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Huang F, He Y. Epigenetic control of gene expression by cellular metabolisms in plants. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102572. [PMID: 38875845 DOI: 10.1016/j.pbi.2024.102572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/09/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
Covalent modifications on DNA and histones can regulate eukaryotic gene expression and are often referred to as epigenetic modifications. These chemical reactions require various metabolites as donors or co-substrates, such as acetyl coenzyme A, S-adenosyl-l-methionine, and α-ketoglutarate. Metabolic processes that take place in the cytoplasm, nucleus, or other cellular compartments may impact epigenetic modifications in the nucleus. Here, we review recent advances on metabolic control of chromatin modifications and thus gene expression in plants, with a focus on the functions of nuclear compartmentalization of metabolic processes and enzymes in DNA and histone modifications. Furthermore, we discuss the functions of cellular metabolisms in fine-tuning gene expression to facilitate the responses or adaptation to environmental changes in plants.
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Affiliation(s)
- Fei Huang
- Peking-Tsinghua Center for Life Sciences & National Key Laboratory of Wheat Improvement, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yuehui He
- Peking-Tsinghua Center for Life Sciences & National Key Laboratory of Wheat Improvement, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China.
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2
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Li H, Chen Y, Ding M, Liu J, Sun H, Fang H, Brady SW, Xu Y, Glaser F, Ma X, Tang Y, Du L, Wu X, Wang S, Zhu L, Li B, Shen S, Zhang J, Zheng L, Yu J, Assaraf YG, Zhou BBS. Folylpolyglutamate synthetase inactivation in relapsed ALL induces a druggable folate metabolic vulnerability. Drug Resist Updat 2024; 77:101141. [PMID: 39181011 DOI: 10.1016/j.drup.2024.101141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/22/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024]
Abstract
AIMS The antifolate methotrexate (MTX) is an anchor drug used in acute lymphoblastic leukemia (ALL) with poorly understood chemoresistance mechanisms in relapse. Herein we find decreased folate polyglutamylation network activities and inactivating FPGS mutations, both of which could induce MTX resistance and folate metabolic vulnerability in relapsed ALL. METHODS We utilized integrated systems biology analysis of transcriptomic and genomic data from relapse ALL cohorts to infer hidden ALL relapse drivers and related genetic alternations during clonal evolution. The drug sensitivity assay was used to determine the impact of relapse-specific FPGS mutations on sensitivity to different antifolates and chemotherapeutics in ALL cells. We used liquid chromatography-mass spectrometry (LC-MS) to quantify MTX and folate polyglutamate levels in folylpoly-γ-glutamate synthetase (FPGS) mutant ALL cells. Enzymatic activity and protein degradation assays were also conducted to characterize the catalytic properties and protein stabilities of FPGS mutants. An ALL cell line-derived mouse leukemia xenograft model was used to evaluate the in vivo impact of FPGS inactivation on leukemogenesis and sensitivity to the polyglutamatable antifolate MTX as well as non-polyglutamatble lipophilic antifolate trimetrexate (TMQ). RESULTS We found a significant decrease in folate polyglutamylation network activities during ALL relapse using RNA-seq data. Supported by functional evidence, we identified multifactorial mechanisms of FPGS inactivation in relapsed ALL, including its decreased network activity and gene expression, focal gene deletion, impaired catalytic activity, and increased protein degradation. These deleterious FPGS alterations induce MTX resistance and inevitably cause marked intracellular folate shrinkage, which could be efficiently targeted by a polyglutamylation-independent lipophilic antifolate TMQ in vitro and in vivo. CONCLUSIONS MTX resistance in relapsed ALL relies on FPGS inactivation, which inevitably induces a folate metabolic vulnerability, allowing for an efficacious antifolate ALL treatment strategy that is based upon TMQ, thereby surmounting chemoresistance in relapsed ALL.
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Affiliation(s)
- Hui Li
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China
| | - Yao Chen
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Ding
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingjing Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Huiying Sun
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Houshun Fang
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yan Xu
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fabian Glaser
- Structural and Computational Biology Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yabin Tang
- Department of Pharmacology and Chemical Biology, School of Basic Medicine and Shanghai Collaborative Innovation Center for Translational Medicine Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Xiaoyu Wu
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuxuan Wang
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Zhu
- Department of Pharmacology and Chemical Biology, School of Basic Medicine and Shanghai Collaborative Innovation Center for Translational Medicine Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Benshang Li
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuhong Shen
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Liang Zheng
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Bin-Bing S Zhou
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China; Department of Pharmacology and Chemical Biology, School of Basic Medicine and Shanghai Collaborative Innovation Center for Translational Medicine Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Hou X, Lu Z, Yu T, Zhang Y, Yao Q, Zhang C, Niu Y, Liang Q. Two maize homologs of mammalian proton-coupled folate transporter, ZmMFS_1-62 and ZmMFS_1-73, are essential to salt and drought tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108623. [PMID: 38626656 DOI: 10.1016/j.plaphy.2024.108623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 04/18/2024]
Abstract
Folates are essential to the maintenance of normal life activities in almost all organisms. Proton-coupled folate transporter (PCFT), belonging to the major facilitator superfamily, is one of the three major folate transporter types widely studied in mammals. However, information about plant PCFTs is limited. Here, a genome-wide identification of maize PCFTs was performed, and two PCFTs, ZmMFS_1-62 and ZmMFS_1-73, were functionally investigated. Both proteins contained the typical 12 transmembrane helixes with N- and C-termini located in the cytoplasm, and were localized in the plasma membrane. Molecular docking analysis indicated their binding activity with folates via hydrogen bonding. Interference with ZmMFS_1-62 and ZmMFS_1-73 in maize seedlings through virus-induced gene silencing disrupted folate homeostasis, mainly in the roots, and reduced tolerance to drought and salt stresses. Moreover, a molecular chaperone protein, ZmHSP20, was found to interact with ZmMFS_1-62 and ZmMFS_1-73, and interference with ZmHSP20 in maize seedlings also led to folate disruption and increased sensitivity to drought and salt stresses. Overall, this is the first report of functional identification of maize PCFTs, which play essential roles in salt and drought stress tolerance, thereby linking folate metabolism with abiotic stress responses in maize.
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Affiliation(s)
- Xiaowan Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China; Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Zhiwei Lu
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
| | - Taifei Yu
- Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, the "Double-First Class" Application Characteristic Discipline of Hunan Province (Pharmaceutical Science), Changsha Medical University, Changsha 410219, China.
| | - Yuanyuan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
| | - Quansheng Yao
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China; National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572000, China.
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China; National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572000, China.
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Zhao Y, Shi J, Feng B, Yuan S, Yue X, Shi W, Yan Z, Xu D, Zuo J, Wang Q. Multi-omic analysis of the extension of broccoli quality during storage by folic acid. J Adv Res 2024; 59:65-78. [PMID: 37406731 PMCID: PMC11081962 DOI: 10.1016/j.jare.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023] Open
Abstract
INTRODUCTION Folic acid (FA) is a critical metabolite in all living organisms and an important nutritional component of broccoli. Few studies have been conducted on the impact of an exogenous application of FA on the postharvest physiology of fruits and vegetables during storage. In this regard, the mechanism by which an exogenous application of FA extends the postharvest quality of broccoli is unclear. OBJECTIVE This study utilized a multicomponent analysis to investigate how an exogenous application of FA effects the postharvest quality of broccoli. METHODS Broccoli was soaked in 5 mg/L FA for 10 min and the effect of the treatment on the appearance and nutritional quality of broccoli was evaluated. These data were combined with transcriptomic, metabolomic, and DNA methylation data to provide insight into the potential mechanism by which FA delays senescence. RESULTS The FA treatment inhibited the yellowing of broccoli during storage. CHH methylation was identified as the main type of methylation that occurs in broccoli and the FA treatment was found to inhibit DNA methylation, promote the accumulation of endogenous FA and chlorophyl, and inhibit ethylene biosynthesis in stored broccoli. The FA treatment also prevented the formation of off-odors by inhibiting the degradation of glucosinolate. CONCLUSIONS FA treatment inhibited the loss of nutrients during the storage of broccoli, delayed its yellowing, and inhibited the generation of off-odors. Our study provides deeper insight into the mechanism by which the postharvest application of FA delays postharvest senescence in broccoli and provides the foundation for further studies of postharvest metabolism in broccoli.
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Affiliation(s)
- Yaqi Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China; State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agriculture, Guangxi University, Nanning 530004, China
| | - Junyan Shi
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bihong Feng
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Shuzhi Yuan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaozhen Yue
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wenlin Shi
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China; College of Agriculture, Guangxi University, Nanning 530004, China
| | - Zhicheng Yan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Dongying Xu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Kawada Y, Hayashi E, Katsuragi Y, Imamura-Jinda A, Hirokawa T, Mizukami T, Hayashi M. Identification of Chemicals That Abrogate Folate-Dependent Inhibition of Starch Accumulation in Non-Photosynthetic Plastids of Arabidopsis. PLANT & CELL PHYSIOLOGY 2023; 64:1551-1562. [PMID: 37801291 DOI: 10.1093/pcp/pcad116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/26/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
Folate, also known as vitamin B9, is an essential cofactor for a variety of enzymes and plays a crucial role in many biological processes. We previously reported that plastidial folate prevents starch biosynthesis triggered by the influx of sugar into non-starch-accumulating plastids, such as etioplasts, and chloroplasts under darkness; hence the loss of plastidial folate induces the accumulation of starch in plastids. To understand the molecular mechanism underlying this phenomenon, we screened our in-house chemical library and searched their derivatives to identify chemicals capable of inducing starch accumulation in etioplasts. The results revealed four chemicals, compounds #120 and #375 and their derivatives, compounds #120d and #375d, respectively. The derivative compounds induced starch accumulation in etioplasts and suppressed hypocotyl elongation in dark-grown Arabidopsis seedlings. They also inhibited the post-germinative growth of seedlings under illumination. All four chemicals contained the sulfonamide group as a consensus structure. The sulfonamide group is also found in sulfa drugs, which exhibit antifolate activity, and in sulfonylurea herbicides. Further analyses revealed that compound #375d induces starch accumulation by inhibiting folate biosynthesis. By contrast, compound #120d neither inhibited folate biosynthesis nor exhibited the herbicide activity. Protein and metabolite analyses suggest that compound #120d abrogates folate-dependent inhibition of starch accumulation in etioplasts by enhancing starch biosynthesis.
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Affiliation(s)
- Yoshihiro Kawada
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Eriko Hayashi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Yuya Katsuragi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Aya Imamura-Jinda
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, Tsukuba University, 1-1-1 Tenmondai, Tsukuba, Ibaragi, 305-8577 Japan
| | - Tamio Mizukami
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
- Frontier Pharma, 1281-8 Tamura, Nagahama, Shiga, 526-0829 Japan
| | - Makoto Hayashi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829 Japan
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Jung H, Lee D, Lee S, Kong HJ, Park J, Seo YS. Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities. Microb Genom 2023; 9:001108. [PMID: 37796250 PMCID: PMC10634447 DOI: 10.1099/mgen.0.001108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/17/2023] [Indexed: 10/06/2023] Open
Abstract
Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein-protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR-Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.
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Affiliation(s)
- Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, South Korea
| | - Duyoung Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
| | - Seungchul Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, South Korea
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, South Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, South Korea
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Tyagi K, Sunkum A, Gupta P, Kilambi HV, Sreelakshmi Y, Sharma R. Reduced γ-glutamyl hydrolase activity likely contributes to high folate levels in Periyakulam-1 tomato. HORTICULTURE RESEARCH 2022; 10:uhac235. [PMID: 36643736 PMCID: PMC9832877 DOI: 10.1093/hr/uhac235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Tomato cultivars show wide variation in nutraceutical folate in ripe fruits, yet the loci regulating folate levels in fruits remain unexplored. To decipher regulatory points, we compared two contrasting tomato cultivars: Periyakulam-1 (PKM-1) with high folate and Arka Vikas (AV) with low folate. The progression of ripening in PKM-1 was nearly similar to AV but had substantially lower ethylene emission. In parallel, the levels of phytohormones salicylic acid, ABA, and jasmonic acid were substantially lower than AV. The fruits of PKM-1 were metabolically distinct from AV, with upregulation of several amino acids. Consistent with higher °Brix, the red ripe fruits also showed upregulation of sugars and sugar-derived metabolites. In parallel with higher folate, PKM-1 fruits also had higher carotenoid levels, especially lycopene and β-carotene. The proteome analysis showed upregulation of carotenoid sequestration and folate metabolism-related proteins in PKM-1. The deglutamylation pathway mediated by γ-glutamyl hydrolase (GGH) was substantially reduced in PKM-1 at the red-ripe stage. The red-ripe fruits had reduced transcript levels of GGHs and lower GGH activity than AV. Conversely, the percent polyglutamylation of folate was much higher in PKM-1. Our analysis indicates the regulation of GGH activity as a potential target to elevate folate levels in tomato fruits.
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Affiliation(s)
| | - Anusha Sunkum
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
| | - Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
| | - Himabindu Vasuki Kilambi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad-500046, India
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He Y, Song S, Li C, Zhang X, Liu H. Effect of germination on the main chemical compounds and 5-methyltetrahydrofolate metabolism of different quinoa varieties. Food Res Int 2022; 159:111601. [DOI: 10.1016/j.foodres.2022.111601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
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Lian T, Wang X, Li S, Jiang H, Zhang C, Wang H, Jiang L. Comparative Transcriptome Analysis Reveals Mechanisms of Folate Accumulation in Maize Grains. Int J Mol Sci 2022; 23:ijms23031708. [PMID: 35163628 PMCID: PMC8836222 DOI: 10.3390/ijms23031708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
Previously, the complexity of folate accumulation in the early stages of maize kernel development has been reported, but the mechanisms of folate accumulation are unclear. Two maize inbred lines, DAN3130 and JI63, with different patterns of folate accumulation and different total folate contents in mature kernels were used to investigate the transcriptional regulation of folate metabolism during late stages of kernel formation by comparative transcriptome analysis. The folate accumulation during DAP 24 to mature kernels could be controlled by circumjacent pathways of folate biosynthesis, such as pyruvate metabolism, glutamate metabolism, and serine/glycine metabolism. In addition, the folate variation between these two inbred lines was related to those genes among folate metabolism, such as genes in the pteridine branch, para-aminobenzoate branch, serine/tetrahydrofolate (THF)/5-methyltetrahydrofolate cycle, and the conversion of THF monoglutamate to THF polyglutamate. The findings provided insight into folate accumulation mechanisms during maize kernel formation to promote folate biofortification.
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Affiliation(s)
- Tong Lian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Plant Genetics, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Xuxia Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
| | - Sha Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
| | - Haiyang Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
- National Agricultural Science and Technology Center, Chengdu 610213, China
- Correspondence: (H.W.); (L.J.)
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Correspondence: (H.W.); (L.J.)
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10
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Li W, Liang Q, Mishra RC, Sanchez-Mu�oz R, Wang H, Chen X, Van Der Straeten D, Zhang C, Xiao Y. The 5-formyl-tetrahydrofolate proteome links folates with C/N metabolism and reveals feedback regulation of folate biosynthesis. THE PLANT CELL 2021; 33:3367-3385. [PMID: 34352110 PMCID: PMC8505879 DOI: 10.1093/plcell/koab198] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/23/2021] [Indexed: 05/31/2023]
Abstract
Folates are indispensable for plant development, but their molecular mode of action remains elusive. We synthesized a probe, "5-F-THF-Dayne," comprising 5-formyl-tetrahydrofolate (THF) coupled to a photoaffinity tag. Exploiting this probe in an affinity proteomics study in Arabidopsis thaliana, we retrieved 51 hits. Thirty interactions were independently validated with in vitro expressed proteins to bind 5-F-THF with high or low affinity. Interestingly, the interactors reveal associations beyond one-carbon metabolism, covering also connections to nitrogen (N) metabolism, carbohydrate metabolism/photosynthesis, and proteostasis. Two of the interactions, one with the folate biosynthetic enzyme DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE 1 (AtDHFR-TS1) and another with N metabolism-associated glutamine synthetase 1;4 (AtGLN1;4), were further characterized. In silico and experimental analyses revealed G35/K36 and E330 as key residues for the binding of 5-F-THF in AtDHFR-TS1 and AtGLN1;4, respectively. Site-directed mutagenesis of AtGLN1;4 E330, which co-localizes with the ATP-binding pocket, abolished 5-F-THF binding as well as AtGLN1;4 activity. Furthermore, 5-F-THF was noted to competitively inhibit the activities of AtDHFR-TS1 and AtGLN1;4. In summary, we demonstrated a regulatory role for 5-F-THF in N metabolism, revealed 5-F-THF-mediated feedback regulation of folate biosynthesis, and identified a total of 14 previously unknown high-affinity binding cellular targets of 5-F-THF. Together, this sets a landmark toward understanding the role of folates in plant development.
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Affiliation(s)
- Weichao Li
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ratnesh Chandra Mishra
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, Gent B-9000, Belgium
| | - Raul Sanchez-Mu�oz
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, Gent B-9000, Belgium
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Chen
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, Gent B-9000, Belgium
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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11
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Sahoo DP, Van Winkle LJ, Díaz de la Garza RI, Dubrovsky JG. Interkingdom Comparison of Threonine Metabolism for Stem Cell Maintenance in Plants and Animals. Front Cell Dev Biol 2021; 9:672545. [PMID: 34557481 PMCID: PMC8454773 DOI: 10.3389/fcell.2021.672545] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/11/2021] [Indexed: 01/12/2023] Open
Abstract
In multicellular organisms, tissue generation, maintenance, and homeostasis depend on stem cells. Cellular metabolic status is an essential component of different differentiated states, from stem to fully differentiated cells. Threonine (Thr) metabolism has emerged as a critical factor required to maintain pluripotent/multipotent stem cells in both plants and animals. Thus, both kingdoms conserved or converged upon this fundamental feature of stem cell function. Here, we examine similarities and differences in Thr metabolism-dependent mechanisms supporting stem cell maintenance in these two kingdoms. We then consider common features of Thr metabolism in stem cell maintenance and predict and speculate that some knowledge about Thr metabolism and its role in stem cell function in one kingdom may apply to the other. Finally, we outline future research directions to explore these hypotheses.
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Affiliation(s)
- Debee Prasad Sahoo
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lon J. Van Winkle
- Department of Biochemistry, Midwestern University, Downers Grove, IL, United States
- Department of Medical Humanities, Rocky Vista University, Parker, CO, United States
| | | | - Joseph G. Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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12
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Sorghum Brown Midrib19 ( Bmr19) Gene Links Lignin Biosynthesis to Folate Metabolism. Genes (Basel) 2021; 12:genes12050660. [PMID: 33924915 PMCID: PMC8146451 DOI: 10.3390/genes12050660] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/02/2022] Open
Abstract
Genetic analysis of brown midrib sorghum (Sorghum bicolor) mutant lines assembled in our program has previously shown that the mutations fall into four allelic groups, bmr2, bmr6, bmr12 or bmr19. Causal genes for allelic groups bmr2, bmr6 and bmr12, have since been identified. In this report, we provide evidence for the nature of the bmr19 mutation. This was accomplished by introgressing each of the four bmr alleles into nine different genetic backgrounds. Polymorphisms from four resequenced bulks of sorghum introgression lines containing either mutation, relative to those of a resequenced bulk of the nine normal midrib recurrent parent lines, were used to locate their respective causal mutations. The analysis confirmed the previously reported causal mutations for bmr2 and bmr6 but failed in the case of bmr12-bulk due to a mixture of mutant alleles at the locus among members of that mutant bulk. In the bmr19-bulk, a common G → A mutation was found among all members in Sobic.001G535500. This gene encodes a putative folylpolyglutamate synthase with high homology to maize Bm4. The brown midrib phenotype co-segregated with this point mutation in two separate F2 populations. Furthermore, an additional variant allele at this locus obtained from a TILLING population also showed a brown midrib phenotype, confirming this locus as Bmr19.
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13
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Li Y, Yang C, Ahmad H, Maher M, Fang C, Luo J. Benefiting others and self: Production of vitamins in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:210-227. [PMID: 33289302 DOI: 10.1111/jipb.13047] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Vitamins maintain growth and development in humans, animals, and plants. Because plants serve as essential producers of vitamins, increasing the vitamin contents in plants has become a goal of crop breeding worldwide. Here, we begin with a summary of the functions of vitamins. We then review the achievements to date in elucidating the molecular mechanisms underlying how vitamins are synthesized, transported, and regulated in plants. We also stress the exploration of variation in vitamins by the use of forward genetic approaches, such as quantitative trait locus mapping and genome-wide association studies. Overall, we conclude that exploring the diversity of vitamins could provide new insights into plant metabolism and crop breeding.
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Affiliation(s)
- Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hasan Ahmad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Mohamed Maher
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuanying Fang
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, 570228, China
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14
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Shohag MJI, Wei Y, Zhang J, Feng Y, Rychlik M, He Z, Yang X. Genetic and physiological regulation of folate in pak choi (Brassica rapa subsp. Chinensis) germplasm. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4914-4929. [PMID: 32639001 PMCID: PMC7410185 DOI: 10.1093/jxb/eraa218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/07/2020] [Indexed: 05/21/2023]
Abstract
Folates are one of the essential micronutrients for all living organisms. Due to inadequate dietary intake, folate deficiency remains prevalent in humans. Genetically diverse germplasms can potentially be used as parents in breeding programs and also for understanding the folate regulatory network. Therefore, we investigated the natural genetic diversity of folates and their physiological regulation in pak choi (Brassica rapa subsp. Chinensis) germplasm. The total folate concentration ranged from 52.7 μg 100 gFW-1 to 166.9 μg 100 gFW-1, with 3.2-fold variation. The main folate vitamer was represented by 5-CH3-H4folate, with 4.5-fold variation. The activities of GTP cyclohydrolase I and aminodeoxy chorismate synthase, the first step of folate synthesis, were high in high folate accessions and low in low folate accessions. Analysis of the transcription levels of 11 genes associated with folate metabolism demonstrated that the difference in folate concentrations may be primarily controlled at the post-transcriptional level. A general correlation between total folate and their precursors was observed. Folate diversity and chlorophyll content were tightly regulated through the methyl cycle. The diverse genetic variation in pak choi germplasm indicated the great genetic potential to integrate breeding programs for folate biofortification and unravel the physiological basis of folate homeostasis in planta.
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Affiliation(s)
- M J I Shohag
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- Department of Agriculture, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
- Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, USA
| | - Yanyan Wei
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- Cultivation Base of Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Jie Zhang
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- International Research Center for Environmental Membrane Biology, Department of Horticulture, Foshan University, Guangdong, China
| | - Ying Feng
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
| | - Michael Rychlik
- Chair of Analytical Food Chemistry, Technische Universitat Munchen, Lise-Meitner-Str. 34, Freising, Germany
| | - Zhenli He
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, USA
| | - Xiaoe Yang
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, USA
- Correspondence:
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15
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Yan Z, Shen Z, Gao ZF, Chao Q, Qian CR, Zheng H, Wang BC. A comprehensive analysis of the lysine acetylome reveals diverse functions of acetylated proteins during de-etiolation in Zea mays. JOURNAL OF PLANT PHYSIOLOGY 2020; 248:153158. [PMID: 32240968 DOI: 10.1016/j.jplph.2020.153158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/02/2020] [Accepted: 02/02/2020] [Indexed: 06/11/2023]
Abstract
Lysine acetylation is one of the most important post-translational modifications and is involved in multiple cellular processes in plants. There is evidence that acetylation may play an important role in light-induced de-etiolation, a key developmental switch from skotomorphogenesis to photomorphogenesis. During this transition, establishment of photosynthesis is of great significance. However, studies on acetylome dynamics during de-etiolation are limited. Here, we performed the first global lysine acetylome analysis for Zea mays seedlings undergoing de-etiolation, using nano liquid chromatography coupled to tandem mass spectrometry, and identified 814 lysine-acetylated sites on 462 proteins. Bioinformatics analysis of this acetylome showed that most of the lysine-acetylated proteins are predicted to be located in the cytoplasm, nucleus, chloroplast, and mitochondria. In addition, we detected ten lysine acetylation motifs and found that the accumulation of 482 lysine-acetylated peptides corresponding to 289 proteins changed significantly during de-etiolation. These proteins include transcription factors, histones, and proteins involved in chlorophyll synthesis, photosynthesis light reaction, carbon assimilation, glycolysis, the TCA cycle, amino acid metabolism, lipid metabolism, and nucleotide metabolism. Our study provides an in-depth dataset that extends our knowledge of in vivo acetylome dynamics during de-etiolation in monocots. This dataset promotes our understanding of the functional consequences of lysine acetylation in diverse cellular metabolic regulatory processes, and will be a useful toolkit for further investigations of the lysine acetylome and de-etiolation in plants.
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Affiliation(s)
- Zhen Yan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhuo Shen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China.
| | - Zhi-Fang Gao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100039, China.
| | - Chun-Rong Qian
- Institute of Crop Cultivation and Farming, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Biological Mass Spectrometry Facility, Rutgers University, Piscataway, New Jersey 08855, USA.
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100039, China.
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16
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Meinke DW. Genome-wide identification of EMBRYO-DEFECTIVE (EMB) genes required for growth and development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:306-325. [PMID: 31334862 DOI: 10.1111/nph.16071] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/10/2019] [Indexed: 05/20/2023]
Abstract
With the emergence of high-throughput methods in plant biology, the importance of long-term projects characterized by incremental advances involving multiple laboratories can sometimes be overlooked. Here, I highlight my 40-year effort to isolate and characterize the most common class of mutants encountered in Arabidopsis (Arabidopsis thaliana): those defective in embryo development. I present an updated dataset of 510 EMBRYO-DEFECTIVE (EMB) genes identified throughout the Arabidopsis community; include important details on 2200 emb mutants and 241 pigment-defective embryo (pde) mutants analyzed in my laboratory; provide curated datasets with key features and publication links for each EMB gene identified; revisit past estimates of 500-1000 total EMB genes in Arabidopsis; document 83 double mutant combinations reported to disrupt embryo development; emphasize the importance of following established nomenclature guidelines and acknowledging allele history in research publications; and consider how best to extend community-based curation and screening efforts to approach saturation for this diverse class of mutants in the future. Continued advances in identifying EMB genes and characterizing their loss-of-function mutant alleles are needed to understand genotype-to-phenotype relationships in Arabidopsis on a broad scale, and to document the contributions of large numbers of essential genes to plant growth and development.
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Affiliation(s)
- David W Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
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17
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Korasick DA, Kandoth PK, Tanner JJ, Mitchum MG, Beamer LJ. Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode. J Biol Chem 2020; 295:3708-3718. [PMID: 32014996 PMCID: PMC7076220 DOI: 10.1074/jbc.ra119.012256] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Management of the agricultural pathogen soybean cyst nematode (SCN) relies on the use of SCN-resistant soybean cultivars, a strategy that has been failing in recent years. An underutilized source of resistance in the soybean genotype Peking is linked to two polymorphisms in serine hydroxy-methyltransferase 8 (SHMT8). SHMT is a pyridoxal 5'-phosphate-dependent enzyme that converts l-serine and (6S)-tetrahydrofolate to glycine and 5,10-methylenetetrahydrofolate. Here, we determined five crystal structures of the 1884-residue SHMT8 tetramers from the SCN-susceptible cultivar (cv.) Essex and the SCN-resistant cv. Forrest (whose resistance is derived from the SHMT8 polymorphisms in Peking); the crystal structures were determined in complex with various ligands at 1.4-2.35 Å resolutions. We find that the two Forrest-specific polymorphic substitutions (P130R and N358Y) impact the mobility of a loop near the entrance of the (6S)-tetrahydrofolate-binding site. Ligand-binding and kinetic studies indicate severely reduced affinity for folate and dramatically impaired enzyme activity in Forrest SHMT8. These findings imply widespread effects on folate metabolism in soybean cv. Forrest that have implications for combating the widespread increase in virulent SCN.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Pramod K Kandoth
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211; Department of Chemistry, University of Missouri, Columbia, Missouri 65211
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Lesa J Beamer
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211; Department of Chemistry, University of Missouri, Columbia, Missouri 65211.
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18
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Expression Levels of the γ-Glutamyl Hydrolase I Gene Predict Vitamin B9 Content in Potato Tubers. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9110734] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biofortification of folates in staple crops is an important strategy to help eradicate human folate deficiencies. Folate biofortification using genetic engineering has shown great success in rice grain, tomato fruit, lettuce, and potato tuber. However, consumers’ skepticism, juridical hurdles, and lack of economic model have prevented the widespread adoption of nutritionally-enhanced genetically-engineered (GE) food crops. Meanwhile, little effort has been made to biofortify food crops with folate by breeding. Previously we reported >10-fold variation in folate content in potato genotypes. To facilitate breeding for enhanced folate content, we attempted to identify genes that control folate content in potato tuber. For this, we analyzed the expression of folate biosynthesis and salvage genes in low- and high-folate potato genotypes. First, RNA-Seq analysis showed that, amongst all folate biosynthesis and salvage genes analyzed, only one gene, which encodes γ-glutamyl hydrolase 1 (GGH1), was consistently expressed at higher levels in high- compared to low-folate segregants of a Solanum boliviense Dunal accession. Second, quantitative PCR showed that GGH1 transcript levels were higher in high- compared to low-folate segregants for seven out of eight pairs of folate segregants analyzed. These results suggest that GGH1 gene expression is an indicator of folate content in potato tubers.
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19
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Eisenhut M, Roell MS, Weber APM. Mechanistic understanding of photorespiration paves the way to a new green revolution. THE NEW PHYTOLOGIST 2019; 223:1762-1769. [PMID: 31032928 DOI: 10.1111/nph.15872] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/11/2019] [Indexed: 05/25/2023]
Abstract
Photorespiration is frequently considered a wasteful and inefficient process. However, mutant analysis demonstrated that photorespiration is essential for recycling of 2-phosphoglycolate in C3 and C4 land plants, in algae, and even in cyanobacteria operating carboxysome-based carbon (C) concentrating mechanisms. Photorespiration links photosynthetic C assimilation with other metabolic processes, such as nitrogen and sulfur assimilation, as well as C1 metabolism, and it may contribute to balancing the redox poise between chloroplasts, peroxisomes, mitochondria and cytoplasm. The high degree of metabolic interdependencies and the pleiotropic phenotypes of photorespiratory mutants impedes the distinction between core and accessory functions. Newly developed synthetic bypasses of photorespiration, beyond holding potential for significant yield increases in C3 crops, will enable us to differentiate between essential and accessory functions of photorespiration.
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Affiliation(s)
- Marion Eisenhut
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, 40225, Germany
| | - Marc-Sven Roell
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, 40225, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, 40225, Germany
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20
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Gorelova V, Bastien O, De Clerck O, Lespinats S, Rébeillé F, Van Der Straeten D. Evolution of folate biosynthesis and metabolism across algae and land plant lineages. Sci Rep 2019; 9:5731. [PMID: 30952916 PMCID: PMC6451014 DOI: 10.1038/s41598-019-42146-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/25/2019] [Indexed: 11/09/2022] Open
Abstract
Tetrahydrofolate and its derivatives, commonly known as folates, are essential for almost all living organisms. Besides acting as one-carbon donors and acceptors in reactions producing various important biomolecules such as nucleic and amino acids, as well as pantothenate, they also supply one-carbon units for methylation reactions. Plants along with bacteria, yeast and fungi synthesize folates de novo and therefore constitute a very important dietary source of folates for animals. All the major steps of folate biosynthesis and metabolism have been identified but only few have been genetically characterized in a handful of model plant species. The possible differences in the folate pathway between various plant and algal species have never been explored. In this study we present a comprehensive comparative study of folate biosynthesis and metabolism of all major land plant lineages as well as green and red algae. The study identifies new features of plant folate metabolism that might open new directions to folate research in plants.
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Affiliation(s)
- V Gorelova
- Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium.,Department of Botany and Plant Biology, Laboratory of Plant Biochemistry and Physiology, University of Geneva, Quai E. Ansermet 30, 1211, Geneva, Switzerland
| | - O Bastien
- Laboratoire de Physiologie Cellulaire Vegetale, UMR168 CNRS-CEA-INRA-Universite Joseph Fourier Grenoble I, Bioscience and Biotechnologies Institute of Grenoble, CEA-Grenoble, 17 rue des Martyrs, 38054, Grenoble, Cedex 9, France
| | - O De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000, Gent, Belgium
| | - S Lespinats
- Laboratoire de Physiologie Cellulaire Vegetale, UMR168 CNRS-CEA-INRA-Universite Joseph Fourier Grenoble I, Bioscience and Biotechnologies Institute of Grenoble, CEA-Grenoble, 17 rue des Martyrs, 38054, Grenoble, Cedex 9, France
| | - F Rébeillé
- Laboratoire de Physiologie Cellulaire Vegetale, UMR168 CNRS-CEA-INRA-Universite Joseph Fourier Grenoble I, Bioscience and Biotechnologies Institute of Grenoble, CEA-Grenoble, 17 rue des Martyrs, 38054, Grenoble, Cedex 9, France
| | - D Van Der Straeten
- Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium.
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21
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Corral MG, Haywood J, Stehl LH, Stubbs KA, Murcha MW, Mylne JS. Targeting plant DIHYDROFOLATE REDUCTASE with antifolates and mechanisms for genetic resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:727-742. [PMID: 29876984 DOI: 10.1111/tpj.13983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
The folate biosynthetic pathway and its key enzyme dihydrofolate reductase (DHFR) is a popular target for drug development due to its essential role in the synthesis of DNA precursors and some amino acids. Despite its importance, little is known about plant DHFRs, which, like the enzymes from the malarial parasite Plasmodium, are bifunctional, possessing DHFR and thymidylate synthase (TS) domains. Here using genetic knockout lines we confirmed that either DHFR-TS1 or DHFR-TS2 (but not DHFR-TS3) was essential for seed development. Screening mutated Arabidopsis thaliana seeds for resistance to antimalarial DHFR-inhibitor drugs pyrimethamine and cycloguanil identified causal lesions in DHFR-TS1 and DHFR-TS2, respectively, near the predicted substrate-binding site. The different drug resistance profiles for the plants, enabled by the G137D mutation in DHFR-TS1 and the A71V mutation in DHFR-TS2, were consistent with biochemical studies using recombinant proteins and could be explained by structural models. These findings provide a great improvement in our understanding of plant DHFR-TS and suggest how plant-specific inhibitors might be developed, as DHFR is not currently targeted by commercial herbicides.
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Affiliation(s)
- Maxime G Corral
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Luca H Stehl
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- Faculty of Biology, The University of Freiburg, Schaenzlestrasse 1, Freiburg, 79104, Germany
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
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22
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Strobbe S, Van Der Straeten D. Toward Eradication of B-Vitamin Deficiencies: Considerations for Crop Biofortification. FRONTIERS IN PLANT SCIENCE 2018; 9:443. [PMID: 29681913 PMCID: PMC5897740 DOI: 10.3389/fpls.2018.00443] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/21/2018] [Indexed: 05/08/2023]
Abstract
'Hidden hunger' involves insufficient intake of micronutrients and is estimated to affect over two billion people on a global scale. Malnutrition of vitamins and minerals is known to cause an alarming number of casualties, even in the developed world. Many staple crops, although serving as the main dietary component for large population groups, deliver inadequate amounts of micronutrients. Biofortification, the augmentation of natural micronutrient levels in crop products through breeding or genetic engineering, is a pivotal tool in the fight against micronutrient malnutrition (MNM). Although these approaches have shown to be successful in several species, a more extensive knowledge of plant metabolism and function of these micronutrients is required to refine and improve biofortification strategies. This review focuses on the relevant B-vitamins (B1, B6, and B9). First, the role of these vitamins in plant physiology is elaborated, as well their biosynthesis. Second, the rationale behind vitamin biofortification is illustrated in view of pathophysiology and epidemiology of the deficiency. Furthermore, advances in biofortification, via metabolic engineering or breeding, are presented. Finally, considerations on B-vitamin multi-biofortified crops are raised, comprising the possible interplay of these vitamins in planta.
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23
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A transcriptomics approach uncovers novel roles for poly(ADP-ribosyl)ation in the basal defense response in Arabidopsis thaliana. PLoS One 2017; 12:e0190268. [PMID: 29284022 PMCID: PMC5746271 DOI: 10.1371/journal.pone.0190268] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/10/2017] [Indexed: 12/20/2022] Open
Abstract
Pharmacological inhibition of poly(ADP-ribose) polymerase (PARP) or loss of Arabidopsis thaliana PARG1 (poly(ADP-ribose) glycohydrolase) disrupt a subset of plant defenses. In the present study we examined the impact of altered poly(ADP-ribosyl)ation on early gene expression induced by the microbe-associate molecular patterns (MAMPs) flagellin (flg22) and EF-Tu (elf18). Stringent statistical analyses and filtering identified 178 genes having MAMP-induced mRNA abundance patterns that were altered by either PARP inhibitor 3-aminobenzamide (3AB) or PARG1 knockout. From the identified set of 178 genes, over fifty Arabidopsis T-DNA insertion lines were chosen and screened for altered basal defense responses. Subtle alterations in callose deposition and/or seedling growth in response to those MAMPs were observed in knockouts of At3g55630 (FPGS3, a cytosolic folylpolyglutamate synthetase), At5g15660 (containing an F-box domain), At1g47370 (a TIR-X (Toll-Interleukin Receptor domain)), and At5g64060 (a predicted pectin methylesterase inhibitor). Over-represented GO terms for the gene expression study included "innate immune response" for elf18/parg1, highlighting a subset of elf18-activated defense-associated genes whose expression is altered in parg1 plants. The study also allowed a tightly controlled comparison of early mRNA abundance responses to flg22 and elf18 in wild-type Arabidopsis, which revealed many differences. The PARP inhibitor 3-methoxybenzamide (3MB) was also used in the gene expression profiling, but pleiotropic impacts of this inhibitor were observed. This transcriptomics study revealed targets for further dissection of MAMP-induced plant immune responses, impacts of PARP inhibitors, and the molecular mechanisms by which poly(ADP-ribosyl)ation regulates plant responses to MAMPs.
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24
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Hayashi M, Tanaka M, Yamamoto S, Nakagawa T, Kanai M, Anegawa A, Ohnishi M, Mimura T, Nishimura M. Plastidial Folate Prevents Starch Biosynthesis Triggered by Sugar Influx into Non-Photosynthetic Plastids of Arabidopsis. PLANT & CELL PHYSIOLOGY 2017; 58:1328-1338. [PMID: 28586467 PMCID: PMC5921527 DOI: 10.1093/pcp/pcx076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/16/2017] [Indexed: 05/22/2023]
Abstract
Regulation of sucrose-starch interconversion in plants is important to maintain energy supplies necessary for viability and growth. Arabidopsis mutants were screened for aberrant responses to sucrose to identify candidates with a defect in the regulation of starch biosynthesis. One such mutant, fpgs1-4, accumulated substantial amounts of starch in non-photosynthetic cells. Dark-grown mutant seedlings exhibited shortened hypocotyls and accumulated starch in etioplasts when supplied with exogenous sucrose/glucose. Similar starch accumulation from exogenous sucrose was observed in mutant chloroplasts, when photosynthesis was prevented by organ culture in darkness. Molecular genetic analyses revealed that the mutant was defective in plastidial folylpolyglutamate synthetase, one of the enzymes engaged in folate biosynthesis. Active folate derivatives are important biomolecules that function as cofactors for a variety of enzymes. Exogenously supplied 5-formyl-tetrahydrofolate abrogated the mutant phenotypes, indicating that the fpgs1-4 mutant produced insufficient folate derivative levels. In addition, the antifolate agents methotrexate and 5-fluorouracil induced starch accumulation from exogenously supplied sucrose in dark-grown seedlings of wild-type Arabidopsis. These results indicate that plastidial folate suppresses starch biosynthesis triggered by sugar influx into non-photosynthetic cells, demonstrating a hitherto unsuspected link between plastidial folate and starch metabolism.
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Affiliation(s)
- Makoto Hayashi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, Tamura 1266, Nagahama, Shiga 526-0829, Japan
- Corresponding author: E-mail,: ; Fax, +81-749-64-8101
| | - Mina Tanaka
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Saki Yamamoto
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, Tamura 1266, Nagahama, Shiga 526-0829, Japan
| | - Taro Nakagawa
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, Tamura 1266, Nagahama, Shiga 526-0829, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Aya Anegawa
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai 1-1, Nada-ku, 657-8501, Japan
| | - Miwa Ohnishi
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai 1-1, Nada-ku, 657-8501, Japan
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Rokkodai 1-1, Nada-ku, 657-8501, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
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25
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Development of a lateral flow dipstick immunoassay for evaluation of folate levels in maize. Anal Bioanal Chem 2017; 409:5655-5660. [DOI: 10.1007/s00216-017-0504-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/22/2017] [Accepted: 06/30/2017] [Indexed: 10/19/2022]
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26
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Maniga A, Ghisaura S, Perrotta L, Marche MG, Cella R, Albani D. Distinctive features and differential regulation of the DRTS genes of Arabidopsis thaliana. PLoS One 2017; 12:e0179338. [PMID: 28594957 PMCID: PMC5464667 DOI: 10.1371/journal.pone.0179338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/26/2017] [Indexed: 01/16/2023] Open
Abstract
In plants and protists, dihydrofolate reductase (DHFR) and thymidylate synthase (TS) are part of a bifunctional enzyme (DRTS) that allows efficient recycling of the dihydrofolate resulting from TS activity. Arabidopsis thaliana possesses three DRTS genes, called AtDRTS1, AtDRTS2 and AtDRTS3, that are located downstream of three members of the sec14-like SFH gene family. In this study, a characterization of the AtDRTS genes identified alternatively spliced transcripts coding for AtDRTS isoforms which may account for monofunctional DHFR enzymes supporting pathways unrelated to DNA synthesis. Moreover, we discovered a complex differential regulation of the AtDRTS genes that confirms the expected involvement of the AtDRTS genes in cell proliferation and endoreduplication, but indicates also functions related to other cellular activities. AtDRTS1 is widely expressed in both meristematic and differentiated tissues, whereas AtDRTS2 expression is almost exclusively limited to the apical meristems and AtDRTS3 is preferentially expressed in the shoot apex, in stipules and in root cap cells. The differential regulation of the AtDRTS genes is associated to distinctive promoter architectures and the expression of AtDRTS1 in the apical meristems is strictly dependent on the presence of an intragenic region that includes the second intron of the gene. Upon activation of cell proliferation in germinating seeds, the activity of the AtDRTS1 and AtDRTS2 promoters in meristematic cells appears to be maximal at the G1/S phase of the cell cycle. In addition, the promoters of AtDRTS2 and AtDRTS3 are negatively regulated through E2F cis-acting elements and both genes, but not AtDRTS1, are downregulated in plants overexpressing the AtE2Fa factor. Our study provides new information concerning the function and the regulation of plant DRTS genes and opens the way to further investigations addressing the importance of folate synthesis with respect to specific cellular activities.
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Affiliation(s)
- Antonio Maniga
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - Stefania Ghisaura
- Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Lara Perrotta
- Department of Agriculture, University of Sassari, Sassari, Italy
- Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | | | - Rino Cella
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Diego Albani
- Department of Agriculture, University of Sassari, Sassari, Italy
- Center of Excellence for Biotechnology Development and Biodiversity Research, University of Sassari, Sassari, Italy
- * E-mail:
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27
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Gorelova V, Ambach L, Rébeillé F, Stove C, Van Der Straeten D. Folates in Plants: Research Advances and Progress in Crop Biofortification. Front Chem 2017; 5:21. [PMID: 28424769 PMCID: PMC5372827 DOI: 10.3389/fchem.2017.00021] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/09/2017] [Indexed: 11/13/2022] Open
Abstract
Folates, also known as B9 vitamins, serve as donors and acceptors in one-carbon (C1) transfer reactions. The latter are involved in synthesis of many important biomolecules, such as amino acids, nucleic acids and vitamin B5. Folates also play a central role in the methyl cycle that provides one-carbon groups for methylation reactions. The important functions fulfilled by folates make them essential in all living organisms. Plants, being able to synthesize folates de novo, serve as an excellent dietary source of folates for animals that lack the respective biosynthetic pathway. Unfortunately, the most important staple crops such as rice, potato and maize are rather poor sources of folates. Insufficient folate consumption is known to cause severe developmental disorders in humans. Two approaches are employed to fight folate deficiency: pharmacological supplementation in the form of folate pills and biofortification of staple crops. As the former approach is considered rather costly for the major part of the world population, biofortification of staple crops is viewed as a decent alternative in the struggle against folate deficiency. Therefore, strategies, challenges and recent progress of folate enhancement in plants will be addressed in this review. Apart from the ever-growing need for the enhancement of nutritional quality of crops, the world population faces climate change catastrophes or environmental stresses, such as elevated temperatures, drought, salinity that severely affect growth and productivity of crops. Due to immense diversity of their biochemical functions, folates take part in virtually every aspect of plant physiology. Any disturbance to the plant folate metabolism leads to severe growth inhibition and, as a consequence, to a lower productivity. Whereas today's knowledge of folate biochemistry can be considered very profound, evidence on the physiological roles of folates in plants only starts to emerge. In the current review we will discuss the implication of folates in various aspects of plant physiology and development.
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Affiliation(s)
- Vera Gorelova
- Laboratory of Functional Plant Biology, Department of Biology, Ghent UniversityGhent, Belgium
| | - Lars Ambach
- Laboratory of Toxicology, Department of Bioanalysis, Ghent UniversityGhent, Belgium
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire Végétale, Bioscience and Biotechnologies Institute of Grenoble, CEA-GrenobleGrenoble, France
| | - Christophe Stove
- Laboratory of Toxicology, Department of Bioanalysis, Ghent UniversityGhent, Belgium
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28
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Arabidopsis plastidial folylpolyglutamate synthetase is required for nitrogen metabolism under nitrate-limited condition in darkness. Biochem Biophys Res Commun 2017; 482:277-281. [DOI: 10.1016/j.bbrc.2016.11.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/16/2022]
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29
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Zhu DZ, Zhao XF, Liu CZ, Ma FF, Wang F, Gao XQ, Zhang XS. Interaction between RNA helicase ROOT INITIATION DEFECTIVE 1 and GAMETOPHYTIC FACTOR 1 is involved in female gametophyte development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5757-5768. [PMID: 27683728 PMCID: PMC5066494 DOI: 10.1093/jxb/erw341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
ROOT INITIATION DEFECTIVE 1 (RID1) is an Arabidopsis DEAH/RHA RNA helicase. It functions in hypocotyl de-differentiation, de novo meristem formation, and cell specification of the mature female gametophyte (FG). However, it is unclear how RID1 regulates FG development. In this study, we observed that mutations to RID1 disrupted the developmental synchrony and retarded the progression of FG development. RID1 exhibited RNA helicase activity, with a preference for unwinding double-stranded RNA in the 3' to 5' direction. Furthermore, we found that RID1 interacts with GAMETOPHYTIC FACTOR 1 (GFA1), which is an integral protein of the spliceosome component U5 small nuclear ribonucleoprotein (snRNP) particle. Substitution of specific RID1 amino acids (Y266F and T267I) inhibited the interaction with GFA1. In addition, the mutated RID1 could not complement the seed-abortion phenotype of the rid1 mutant. The rid1 and gfa1 mutants exhibited similar abnormalities in pre-mRNA splicing and down-regulated expression of some genes involved in FG development. Our results suggest that an interaction between RID1 and the U5 snRNP complex regulates essential pre-mRNA splicing of the genes required for FG development. This study provides new information regarding the mechanism underlying the FG developmental process.
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Affiliation(s)
- Dong Zi Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xue Fang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Chang Zhen Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Fang Fang Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Fang Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xin-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, China
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30
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Upadhyaya P, Tyagi K, Sarma S, Tamboli V, Sreelakshmi Y, Sharma R. Natural variation in folate levels among tomato (Solanum lycopersicum) accessions. Food Chem 2016; 217:610-619. [PMID: 27664678 DOI: 10.1016/j.foodchem.2016.09.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 06/02/2016] [Accepted: 09/05/2016] [Indexed: 11/17/2022]
Abstract
Folate content was estimated in tomato (Solanum lycopersicum) accessions using microbiological assay (MA) and by LC-MS. The MA revealed that in red-ripe fruits folate levels ranged from 4 to 60μg/100g fresh weight. The LC-MS estimation of red-ripe fruits detected three folate forms, 5-CH3-THF, 5-CHO-THF, 5,10-CH(+)THF and folate levels ranged from 14 to 46μg/100g fresh weight. In mature green and red ripe fruit, 5-CH3-THF was the most abundant folate form. Comparison of LC-MS with MA revealed that MA inaccurately estimates folate levels. The accumulation of folate forms and their distribution varied among accessions. The single nucleotide polymorphism was examined in the key genes of the folate pathway to understand its linkage with folate levels. Despite the significant variation in folate levels among tomato accessions, little polymorphism was found in folate biosynthesis genes. Our results indicate that variation in folate level is governed by a more complex regulation at cellular homeostasis level.
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Affiliation(s)
- Pallawi Upadhyaya
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Kamal Tyagi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Supriya Sarma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Vajir Tamboli
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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31
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Raz S, Stark M, Assaraf YG. Folylpoly-γ-glutamate synthetase: A key determinant of folate homeostasis and antifolate resistance in cancer. Drug Resist Updat 2016; 28:43-64. [PMID: 27620954 DOI: 10.1016/j.drup.2016.06.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 06/10/2016] [Accepted: 06/16/2016] [Indexed: 01/26/2023]
Abstract
Mammalians are devoid of autonomous biosynthesis of folates and hence must obtain them from the diet. Reduced folate cofactors are B9-vitamins which play a key role as donors of one-carbon units in the biosynthesis of purine nucleotides, thymidylate and amino acids as well as in a multitude of methylation reactions including DNA, RNA, histone and non-histone proteins, phospholipids, as well as intermediate metabolites. The products of these S-adenosylmethionine (SAM)-dependent methylations are involved in the regulation of key biological processes including transcription, translation and intracellular signaling. Folate-dependent one-carbon metabolism occurs in several subcellular compartments including the cytoplasm, mitochondria, and nucleus. Since folates are essential for DNA replication, intracellular folate cofactors play a central role in cancer biology and inflammatory autoimmune disorders. In this respect, various folate-dependent enzymes catalyzing nucleotide biosynthesis have been targeted by specific folate antagonists known as antifolates. Currently, antifolates are used in drug treatment of multiple human cancers, non-malignant chronic inflammatory disorders as well as bacterial and parasitic infections. An obligatory key component of intracellular folate retention and intracellular homeostasis is (anti)folate polyglutamylation, mediated by the unique enzyme folylpoly-γ-glutamate synthetase (FPGS), which resides in both the cytoplasm and mitochondria. Consistently, knockout of the FPGS gene in mice results in embryonic lethality. FPGS catalyzes the addition of a long polyglutamate chain to folates and antifolates, hence rendering them polyanions which are efficiently retained in the cell and are now bound with enhanced affinity by various folate-dependent enzymes. The current review highlights the crucial role that FPGS plays in maintenance of folate homeostasis under physiological conditions and delineates the plethora of the molecular mechanisms underlying loss of FPGS function and consequent antifolate resistance in cancer.
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Affiliation(s)
- Shachar Raz
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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32
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Abstract
DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. Here, we identify the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Decreased levels of oxidized tetrahydrofolates in mthfd1-1 and lethality of loss-of-function demonstrate the essential enzymatic role of MTHFD1 in Arabidopsis. Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1. Comparative analysis of DNA methylation revealed that the CMT3 and CMT2 pathways involving positive feedback with H3K9me are mostly affected. Our work highlights the sensitivity of epigenetic networks to one-carbon metabolism due to their common S-adenosylmethionine-dependent transmethylation and has implications for human MTHFD1-associated diseases.
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Li L, Hill-Skinner S, Liu S, Beuchle D, Tang HM, Yeh CT, Nettleton D, Schnable PS. The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:493-504. [PMID: 25495051 PMCID: PMC4329605 DOI: 10.1111/tpj.12745] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/03/2014] [Accepted: 12/08/2014] [Indexed: 05/02/2023]
Abstract
Mutations in the brown midrib4 (bm4) gene affect the accumulation and composition of lignin in maize. Fine-mapping analysis of bm4 narrowed the candidate region to an approximately 105 kb interval on chromosome 9 containing six genes. Only one of these six genes, GRMZM2G393334, showed decreased expression in mutants. At least four of 10 Mu-induced bm4 mutant alleles contain a Mu insertion in the GRMZM2G393334 gene. Based on these results, we concluded that GRMZM2G393334 is the bm4 gene. GRMZM2G393334 encodes a putative folylpolyglutamate synthase (FPGS), which functions in one-carbon (C1) metabolism to polyglutamylate substrates of folate-dependent enzymes. Yeast complementation experiments demonstrated that expression of the maize bm4 gene in FPGS-deficient met7 yeast is able to rescue the yeast mutant phenotype, thus demonstrating that bm4 encodes a functional FPGS. Consistent with earlier studies, bm4 mutants exhibit a modest decrease in lignin concentration and an overall increase in the S:G lignin ratio relative to wild-type. Orthologs of bm4 include at least one paralogous gene in maize and various homologs in other grasses and dicots. Discovery of the gene underlying the bm4 maize phenotype illustrates a role for FPGS in lignin biosynthesis.
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Affiliation(s)
- Li Li
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- College of Agronomy, Northwest Agriculture and Forestry University#3, Taicheng road, Yangling, Shaanxi, 712100, China
| | - Sarah Hill-Skinner
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
| | - Danielle Beuchle
- Department of Genetics, Development and Cell Biology, Iowa State University1210 Molecular Biology Building, Ames, IA 50011-3260, USA
| | - Ho Man Tang
- Department of Genetics, Development and Cell Biology, Iowa State University1210 Molecular Biology Building, Ames, IA 50011-3260, USA
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
| | - Dan Nettleton
- Center for Plant Genomics, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- Department of Statistics, Iowa State University2115 Snedecor, Ames, IA, 50011, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- Department of Genetics, Development and Cell Biology, Iowa State University1210 Molecular Biology Building, Ames, IA 50011-3260, USA
- Center for Plant Genomics, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- *
For correspondence (e-mail )
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Srivastava AC, Chen F, Ray T, Pattathil S, Peña MJ, Avci U, Li H, Huhman DV, Backe J, Urbanowicz B, Miller JS, Bedair M, Wyman CE, Sumner LW, York WS, Hahn MG, Dixon RA, Blancaflor EB, Tang Y. Loss of function of folylpolyglutamate synthetase 1 reduces lignin content and improves cell wall digestibility in Arabidopsis. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:224. [PMID: 26697113 PMCID: PMC4687376 DOI: 10.1186/s13068-015-0403-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/30/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND One-carbon (C1) metabolism is important for synthesizing a range of biologically important compounds that are essential for life. In plants, the C1 pathway is crucial for the synthesis of a large number of secondary metabolites, including lignin. Tetrahydrofolate and its derivatives, collectively referred to as folates, are crucial co-factors for C1 metabolic pathway enzymes. Given the link between the C1 and phenylpropanoid pathways, we evaluated whether folylpolyglutamate synthetase (FPGS), an enzyme that catalyzes the addition of a glutamate tail to folates to form folylpolyglutamates, can be a viable target for reducing cell wall recalcitrance in plants. RESULTS Consistent with its role in lignocellulosic formation, FPGS1 was preferentially expressed in vascular tissues. Total lignin was low in fpgs1 plants leading to higher saccharification efficiency of the mutant. The decrease in total lignin in fpgs1 was mainly due to lower guaiacyl (G) lignin levels. Glycome profiling revealed subtle alterations in the cell walls of fpgs1. Further analyses of hemicellulosic polysaccharides by NMR showed that the degree of methylation of 4-O-methyl glucuronoxylan was reduced in the fpgs1 mutant. Microarray analysis and real-time qRT-PCR revealed that transcripts of a number of genes in the C1 and lignin pathways had altered expression in fpgs1 mutants. Consistent with the transcript changes of C1-related genes, a significant reduction in S-adenosyl-l-methionine content was detected in the fpgs1 mutant. The modified expression of the various methyltransferases and lignin-related genes indicate possible feedback regulation of C1 pathway-mediated lignin biosynthesis. CONCLUSIONS Our observations provide genetic and biochemical support for the importance of folylpolyglutamates in the lignocellulosic pathway and reinforces previous observations that targeting a single FPGS isoform for down-regulation leads to reduced lignin in plants. Because fpgs1 mutants had no dramatic defects in above ground biomass, selective down-regulation of individual components of C1 metabolism is an approach that should be explored further for the improvement of lignocellulosic feedstocks.
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Affiliation(s)
- Avinash C. Srivastava
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Fang Chen
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
| | - Tui Ray
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Sivakumar Pattathil
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- />Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
| | - Maria J. Peña
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
| | - Utku Avci
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- />Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
| | - Hongjia Li
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, CA 92507 USA
| | - David V. Huhman
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Jason Backe
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
| | - Breeanna Urbanowicz
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
| | - Jeffrey S. Miller
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
| | - Mohamed Bedair
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Charles E. Wyman
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, CA 92507 USA
| | - Lloyd W. Sumner
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - William S. York
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- />Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
| | - Michael G. Hahn
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602 USA
- />Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
| | - Richard A. Dixon
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
- />Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
| | - Elison B. Blancaflor
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
| | - Yuhong Tang
- />Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
- />BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN 37831 USA
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Meng H, Jiang L, Xu B, Guo W, Li J, Zhu X, Qi X, Duan L, Meng X, Fan Y, Zhang C. Arabidopsis plastidial folylpolyglutamate synthetase is required for seed reserve accumulation and seedling establishment in darkness. PLoS One 2014; 9:e101905. [PMID: 25000295 PMCID: PMC4084893 DOI: 10.1371/journal.pone.0101905] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/12/2014] [Indexed: 01/16/2023] Open
Abstract
Interactions among metabolic pathways are important in plant biology. At present, not much is known about how folate metabolism affects other metabolic pathways in plants. Here we report a T-DNA insertion mutant (atdfb-3) of the plastidial folylpolyglutamate synthetase gene (AtDFB) was defective in seed reserves and skotomorphogenesis. Lower carbon (C) and higher nitrogen (N) content in the mutant seeds than that of the wild type were indicative of an altered C and N partitioning capacity. Higher levels of organic acids and sugars were detected in the mutant seeds compared with the wild type. Further analysis revealed that atdfb-3 seeds contained less total amino acids and individual Asn and Glu as well as NO3−. These results indicate significant changes in seed storage in the mutant. Defects in hypocotyl elongation were observed in atdfb-3 in darkness under sufficient NO3− conditions, and further enhanced under NO3− limited conditions. The strong expression of AtDFB in cotyledons and hypocotyl during early developmental stage was consistent with the mutant sensitivity to limited NO3− during a narrow developmental window. Exogenous 5-formyl-tetrahydrofolate completely restored the hypocotyl length in atdfb-3 seedlings with NO3− as the sole N source. Further study demonstrated that folate profiling and N metabolism were perturbed in atdfb-3 etiolated seedlings. The activity of enzymes involved in N reduction and assimilation was altered in atdfb-3. Taken together, these results indicate that AtDFB is required for seed reserves, hypocotyl elongation and N metabolism in darkness, providing novel insights into potential associations of folate metabolism with seed reserve accumulation, N metabolism and hypocotyl development in Arabidopsis.
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Affiliation(s)
- Hongyan Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, People’s Republic of China
| | - Bosi Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Wenzhu Guo
- Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Jinglai Li
- Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Xiuqing Zhu
- Beijing Institute of Pharmacology and Toxicology, Beijing, People’s Republic of China
| | - Xiaoquan Qi
- Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Lixin Duan
- Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xianbin Meng
- Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yunliu Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, People’s Republic of China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, People’s Republic of China
- * E-mail:
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Reyes-Hernández BJ, Srivastava AC, Ugartechea-Chirino Y, Shishkova S, Ramos-Parra PA, Lira-Ruan V, Díaz de la Garza RI, Dong G, Moon JC, Blancaflor EB, Dubrovsky JG. The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2014; 202:1223-1236. [PMID: 24635769 DOI: 10.1111/nph.12757] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/02/2014] [Indexed: 05/02/2023]
Abstract
Roots have both indeterminate and determinate developmental programs. The latter is preceded by the former. It is not well understood how the indeterminacy-to-determinacy switch (IDS) is regulated. We isolated a moots koom2 (mko2; 'short root' in Mayan) Arabidopsis thaliana mutant with determinate primary root growth and analyzed the root apical meristem (RAM) behavior using various marker lines. Deep sequencing and genetic and pharmacological complementation permitted the identification of a point mutation in the FOLYLPOLYGLUTAMATE SYNTHETASE1 (FPGS1) gene responsible for the mko2 phenotype. Wild-type FPGS1 is required to maintain the IDS in the 'off' state. When FPGS1 function is compromised, the IDS is turned on and the RAM becomes completely consumed. The polyglutamate-dependent pathway of the IDS involves activation of the quiescent center independently of auxin gradients and regulatory modules participating in RAM maintenance (WUSCHEL-RELATED HOMEOBOX5 (WOX5), PLETHORA, and SCARECROW (SCR)). The mko2 mutation causes drastic changes in folate metabolism and also affects lateral root primordium morphogenesis but not initiation. We identified a metabolism-dependent pathway involved in the IDS in roots. We suggest that the root IDS represents a specific developmental pathway that regulates RAM behaviour and is a different level of regulation in addition to RAM maintenance.
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Affiliation(s)
- Blanca Jazmín Reyes-Hernández
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Mexico
| | - Avinash C Srivastava
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Yamel Ugartechea-Chirino
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Mexico
| | - Svetlana Shishkova
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Mexico
| | - Perla A Ramos-Parra
- Escuela de Biotecnología y Alimentos, Centro de Biotecnología - FEMSA, Monterrey, 64849, Mexico
| | - Verónica Lira-Ruan
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Mexico
| | | | - Gaofeng Dong
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Mexico
| | - Jun-Cheol Moon
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Mexico
| | - Elison B Blancaflor
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250, Cuernavaca, Mexico
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Plant amino acid-derived vitamins: biosynthesis and function. Amino Acids 2013; 46:809-24. [PMID: 24368523 DOI: 10.1007/s00726-013-1653-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 12/14/2013] [Indexed: 02/06/2023]
Abstract
Vitamins are essential organic compounds for humans, having lost the ability to de novo synthesize them. Hence, they represent dietary requirements, which are covered by plants as the main dietary source of most vitamins (through food or livestock's feed). Most vitamins synthesized by plants present amino acids as precursors (B1, B2, B3, B5, B7, B9 and E) and are therefore linked to plant nitrogen metabolism. Amino acids play different roles in their biosynthesis and metabolism, either incorporated into the backbone of the vitamin or as amino, sulfur or one-carbon group donors. There is a high natural variation in vitamin contents in crops and its exploitation through breeding, metabolic engineering and agronomic practices can enhance their nutritional quality. While the underlying biochemical roles of vitamins as cosubstrates or cofactors are usually common for most eukaryotes, the impact of vitamins B and E in metabolism and physiology can be quite different on plants and animals. Here, we first aim at giving an overview of the biosynthesis of amino acid-derived vitamins in plants, with a particular focus on how this knowledge can be exploited to increase vitamin contents in crops. Second, we will focus on the functions of these vitamins in both plants and animals (and humans in particular), to unravel common and specific roles for vitamins in evolutionary distant organisms, in which these amino acid-derived vitamins play, however, an essential role.
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38
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Matityahu I, Godo I, Hacham Y, Amir R. Tobacco seeds expressing feedback-insensitive cystathionine gamma-synthase exhibit elevated content of methionine and altered primary metabolic profile. BMC PLANT BIOLOGY 2013; 13:206. [PMID: 24314105 PMCID: PMC3878949 DOI: 10.1186/1471-2229-13-206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 12/03/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND The essential sulfur-containing amino acid methionine plays a vital role in plant metabolism and human nutrition. In this study, we aimed to elucidate the regulatory role of the first committed enzyme in the methionine biosynthesis pathway, cystathionine γ-synthase (CGS), on methionine accumulation in tobacco seeds. We also studied the effect of this manipulation on the seed's metabolism. RESULTS Two forms of Arabidopsis CGS (AtCGS) were expressed under the control of the seeds-specific promoter of legumin B4: feedback-sensitive F-AtCGS (LF seeds), and feedback-insensitive T-AtCGS (LT seeds). Unexpectedly, the soluble content of methionine was reduced significantly in both sets of transgenic seeds. Amino acids analysis and feeding experiments indicated that although the level of methionine was reduced, the flux through its synthesis had increased. As a result, the level of protein-incorporated methionine had increased significantly in LT seeds by up to 60%, but this was not observed in LF seeds, whose methionine content is tightly regulated. This increase was accompanied by a higher content of other protein-incorporated amino acids, which led to 27% protein content in the seeds although this was statistically insignificantly. In addition, the levels of reducing sugars (representing starch) were slightly but significantly reduced, while that of oil was insignificantly reduced. To assess the impact of the high expression level of T-AtCGS in seeds on other primary metabolites, metabolic profiling using GC-MS was performed. This revealed significant alterations to the primary seed metabolism manifested by a significant increase in eight annotated metabolites (mostly sugars and their oxidized derivatives), while the levels of 12 other metabolites were reduced significantly in LT compared to wild-type seeds. CONCLUSION Expression of T-AtCGS leads to an increase in the level of total Met, higher contents of total amino acids, and significant changes in the levels of 20 annotated metabolites. The high level of oxidized metabolites, the two stress-associated amino acids, proline and serine, and low level of glutathione suggest oxidative stress that occurs during LT seed development. This study provides information on the metabolic consequence of increased CGS activity in seeds and how it affects the seed's nutritional quality.
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Affiliation(s)
- Ifat Matityahu
- Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - Itamar Godo
- Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - Yael Hacham
- Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
| | - Rachel Amir
- Laboratory of Plant Science, Migal Galilee Technology Center, P.O. Box 831, Kiryat Shmona 12100, Israel
- Tel Hai College, Upper Galilee, Israel
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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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40
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Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis. Biochem J 2013; 451:145-54. [PMID: 23535167 DOI: 10.1042/bj20121744] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Both Met (methionine) and SAM (S-adenosylmethionine), the activated form of Met, participate in a number of essential metabolic pathways in plants. The subcellular compartmentalization of Met fluxes will be discussed in the present review with respect to regulation and communication with the sulfur assimilation pathway, the network of the aspartate-derived amino acids and the demand for production of SAM. SAM enters the ethylene, nicotianamine and polyamine biosynthetic pathways and provides the methyl group for the majority of methylation reactions required for plant growth and development. The multiple essential roles of SAM require regulation of its synthesis, recycling and distribution to sustain these different pathways. A particular focus of the present review will be on the function of recently identified genes of the Met salvage cycle or Yang cycle and the importance of the Met salvage cycle in the metabolism of MTA (5'-methylthioadenosine). MTA has the potential for product inhibition of ethylene, nicotianamine and polyamine biosynthesis which provides an additional link between these pathways. Interestingly, regulation of Met cycle genes was found to differ between plant species as shown for Arabidopsis thaliana and Oryza sativa.
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Ramos-Parra PA, García-Salinas C, Hernández-Brenes C, de la Garza RID. Folate levels and polyglutamylation profiles of papaya (Carica papaya cv. Maradol) during fruit development and ripening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:3949-3956. [PMID: 23574547 DOI: 10.1021/jf305364x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Folates are essential micronutrients for humans, and their deficiency causes several detrimental effects on human health. Papaya fruit is an important natural source of some micronutrients. This paper presents a first complete characterization of folate derivatives accumulated in cv. Maradol papaya during fruit development and ripening processes. During postharvest ripening, the fruit accumulated up to 24.5% of the daily folate recommended dietary allowance (RDA) for an adult in a 1 cup (145 g) portion. Tetrahydrofolate (THF) and 5-methyl-THF were the predominant folate classes observed. Surprisingly, an unusually long polyglutamylation profile of tentatively up to 17 glutamates linked to 5-methyl-THF was detected; to the authors' knowledge, this very long polyglutamyl tail has not been reported for any organism, and it is probably characteristic of this plant species. This polyglutamylation degree changed throughout fruit development and ripening, showing the largest differences at the onset of ripening. This work raises questions about the functional role of folate derivatives in fruit development.
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Affiliation(s)
- Perla A Ramos-Parra
- Escuela de Biotecnología y Alimentos, Centro de Biotechnologı́a - FEMSA, Tecnológico de Monterrey , Campus-Monterrey 64849, Mexico
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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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Jiang L, Liu Y, Sun H, Han Y, Li J, Li C, Guo W, Meng H, Li S, Fan Y, Zhang C. The mitochondrial folylpolyglutamate synthetase gene is required for nitrogen utilization during early seedling development in arabidopsis. PLANT PHYSIOLOGY 2013; 161:971-89. [PMID: 23129207 PMCID: PMC3561033 DOI: 10.1104/pp.112.203430] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Investigations into the biochemical processes and regulatory mechanisms of nitrogen (N) utilization can aid in understanding how N is used efficiently in plants. This report describes a deficiency in N utilization in an Arabidopsis (Arabidopsis thaliana) transfer DNA insertion mutant of the mitochondrial folylpolyglutamate synthetase gene DFC, which catalyzes the conjugation of glutamate residues to the tetrahydrofolate during folate synthesis. The mutant seedlings displayed several metabolic changes that are typical of plant responses to low-N stress, including increased levels of starch and anthocyanin synthesis as well as decreased levels of soluble protein and free amino acid, as compared with those in wild-type seedlings when external N was sufficient. More striking changes were observed when dfc seedlings were grown under N-limited conditions, including shorter primary roots, fewer lateral roots, higher levels of glycine and carbon-N ratios, and lower N content than those in wild-type seedlings. Gene expression studies in mutant seedlings revealed altered transcript levels of several genes involved in folate biosynthesis and N metabolism. The biochemical and metabolic changes also suggested that N assimilation is drastically perturbed due to a loss of DFC function. The observation that elevated CO(2) partly rescued the dfc phenotypes suggests that the alterations in N metabolism in dfc may be mainly due to a defect in photorespiration. These results indicate that DFC is required for N utilization in Arabidopsis and provide new insight into a potential interaction between folate and N metabolism.
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Sha L, Ling J, Chongying W, Chunyi Z. Research Advances in the Functions of Plant Folates. ACTA ACUST UNITED AC 2013. [DOI: 10.3724/sp.j.1259.2012.00525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Capron A, Chang XF, Hall H, Ellis B, Beatson RP, Berleth T. Identification of quantitative trait loci controlling fibre length and lignin content in Arabidopsis thaliana stems. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:185-97. [PMID: 23136168 PMCID: PMC3528028 DOI: 10.1093/jxb/ers319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Fibre properties and the biochemical composition of cell walls are important traits in many applications. For example, the lengths of fibres define the strength and quality of paper, and lignin content is a critical parameter for the use of biomass in biofuel production. Identifying genes controlling these traits is comparatively difficult in woody species, because of long generation times and limited amenability to high-resolution genetic mapping. To address this problem, this study mapped quantitative trait loci (QTLs) defining fibre length and lignin content in the Arabidopsis recombinant inbred line population Col-4 × Ler-0. Adapting high-throughput phenotyping techniques for both traits for measurements in Arabidopsis inflorescence stems identified significant QTLs for fibre length on chromosomes 2 and 5, as well as one significant QTL affecting lignin content on chromosome 2. For fibre length, total variation within the population was 208% higher than between parental lines and the identified QTLs explained 50.58% of the observed variation. For lignin content, the values were 261 and 26.51%, respectively. Bioinformatics analysis of the associated intervals identified a number of candidate genes for fibre length and lignin content. This study demonstrates that molecular mapping of QTLs pertaining to wood and fibre properties is possible in Arabidopsis, which substantially broadens the use of Arabidopsis as a model species for the functional characterization of plant genes.
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Affiliation(s)
- Arnaud Capron
- University of Toronto-CSB, 25 Willcocks Street, Toronto, ON, Canada, M5S 3B2
| | - Xue Feng Chang
- British Columbia Institute of Technology, 3700 Willingdon Avenue, Burnaby, BC, Canada, V5G 3H2
| | - Hardy Hall
- University of British Columbia – Michael Smith Laboratories, #301–2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Brian Ellis
- University of British Columbia – Michael Smith Laboratories, #301–2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Rodger P. Beatson
- British Columbia Institute of Technology, 3700 Willingdon Avenue, Burnaby, BC, Canada, V5G 3H2
| | - Thomas Berleth
- University of Toronto-CSB, 25 Willcocks Street, Toronto, ON, Canada, M5S 3B2
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Gerdes S, Lerma-Ortiz C, Frelin O, Seaver SMD, Henry CS, de Crécy-Lagard V, Hanson AD. Plant B vitamin pathways and their compartmentation: a guide for the perplexed. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5379-95. [PMID: 22915736 DOI: 10.1093/jxb/ers208] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The B vitamins and the cofactors derived from them are essential for life. B vitamin synthesis in plants is consequently as crucial to plants themselves as it is to humans and animals, whose B vitamin nutrition depends largely on plants. The synthesis and salvage pathways for the seven plant B vitamins are now broadly known, but certain enzymes and many transporters have yet to be identified, and the subcellular locations of various reactions are unclear. Although very substantial, what is not known about plant B vitamin pathways is regrettably difficult to discern from the literature or from biochemical pathway databases. Nor do databases accurately represent all that is known about B vitamin pathways-above all their compartmentation-because the facts are scattered throughout the literature, and thus hard to piece together. These problems (i) deter discoveries because newcomers to B vitamins cannot see which mysteries still need solving; and (ii) impede metabolic reconstruction and modelling of B vitamin pathways because genes for reactions or transport steps are missing. This review therefore takes a fresh approach to capture current knowledge of B vitamin pathways in plants. The synthesis pathways, key salvage routes, and their subcellular compartmentation are surveyed in depth, and encoded in the SEED database (http://pubseed.theseed.org/seedviewer.cgi?page=PlantGateway) for Arabidopsis and maize. The review itself and the encoded pathways specifically identify enigmatic or missing reactions, enzymes, and transporters. The SEED-encoded B vitamin pathway collection is a publicly available, expertly curated, one-stop resource for metabolic reconstruction and modeling.
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Affiliation(s)
- Svetlana Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
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Srivastava AC, Tang Y, de la Garza RID, Blancaflor EB. The plastidial folylpolyglutamate synthetase and root apical meristem maintenance. PLANT SIGNALING & BEHAVIOR 2011; 6:751-4. [PMID: 21502816 PMCID: PMC3172856 DOI: 10.4161/psb.6.5.15403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 03/07/2011] [Indexed: 05/02/2023]
Abstract
Folylpolyglutamate synthetase (FPGS) catalyzes the attachment of glutamate residues to the folate molecule in plants. Three isoforms of FPGS have been identified in Arabidopsis and these are localized in the plastid (AtDFB), mitochondria (AtDFC), and cytosol (AtDFD). We recently determined that mutants in the AtDFB (At5G05980) gene disrupt primary root development in Arabidopsis thaliana seedlings. Transient expression of AtDFB-green fluorescent protein (GFP) fusion under the control of the native AtDFB promoter in Nicotiana tabacum leaf epidermal cells verified the plastid localization of AtDFB. Furthermore, low concentrations of methotrexate (MTX), a compound commonly used as a folate antagonist in plant and mammalian cells induced primary root defects in wild type seedlings that were similar to atdfb. In addition, atdfb seedlings were more sensitive to MTX when compared to wild type. Quantitative (q) RT-PCR showed lower transcript levels of the mitochondrial and cytosolic FPGS in roots of 7 day old atdfb seedling suggesting feedback regulation of AtDFB on the expression of other FPGS isoforms during early seedling development. The primary root defects of atdfb, which can be traced in part to altered quiescent center (QC) identity, pave the way for future studies that could link cell type specific folate and FPGS isoform requirements to whole organ development.
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Srivastava AC, Ramos-Parra PA, Bedair M, Robledo-Hernández AL, Tang Y, Sumner LW, Díaz de la Garza RI, Blancaflor EB. The folylpolyglutamate synthetase plastidial isoform is required for postembryonic root development in Arabidopsis. PLANT PHYSIOLOGY 2011; 155:1237-51. [PMID: 21233333 PMCID: PMC3046582 DOI: 10.1104/pp.110.168278] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A recessive Arabidopsis (Arabidopsis thaliana) mutant with short primary roots and root hairs was identified from a forward genetic screen. The disrupted gene in the mutant encoded the plastidial isoform of folylpolyglutamate synthetase (FPGS), previously designated as AtDFB, an enzyme that catalyzes the addition of glutamate residues to the folate molecule to form folylpolyglutamates. The short primary root of atdfb was associated with a disorganized quiescent center, dissipated auxin gradient in the root cap, bundled actin cytoskeleton, and reduced cell division and expansion. The accumulation of monoglutamylated forms of some folate classes in atdfb was consistent with impaired FPGS function. The observed cellular defects in roots of atdfb underscore the essential role of folylpolyglutamates in the highly compartmentalized one-carbon transfer reactions (C1 metabolism) that lead to the biosynthesis of compounds required for metabolically active cells found in the growing root apex. Indeed, metabolic profiling uncovered a depletion of several amino acids and nucleotides in atdfb indicative of broad alterations in metabolism. Methionine and purines, which are synthesized de novo in plastids via C1 enzymatic reactions, were particularly depleted. The root growth and quiescent center defects of atdfb were rescued by exogenous application of 5-formyl-tetrahydrofolate, a stable folate that was readily converted to metabolically active folates. Collectively, our results indicate that AtDFB is the predominant FPGS isoform that generates polyglutamylated folate cofactors to support C1 metabolism required for meristem maintenance and cell expansion during postembryonic root development in Arabidopsis.
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Hanson AD, Gregory JF. Folate biosynthesis, turnover, and transport in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 62:105-25. [PMID: 21275646 DOI: 10.1146/annurev-arplant-042110-103819] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Folates are essential cofactors for one-carbon transfer reactions and are needed in the diets of humans and animals. Because plants are major sources of dietary folate, plant folate biochemistry has long been of interest but progressed slowly until the genome era. Since then, genome-enabled approaches have brought rapid advances: We now know (a) all the plant folate synthesis genes and some genes of folate turnover and transport, (b) certain mechanisms governing folate synthesis, and (c) the subcellular locations of folate synthesis enzymes and of folates themselves. Some of this knowledge has been applied, simply and successfully, to engineer folate-enriched food crops (i.e., biofortification). Much remains to be discovered about folates, however, particularly in relation to homeostasis, catabolism, membrane transport, and vacuolar storage. Understanding these processes, which will require both biochemical and -omics research, should lead to improved biofortification strategies based on transgenic or conventional approaches.
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Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
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Pribat A, Noiriel A, Morse AM, Davis JM, Fouquet R, Loizeau K, Ravanel S, Frank W, Haas R, Reski R, Bedair M, Sumner LW, Hanson AD. Nonflowering plants possess a unique folate-dependent phenylalanine hydroxylase that is localized in chloroplasts. THE PLANT CELL 2010; 22:3410-22. [PMID: 20959559 PMCID: PMC2990131 DOI: 10.1105/tpc.110.078824] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 08/18/2010] [Accepted: 10/05/2010] [Indexed: 05/07/2023]
Abstract
Tetrahydropterin-dependent aromatic amino acid hydroxylases (AAHs) are known from animals and microbes but not plants. A survey of genomes and ESTs revealed AAH-like sequences in gymnosperms, mosses, and algae. Analysis of full-length AAH cDNAs from Pinus taeda, Physcomitrella patens, and Chlamydomonas reinhardtii indicated that the encoded proteins form a distinct clade within the AAH family. These proteins were shown to have Phe hydroxylase activity by functional complementation of an Escherichia coli Tyr auxotroph and by enzyme assays. The P. taeda and P. patens AAHs were specific for Phe, required iron, showed Michaelian kinetics, and were active as monomers. Uniquely, they preferred 10-formyltetrahydrofolate to any physiological tetrahydropterin as cofactor and, consistent with preferring a folate cofactor, retained activity in complementation tests with tetrahydropterin-depleted E. coli host strains. Targeting assays in Arabidopsis thaliana mesophyll protoplasts using green fluorescent protein fusions, and import assays with purified Pisum sativum chloroplasts, indicated chloroplastic localization. Targeting assays further indicated that pterin-4a-carbinolamine dehydratase, which regenerates the AAH cofactor, is also chloroplastic. Ablating the single AAH gene in P. patens caused accumulation of Phe and caffeic acid esters. These data show that nonflowering plants have functional plastidial AAHs, establish an unprecedented electron donor role for a folate, and uncover a novel link between folate and aromatic metabolism.
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Affiliation(s)
- Anne Pribat
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Alexandre Noiriel
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Alison M. Morse
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611
| | - John M. Davis
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611
| | - Romain Fouquet
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Karen Loizeau
- Laboratoire de Physiologie Cellulaire Végétale, Centre National de la Recherche Scientifique/Commissariat à l’Energie Atomique/Institut National de la Recherche Agronomique/Université Joseph Fourier, Commissariat à l’Energie Atomique-Grenoble, F-38054 Grenoble Cedex 9, France
| | - Stéphane Ravanel
- Laboratoire de Physiologie Cellulaire Végétale, Centre National de la Recherche Scientifique/Commissariat à l’Energie Atomique/Institut National de la Recherche Agronomique/Université Joseph Fourier, Commissariat à l’Energie Atomique-Grenoble, F-38054 Grenoble Cedex 9, France
| | - Wolfgang Frank
- Plant Biotechnology, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Richard Haas
- Plant Biotechnology, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Mohamed Bedair
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Lloyd W. Sumner
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
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