen
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ping Zhu
- Guangdong Academy of Medical Sciences, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Jiabi Qin
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China.,National Health Committee Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.,Guangdong Academy of Medical Sciences, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangzhou, China.,Hunan Provincial Key Laboratory of Clinical Epidemiology, Changsha, China
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9
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Comparative Proteomic Profiling of Marine and Freshwater Synechocystis Strains Using Liquid Chromatography-Tandem Mass Spectrometry. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8100790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Freshwater Synechocystis sp. PCC 6803 has been considered to be a platform for the production of the next generation of biofuels and is used as a model organism in various fields. Various genomics, transcriptomics, metabolomics, and proteomics studies have been performed on this strain, whereas marine Synechocystis sp. PCC 7338 has not been widely studied despite its wide distribution. This study analyzed the proteome profiles of two Synechocystis strains using a liquid chromatography–tandem mass spectrometry-based bottom-up proteomic approach. Proteomic profiling of Synechocystis sp. PCC 7338 was performed for the first time with a data-dependent acquisition method, revealing 18,779 unique peptides and 1794 protein groups. A data-independent acquisition method was carried out for the comparative quantitation of Synechocystis sp. PCC 6803 and 7338. Among 2049 quantified proteins, 185 up- and 211 down-regulated proteins were defined in Synechocystis sp. PCC 7338. Some characteristics in the proteome of Synechocystis sp. PCC 7338 were revealed, such as its adaptation to living conditions, including the down-regulation of some photosynthesis proteins, the up-regulation of kdpB, and the use of osmolyte glycine as a substrate in C1 metabolism for the regulation of carbon flow. This study will facilitate further studies on Synechocystis 7338 to define in depth the proteomic differences between it and other Synechocystis strains.
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10
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Bidla G, Watkins D, Chéry C, Froese DS, Ells C, Kerachian M, Saskin A, Christensen KE, Gilfix BM, Guéant JL, Rosenblatt DS. Biochemical analysis of patients with mutations in MTHFD1 and a diagnosis of methylenetetrahydrofolate dehydrogenase 1 deficiency. Mol Genet Metab 2020; 130:179-182. [PMID: 32414565 DOI: 10.1016/j.ymgme.2020.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
MTHFD1 is a trifunctional protein containing 10-formyltetrahydrofolate synthetase, 5,10-methenyltetrahydrofolate cyclohydrolase and 5,10-methylenetetrahydrofolate dehydrogenase activities. It is encoded by MTHFD1 and functions in the cytoplasmic folate cycle where it is involved in de novo purine synthesis, synthesis of thymidylate and remethylation of homocysteine to methionine. Since the first reported case of severe combined immunodeficiency resulting from MTHFD1 mutations, seven additional patients ascertained through molecular analysis have been reported with variable phenotypes, including megaloblastic anemia, atypical hemolytic uremic syndrome, hyperhomocysteinemia, microangiopathy, infections and autoimmune diseases. We determined the level of MTHFD1 expression and dehydrogenase specific activity in cell extracts from cultured fibroblasts of three previously reported patients, as well as a patient with megaloblastic anemia and recurrent infections with compound heterozygous MTHFD1 variants that were predicted to be deleterious. MTHFD1 protein expression determined by Western blotting in fibroblast extracts from three of the patients was markedly decreased compared to expression in wild type cells (between 4.8 and 14.3% of mean control values). MTHFD1 expression in the fourth patient was approximately 44% of mean control values. There was no detectable methylenetetrahydrofolate dehydrogenase specific activity in extracts from any of the four patients. This is the first measurement of MTHFD1 function in MTHFD1 deficient patients and confirms the previous molecular diagnoses.
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Affiliation(s)
- Gawa Bidla
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David Watkins
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.; Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada.; Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada..
| | - Céline Chéry
- Inserm-U954, National reference centre for inherited metabolic diseases, University Hospital Centre, Nancy, France
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zürich, Switzerland
| | - Courtney Ells
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Matin Kerachian
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Avi Saskin
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Karen E Christensen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.; Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Brian M Gilfix
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.; Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Jean-Louis Guéant
- Inserm-U954, National reference centre for inherited metabolic diseases, University Hospital Centre, Nancy, France
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.; Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada.; Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.; Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada
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11
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Praveen G, Shalini T, Sivaprasad M, Reddy GB. Relative telomere length and mitochondrial DNA copy number variation with age: Association with plasma folate and vitamin B12. Mitochondrion 2020; 51:79-87. [PMID: 31935457 DOI: 10.1016/j.mito.2020.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/01/2019] [Accepted: 01/10/2020] [Indexed: 01/03/2023]
Abstract
Telomere attrition and mitochondrial DNA variations are implicated in the biological aging process and genomic stability can be influenced by nutritional factors. This study aims to analyze the relative telomere length (rTL) and mitochondrial DNA copy number (mtCN) in aged individuals and their association with plasma folate and vitamin B12 levels. This community-based cross-sectional study involves 428 subjects (<60 years: 242 & ≥60 years: 186). Quantitative real-time PCR was used to measure rTL and mtCN variation, and radioimmunoassay to measure plasma folate and vitamin B12 levels. The subjects in the ≥60 years age group have significantly shorter telomeres and lower mtCN compared to the <60 years age group. A significant positive correlation was observed between the rTL and mtCN, and both of them were positively associated with plasma folate and vitamin B12 levels. In the ≥60 age group; folate and vitamin B12 positively correlated with rTL and vitamin B12 with mtCN. The study revealed a decline of rTL and mtCN with age in the Indian population and their association suggests that they may co-regulate each other with age. In conclusion, folate and vitamin B12 may delay aging by preventing the reduction in rTL length and mtCN.
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Affiliation(s)
- Guruvaiah Praveen
- Department of Biochemistry, National Institute of Nutrition (ICMR), Hyderabad, Telangana, India
| | - Tattari Shalini
- Department of Biochemistry, National Institute of Nutrition (ICMR), Hyderabad, Telangana, India
| | - Mudili Sivaprasad
- Department of Biochemistry, National Institute of Nutrition (ICMR), Hyderabad, Telangana, India
| | - G Bhanuprakash Reddy
- Department of Biochemistry, National Institute of Nutrition (ICMR), Hyderabad, Telangana, India.
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12
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Mitochondrial One-Carbon Pathway Supports Cytosolic Folate Integrity in Cancer Cells. Cell 2019; 175:1546-1560.e17. [PMID: 30500537 DOI: 10.1016/j.cell.2018.09.041] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/25/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
Mammalian folate metabolism is comprised of cytosolic and mitochondrial pathways with nearly identical core reactions, yet the functional advantages of such an organization are not well understood. Using genome-editing and biochemical approaches, we find that ablating folate metabolism in the mitochondria of mammalian cell lines results in folate degradation in the cytosol. Mechanistically, we show that QDPR, an enzyme in tetrahydrobiopterin metabolism, moonlights to repair oxidative damage to tetrahydrofolate (THF). This repair capacity is overwhelmed when cytosolic THF hyperaccumulates in the absence of mitochondrially produced formate, leading to THF degradation. Unexpectedly, we also find that the classic antifolate methotrexate, by inhibiting its well-known target DHFR, causes even more extensive folate degradation in nearly all tested cancer cell lines. These findings shed light on design features of folate metabolism, provide a biochemical basis for clinically observed folate deficiency in QDPR-deficient patients, and reveal a hitherto unknown and unexplored cellular effect of methotrexate.
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13
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Fan LH, Wang ZB, Li QN, Meng TG, Dong MZ, Hou Y, Ouyang YC, Schatten H, Sun QY. Absence of mitochondrial DNA methylation in mouse oocyte maturation, aging and early embryo development. Biochem Biophys Res Commun 2019; 513:912-918. [PMID: 31005257 DOI: 10.1016/j.bbrc.2019.04.100] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/14/2019] [Indexed: 01/24/2023]
Abstract
Mitochondrial DNA (mtDNA) is important for oxidative phosphorylation; dysfunctions can play a role in many mitochondrial diseases and can also affect the aging of cells and individuals. DNA methylation is an important epigenetic modification that plays a critical role in regulating gene expression. While recent studies have revealed the existence of mtDNA methylation there are still controversies about mtDNA methylation due to the special structure of mtDNA. Mitochondria and DNA methylation are both essential for regulating oocyte maturation and early embryo development, but whether mtDNA methylation changes during this process is unknown. By employing bisulfite sequencing, we found that in the process of mouse oocyte maturation, postovulatory oocyte aging, and early embryo development, all analyzed mitochondrial genes, including 16S-CpGI, DCR, ND6, 12S, and ATP8, lacked 5'mC. Thus, mtDNA methylation does not occur in the oocyte and early embryo.
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Affiliation(s)
- Li-Hua Fan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Qian-Nan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Tie-Gang Meng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Ming-Zhe Dong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Yi Hou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Ying-Chun Ouyang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, 65211, USA
| | - Qing-Yuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100101, PR China.
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14
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Zheng Y, Cantley LC. Toward a better understanding of folate metabolism in health and disease. J Exp Med 2019; 216:253-266. [PMID: 30587505 PMCID: PMC6363433 DOI: 10.1084/jem.20181965] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/18/2018] [Accepted: 12/03/2018] [Indexed: 12/15/2022] Open
Abstract
Folate metabolism is crucial for many biochemical processes, including purine and thymidine monophosphate (dTMP) biosynthesis, mitochondrial protein translation, and methionine regeneration. These biochemical processes in turn support critical cellular functions such as cell proliferation, mitochondrial respiration, and epigenetic regulation. Not surprisingly, abnormal folate metabolism has been causally linked with a myriad of diseases. In this review, we provide a historical perspective, delve into folate chemistry that is often overlooked, and point out various missing links and underdeveloped areas in folate metabolism for future exploration.
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Affiliation(s)
- Yuxiang Zheng
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Lewis C Cantley
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, NY
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15
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Hilgers EJA, Schöttler MA, Mettler-Altmann T, Krueger S, Dörmann P, Eicks M, Flügge UI, Häusler RE. The Combined Loss of Triose Phosphate and Xylulose 5-Phosphate/Phosphate Translocators Leads to Severe Growth Retardation and Impaired Photosynthesis in Arabidopsis thaliana tpt/xpt Double Mutants. FRONTIERS IN PLANT SCIENCE 2018; 9:1331. [PMID: 30333839 PMCID: PMC6175978 DOI: 10.3389/fpls.2018.01331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/24/2018] [Indexed: 05/18/2023]
Abstract
The xylulose 5-phosphate/phosphate translocator (XPT) represents the fourth functional member of the phosphate translocator (PT) family residing in the plastid inner envelope membrane. In contrast to the other three members, little is known on the physiological role of the XPT. Based on its major transport substrates (i.e., pentose phosphates) the XPT has been proposed to act as a link between the plastidial and extraplastidial branches of the oxidative pentose phosphate pathway (OPPP). As the XPT is also capable of transporting triose phosphates, it might as well support the triose phosphate PT (TPT) in exporting photoassimilates from the chloroplast in the light ('day path of carbon') and hence in supplying the whole plant with carbohydrates. Two independent knockout mutant alleles of the XPT (xpt-1 and xpt-2) lacked any specific phenotype, suggesting that the XPT function is redundant. However, double mutants generated from crossings of xpt-1 to different mutant alleles of the TPT (tpt-1 and tpt-2) were severely retarded in size, exhibited a high chlorophyll fluorescence phenotype, and impaired photosynthetic electron transport rates. In the double mutant the export of triose phosphates from the chloroplasts is completely blocked. Hence, precursors for sucrose biosynthesis derive entirely from starch turnover ('night path of carbon'), which was accompanied by a marked accumulation of maltose as a starch breakdown product. Moreover, pentose phosphates produced by the extraplastidial branch of the OPPP also accumulated in the double mutants. Thus, an active XPT indeed retrieves excessive pentose phosphates from the extra-plastidial space and makes them available to the plastids. Further metabolic profiling revealed that phosphorylated intermediates remained largely unaffected, whereas fumarate and glycine contents were diminished in the double mutants. The assessment of C/N-ratios suggested co-limitations of C- and N-metabolism as possible cause for growth retardation of the double mutants. Feeding of sucrose partially rescued the growth and photosynthesis phenotypes of the double mutants. Immunoblots of thylakoid proteins, spectroscopic determinations of photosynthesis complexes, and chlorophyll a fluorescence emission spectra at 77 Kelvin could only partially explain constrains in photosynthesis observed in the double mutants. The data are discussed together with aspects of the OPPP and central carbon metabolism.
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Affiliation(s)
- Elke J. A. Hilgers
- Department of Biology, Cologne Biocenter, Botanical Institute II and Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | | | | | - Stephan Krueger
- Department of Biology, Cologne Biocenter, Botanical Institute II and Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Peter Dörmann
- Molecular Biotechnology and Biochemistry, Universität Bonn, Bonn, Germany
| | | | - Ulf-Ingo Flügge
- Department of Biology, Cologne Biocenter, Botanical Institute II and Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Rainer E. Häusler
- Department of Biology, Cologne Biocenter, Botanical Institute II and Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
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16
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Bar-Even A. Daring metabolic designs for enhanced plant carbon fixation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:71-83. [PMID: 29907311 DOI: 10.1016/j.plantsci.2017.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/16/2017] [Accepted: 12/16/2017] [Indexed: 05/07/2023]
Abstract
Increasing agricultural productivity is one of the major challenges our society faces. While multiple strategies to enhance plant carbon fixation have been suggested, and partially implemented, most of them are restricted to relatively simple modifications of endogenous metabolism, i.e., "low hanging fruit". Here, I portray the next generation of metabolic solutions to increase carbon fixation rate and yield. These strategies involve major rewiring of central metabolism, including dividing Rubisco's catalysis between several enzymes, replacing Rubisco with a different carboxylation reaction, substituting the Calvin Cycle with alternative carbon fixation pathways, and engineering photorespiration bypass routes that do not release carbon. While the barriers for implementing these elaborated metabolic architectures are quite significant, if we truly want to revolutionize carbon fixation, only daring engineering efforts will lead the way.
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Affiliation(s)
- Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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17
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Simultaneous measurement of folate cycle intermediates in different biological matrices using liquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1092:168-178. [PMID: 29906678 DOI: 10.1016/j.jchromb.2018.06.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/31/2018] [Accepted: 06/03/2018] [Indexed: 11/23/2022]
Abstract
The folate cycle is an essential metabolic pathway in the cell, involved in nucleotide synthesis, maintenance of the redox balance in the cell, methionine metabolism and re-methylation reactions. Standardised methods for the measurement of folate cycle intermediates in different biological matrices are in great demand. Here we describe a rapid, sensitive, precise and accurate liquid chromatographic-tandem mass spectrometric (LC-MS/MS) method with a wide calibration curve range and a short run time for the simultaneous determination of folate cycle metabolites, including tetrahydrofolic acid (THF), 5‑methyl THF, 5‑formyl THF, 5,10‑methenyl THF, 5,10‑methylene THF, dihydrofolic acid (DHF) and folic acid in different biological matrices. Extraction of folate derivatives from soft and hard tissue samples as well as from adherent cells was achieved using homogenisation in buffer, while extraction from the whole blood and plasma relied on the anion exchange solid-phase extraction (SPE) method. Chromatographic separation was completed using a Waters Atlantis dC18 2.0 × 100 mm, 3-μ column with a gradient elution using formic acid in water (0.1% v/v) and acetonitrile as the mobile phases. LC gradient started with 95% of the aqueous phase which was gradually changed to 95% of the organic phase during 2.70 min in order to separate the selected metabolites. The analytes were separated with a run time of 5 min at a flow rate of 0.300 mL/min and detected using a Waters Xevo-TQS triple quadrupole mass spectrometer in the multiple reaction monitoring mode (MRM) at positive polarity. The instrument response was linear over a calibration range of 0.5 to 2500 ng/mL (r2 > 0.980). The developed bioanalytical method was thoroughly validated in terms of accuracy, precision, linearity, recovery, sensitivity and stability for tissue and blood samples. The matrix effect was compensated by using structurally similar isotope labelled internal standard (IS), 13C5‑methyl THF, for all folate metabolites. However, not all folate metabolites can be accurately quantified using this method due to their high interconversion rates especially at low pH. This applies to 5,10‑methylene THF which interconverts into THF, and 5,10‑methenyl‑THF interconverting into 5‑formyl‑THF. Using this method, we measured folate cycle intermediates in mouse bone marrow cells and plasma, in human whole blood; in mouse muscle, liver, heart and brain samples.
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18
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Wybouw N, Van Leeuwen T, Dermauw W. A massive incorporation of microbial genes into the genome of Tetranychus urticae, a polyphagous arthropod herbivore. INSECT MOLECULAR BIOLOGY 2018; 27:333-351. [PMID: 29377385 DOI: 10.1111/imb.12374] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A number of horizontal gene transfers (HGTs) have been identified in the spider mite Tetranychus urticae, a chelicerate herbivore. However, the genome of this mite species has at present not been thoroughly mined for the presence of HGT genes. Here, we performed a systematic screen for HGT genes in the T. urticae genome using the h-index metric. Our results not only validated previously identified HGT genes but also uncovered 25 novel HGT genes. In addition to HGT genes with a predicted biochemical function in carbohydrate, lipid and folate metabolism, we also identified the horizontal transfer of a ketopantoate hydroxymethyltransferase and a pantoate β-alanine ligase gene. In plants and bacteria, both genes are essential for vitamin B5 biosynthesis and their presence in the mite genome strongly suggests that spider mites, similar to Bemisia tabaci and nematodes, can synthesize their own vitamin B5. We further show that HGT genes were physically embedded within the mite genome and were expressed in different life stages. By screening chelicerate genomes and transcriptomes, we were able to estimate the evolutionary histories of these HGTs during chelicerate evolution. Our study suggests that HGT has made a significant and underestimated impact on the metabolic repertoire of plant-feeding spider mites.
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Affiliation(s)
- N Wybouw
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - T Van Leeuwen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - W Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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19
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Enzymes of the one-carbon folate metabolism as anticancer targets predicted by survival rate analysis. Sci Rep 2018; 8:303. [PMID: 29321536 PMCID: PMC5762868 DOI: 10.1038/s41598-017-18456-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/12/2017] [Indexed: 01/15/2023] Open
Abstract
The significance of mitochondrial metabolism in cancer cells has recently been gaining attention. Among other findings, One-carbon folate metabolism has been reported to be closely associated with cellular characteristics in cancer. To study molecular targets for efficient cancer therapy, we investigated the association between the expressions of genes that code enzymes involved in one-carbon metabolism and survival rate of patients with adenocarcinomas of the colorectum and lung. Patients with high expression of genes that control the metabolic cycle of tetrahydrofolate (THF) in mitochondria, SHMT2, MTHFD2, and ALDH1L2, have a shorter overall survival rate compared with patients with low expression of these genes. Our results revealed that these genes could be novel and more promising anticancer targets than dihydrofolate reductase (DHFR), the current target of drug therapy linked with folate metabolism, suggesting the rationale of drug discovery in cancer medicine.
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20
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Natural Variation in SER1 and ENA6 Underlie Condition-Specific Growth Defects in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2018; 8:239-251. [PMID: 29138237 PMCID: PMC5765352 DOI: 10.1534/g3.117.300392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite their ubiquitous use in laboratory strains, naturally occurring loss-of-function mutations in genes encoding core metabolic enzymes are relatively rare in wild isolates of Saccharomyces cerevisiae. Here, we identify a naturally occurring serine auxotrophy in a sake brewing strain from Japan. Through a cross with a honey wine (white tecc) brewing strain from Ethiopia, we map the minimal medium growth defect to SER1, which encodes 3-phosphoserine aminotransferase and is orthologous to the human disease gene, PSAT1. To investigate the impact of this polymorphism under conditions of abundant external nutrients, we examine growth in rich medium alone or with additional stresses, including the drugs caffeine and rapamycin and relatively high concentrations of copper, salt, and ethanol. Consistent with studies that found widespread effects of different auxotrophies on RNA expression patterns in rich media, we find that the SER1 loss-of-function allele dominates the quantitative trait locus (QTL) landscape under many of these conditions, with a notable exacerbation of the effect in the presence of rapamycin and caffeine. We also identify a major-effect QTL associated with growth on salt that maps to the gene encoding the sodium exporter, ENA6. We demonstrate that the salt phenotype is largely driven by variation in the ENA6 promoter, which harbors a deletion that removes binding sites for the Mig1 and Nrg1 transcriptional repressors. Thus, our results identify natural variation associated with both coding and regulatory regions of the genome that underlie strong growth phenotypes.
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21
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The natural product carolacton inhibits folate-dependent C1 metabolism by targeting FolD/MTHFD. Nat Commun 2017; 8:1529. [PMID: 29142318 PMCID: PMC5688156 DOI: 10.1038/s41467-017-01671-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/05/2017] [Indexed: 01/26/2023] Open
Abstract
The natural product carolacton is a macrolide keto-carboxylic acid produced by the myxobacterium Sorangium cellulosum, and was originally described as an antibacterial compound. Here we show that carolacton targets FolD, a key enzyme from the folate-dependent C1 metabolism. We characterize the interaction between bacterial FolD and carolacton biophysically, structurally and biochemically. Carolacton binds FolD with nanomolar affinity, and the crystal structure of the FolD–carolacton complex reveals the mode of binding. We show that the human FolD orthologs, MTHFD1 and MTHFD2, are also inhibited in the low nM range, and that micromolar concentrations of carolacton inhibit the growth of cancer cell lines. As mitochondrial MTHFD2 is known to be upregulated in cancer cells, it may be possible to use carolacton as an inhibitor tool compound to assess MTHFD2 as an anti-cancer target. The mechanisms behind the antibacterial activity of the natural product carolacton are unknown. Here, the authors show that carolacton is a potent inhibitor of FolD/MTHFD enzymes (involved in folate-dependent C1 metabolism in bacteria and humans) and inhibits the growth of cancer cell lines
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22
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Kandoth PK, Liu S, Prenger E, Ludwig A, Lakhssassi N, Heinz R, Zhou Z, Howland A, Gunther J, Eidson S, Dhroso A, LaFayette P, Tucker D, Johnson S, Anderson J, Alaswad A, Cianzio SR, Parrott WA, Korkin D, Meksem K, Mitchum MG. Systematic Mutagenesis of Serine Hydroxymethyltransferase Reveals an Essential Role in Nematode Resistance. PLANT PHYSIOLOGY 2017; 175:1370-1380. [PMID: 28912378 PMCID: PMC5664460 DOI: 10.1104/pp.17.00553] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 09/11/2017] [Indexed: 05/27/2023]
Abstract
Rhg4 is a major genetic locus that contributes to soybean cyst nematode (SCN) resistance in the Peking-type resistance of soybean (Glycine max), which also requires the rhg1 gene. By map-based cloning and functional genomic approaches, we previously showed that the Rhg4 gene encodes a predicted cytosolic serine hydroxymethyltransferase (GmSHMT08); however, the novel gain of function of GmSHMT08 in SCN resistance remains to be characterized. Using a forward genetic screen, we identified an allelic series of GmSHMT08 mutants that shed new light on the mechanistic aspects of GmSHMT08-mediated resistance. The new mutants provide compelling genetic evidence that Peking-type rhg1 resistance in cv Forrest is fully dependent on the GmSHMT08 gene and demonstrates that this resistance is mechanistically different from the PI 88788-type of resistance that only requires rhg1 We also demonstrated that rhg1-a from cv Forrest, although required, does not exert selection pressure on the nematode to shift from HG type 7, which further validates the bigenic nature of this resistance. Mapping of the identified mutations onto the SHMT structural model uncovered key residues for structural stability, ligand binding, enzyme activity, and protein interactions, suggesting that GmSHMT08 has additional functions aside from its main enzymatic role in SCN resistance. Lastly, we demonstrate the functionality of the GmSHMT08 SCN resistance gene in a transgenic soybean plant.
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Affiliation(s)
- Pramod K Kandoth
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Elizabeth Prenger
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Andrew Ludwig
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Robert Heinz
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Amanda Howland
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Joshua Gunther
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Samantha Eidson
- Mathematics and Computer Science Department, Fontbonne University, St. Louis, Missouri 63105
| | - Andi Dhroso
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Peter LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Donna Tucker
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Sarah Johnson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - James Anderson
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Alaa Alaswad
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | | | - Wayne A Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Dmitry Korkin
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
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23
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Khan NA, Nikkanen J, Yatsuga S, Jackson C, Wang L, Pradhan S, Kivelä R, Pessia A, Velagapudi V, Suomalainen A. mTORC1 Regulates Mitochondrial Integrated Stress Response and Mitochondrial Myopathy Progression. Cell Metab 2017; 26:419-428.e5. [PMID: 28768179 DOI: 10.1016/j.cmet.2017.07.007] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/15/2017] [Accepted: 07/14/2017] [Indexed: 01/28/2023]
Abstract
Mitochondrial dysfunction elicits various stress responses in different model systems, but how these responses relate to each other and contribute to mitochondrial disease has remained unclear. Mitochondrial myopathy (MM) is the most common manifestation of adult-onset mitochondrial disease and shows a multifaceted tissue-specific stress response: (1) transcriptional response, including metabolic cytokines FGF21 and GDF15; (2) remodeling of one-carbon metabolism; and (3) mitochondrial unfolded protein response. We show that these processes are part of one integrated mitochondrial stress response (ISRmt), which is controlled by mTORC1 in muscle. mTORC1 inhibition by rapamycin downregulated all components of ISRmt, improved all MM hallmarks, and reversed the progression of even late-stage MM, without inducing mitochondrial biogenesis. Our evidence suggests that (1) chronic upregulation of anabolic pathways contributes to MM progression, (2) long-term induction of ISRmt is not protective for muscle, and (3) rapamycin treatment trials should be considered for adult-type MM with raised FGF21.
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Affiliation(s)
- Nahid A Khan
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland
| | - Joni Nikkanen
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland
| | - Shuichi Yatsuga
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland; Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
| | - Christopher Jackson
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland
| | - Liya Wang
- Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Swagat Pradhan
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland
| | - Riikka Kivelä
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, 00290 Helsinki, Finland
| | - Alberto Pessia
- Metabolomics Unit, Institute for Molecular Medicine Finland, University of Helsinki, 00290 Helsinki, Finland
| | - Vidya Velagapudi
- Metabolomics Unit, Institute for Molecular Medicine Finland, University of Helsinki, 00290 Helsinki, Finland
| | - Anu Suomalainen
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland; Department of Neurology, Helsinki University Hospital, 00290 Helsinki, Finland; Neuroscience Center, University of Helsinki, 00790 Helsinki, Finland.
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24
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Gustafsson R, Jemth AS, Gustafsson NMS, Färnegårdh K, Loseva O, Wiita E, Bonagas N, Dahllund L, Llona-Minguez S, Häggblad M, Henriksson M, Andersson Y, Homan E, Helleday T, Stenmark P. Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor. Cancer Res 2016; 77:937-948. [PMID: 27899380 DOI: 10.1158/0008-5472.can-16-1476] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/23/2016] [Accepted: 11/04/2016] [Indexed: 11/16/2022]
Abstract
To sustain their proliferation, cancer cells become dependent on one-carbon metabolism to support purine and thymidylate synthesis. Indeed, one of the most highly upregulated enzymes during neoplastic transformation is MTHFD2, a mitochondrial methylenetetrahydrofolate dehydrogenase and cyclohydrolase involved in one-carbon metabolism. Because MTHFD2 is expressed normally only during embryonic development, it offers a disease-selective therapeutic target for eradicating cancer cells while sparing healthy cells. Here we report the synthesis and preclinical characterization of the first inhibitor of human MTHFD2. We also disclose the first crystal structure of MTHFD2 in complex with a substrate-based inhibitor and the enzyme cofactors NAD+ and inorganic phosphate. Our work provides a rationale for continued development of a structural framework for the generation of potent and selective MTHFD2 inhibitors for cancer treatment. Cancer Res; 77(4); 937-48. ©2017 AACR.
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Affiliation(s)
- Robert Gustafsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nina M S Gustafsson
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Katarina Färnegårdh
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Solna, Sweden
| | - Olga Loseva
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nadilly Bonagas
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Leif Dahllund
- Drug Discovery and Development Platform, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Sabin Llona-Minguez
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Maria Häggblad
- Biochemical and Cellular Screening, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Henriksson
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yasmin Andersson
- Drug Discovery and Development Platform, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Evert Homan
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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Kalhan SC. One carbon metabolism in pregnancy: Impact on maternal, fetal and neonatal health. Mol Cell Endocrinol 2016; 435:48-60. [PMID: 27267668 PMCID: PMC5014566 DOI: 10.1016/j.mce.2016.06.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 02/07/2023]
Abstract
One carbon metabolism or methyl transfer, a crucial component of metabolism in all cells and tissues, supports the critical function of synthesis of purines, thymidylate and methylation via multiple methyl transferases driven by the ubiquitous methyl donor s-adenosylmethionine. Serine is the primary methyl donor to the one carbon pool. Intracellular folates and methionine metabolism are the critical components of one carbon transfer. Methionine metabolism requires vitamin B12, B6 as cofactors and is modulated by endocrine signals and is responsive to nutrient intake. Perturbations in one carbon transfer can have profound effects on cell proliferation, growth and function. Epidemiological studies in humans and experimental model have established a strong relationship between impaired fetal growth and the immediate and long term consequences to the health of the offspring. It is speculated that during development, maternal environmental and nutrient influences by their effects on one carbon transfer can impact the health of the mother, impair growth and reprogram metabolism of the fetus, and cause long term morbidity in the offspring. The potential for such effects is underscored by the unique responses in methionine metabolism in the human mother during pregnancy, the absence of transsulfuration activity in the fetus, ontogeny of methionine metabolism in the placenta and the unique metabolism of serine and glycine in the fetus. Dietary protein restriction in animals and marginal protein intake in humans causes characteristic changes in one carbon metabolism. The impact of perturbations in one carbon metabolism on the health of the mother during pregnancy, on fetal growth and the neonate are discussed and their possible mechanism explored.
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Affiliation(s)
- Satish C Kalhan
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Department of Pathobiology, Lerner Research Institute, NE-40, Cleveland Clinic, 9500 Euclid Av, Cleveland, OH, 44195, USA.
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26
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Prasoona KR, Sunitha T, Srinadh B, Deepika MLN, Kumari TM, Jyothy A. Paternal transmission of MTHFD1 G1958A variant predisposes to neural tube defects in the offspring. Dev Med Child Neurol 2016; 58:625-31. [PMID: 26394717 DOI: 10.1111/dmcn.12929] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/16/2015] [Indexed: 01/15/2023]
Abstract
AIM This study aimed to evaluate the role of methylenetetrahydrofolate dehydrogenase (MTHFD1) G1958A variant (rs2236225) as a 'maternal, paternal, or embryonic' genetic risk factor for neural tube defect (NTD) susceptibility. It also estimated differential associations based on type of NTD, offspring sex, maternal-paternal-offspring genotype incompatibility, and parent-of-origin effects (POE) using both case-control and family-based approach. In addition, genotype impact on serum folate levels was also assessed. METHOD The study population (n=900) consisted of 120 NTD case-parent triads (n=120×3=360) and 180 healthy control-parent triads (n=180×3=540) from South India. Umbilical cord tissues were collected from those with NTD and control newborn infants, and blood samples from case and control parents. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism. Statistical analysis used were SPSS, transmission disequilibrium test and POE. Serum folate levels were estimated using enzyme-linked immunosorbent assay. RESULTS In the case-control study, those with the MTHFD1 G1958A variant were associated with around twofold risk of anencephaly (p=0.01) and spina bifida (p<0.01). Among parents, fathers were associated with around twofold risk of having an offspring with anencephaly (p<0.01). Considering offspring sex, the A allele in single or double dose conferred around two- to fourfold risk of anencephaly (p=0.01), spina bifida (p<0.01), and encephalocele (p<0.05) in females only. Maternal AA genotype was not associated independently but conferred threefold risk when combined with paternal GA genotype (p=0.01). Transmission disequilibrium and POE were not observed in controls (p>0.05) but revealed excess total (odds ratio [OR]=2.21; p<0.01) and paternal transmission (OR=7.00; p<0.01) of the G1958A allele to those with spina bifida, which remained the same for female cases (total transmission OR=3.00, p=0.01; paternal transmission OR=12.00, p<0.01). Increased serum folate levels were observed in case fathers with GA and AA genotypes than control fathers (p<0.01). INTERPRETATION Our research provides the first evidence supporting a paternal, rather than a maternal, transmission bias of MTHFD1 G1958A variant for NTD susceptibility in the offspring.
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Affiliation(s)
- Kattekola R Prasoona
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana, India
| | - Tella Sunitha
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana, India
| | - Buragadda Srinadh
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana, India
| | - Madireddy L N Deepika
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana, India
| | | | - Akka Jyothy
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana, India
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27
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Antunes-Fernandes EC, van Gastelen S, Dijkstra J, Hettinga KA, Vervoort J. Milk metabolome relates enteric methane emission to milk synthesis and energy metabolism pathways. J Dairy Sci 2016; 99:6251-6262. [PMID: 27236769 DOI: 10.3168/jds.2015-10248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 04/15/2016] [Indexed: 01/15/2023]
Abstract
Methane (CH4) emission of dairy cows contributes significantly to the carbon footprint of the dairy chain; therefore, a better understanding of CH4 formation is urgently needed. The present study explored the milk metabolome by gas chromatography-mass spectrometry (milk volatile metabolites) and nuclear magnetic resonance (milk nonvolatile metabolites) to better understand the biological pathways involved in CH4 emission in dairy cattle. Data were used from a randomized block design experiment with 32 multiparous Holstein-Friesian cows and 4 diets. All diets had a roughage:concentrate ratio of 80:20 (dry matter basis) and the roughage was grass silage (GS), corn silage (CS), or a mixture of both (67% GS, 33% CS; 33% GS, 67% CS). Methane emission was measured in climate respiration chambers and expressed as CH4 yield (per unit of dry matter intake) and CH4 intensity (per unit of fat- and protein-corrected milk; FPCM). No volatile or nonvolatile metabolite was positively related to CH4 yield, and acetone (measured as a volatile and as a nonvolatile metabolite) was negatively related to CH4 yield. The volatile metabolites 1-heptanol-decanol, 3-nonanone, ethanol, and tetrahydrofuran were positively related to CH4 intensity. None of the volatile metabolites was negatively related to CH4 intensity. The nonvolatile metabolites acetoacetate, creatinine, ethanol, formate, methylmalonate, and N-acetylsugar A were positively related to CH4 intensity, and uridine diphosphate (UDP)-hexose B and citrate were negatively related to CH4 intensity. Several volatile and nonvolatile metabolites that were correlated with CH4 intensity also were correlated with FPCM and not significantly related to CH4 intensity anymore when FPCM was included as covariate. This suggests that changes in these milk metabolites may be related to changes in milk yield or metabolic processes involved in milk synthesis. The UDP-hexose B was correlated with FPCM, whereas citrate was not. Both metabolites were still related to CH4 intensity when FPCM was included as covariate. The UDP-hexose B is an intermediate of lactose metabolism, and citrate is an important intermediate of Krebs cycle-related energy processes. Therefore, the negative correlation of UDP-hexose B and citrate with CH4 intensity may reflect a decrease in metabolic activity in the mammary gland. Our results suggest that an integrative approach including milk yield and composition, and dietary and animal traits will help to explain the biological metabolism of dairy cows in relation to methane CH4 emission.
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Affiliation(s)
- E C Antunes-Fernandes
- Top Institute Food and Nutrition, PO Box 557, 6700 AN Wageningen, the Netherlands; Food Quality and Design Group, Wageningen University, PO Box 17, 6700 AH Wageningen, the Netherlands
| | - S van Gastelen
- Top Institute Food and Nutrition, PO Box 557, 6700 AN Wageningen, the Netherlands; Animal Nutrition Group, Wageningen University, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - J Dijkstra
- Animal Nutrition Group, Wageningen University, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - K A Hettinga
- Food Quality and Design Group, Wageningen University, PO Box 17, 6700 AH Wageningen, the Netherlands.
| | - J Vervoort
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, the Netherlands
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28
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Mitochondrial DNA Replication Defects Disturb Cellular dNTP Pools and Remodel One-Carbon Metabolism. Cell Metab 2016; 23:635-48. [PMID: 26924217 DOI: 10.1016/j.cmet.2016.01.019] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/07/2015] [Accepted: 01/28/2016] [Indexed: 01/12/2023]
Abstract
Mitochondrial dysfunction affects cellular energy metabolism, but less is known about the consequences for cytoplasmic biosynthetic reactions. We report that mtDNA replication disorders caused by TWINKLE mutations-mitochondrial myopathy (MM) and infantile onset spinocerebellar ataxia (IOSCA)-remodel cellular dNTP pools in mice. MM muscle shows tissue-specific induction of the mitochondrial folate cycle, purine metabolism, and imbalanced and increased dNTP pools, consistent with progressive mtDNA mutagenesis. IOSCA-TWINKLE is predicted to hydrolyze dNTPs, consistent with low dNTP pools and mtDNA depletion in the disease. MM muscle also modifies the cytoplasmic one-carbon cycle, transsulfuration, and methylation, as well as increases glucose uptake and its utilization for de novo serine and glutathione biosynthesis. Our evidence indicates that the mitochondrial replication machinery communicates with cytoplasmic dNTP pools and that upregulation of glutathione synthesis through glucose-driven de novo serine biosynthesis contributes to the metabolic stress response. These results are important for disorders with primary or secondary mtDNA instability and offer targets for metabolic therapy.
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Guerreiro JF, Sampaio-Marques B, Soares R, Coelho AV, Leão C, Ludovico P, Sá-Correia I. Mitochondrial proteomics of the acetic acid - induced programmed cell death response in a highly tolerant Zygosaccharomyces bailii - derived hybrid strain. MICROBIAL CELL 2016; 3:65-78. [PMID: 28357336 PMCID: PMC5349105 DOI: 10.15698/mic2016.02.477] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Very high concentrations of acetic acid at low pH induce programmed cell death
(PCD) in both the experimental model Saccharomyces cerevisiae
and in Zygosaccharomyces bailii, the latter being considered
the most problematic acidic food spoilage yeast due to its remarkable intrinsic
resistance to this food preservative. However, while the mechanisms underlying
S. cerevisiae PCD induced by acetic acid have been
previously examined, the corresponding molecular players remain largely unknown
in Z. bailii. Also, the reason why acetic acid concentrations
known to be necrotic for S. cerevisiae induce PCD with an
apoptotic phenotype in Z. bailii remains to be elucidated. In
this study, a 2-DE-based expression mitochondrial proteomic analysis was
explored to obtain new insights into the mechanisms involved in PCD in the
Z. bailii derived hybrid strain ISA1307. This allowed the
quantitative assessment of expression of protein species derived from each of
the parental strains, with special emphasis on the processes taking place in the
mitochondria known to play a key role in acetic acid - induced PCD. A marked
decrease in the content of proteins involved in mitochondrial metabolism, in
particular, in respiratory metabolism (Cor1, Rip1, Lpd1, Lat1 and Pdb1), with a
concomitant increase in the abundance of proteins involved in fermentation
(Pdc1, Ald4, Dld3) was registered. Other differentially expressed identified
proteins also suggest the involvement of the oxidative stress response, protein
translation, amino acid and nucleotide metabolism, among other processes, in the
PCD response. Overall, the results strengthen the emerging concept of the
importance of metabolic regulation of yeast PCD.
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Affiliation(s)
- Joana F Guerreiro
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal. ; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Renata Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Ana V Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Cecília Leão
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal. ; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal. ; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
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McKeague M, Wang YH, Smolke CD. In Vitro Screening and in Silico Modeling of RNA-Based Gene Expression Control. ACS Chem Biol 2015; 10:2463-2467. [PMID: 26359915 DOI: 10.1021/acschembio.5b00518] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Molecular tools for controlling gene expression are essential for manipulating biological systems. One class of tools includes RNA switches that incorporate RNA-based sensors, known as aptamers. However, most switches reported to date are responsive to toxic molecules or to endogenous metabolites. For effective conditional control, switches must incorporate RNA aptamers that exhibit selectivity against such endogenous metabolites. We report a systematic approach which combines a rapid in vitro assay and an in silico model to support an efficient, streamlined application of aptamers into RNA switches. Model predictions were validated in vivo and demonstrate that the RNA switches enable selective and programmable gene regulation. We demonstrate the method using aptamers that bind the FDA-approved small molecule (6R)-folinic acid, providing access to new molecular targets for gene expression control and much-needed clinically relevant tools for advancing RNA-based therapeutics.
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Affiliation(s)
- Maureen McKeague
- Department of Bioengineering, Stanford University, 443 Via Ortega,
MC 4245, Stanford, California 94305, United States
| | - Yen-Hsiang Wang
- Department of Bioengineering, Stanford University, 443 Via Ortega,
MC 4245, Stanford, California 94305, United States
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, 443 Via Ortega,
MC 4245, Stanford, California 94305, United States
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31
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Review: can diet influence the selective advantage of mitochondrial DNA haplotypes? Biosci Rep 2015; 35:BSR20150232. [PMID: 26543031 PMCID: PMC4708006 DOI: 10.1042/bsr20150232] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 01/12/2023] Open
Abstract
This review explores the potential for changes in dietary macronutrients to differentially influence mitochondrial bioenergetics and thereby the frequency of mtDNA haplotypes in natural populations. Such dietary modification may be seasonal or result from biogeographic or demographic shifts. Mechanistically, mtDNA haplotypes may influence the activity of the electron transport system (ETS), retrograde signalling to the nuclear genome and affect epigenetic modifications. Thus, differential provisioning by macronutrients may lead to selection through changes in the levels of ATP production, modulation of metabolites (including AMP, reactive oxygen species (ROS) and the NAD+/NADH ratio) and potentially complex epigenetic effects. The exquisite complexity of dietary influence on haplotype frequency is further illustrated by the fact that macronutrients may differentially influence the selective advantage of specific mutations in different life-history stages. In Drosophila, complex I mutations may affect larval growth because dietary nutrients are fed through this complex in immaturity. In contrast, the majority of electrons are provided to complex III in adult flies. We conclude the review with a case study that considers specific interactions between diet and complex I of the ETS. Complex I is the first enzyme of the mitochondrial ETS and co-ordinates in the oxidation of NADH and transfer of electrons to ubiquinone. Although the supposition that mtDNA variants may be selected upon by dietary macronutrients could be intuitively consistent to some and counter intuitive to others, it must face a multitude of scientific hurdles before it can be recognized.
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Bailey LB, Stover PJ, McNulty H, Fenech MF, Gregory JF, Mills JL, Pfeiffer CM, Fazili Z, Zhang M, Ueland PM, Molloy AM, Caudill MA, Shane B, Berry RJ, Bailey RL, Hausman DB, Raghavan R, Raiten DJ. Biomarkers of Nutrition for Development-Folate Review. J Nutr 2015; 145:1636S-1680S. [PMID: 26451605 PMCID: PMC4478945 DOI: 10.3945/jn.114.206599] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/11/2014] [Accepted: 04/14/2015] [Indexed: 12/13/2022] Open
Abstract
The Biomarkers of Nutrition for Development (BOND) project is designed to provide evidence-based advice to anyone with an interest in the role of nutrition in health. Specifically, the BOND program provides state-of-the-art information and service with regard to selection, use, and interpretation of biomarkers of nutrient exposure, status, function, and effect. To accomplish this objective, expert panels are recruited to evaluate the literature and to draft comprehensive reports on the current state of the art with regard to specific nutrient biology and available biomarkers for assessing nutrients in body tissues at the individual and population level. Phase I of the BOND project includes the evaluation of biomarkers for 6 nutrients: iodine, iron, zinc, folate, vitamin A, and vitamin B-12. This review represents the second in the series of reviews and covers all relevant aspects of folate biology and biomarkers. The article is organized to provide the reader with a full appreciation of folate's history as a public health issue, its biology, and an overview of available biomarkers (serum folate, RBC folate, and plasma homocysteine concentrations) and their interpretation across a range of clinical and population-based uses. The article also includes a list of priority research needs for advancing the area of folate biomarkers related to nutritional health status and development.
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Affiliation(s)
- Lynn B Bailey
- Department of Foods and Nutrition, University of Georgia, Athens, GA;
| | - Patrick J Stover
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Helene McNulty
- Northern Ireland Centre for Food and Health, Biomedical Sciences Research Institute, University of Ulster, Londonderry, United Kingdom
| | - Michael F Fenech
- Genome Health Nutrigenomics Laboratory, Food, Nutrition, and Bioproducts Flagship, Commonwealth Scientific and Industrial Research Organization, Adelaide, Australia
| | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL
| | - James L Mills
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | | | - Zia Fazili
- National Center for Environmental Health, CDC, Atlanta, GA
| | - Mindy Zhang
- National Center for Environmental Health, CDC, Atlanta, GA
| | - Per M Ueland
- Department of Clinical Science, Univeristy of Bergen, Bergen, Norway
| | - Anne M Molloy
- Institute of Molecular Medicine, Trinity College, Dublin, Ireland
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Barry Shane
- Department of Nutritional Sciences and Toxicology, University of California-Berkeley, Berkeley, CA
| | - Robert J Berry
- National Center on Birth Defects and Developmental Disabilities, CDC, Atlanta, GA; and
| | | | - Dorothy B Hausman
- Department of Foods and Nutrition, University of Georgia, Athens, GA
| | - Ramkripa Raghavan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | - Daniel J Raiten
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD;
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Abstract
Activation of oncogenes and loss of tumour suppressors promote metabolic reprogramming in cancer, resulting in enhanced nutrient uptake to supply energetic and biosynthetic pathways. However, nutrient limitations within solid tumours may require that malignant cells exhibit metabolic flexibility to sustain growth and survival. Here, we highlight these adaptive mechanisms and also discuss emerging approaches to probe tumour metabolism in vivo and their potential to expand the metabolic repertoire of malignant cells even further.
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Ferreira A, Serafim TL, Sardão VA, Cunha-Oliveira T. Role of mtDNA-related mitoepigenetic phenomena in cancer. Eur J Clin Invest 2015; 45 Suppl 1:44-9. [PMID: 25524586 DOI: 10.1111/eci.12359] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 10/20/2014] [Indexed: 12/25/2022]
Abstract
BACKGROUND Abnormal mitochondrial function has long been associated with the development and the progression of cancer. Multiple defects in the mitochondrial genome have been reported for various cancers, however the often disregarded mitochondrial epigenetic landscape provides an additional source of deregulation that may contribute to carcinogenesis. DESIGN This article reviews the current understanding of mitochondrial epigenetics and how it may relate to cancer progression and development. Relevant studies were found through electronic databases (Web of Science and PubMed). RESULTS AND CONCLUSIONS The remarkably unexplored field of mitochondrial epigenetics has the potential to shed light on several cancer-related mitochondrial abnormalities. More studies using innovative, genome-wide sequencing technologies are highly warranted to assess whether and how altered mtDNA methylation patterns affect cancer initiation and progression.
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Affiliation(s)
- André Ferreira
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra, Cantanhede, Portugal
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de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
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Castro SV, Carvalho AA, Silva CMG, Santos FW, Campello CC, de Figueiredo JR, Rodrigues APR. Frozen and Fresh Ovarian Tissue Require Different Culture Media to Promote in Vitro Development of Bovine Preantral Follicles. Biopreserv Biobank 2014; 12:317-24. [DOI: 10.1089/bio.2014.0020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Simone Vieira Castro
- Laboratory of Manipulation of Oocytes and Preantral Follicles (LAMOFOPA), Veterinary Faculty, State University of Ceará, Fortaleza-CE, Brazil
| | - Adeline Andrade Carvalho
- Laboratory of Manipulation of Oocytes and Preantral Follicles (LAMOFOPA), Veterinary Faculty, State University of Ceará, Fortaleza-CE, Brazil
| | - Cleidson Manoel Gomes Silva
- Laboratory of Manipulation of Oocytes and Preantral Follicles (LAMOFOPA), Veterinary Faculty, State University of Ceará, Fortaleza-CE, Brazil
| | - Francielli Weber Santos
- Department of Chemistry, Center of Natural and Exact Sciences, Federal University of Santa Maria, Santa Maria-RS, Brazil
| | - Cláudio Cabral Campello
- Laboratory of Manipulation of Oocytes and Preantral Follicles (LAMOFOPA), Veterinary Faculty, State University of Ceará, Fortaleza-CE, Brazil
| | - José Ricardo de Figueiredo
- Laboratory of Manipulation of Oocytes and Preantral Follicles (LAMOFOPA), Veterinary Faculty, State University of Ceará, Fortaleza-CE, Brazil
| | - Ana Paula Ribeiro Rodrigues
- Laboratory of Manipulation of Oocytes and Preantral Follicles (LAMOFOPA), Veterinary Faculty, State University of Ceará, Fortaleza-CE, Brazil
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Shin M, Bryant JD, Momb J, Appling DR. Mitochondrial MTHFD2L is a dual redox cofactor-specific methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase expressed in both adult and embryonic tissues. J Biol Chem 2014; 289:15507-17. [PMID: 24733394 DOI: 10.1074/jbc.m114.555573] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian mitochondria are able to produce formate from one-carbon donors such as serine, glycine, and sarcosine. This pathway relies on the mitochondrial pool of tetrahydrofolate (THF) and several folate-interconverting enzymes in the mitochondrial matrix. We recently identified MTHFD2L as the enzyme that catalyzes the oxidation of 5,10-methylenetetrahydrofolate (CH2-THF) in adult mammalian mitochondria. We show here that the MTHFD2L enzyme is bifunctional, possessing both CH2-THF dehydrogenase and 5,10-methenyl-THF cyclohydrolase activities. The dehydrogenase activity can use either NAD(+) or NADP(+) but requires both phosphate and Mg(2+) when using NAD(+). The NADP(+)-dependent dehydrogenase activity is inhibited by inorganic phosphate. MTHFD2L uses the mono- and polyglutamylated forms of CH2-THF with similar catalytic efficiencies. Expression of the MTHFD2L transcript is low in early mouse embryos but begins to increase at embryonic day 10.5 and remains elevated through birth. In adults, MTHFD2L is expressed in all tissues examined, with the highest levels observed in brain and lung.
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Affiliation(s)
- Minhye Shin
- From the Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Joshua D Bryant
- From the Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Jessica Momb
- From the Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Dean R Appling
- From the Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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Utility of the Biosynthetic Folate Pathway for Targets in Antimicrobial Discovery. Antibiotics (Basel) 2014; 3:1-28. [PMID: 27025730 PMCID: PMC4790348 DOI: 10.3390/antibiotics3010001] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 01/07/2023] Open
Abstract
The need for new antimicrobials is great in face of a growing pool of resistant pathogenic organisms. This review will address the potential for antimicrobial therapy based on polypharmacological activities within the currently utilized bacterial biosynthetic folate pathway. The folate metabolic pathway leads to synthesis of required precursors for cellular function and contains a critical node, dihydrofolate reductase (DHFR), which is shared between prokaryotes and eukaryotes. The DHFR enzyme is currently targeted by methotrexate in anti-cancer therapies, by trimethoprim for antibacterial uses, and by pyrimethamine for anti-protozoal applications. An additional anti-folate target is dihyropteroate synthase (DHPS), which is unique to prokaryotes as they cannot acquire folate through dietary means. It has been demonstrated as a primary target for the longest standing antibiotic class, the sulfonamides, which act synergistically with DHFR inhibitors. Investigations have revealed most DHPS enzymes possess the ability to utilize sulfa drugs metabolically, producing alternate products that presumably inhibit downstream enzymes requiring the produced dihydropteroate. Recent work has established an off-target effect of sulfonamide antibiotics on a eukaryotic enzyme, sepiapterin reductase, causing alterations in neurotransmitter synthesis. Given that inhibitors of both DHFR and DHPS are designed to mimic their cognate substrate, which contain shared substructures, it is reasonable to expect such “off-target” effects. These inhibitors are also likely to interact with the enzymatic neighbors in the folate pathway that bind products of the DHFR or DHPS enzymes and/or substrates of similar substructure. Computational studies designed to assess polypharmacology reiterate these conclusions. This leads to hypotheses exploring the vast utility of multiple members of the folate pathway for modulating cellular metabolism, and includes an appealing capacity for prokaryotic-specific polypharmacology for antimicrobial applications.
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Iacobazzi V, Castegna A, Infantino V, Andria G. Mitochondrial DNA methylation as a next-generation biomarker and diagnostic tool. Mol Genet Metab 2013; 110:25-34. [PMID: 23920043 DOI: 10.1016/j.ymgme.2013.07.012] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/12/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
Recent expansion of our knowledge on epigenetic changes strongly suggests that not only nuclear DNA (nDNA), but also mitochondrial DNA (mtDNA) may be subjected to epigenetic modifications related to disease development, environmental exposure, drug treatment and aging. Thus, mtDNA methylation is attracting increasing attention as a potential biomarker for the detection and diagnosis of diseases and the understanding of cellular behavior in particular conditions. In this paper we review the current advances in mtDNA methylation studies with particular attention to the evidences of mtDNA methylation changes in diseases and physiological conditions so far investigated. Technological advances for the analysis of epigenetic variations are promising tools to provide insights into methylation of mtDNA with similar resolution levels as those reached for nDNA. However, many aspects related to mtDNA methylation are still unclear. More studies are needed to understand whether and how changes in mtDNA methylation patterns, global and gene specific, are associated to diseases or risk factors.
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Affiliation(s)
- Vito Iacobazzi
- Department of Biosciences, Biotechnology and Pharmacological Sciences, University of Bari, via Orabona 4, 70125 Bari, Italy.
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40
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Wei Z, Sun K, Sandoval FJ, Cross JM, Gordon C, Kang C, Roje S. Folate polyglutamylation eliminates dependence of activity on enzyme concentration in mitochondrial serine hydroxymethyltransferases from Arabidopsis thaliana. Arch Biochem Biophys 2013; 536:87-96. [DOI: 10.1016/j.abb.2013.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 06/11/2013] [Accepted: 06/11/2013] [Indexed: 11/27/2022]
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Abstract
Mechanisms postulated to link folate and B12 metabolism with cancer, including genome-wide hypomethylation, gene-specific promoter hypermethylation, and DNA uracil misincorporation, have been observed in prostate tumor cells. However, epidemiological studies of prostate cancer risk, based on dietary intakes and blood levels of folate and vitamin B12 and on folate-pathway gene variants, have generated contradictory findings. In a meta-analysis, circulating concentrations of B12 (seven studies, OR = 1.10; 95% CI 1.01, 1.19; P = 0.002) and (in cohort studies) folate (five studies, OR = 1.18; 95% CI 1.00, 1.40; P = 0.02) were positively associated with an increased risk of prostate cancer. Homocysteine was not associated with risk of prostate cancer (four studies, OR = 0.91; 95% CI 0.69, 1.19; P = 0.5). In a meta-analysis of folate-pathway polymorphisms, MTR 2756A > G (eight studies, OR = 1.06; 95% CI 1.00, 1.12; P = 0.06) and SHMT1 1420C > T (two studies, OR = 1.11; 95% CI 1.00, 1.22; P = 0.05) were positively associated with prostate cancer risk. There were no effects due to any other polymorphisms, including MTHFR 677C > T (12 studies, OR = 1.04; 95% CI 0.97, 1.12; P = 0.3). The positive association of circulating B12 with an increased risk of prostate cancer could be explained by reverse causality. However, given current controversies over mandatory B12 fortification, further research to eliminate a causal role of B12 in prostate cancer initiation and/or progression is required. Meta-analysis does not entirely rule out a positive association of circulating folate with increased prostate cancer risk. As with B12, even a weak positive association would be a significant public health issue, given the high prevalence of prostate cancer and concerns about the potential harms versus benefits of mandatory folic acid fortification.
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42
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Christensen KE, Deng L, Leung KY, Arning E, Bottiglieri T, Malysheva OV, Caudill MA, Krupenko NI, Greene ND, Jerome-Majewska L, MacKenzie RE, Rozen R. A novel mouse model for genetic variation in 10-formyltetrahydrofolate synthetase exhibits disturbed purine synthesis with impacts on pregnancy and embryonic development. Hum Mol Genet 2013; 22:3705-19. [PMID: 23704330 DOI: 10.1093/hmg/ddt223] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genetic variants in one-carbon folate metabolism have been identified as risk factors for disease because they may impair the production or use of one-carbon folates required for nucleotide synthesis and methylation. p.R653Q (1958G>A) is a single-nucleotide polymorphism (SNP) in the 10-formyltetrahydrofolate (formylTHF) synthetase domain of the trifunctional enzyme MTHFD1; this domain produces the formylTHF which is required for the de novo synthesis of purines. Approximately 20% of Caucasians are homozygous for the Q allele. MTHFD1 p.R653Q has been proposed as a risk factor for neural tube defects (NTDs), congenital heart defects (CHDs) and pregnancy losses. We have generated a novel mouse model in which the MTHFD1 synthetase activity is inactivated without affecting protein expression or the other activities of this enzyme. Complete loss of synthetase activity (Mthfd1S(-/-)) is incompatible with life; embryos die shortly after 10.5 days gestation, and are developmentally delayed or abnormal. The proportion of 10-formylTHF in the plasma and liver of Mthfd1S(+/-) mice is reduced (P < 0.05), and de novo purine synthesis is impaired in Mthfd1S(+/-) mouse embryonic fibroblasts (MEFs, P < 0.005). Female Mthfd1S(+/-) mice had decreased neutrophil counts (P < 0.05) during pregnancy and increased incidence of developmental defects in embryos (P = 0.052). These findings suggest that synthetase deficiency may lead to pregnancy complications through decreased purine synthesis and reduced cellular proliferation. Additional investigation of the impact of synthetase polymorphisms on human pregnancy is warranted.
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Affiliation(s)
- K E Christensen
- Departments of Human Genetics and Pediatrics, McGill University, and Montreal Children's Hospital site/McGill University Health Centre Research Institute, Montreal, Quebec, Canada
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43
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Folate metabolism in human malaria parasites—75 years on. Mol Biochem Parasitol 2013; 188:63-77. [DOI: 10.1016/j.molbiopara.2013.02.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 12/21/2022]
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Scotti M, Stella L, Shearer EJ, Stover PJ. Modeling cellular compartmentation in one-carbon metabolism. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:343-65. [PMID: 23408533 DOI: 10.1002/wsbm.1209] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Folate-mediated one-carbon metabolism (FOCM) is associated with risk for numerous pathological states including birth defects, cancers, and chronic diseases. Although the enzymes that constitute the biological pathways have been well described and their interdependency through the shared use of folate cofactors appreciated, the biological mechanisms underlying disease etiologies remain elusive. The FOCM network is highly sensitive to nutritional status of several B-vitamins and numerous penetrant gene variants that alter network outputs, but current computational approaches do not fully capture the dynamics and stochastic noise of the system. Combining the stochastic approach with a rule-based representation will help model the intrinsic noise displayed by FOCM, address the limited flexibility of standard simulation methods for coarse-graining the FOCM-associated biochemical processes, and manage the combinatorial complexity emerging from reactions within FOCM that would otherwise be intractable.
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Affiliation(s)
- Marco Scotti
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
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45
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Cordeiro OD, Silva TS, Alves RN, Costas B, Wulff T, Richard N, de Vareilles M, Conceição LEC, Rodrigues PM. Changes in liver proteome expression of Senegalese sole (Solea senegalensis) in response to repeated handling stress. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:714-729. [PMID: 22327442 DOI: 10.1007/s10126-012-9437-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 01/16/2012] [Indexed: 05/28/2023]
Abstract
The Senegalese sole, a high-value flatfish, is a good candidate for aquaculture production. Nevertheless, there are still issues regarding this species' sensitivity to stress in captivity. We aimed to characterize the hepatic proteome expression for this species in response to repeated handling and identify potential molecular markers that indicate a physiological response to chronic stress. Two groups of fish were reared in duplicate for 28 days, one of them weekly exposed to handling stress (including hypoxia) for 3 min, and the other left undisturbed. Two-dimensional electrophoresis enabled the detection of 287 spots significantly affected by repeated handling stress (Wilcoxon-Mann-Whitney U test, p < 0.05), 33 of which could be reliably identified by peptide mass spectrometry. Chronic exposure to stress seems to have affected protein synthesis, folding and turnover (40S ribosomal protein S12, cathepsin B, disulfide-isomerase A3 precursor, cell-division cycle 48, and five distinct heat shock proteins), amino acid metabolism, urea cycle and methylation/folate pathways (methionine adenosyltransferase I α, phenylalanine hydroxylase, mitochondrial agmatinase, serine hydroxymethyltransferase, 3-hydroxyanthranilate 3,4-dioxygenase, and betaine homocysteine methyltransferase), cytoskeletal (40S ribosomal protein SA, α-actin, β-actin, α-tubulin, and cytokeratin K18), aldehyde detoxification (aldehyde dehydrogenase 4A1 family and aldehyde dehydrogenase 7A1 family), carbohydrate metabolism and energy homeostasis (fatty acid-binding protein, enolase 3, enolase 1, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, aconitase 1, mitochondrial ATP synthase α-subunit, and electron-transfer flavoprotein α polypeptide), iron and selenium homeostasis (transferrin and selenium binding protein 1), steroid hormone metabolism (3-oxo-5-β-steroid 4-dehydrogenase), and purine salvage (hypoxanthine phosphoribosyltransferase). Further characterization is required to fully assess the potential of these markers for the monitoring of fish stress response to chronic stressors of aquaculture environment.
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Affiliation(s)
- Odete D Cordeiro
- Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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Eadsforth TC, Maluf FV, Hunter WN. Acinetobacter baumannii FolD ligand complexes --potent inhibitors of folate metabolism and a re-evaluation of the structure of LY374571. FEBS J 2012; 279:4350-60. [PMID: 23050773 DOI: 10.1111/febs.12025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/07/2012] [Accepted: 10/04/2012] [Indexed: 01/26/2023]
Abstract
The bifunctional N(5),N(10)-methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DHCH or FolD), which is widely distributed in prokaryotes and eukaryotes, is involved in the biosynthesis of folate cofactors that are essential for growth and cellular development. The enzyme activities represent a potential antimicrobial drug target. We have characterized the kinetic properties of FolD from the Gram-negative pathogen Acinetobacter baumanni and determined high-resolution crystal structures of complexes with a cofactor and two potent inhibitors. The data reveal new details with respect to the molecular basis of catalysis and potent inhibition. A unexpected finding was that our crystallographic data revealed a different structure for LY374571 (an inhibitor studied as an antifolate) than that previously published. The implications of this observation are discussed.
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Affiliation(s)
- Thomas C Eadsforth
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
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47
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Ikeda S, Koyama H, Sugimoto M, Kume S. Roles of one-carbon metabolism in preimplantation period--effects on short-term development and long-term programming--. J Reprod Dev 2012; 58:38-43. [PMID: 22450283 DOI: 10.1262/jrd.2011-002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One-carbon metabolism (OCM) can be seen as integrated metabolic pathways centered on the metabolism of two nutritional substances, folate and methionine. Mammalian oocytes and preimplantation embryos express almost all enzymes that participate in OCM, suggesting that they can independently metabolize OCM nutrients. A deficiency or excess of OCM nutrients and their metabolites during in vitro culture affects preimplantation development of mammalian embryos. Recent in vivo studies have demonstrated that specific OCM dietary interventions during the periconceptional (mainly oocyte growth and preimplantation) period can cause epigenetic alterations in DNA of offspring and program the long-term consequences in their health in adulthood. The epigenetic processes are likely to be implicated in the effects of OCM nutrients; however, understanding their effects at the level of specific genes and their implications in assisted reproductive technology will require further investigations.
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Affiliation(s)
- Shuntaro Ikeda
- Laboratory of Animal Physiology and Functional Anatomy, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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48
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Abstract
Trypanosomatid parasitic protozoans of the genus Leishmania are autotrophic for both folate and unconjugated pteridines. Leishmania salvage these metabolites from their mammalian hosts and insect vectors through multiple transporters. Within the parasite, folates are reduced by a bifunctional DHFR (dihydrofolate reductase)-TS (thymidylate synthase) and by a novel PTR1 (pteridine reductase 1), which reduces both folates and unconjugated pteridines. PTR1 can act as a metabolic bypass of DHFR inhibition, reducing the effectiveness of existing antifolate drugs. Leishmania possess a reduced set of folate-dependent metabolic reactions and can salvage many of the key products of folate metabolism from their hosts. For example, they lack purine synthesis, which normally requires 10-formyltetrahydrofolate, and instead rely on a network of purine salvage enzymes. Leishmania elaborate at least three pathways for the synthesis of the key metabolite 5,10-methylene-tetrahydrofolate, required for the synthesis of thymidylate, and for 10-formyltetrahydrofolate, whose presumptive function is for methionyl-tRNAMet formylation required for mitochondrial protein synthesis. Genetic studies have shown that the synthesis of methionine using 5-methyltetrahydrofolate is dispensable, as is the activity of the glycine cleavage complex, probably due to redundancy with serine hydroxymethyltransferase. Although not always essential, the loss of several folate metabolic enzymes results in attenuation or loss of virulence in animal models, and a null DHFR-TS mutant has been used to induce protective immunity. The folate metabolic pathway provides numerous opportunities for targeted chemotherapy, with strong potential for 'repurposing' of compounds developed originally for treatment of human cancers or other infectious agents.
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50
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Dikicioglu D, Dunn WB, Kell DB, Kirdar B, Oliver SG. Short- and long-term dynamic responses of the metabolic network and gene expression in yeast to a transient change in the nutrient environment. MOLECULAR BIOSYSTEMS 2012; 8:1760-74. [PMID: 22491778 DOI: 10.1039/c2mb05443d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Quantitative data on the dynamic changes in the transcriptome and the metabolome of yeast in response to an impulse-like perturbation in nutrient availability was integrated with the metabolic pathway information in order to elucidate the long-term dynamic re-organization of the cells. This study revealed that, in addition to the dynamic re-organization of the de novo biosynthetic pathways, salvage pathways were also re-organized in a time-dependent manner upon catabolite repression. The transcriptional and the metabolic responses observed for nitrogen catabolite repression were not as severe as those observed for carbon catabolite repression. Selective up- or down regulation of a single member of a paralogous gene pair during the response to the relaxation from nutritional limitation was identified indicating a differentiation of functions among paralogs. Our study highlighted the role of inosine accumulation and recycling in energy homeostasis and indicated possible bottlenecks in the process.
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Affiliation(s)
- Duygu Dikicioglu
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.
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