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de la Torre F, Medina-Morales B, Blanca-Reyes I, Pascual MB, Ávila C, Cánovas FM, Castro-Rodríguez V. Properties and Functional Analysis of Two Chorismate Mutases from Maritime Pine. Cells 2024; 13:929. [PMID: 38891061 PMCID: PMC11171525 DOI: 10.3390/cells13110929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/20/2024] Open
Abstract
Through the shikimate pathway, a massive metabolic flux connects the central carbon metabolism with the synthesis of chorismate, the common precursor of the aromatic amino acids phenylalanine, tyrosine, and tryptophan, as well as other compounds, including salicylate or folate. The alternative metabolic channeling of chorismate involves a key branch-point, finely regulated by aromatic amino acid levels. Chorismate mutase catalyzes the conversion of chorismate to prephenate, a precursor of phenylalanine and tyrosine and thus a vast repertoire of fundamental derived compounds, such as flavonoids or lignin. The regulation of this enzyme has been addressed in several plant species, but no study has included conifers or other gymnosperms, despite the importance of the phenolic metabolism for these plants in processes such as lignification and wood formation. Here, we show that maritime pine (Pinus pinaster Aiton) has two genes that encode for chorismate mutase, PpCM1 and PpCM2. Our investigations reveal that these genes encode plastidial isoenzymes displaying activities enhanced by tryptophan and repressed by phenylalanine and tyrosine. Using phylogenetic studies, we have provided new insights into the possible evolutionary origin of the cytosolic chorismate mutases in angiosperms involved in the synthesis of phenylalanine outside the plastid. Studies based on different platforms of gene expression and co-expression analysis have allowed us to propose that PpCM2 plays a central role in the phenylalanine synthesis pathway associated with lignification.
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Affiliation(s)
- Fernando de la Torre
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071 Málaga, Spain; (B.M.-M.); (I.B.-R.); (M.B.P.); (C.Á.); (F.M.C.)
| | | | | | | | | | | | - Vanessa Castro-Rodríguez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071 Málaga, Spain; (B.M.-M.); (I.B.-R.); (M.B.P.); (C.Á.); (F.M.C.)
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2
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Jiang Y, Zhu Q, Yang H, Zhi T, Ren C. Phenylalanine suppresses cell death caused by loss of fumarylacetoacetate hydrolase in Arabidopsis. Sci Rep 2022; 12:13546. [PMID: 35941360 PMCID: PMC9360007 DOI: 10.1038/s41598-022-17819-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Fumarylacetoacetate hydrolase (FAH) catalyzes the final step of Tyrosine (Tyr) degradation pathway essential to animals and the deficiency of FAH causes an inborn lethal disease. In plants, a role of this pathway was unknown until we found that mutation of Short-day Sensitive Cell Death1 (SSCD1), encoding Arabidopsis FAH, results in cell death under short day. Phenylalanine (Phe) could be converted to Tyr and then degraded in both animals and plants. Phe ingestion in animals worsens the disease caused by FAH defect. However, in this study we found that Phe represses cell death caused by FAH defect in plants. Phe treatment promoted chlorophyll biosynthesis and suppressed the up-regulation of reactive oxygen species marker genes in the sscd1 mutant. Furthermore, the repression of sscd1 cell death by Phe could be reduced by α-aminooxi-β-phenylpropionic acid but increased by methyl jasmonate, which inhibits or activates Phe ammonia-lyase catalyzing the first step of phenylpropanoid pathway, respectively. In addition, we found that jasmonate signaling up-regulates Phe ammonia-lyase 1 and mediates the methyl jasmonate enhanced repression of sscd1 cell death by Phe. These results uncovered the relation between chlorophyll biosynthesis, phenylpropanoid pathway and jasmonate signaling in regulating the cell death resulting from loss of FAH in plants.
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Affiliation(s)
- Yihe Jiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Qi Zhu
- College of Horticulture, Hunan Agricultural University, Changsha, 410128, China
| | - Hua Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.,Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China
| | - Tiantian Zhi
- Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China.,College of Life Sciences and Resources and Environment, Yichun University, Yichun, 336000, China
| | - Chunmei Ren
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China. .,Crop Gene Engineering Key Laboratory of Hunan Province, Hunan Agricultural University, Changsha, 410128, China.
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3
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Wang S, Li Y, He L, Yang J, Fernie AR, Luo J. Natural variance at the interface of plant primary and specialized metabolism. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102201. [PMID: 35349968 DOI: 10.1016/j.pbi.2022.102201] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/01/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Plants produce a large number of diverse metabolites when they grow and develop as well as when they respond to the changing external environment. These are an important source of human nutrition and medicine. In this review we emphasized the major issues of the primary-specialized metabolic interface in plant metabolism, described the metabolic flow from primary to specialized metabolism, and the conservation and diversity of primary and specialized metabolites. At the same time, we summarized the regulatory mechanisms underpinning the dynamic balance primary and specialized metabolism based on multi-omics integration analysis, as well as the natural variation of primary and specialized metabolic pathways and genes during the plant evolution. Moreover, the discovery and optimization of the synthesis and regulation elements of various primary to specialized metabolic flows provide the possibility for precise modification and personalized customization of metabolic pathways, which will greatly promote the development of synthetic biology.
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Affiliation(s)
| | - Yan Li
- College of Tropical Crops, Hainan University, Haikou, China
| | - Liqiang He
- College of Tropical Crops, Hainan University, Haikou, China
| | - Jun Yang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China.
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4
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Phenylketonuria monitoring in human blood serum by mosses extract/ZnO@Au nanoarrays-loaded filter paper as a novel electrochemical biosensor. Microchem J 2021. [DOI: 10.1016/j.microc.2020.105739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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5
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Suppression of chorismate synthase, which is localized in chloroplasts and peroxisomes, results in abnormal flower development and anthocyanin reduction in petunia. Sci Rep 2020; 10:10846. [PMID: 32616740 PMCID: PMC7331636 DOI: 10.1038/s41598-020-67671-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/12/2020] [Indexed: 12/18/2022] Open
Abstract
In plants, the shikimate pathway generally occurs in plastids and leads to the biosynthesis of aromatic amino acids. Chorismate synthase (CS) catalyses the last step of the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP) to chorismate, but the role of CS in the metabolism of higher plants has not been reported. In this study, we found that PhCS, which is encoded by a single-copy gene in petunia (Petunia hybrida), contains N-terminal plastidic transit peptides and peroxisomal targeting signals. Green fluorescent protein (GFP) fusion protein assays revealed that PhCS was localized in chloroplasts and, unexpectedly, in peroxisomes. Petunia plants with reduced PhCS activity were generated through virus-induced gene silencing and further characterized. PhCS silencing resulted in reduced CS activity, severe growth retardation, abnormal flower and leaf development and reduced levels of folate and pigments, including chlorophylls, carotenoids and anthocyanins. A widely targeted metabolomics analysis showed that most primary and secondary metabolites were significantly changed in pTRV2-PhCS-treated corollas. Overall, the results revealed a clear connection between primary and specialized metabolism related to the shikimate pathway in petunia.
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6
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Lynch JH, Dudareva N. Aromatic Amino Acids: A Complex Network Ripe for Future Exploration. TRENDS IN PLANT SCIENCE 2020; 25:670-681. [PMID: 32526172 DOI: 10.1016/j.tplants.2020.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 05/28/2023]
Abstract
In plants, high carbon flux is committed to the biosynthesis of phenylalanine, tyrosine, and tryptophan, owing to their roles not only in the production of proteins, but also as precursors to thousands of primary and specialized metabolites. The core plastidial pathways that supply the majority of aromatic amino acids (AAAs) have previously been described in detail. More recently, the discovery of cytosolic enzymes contributing to overall AAA biosynthesis, as well as the identification of intracellular transporters and the continuing elucidation of transcriptional and post-transcriptional regulatory mechanisms, have revealed the complexity of this intercompartmental metabolic network. Here, we review the latest breakthroughs in AAA production and use the newest findings to highlight both longstanding and newly developed questions.
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Affiliation(s)
- Joseph H Lynch
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN 47907-2063, USA
| | - Natalia Dudareva
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
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7
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Luo H, Yang L, Kim SH, Wulff T, Feist AM, Herrgard M, Palsson BØ. Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli. ACS Synth Biol 2020; 9:494-499. [PMID: 32149495 DOI: 10.1021/acssynbio.9b00488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tetrahydrobiopterin-dependent hydroxylation of aromatic amino acids is the first step in the biosynthesis of many neuroactive compounds in humans. A fundamental challenge in building these pathways in Escherichia coli is the provision of the non-native hydroxylase cofactor, tetrahydrobiopterin. To solve this, we designed a genetic selection that relies on the tyrosine synthesis activity of phenylalanine hydroxylase. Using adaptive laboratory evolution, we demonstrate the use of this selection to discover: (1) a minimum set of heterologous enzymes and a host folE (T198I) mutation for achieving this type of hydroxylation chemistry in whole cells, (2) functional complementation of tetrahydrobiopterin by indigenous cofactors, and (3) a tryptophan hydroxylase mutation for improving protein abundance. Thus, the goal of having functional aromatic-amino-acid hydroxylation in E. coli was achieved through directed metabolic pathway evolution.
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Affiliation(s)
- Hao Luo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Lei Yang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Se Hyeuk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States of America
| | - Markus Herrgard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bernhard Ø Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States of America
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8
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Metabolic engineering of Synechocystis sp. PCC 6803 for the production of aromatic amino acids and derived phenylpropanoids. Metab Eng 2020; 57:129-139. [DOI: 10.1016/j.ymben.2019.11.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/14/2019] [Accepted: 11/08/2019] [Indexed: 11/22/2022]
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9
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Maeda HA. Harnessing evolutionary diversification of primary metabolism for plant synthetic biology. J Biol Chem 2019; 294:16549-16566. [PMID: 31558606 DOI: 10.1074/jbc.rev119.006132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Plants produce numerous natural products that are essential to both plant and human physiology. Recent identification of genes and enzymes involved in their biosynthesis now provides exciting opportunities to reconstruct plant natural product pathways in heterologous systems through synthetic biology. The use of plant chassis, although still in infancy, can take advantage of plant cells' inherent capacity to synthesize and store various phytochemicals. Also, large-scale plant biomass production systems, driven by photosynthetic energy production and carbon fixation, could be harnessed for industrial-scale production of natural products. However, little is known about which plants could serve as ideal hosts and how to optimize plant primary metabolism to efficiently provide precursors for the synthesis of desirable downstream natural products or specialized (secondary) metabolites. Although primary metabolism is generally assumed to be conserved, unlike the highly-diversified specialized metabolism, primary metabolic pathways and enzymes can differ between microbes and plants and also among different plants, especially at the interface between primary and specialized metabolisms. This review highlights examples of the diversity in plant primary metabolism and discusses how we can utilize these variations in plant synthetic biology. I propose that understanding the evolutionary, biochemical, genetic, and molecular bases of primary metabolic diversity could provide rational strategies for identifying suitable plant hosts and for further optimizing primary metabolism for sizable production of natural and bio-based products in plants.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
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10
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Schenck CA, Maeda HA. Tyrosine biosynthesis, metabolism, and catabolism in plants. PHYTOCHEMISTRY 2018; 149:82-102. [PMID: 29477627 DOI: 10.1016/j.phytochem.2018.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/26/2018] [Accepted: 02/02/2018] [Indexed: 05/22/2023]
Abstract
L-Tyrosine (Tyr) is an aromatic amino acid (AAA) required for protein synthesis in all organisms, but synthesized de novo only in plants and microorganisms. In plants, Tyr also serves as a precursor of numerous specialized metabolites that have diverse physiological roles as electron carriers, antioxidants, attractants, and defense compounds. Some of these Tyr-derived plant natural products are also used in human medicine and nutrition (e.g. morphine and vitamin E). While the Tyr biosynthesis and catabolic pathways have been extensively studied in microbes and animals, respectively, those of plants have received much less attention until recently. Accumulating evidence suggest that the Tyr biosynthetic pathways differ between microbes and plants and even within the plant kingdom, likely to support the production of lineage-specific plant specialized metabolites derived from Tyr. The interspecies variations of plant Tyr pathway enzymes can now be used to enhance the production of Tyr and Tyr-derived compounds in plants and other synthetic biology platforms.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.
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11
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Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO. A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals. Front Mol Biosci 2018; 5:29. [PMID: 29682508 PMCID: PMC5897657 DOI: 10.3389/fmolb.2018.00029] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Penelope J. Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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Watanabe S, Ohtani Y, Tatsukami Y, Aoki W, Amemiya T, Sukekiyo Y, Kubokawa S, Ueda M. Folate Biofortification in Hydroponically Cultivated Spinach by the Addition of Phenylalanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4605-4610. [PMID: 28548831 DOI: 10.1021/acs.jafc.7b01375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Folate is an important vitamin mainly ingested from vegetables, and folate deficiency causes various health problems. Recently, several studies demonstrated folate biofortification in plants or food crops by metabolic engineering through genetic modifications. However, the production and sales of genetically modified foods are under strict regulation. Here, we developed a new approach to achieve folate biofortification in spinach (Spinacia oleracea) without genetic modification. We hydroponically cultivated spinach with the addition of three candidate compounds expected to fortify folate. As a result of liquid chromatography tandem mass spectrometry analysis, we found that the addition of phenylalanine increased the folate content up to 2.0-fold (306 μg in 100 g of fresh spinach), representing 76.5% of the recommended daily allowance for adults. By measuring the intermediates of folate biosynthesis, we revealed that phenylalanine activated folate biosynthesis in spinach by increasing the levels of pteridine and p-aminobenzoic acid. Our approach is a promising and practical approach to cultivate nutrient-enriched vegetables.
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Affiliation(s)
- Sho Watanabe
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuta Ohtani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
| | - Yohei Tatsukami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
- Japan Society for the Promotion of Science , Sakyo-ku, Kyoto 606-8502, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center , Shimogyo-ku, Kyoto 600-8813, Japan
| | - Takashi Amemiya
- Mitsubishi Plastic, Inc. , Chiyoda-ku, Tokyo 100-8252, Japan
| | | | | | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center , Shimogyo-ku, Kyoto 600-8813, Japan
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13
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Simonet P, Gaget K, Parisot N, Duport G, Rey M, Febvay G, Charles H, Callaerts P, Colella S, Calevro F. Disruption of phenylalanine hydroxylase reduces adult lifespan and fecundity, and impairs embryonic development in parthenogenetic pea aphids. Sci Rep 2016; 6:34321. [PMID: 27694983 PMCID: PMC5046115 DOI: 10.1038/srep34321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/12/2016] [Indexed: 11/11/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) is a key tyrosine-biosynthetic enzyme involved in neurological and melanin-associated physiological processes. Despite extensive investigations in holometabolous insects, a PAH contribution to insect embryonic development has never been demonstrated. Here, we have characterized, for the first time, the PAH gene in a hemimetabolous insect, the aphid Acyrthosiphon pisum. Phylogenetic and sequence analyses confirmed that ApPAH is closely related to metazoan PAH, exhibiting the typical ACT regulatory and catalytic domains. Temporal expression patterns suggest that ApPAH has an important role in aphid developmental physiology, its mRNA levels peaking at the end of embryonic development. We used parental dsApPAH treatment to generate successful knockdown in aphid embryos and to study its developmental role. ApPAH inactivation shortens the adult aphid lifespan and considerably affects fecundity by diminishing the number of nymphs laid and impairing embryonic development, with newborn nymphs exhibiting severe morphological defects. Using single nymph HPLC analyses, we demonstrated a significant tyrosine deficiency and a consistent accumulation of the upstream tyrosine precursor, phenylalanine, in defective nymphs, thus confirming the RNAi-mediated disruption of PAH activity. This study provides first insights into the role of PAH in hemimetabolous insects and demonstrates that this metabolic gene is essential for insect embryonic development.
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Affiliation(s)
- Pierre Simonet
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Karen Gaget
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Gabrielle Duport
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Marjolaine Rey
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Patrick Callaerts
- KU Leuven, University of Leuven, Department of Human Genetics, Laboratory of Behavioral and Developmental Genetics, B-3000, Leuven, Belgium
- VIB Center for the Biology of Disease, B-3000, Leuven, Belgium
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
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14
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Pascual MB, El-Azaz J, de la Torre FN, Cañas RA, Avila C, Cánovas FM. Biosynthesis and Metabolic Fate of Phenylalanine in Conifers. FRONTIERS IN PLANT SCIENCE 2016; 7:1030. [PMID: 27468292 PMCID: PMC4942462 DOI: 10.3389/fpls.2016.01030] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/30/2016] [Indexed: 05/18/2023]
Abstract
The amino acid phenylalanine (Phe) is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development, and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids. The study of this metabolic pathway is particularly relevant in trees, which divert large amounts of carbon into the biosynthesis of Phe-derived compounds, particularly lignin, an important constituent of wood. The trunks of trees are metabolic sinks that consume a considerable percentage of carbon and energy from photosynthesis, and carbon is finally immobilized in wood. This paper reviews recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees. Two alternative routes have been identified: the ancient phenylpyruvate pathway that is present in microorganisms, and the arogenate pathway that possibly evolved later during plant evolution. Additionally, an efficient nitrogen recycling mechanism is required to maintain sustained growth during xylem formation. The relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions, and ultraviolet protection is discussed. The genetic manipulation and transcriptional regulation of the pathways are also outlined.
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Affiliation(s)
| | | | | | | | | | - Francisco M. Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de MálagaMálaga, Spain
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15
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Hildebrandt TM, Nunes Nesi A, Araújo WL, Braun HP. Amino Acid Catabolism in Plants. MOLECULAR PLANT 2015; 8:1563-79. [PMID: 26384576 DOI: 10.1016/j.molp.2015.09.005] [Citation(s) in RCA: 546] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 05/19/2023]
Abstract
Amino acids have various prominent functions in plants. Besides their usage during protein biosynthesis, they also represent building blocks for several other biosynthesis pathways and play pivotal roles during signaling processes as well as in plant stress response. In general, pool sizes of the 20 amino acids differ strongly and change dynamically depending on the developmental and physiological state of the plant cell. Besides amino acid biosynthesis, which has already been investigated in great detail, the catabolism of amino acids is of central importance for adjusting their pool sizes but so far has drawn much less attention. The degradation of amino acids can also contribute substantially to the energy state of plant cells under certain physiological conditions, e.g. carbon starvation. In this review, we discuss the biological role of amino acid catabolism and summarize current knowledge on amino acid degradation pathways and their regulation in the context of plant cell physiology.
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Affiliation(s)
- Tatjana M Hildebrandt
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany.
| | - Adriano Nunes Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil.
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
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Ibarra-Laclette E, Zamudio-Hernández F, Pérez-Torres CA, Albert VA, Ramírez-Chávez E, Molina-Torres J, Fernández-Cortes A, Calderón-Vázquez C, Olivares-Romero JL, Herrera-Estrella A, Herrera-Estrella L. De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis. BMC Genomics 2015; 16:657. [PMID: 26330142 PMCID: PMC4557841 DOI: 10.1186/s12864-015-1821-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 08/07/2015] [Indexed: 12/04/2022] Open
Abstract
Background Lophophora williamsii (commonly named peyote) is a small, spineless cactus with psychoactive alkaloids, particularly mescaline. Peyote utilizes crassulacean acid metabolism (CAM), an alternative form of photosynthesis that exists in succulents such as cacti and other desert plants. Therefore, its transcriptome can be considered an important resource for future research focused on understanding how these plants make more efficient use of water in marginal environments and also for research focused on better understanding of the overall mechanisms leading to production of plant natural products and secondary metabolites. Results In this study, two cDNA libraries were generated from L. williamsii. These libraries, representing buttons (tops of stems) and roots were sequenced using different sequencing platforms (GS-FLX, GS-Junior and PGM, respectively). A total of 5,541,550 raw reads were generated, which were assembled into 63,704 unigenes with an average length of 564.04 bp. A total of 25,149 unigenes (62.19 %) was annotated using public databases. 681 unigenes were found to be differentially expressed when comparing the two libraries, where 400 were preferentially expressed in buttons and 281 in roots. Some of the major alkaloids, including mescaline, were identified by GC-MS and relevant metabolic pathways were reconstructed using the Kyoto encyclopedia of genes and genomes database (KEGG). Subsequently, the expression patterns of preferentially expressed genes putatively involved in mescaline production were examined and validated by qRT-PCR. Conclusions High throughput transcriptome sequencing (RNA-seq) analysis allowed us to efficiently identify candidate genes involved in mescaline biosynthetic pathway in L. williamsii; these included tyrosine/DOPA decarboxylase, hydroxylases, and O-methyltransferases. This study sets the theoretical foundation for bioassay design directed at confirming the participation of these genes in mescaline production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1821-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Flor Zamudio-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Claudia Anahí Pérez-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México. .,Investigador Cátedra CONACyT, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, 14260, USA.
| | - Enrique Ramírez-Chávez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Jorge Molina-Torres
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Araceli Fernández-Cortes
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Carlos Calderón-Vázquez
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Instituto Politécnico Nacional, 81000, Guasave, Sinaloa, México.
| | | | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
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Tohge T, Obata T, Fernie AR. Biosynthesis of the essential respiratory cofactor ubiquinone from phenylalanine in plants. MOLECULAR PLANT 2014; 7:1403-1405. [PMID: 25013082 DOI: 10.1093/mp/ssu081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Toshihiro Obata
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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Block A, Widhalm JR, Fatihi A, Cahoon RE, Wamboldt Y, Elowsky C, Mackenzie SA, Cahoon EB, Chapple C, Dudareva N, Basset GJ. The Origin and Biosynthesis of the Benzenoid Moiety of Ubiquinone (Coenzyme Q) in Arabidopsis. THE PLANT CELL 2014; 26:1938-1948. [PMID: 24838974 PMCID: PMC4079360 DOI: 10.1105/tpc.114.125807] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/15/2014] [Accepted: 04/24/2014] [Indexed: 05/18/2023]
Abstract
It is not known how plants make the benzenoid ring of ubiquinone, a vital respiratory cofactor. Here, we demonstrate that Arabidopsis thaliana uses for that purpose two separate biosynthetic branches stemming from phenylalanine and tyrosine. Gene network modeling and characterization of T-DNA mutants indicated that acyl-activating enzyme encoded by At4g19010 contributes to the biosynthesis of ubiquinone specifically from phenylalanine. CoA ligase assays verified that At4g19010 prefers para-coumarate, ferulate, and caffeate as substrates. Feeding experiments demonstrated that the at4g19010 knockout cannot use para-coumarate for ubiquinone biosynthesis and that the supply of 4-hydroxybenzoate, the side-chain shortened version of para-coumarate, can bypass this blockage. Furthermore, a trans-cinnamate 4-hydroxylase mutant, which is impaired in the conversion of trans-cinnamate into para-coumarate, displayed similar defects in ubiquinone biosynthesis to that of the at4g19010 knockout. Green fluorescent protein fusion experiments demonstrated that At4g19010 occurs in peroxisomes, resulting in an elaborate biosynthetic architecture where phenylpropanoid intermediates have to be transported from the cytosol to peroxisomes and then to mitochondria where ubiquinone is assembled. Collectively, these results demonstrate that At4g19010 activates the propyl side chain of para-coumarate for its subsequent β-oxidative shortening. Evidence is shown that the peroxisomal ABCD transporter (PXA1) plays a critical role in this branch.
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Affiliation(s)
- Anna Block
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Joshua R Widhalm
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Abdelhak Fatihi
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Rebecca E Cahoon
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Yashitola Wamboldt
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Christian Elowsky
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Sally A Mackenzie
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Edgar B Cahoon
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Gilles J Basset
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
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Wang H, Chen H, Hao G, Yang B, Feng Y, Wang Y, Feng L, Zhao J, Song Y, Zhang H, Chen YQ, Wang L, Chen W. Role of the phenylalanine-hydroxylating system in aromatic substance degradation and lipid metabolism in the oleaginous fungus Mortierella alpina. Appl Environ Microbiol 2013; 79:3225-33. [PMID: 23503309 PMCID: PMC3685260 DOI: 10.1128/aem.00238-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/05/2013] [Indexed: 11/20/2022] Open
Abstract
Mortierella alpina is a filamentous fungus commonly found in soil that is able to produce lipids in the form of triacylglycerols that account for up to 50% of its dry weight. Analysis of the M. alpina genome suggests that there is a phenylalanine-hydroxylating system for the catabolism of phenylalanine, which has never been found in fungi before. We characterized the phenylalanine-hydroxylating system in M. alpina to explore its role in phenylalanine metabolism and its relationship to lipid biosynthesis. Significant changes were found in the profile of fatty acids in M. alpina grown on medium containing an inhibitor of the phenylalanine-hydroxylating system compared to M. alpina grown on medium without inhibitor. Genes encoding enzymes involved in the phenylalanine-hydroxylating system (phenylalanine hydroxylase [PAH], pterin-4α-carbinolamine dehydratase, and dihydropteridine reductase) were expressed heterologously in Escherichia coli, and the resulting proteins were purified to homogeneity. Their enzymatic activity was investigated by high-performance liquid chromatography (HPLC) or visible (Vis)-UV spectroscopy. Two functional PAH enzymes were observed, encoded by distinct gene copies. A novel role for tetrahydrobiopterin in fungi as a cofactor for PAH, which is similar to its function in higher life forms, is suggested. This study establishes a novel scheme for the fungal degradation of an aromatic substance (phenylalanine) and suggests that the phenylalanine-hydroxylating system is functionally significant in lipid metabolism.
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Affiliation(s)
- Hongchao Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Haiqin Chen
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Guangfei Hao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yun Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Yu Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Lu Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Jianxin Zhao
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yuanda Song
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Yong Q. Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin, People's Republic of China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
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20
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Flydal MI, Martinez A. Phenylalanine hydroxylase: function, structure, and regulation. IUBMB Life 2013; 65:341-9. [PMID: 23457044 DOI: 10.1002/iub.1150] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 01/09/2013] [Indexed: 11/08/2022]
Abstract
Mammalian phenylalanine hydroxylase (PAH) catalyzes the rate-limiting step in the phenylalanine catabolism, consuming about 75% of the phenylalanine input from the diet and protein catabolism under physiological conditions. In humans, mutations in the PAH gene lead to phenylketonuria (PKU), and most mutations are mainly associated with PAH misfolding and instability. The established treatment for PKU is a phenylalanine-restricted diet and, recently, supplementation with preparations of the natural tetrahydrobiopterin cofactor also shows effectiveness for some patients. Since 1997 there has been a significant increase in the understanding of the structure, catalytic mechanism, and regulation of PAH by its substrate and cofactor, in addition to improved correlations between genotype and phenotype in PKU. Importantly, there has also been an increased number of studies on the structure and function of PAH from bacteria and lower eukaryote organisms, revealing an additional anabolic role of the enzyme in the synthesis of melanin-like pigments. In this review, we discuss these recent studies, which contribute to define the evolutionary adaptation of the PAH structure and function leading to sophisticated regulation for effective catabolic processing of phenylalanine in mammalian organisms.
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Affiliation(s)
- Marte I Flydal
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Jonas Lies vei 91, 5009-Bergen, Norway
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Hasnain G, Frelin O, Roje S, Ellens KW, Ali K, Guan JC, Garrett TJ, de Crécy-Lagard V, Gregory JF, McCarty DR, Hanson AD. Identification and characterization of the missing pyrimidine reductase in the plant riboflavin biosynthesis pathway. PLANT PHYSIOLOGY 2013; 161:48-56. [PMID: 23150645 PMCID: PMC3532277 DOI: 10.1104/pp.112.208488] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/08/2012] [Indexed: 05/21/2023]
Abstract
Riboflavin (vitamin B₂) is the precursor of the flavin coenzymes flavin mononucleotide and flavin adenine dinucleotide. In Escherichia coli and other bacteria, sequential deamination and reduction steps in riboflavin biosynthesis are catalyzed by RibD, a bifunctional protein with distinct pyrimidine deaminase and reductase domains. Plants have two diverged RibD homologs, PyrD and PyrR; PyrR proteins have an extra carboxyl-terminal domain (COG3236) of unknown function. Arabidopsis (Arabidopsis thaliana) PyrD (encoded by At4g20960) is known to be a monofunctional pyrimidine deaminase, but no pyrimidine reductase has been identified. Bioinformatic analyses indicated that plant PyrR proteins have a catalytically competent reductase domain but lack essential zinc-binding residues in the deaminase domain, and that the Arabidopsis PyrR gene (At3g47390) is coexpressed with riboflavin synthesis genes. These observations imply that PyrR is a pyrimidine reductase without deaminase activity. Consistent with this inference, Arabidopsis or maize (Zea mays) PyrR (At3g47390 or GRMZM2G090068) restored riboflavin prototrophy to an E. coli ribD deletant strain when coexpressed with the corresponding PyrD protein (At4g20960 or GRMZM2G320099) but not when expressed alone; the COG3236 domain was unnecessary for complementing activity. Furthermore, recombinant maize PyrR mediated NAD(P)H-dependent pyrimidine reduction in vitro. Import assays with pea (Pisum sativum) chloroplasts showed that PyrR and PyrD are taken up and proteolytically processed. Ablation of the maize PyrR gene caused early seed lethality. These data argue that PyrR is the missing plant pyrimidine reductase, that it is plastid localized, and that it is essential. The role of the COG3236 domain remains mysterious; no evidence was obtained for the possibility that it catalyzes the dephosphorylation that follows pyrimidine reduction.
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Affiliation(s)
- Ghulam Hasnain
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Océane Frelin
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Sanja Roje
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Kenneth W. Ellens
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Kashif Ali
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Jiahn-Chou Guan
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Timothy J. Garrett
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Valérie de Crécy-Lagard
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Jesse F. Gregory
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Donald R. McCarty
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
| | - Andrew D. Hanson
- Department of Horticultural Sciences (G.H., O.F., K.W.E., J.-C.G., D.R.M., A.D.H.), Department of Food Science and Human Nutrition (K.A., J.F.G.), and Department of Microbiology and Cell Science (V.d.C.-L.), University of Florida, Gainesville, Florida 32611; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (S.R.); and Department of Pathology, University of Florida, Gainesville, Florida 32610 (T.J.G.)
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Dictyostelium
phenylalanine hydroxylase is activated by its substrate phenylalanine. FEBS Lett 2012; 586:3596-600. [DOI: 10.1016/j.febslet.2012.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 09/08/2012] [Accepted: 09/10/2012] [Indexed: 11/20/2022]
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Tzin V, Malitsky S, Zvi MMB, Bedair M, Sumner L, Aharoni A, Galili G. Expression of a bacterial feedback-insensitive 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase of the shikimate pathway in Arabidopsis elucidates potential metabolic bottlenecks between primary and secondary metabolism. THE NEW PHYTOLOGIST 2012; 194:430-439. [PMID: 22296303 DOI: 10.1111/j.1469-8137.2012.04052.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The shikimate pathway of plants mediates the conversion of primary carbon metabolites via chorismate into the three aromatic amino acids and to numerous secondary metabolites derived from them. However, the regulation of the shikimate pathway is still far from being understood. We hypothesized that 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAHPS) is a key enzyme regulating flux through the shikimate pathway. To test this hypothesis, we expressed a mutant bacterial AroG gene encoding a feedback-insensitive DAHPS in transgenic Arabidopsis plants. The plants were subjected to detailed analysis of primary metabolism, using GC-MS, as well as secondary metabolism, using LC-MS. Our results exposed a major effect of bacterial AroG expression on the levels of shikimate intermediate metabolites, phenylalanine, tryptophan and broad classes of secondary metabolite, such as phenylpropanoids, glucosinolates, auxin and other hormone conjugates. We propose that DAHPS is a key regulatory enzyme of the shikimate pathway. Moreover, our results shed light on additional potential metabolic bottlenecks bridging plant primary and secondary metabolism.
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Affiliation(s)
- Vered Tzin
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sergey Malitsky
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Moyal Ben Zvi
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel
| | - Mohamed Bedair
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Lloyd Sumner
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Asaph Aharoni
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gad Galili
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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Frelin O, Agrimi G, Laera VL, Castegna A, Richardson LGL, Mullen RT, Lerma-Ortiz C, Palmieri F, Hanson AD. Identification of mitochondrial thiamin diphosphate carriers from Arabidopsis and maize. Funct Integr Genomics 2012; 12:317-26. [DOI: 10.1007/s10142-012-0273-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/17/2012] [Accepted: 03/02/2012] [Indexed: 10/28/2022]
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Waller JC, Ellens KW, Alvarez S, Loizeau K, Ravanel S, Hanson AD. Mitochondrial and plastidial COG0354 proteins have folate-dependent functions in iron-sulphur cluster metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:403-11. [PMID: 21984653 PMCID: PMC3245475 DOI: 10.1093/jxb/err286] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/04/2011] [Accepted: 08/12/2011] [Indexed: 05/07/2023]
Abstract
COG0354 proteins have been implicated in synthesis or repair of iron/sulfur (Fe/S) clusters in all domains of life, and those of bacteria, animals, and protists have been shown to require a tetrahydrofolate to function. Two COG0354 proteins were identified in Arabidopsis and many other plants, one (At4g12130) related to those of α-proteobacteria and predicted to be mitochondrial, the other (At1g60990) related to those of cyanobacteria and predicted to be plastidial. Grasses and poplar appear to lack the latter. The predicted subcellular locations of the Arabidopsis proteins were validated by in vitro import assays with purified pea organelles and by targeting assays in Arabidopsis and tobacco protoplasts using green fluorescent protein fusions. The At4g12130 protein was shown to be expressed mainly in flowers, siliques, and seeds, whereas the At1g60990 protein was expressed mainly in young leaves. The folate dependence of both Arabidopsis proteins was established by functional complementation of an Escherichia coli COG0354 (ygfZ) deletant; both plant genes restored in vivo activity of the Fe/S enzyme MiaB but restoration was abrogated when folates were eliminated by deleting folP. Insertional inactivation of At4g12130 was embryo lethal; this phenotype was reversed by genetic complementation of the mutant. These data establish that COG0354 proteins have a folate-dependent function in mitochondria and plastids, and that the mitochondrial protein is essential. That plants retain mitochondrial and plastidial COG0354 proteins with distinct phylogenetic origins emphasizes how deeply the extant Fe/S cluster assembly machinery still reflects the ancient endosymbioses that gave rise to plants.
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Affiliation(s)
- Jeffrey C. Waller
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Kenneth W. Ellens
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Sophie Alvarez
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Karen Loizeau
- Laboratoire de Physiologie Cellulaire Végétale, CNRS/CEA/INRA/Université Joseph Fourier, CEA-Grenoble, F-38054 Grenoble cedex 9, France
| | - Stéphane Ravanel
- Laboratoire de Physiologie Cellulaire Végétale, CNRS/CEA/INRA/Université Joseph Fourier, CEA-Grenoble, F-38054 Grenoble cedex 9, France
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
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Maeda H, Dudareva N. The shikimate pathway and aromatic amino Acid biosynthesis in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:73-105. [PMID: 22554242 DOI: 10.1146/annurev-arplant-042811-105439] [Citation(s) in RCA: 722] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
L-tryptophan, L-phenylalanine, and L-tyrosine are aromatic amino acids (AAAs) that are used for the synthesis of proteins and that in plants also serve as precursors of numerous natural products, such as pigments, alkaloids, hormones, and cell wall components. All three AAAs are derived from the shikimate pathway, to which ≥30% of photosynthetically fixed carbon is directed in vascular plants. Because their biosynthetic pathways have been lost in animal lineages, the AAAs are essential components of the diets of humans, and the enzymes required for their synthesis have been targeted for the development of herbicides. This review highlights recent molecular identification of enzymes of the pathway and summarizes the pathway organization and the transcriptional/posttranscriptional regulation of the AAA biosynthetic network. It also identifies the current limited knowledge of the subcellular compartmentalization and the metabolite transport involved in the plant AAA pathways and discusses metabolic engineering efforts aimed at improving production of the AAA-derived plant natural products.
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Affiliation(s)
- Hiroshi Maeda
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907-2010, USA.
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Fouquet R, Martin F, Fajardo DS, Gault CM, Gómez E, Tseung CW, Policht T, Hueros G, Settles AM. Maize rough endosperm3 encodes an RNA splicing factor required for endosperm cell differentiation and has a nonautonomous effect on embryo development. THE PLANT CELL 2011; 23:4280-97. [PMID: 22138152 PMCID: PMC3269866 DOI: 10.1105/tpc.111.092163] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 09/30/2011] [Accepted: 11/18/2011] [Indexed: 05/18/2023]
Abstract
Endosperm and embryo development are coordinated via epigenetic regulation and signaling between these tissues. In maize (Zea mays), the endosperm-embryo signals are not known, but endosperm cellularization is a key event for embryos to form shoots and roots. We screened seed mutants for nonautonomous functions in endosperm and embryo development with genetically nonconcordant seeds and identified the recessive mutant rough endosperm3 (rgh3). The wild-type Rgh3 allele is required in the endosperm for embryos to develop and has an autonomous role in embryo and seedling development. Endosperm cell differentiation is defective in rgh3. Results from endosperm cell culture indicate that rgh3 mutants remain in a proliferative state through mid-seed development. Rgh3 encodes the maize U2AF(35) Related Protein (URP), an RNA splicing factor involved in both U2 and U12 splicing. The Rgh3 allele produces at least 19 alternative splice variants with only one isoform encoding a full-length ortholog to URP. The full-length RGH3α isoform localizes to the nucleolus and displays a speckled pattern within the nucleoplasm, and RGH3α colocalizes with U2AF(65). A survey of alternatively spliced transcripts found that, in the rgh3 mutant, a fraction of noncanonical splicing events are altered. Our findings suggest that differentiation of maize endosperm cell types is necessary for embryos to develop. The molecular cloning of Rgh3 suggests that alternative RNA splicing is needed for cell differentiation, development, and plant viability.
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Affiliation(s)
- Romain Fouquet
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Federico Martin
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Diego S. Fajardo
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Christine M. Gault
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Elisa Gómez
- Departamento de Biología Celular y Genética, Universidad de Alcalá, 28871 Alcalá de Henares (Madrid), Spain
| | - Chi-Wah Tseung
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Tyler Policht
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Gregorio Hueros
- Departamento de Biología Celular y Genética, Universidad de Alcalá, 28871 Alcalá de Henares (Madrid), Spain
| | - A. Mark Settles
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
- Address correspondence to
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Pribat A, Blaby IK, Lara-Núñez A, Jeanguenin L, Fouquet R, Frelin O, Gregory JF, Philmus B, Begley TP, de Crécy-Lagard V, Hanson AD. A 5-formyltetrahydrofolate cycloligase paralog from all domains of life: comparative genomic and experimental evidence for a cryptic role in thiamin metabolism. Funct Integr Genomics 2011; 11:467-78. [PMID: 21538139 PMCID: PMC6078417 DOI: 10.1007/s10142-011-0224-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/19/2011] [Accepted: 04/03/2011] [Indexed: 12/18/2022]
Abstract
A paralog (here termed COG0212) of the ATP-dependent folate salvage enzyme 5-formyltetrahydrofolate cycloligase (5-FCL) occurs in all domains of life and, although typically annotated as 5-FCL in pro- and eukaryotic genomes, is of unknown function. COG0212 is similar in overall structure to 5-FCL, particularly in the substrate binding region, and has distant similarity to other kinases. The Arabidopsis thaliana COG0212 protein was shown to be targeted to chloroplasts and to be required for embryo viability. Comparative genomic analysis revealed that a high proportion (19%) of archaeal and bacterial COG0212 genes are clustered on the chromosome with various genes implicated in thiamin metabolism or transport but showed no such association between COG0212 and folate metabolism. Consistent with the bioinformatic evidence for a role in thiamin metabolism, ablating COG0212 in the archaeon Haloferax volcanii caused accumulation of thiamin monophosphate. Biochemical and functional complementation tests of several known and hypothetical thiamin-related activities (involving thiamin, its breakdown products, and their phosphates) were, however, negative. Also consistent with the bioinformatic evidence, the COG0212 proteins from A. thaliana and prokaryote sources lacked 5-FCL activity in vitro and did not complement the growth defect or the characteristic 5-formyltetrahydrofolate accumulation of a 5-FCL-deficient (ΔygfA) Escherichia coli strain. We therefore propose (a) that COG0212 has an unrecognized yet sometimes crucial role in thiamin metabolism, most probably in salvage or detoxification, and (b) that is not a 5-FCL and should no longer be so annotated.
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Affiliation(s)
- Anne Pribat
- Horticultural Sciences Department, University of Florida, Gainesville, 32611, USA
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