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Zhao Y, Hu J, Zhou Z, Li L, Zhang X, He Y, Zhang C, Wang J, Hong G. Biofortified Rice Provides Rich Sakuranetin in Endosperm. RICE (NEW YORK, N.Y.) 2024; 17:19. [PMID: 38430431 PMCID: PMC10908774 DOI: 10.1186/s12284-024-00697-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
Sakuranetin plays a key role as a phytoalexin in plant resistance to biotic and abiotic stresses, and possesses diverse health-promoting benefits. However, mature rice seeds do not contain detectable levels of sakuranetin. In the present study, a transgenic rice plant was developed in which the promoter of an endosperm-specific glutelin gene OsGluD-1 drives the expression of a specific enzyme naringenin 7-O-methyltransferase (NOMT) for sakuranetin biosynthesis. The presence of naringenin, which serves as the biosynthetic precursor of sakuranetin made this modification feasible in theory. Liquid chromatography tandem mass spectrometry (LC-MS/MS) validated that the seeds of transgenic rice accumulated remarkable sakuranetin at the mature stage, and higher at the filling stage. In addition, the panicle blast resistance of transgenic rice was significantly higher than that of the wild type. Specially, the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging was performed to detect the content and spatial distribution of sakuranetin and other nutritional metabolites in transgenic rice seeds. Notably, this genetic modification also did not change the nutritional and quality indicators such as soluble sugars, total amino acids, total flavonoids, amylose, total protein, and free amino acid content in rice. Meanwhile, the phenotypes of the transgenic plant during the whole growth and developmental periods and agricultural traits such as grain width, grain length, and 1000-grain weight exhibited no significant differences from the wild type. Collectively, the study provides a conceptual advance on cultivating sakuranetin-rich biofortified rice by metabolic engineering. This new breeding idea may not only enhance the disease resistance of cereal crop seeds but also improve the nutritional value of grains for human health benefits.
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Affiliation(s)
- Yao Zhao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Jitao Hu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Zhongjing Zhou
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Linying Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Xueying Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Yuqing He
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Chi Zhang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Junmin Wang
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Gaojie Hong
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China.
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2
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Feng Y, Chang SK, Portnoy DA. The major role of Listeria monocytogenes folic acid metabolism during infection is the generation of N-formylmethionine. mBio 2023; 14:e0107423. [PMID: 37695058 PMCID: PMC10653936 DOI: 10.1128/mbio.01074-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 09/12/2023] Open
Abstract
IMPORTANCE Folic acid is an essential vitamin for bacteria, plants, and animals. The lack of folic acid leads to various consequences such as a shortage of amino acids and nucleotides that are fundamental building blocks for life. Though antifolate drugs are widely used for antimicrobial treatments, the underlying mechanism of bacterial folate deficiency during infection is unclear. This study compares the requirements of different folic acid end-products during the infection of Listeria monocytogenes, a facultative intracellular pathogen of animals and humans. The results reveal the critical importance of N-formylmethionine, the amino acid used by bacteria to initiate protein synthesis. This work extends the current understanding of folic acid metabolism in pathogens and potentially provides new insights into antifolate drug development in the future.
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Affiliation(s)
- Ying Feng
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Shannon K. Chang
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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3
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Li X, Meng H, Liu L, Hong C, Zhang C. Metabolic network changes during skotomorphogenesis in Arabidopsis thaliana mutant ( atdfb-3). PLANT DIRECT 2022; 6:e00467. [PMID: 36438611 PMCID: PMC9684686 DOI: 10.1002/pld3.467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
The metabolic networks underlying skotomorphogenesis in seedlings remain relatively unknown. On the basis of our previous study on the folate metabolism in seedlings grown in darkness, the plastidial folylpolyglutamate synthetase gene (AtDFB) T-DNA insertion Arabidopsis thaliana mutant (atdfb-3) was examined. Under the nitrate-sufficient condition, the mutant exhibited deficient folate metabolism and hypocotyl elongation, which affected skotomorphogenesis. Further analyses revealed changes to multiple intermediate metabolites related to carbon and nitrogen metabolism in the etiolated atdfb-3 seedlings. Specifically, the sugar, polyol, and fatty acid contents decreased in the atdfb-3 mutant under the nitrate-sufficient condition, whereas the abundance of various organic acids and amino acids increased. In response to nitrate-limited stress, multiple metabolites, including sugars, polyols, fatty acids, organic acids, and amino acids, accumulated more in the mutant than in the wild-type control. The differences in the contents of multiple metabolites between the atdfb-3 and wild-type seedlings decreased following the addition of exogenous 5-F-THF under both nitrogen conditions. Additionally, the mutant accumulated high levels of one-carbon metabolites, such as Cys, S-adenosylmethionine, and S-adenosylhomocysteine, under both nitrogen conditions. Thus, our data demonstrated that the perturbed folate metabolism in the atdfb-3 seedlings, which was caused by the loss-of-function mutation to AtDFB, probably altered carbon and nitrogen metabolism, thereby modulating skotomorphogenesis. Furthermore, the study findings provide new evidence of the links among folate metabolism, metabolic networks, and skotomorphogenesis.
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Affiliation(s)
- Xingjuan Li
- College of BioengineeringBeijing PolytechnicBeijingChina
| | - Hongyan Meng
- Fujian Provincial Key Laboratory of Subtropical Plant Physiology and BiochemistryFujian Institute of Subtropical BotanyXiamenChina
| | - Liqing Liu
- Fujian Provincial Key Laboratory of Subtropical Plant Physiology and BiochemistryFujian Institute of Subtropical BotanyXiamenChina
| | - Cuiyun Hong
- Fujian Provincial Key Laboratory of Subtropical Plant Physiology and BiochemistryFujian Institute of Subtropical BotanyXiamenChina
| | - Chunyi Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
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4
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Vadlamani G, Sukhoverkov KV, Haywood J, Breese KJ, Fisher MF, Stubbs KA, Bond CS, Mylne JS. Crystal structure of Arabidopsis thaliana HPPK/DHPS, a bifunctional enzyme and target of the herbicide asulam. PLANT COMMUNICATIONS 2022; 3:100322. [PMID: 35605193 PMCID: PMC9284294 DOI: 10.1016/j.xplc.2022.100322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/21/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Herbicides are vital for modern agriculture, but their utility is threatened by genetic or metabolic resistance in weeds, as well as regulatory barriers. Of the known herbicide modes of action, 7,8-dihydropterin synthase (DHPS), which is involved in folate biosynthesis, is targeted by just one commercial herbicide, asulam. A mimic of the substrate para-aminobenzoic acid, asulam is chemically similar to sulfonamide antibiotics, and although it is still in widespread use, asulam has faced regulatory scrutiny. With an entire mode of action represented by just one commercial agrochemical, we sought to improve the understanding of its plant target. Here we solve a 2.3 Å resolution crystal structure for Arabidopsis thaliana DHPS that is conjoined to 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), and we reveal a strong structural conservation with bacterial counterparts at the sulfonamide-binding pocket of DHPS. We demonstrate that asulam and the antibiotic sulfamethoxazole have herbicidal as well as antibacterial activity, and we explore the structural basis of their potency by modeling these compounds in mitochondrial HPPK/DHPS. Our findings suggest limited opportunity for the rational design of plant selectivity from asulam and indicate that pharmacokinetic or delivery differences between plants and microbes might be the best ways to safeguard this mode of action.
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Affiliation(s)
- Grishma Vadlamani
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Kirill V Sukhoverkov
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Karen J Breese
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Mark F Fisher
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia.
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5
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Sanchez-Arcos C, Ueberschaar N, Pohnert G. Aquifer system and depth specific chemical patterns in fractured-rock groundwater from the Critical Zone revealed by untargeted LC-MS-based metabolomics. WATER RESEARCH 2022; 219:118566. [PMID: 35580391 DOI: 10.1016/j.watres.2022.118566] [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: 12/15/2021] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
In the Earth's Critical Zone, water plays an essential role as a collector and transporter of metabolites and their transformation products. It is generally believed that the chemical profiles of groundwater are strongly impacted by land use. However, predictors for the effects of above-ground natural and anthropogenic activities on below-ground chemistry are rare. We reasoned that comparing groundwater metabolomes from different land-use sites and depths can give insight into this coupling of above and below-ground processes in the Critical Zone. This study used an LC-MS-based untargeted metabolomic approach to identify links between groundwater metabolomes from monitoring wells in fractured carbonate-/siliciclastic alternations along a hillslope of the Hainich Critical Zone Exploratory (CZE) in Thuringia, Germany. Our results identify the land-use type, aquifer system, and sampling depth as critical factors determining the differences among groundwater metabolomes. We established five groundwater metabolic clusters and correlated these to the aquifer systems, hydrogeochemistry, and microbial community composition. Our untargeted metabolomic approach reveals the limited connectivity of groundwater chemical profiles with above-ground activities and illustrates how deep the input signals can travel.
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Affiliation(s)
- Carlos Sanchez-Arcos
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743, Jena, Germany
| | - Nico Ueberschaar
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743, Jena, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743, Jena, Germany.
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6
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B Vitamins and Their Roles in Gut Health. Microorganisms 2022; 10:microorganisms10061168. [PMID: 35744686 PMCID: PMC9227236 DOI: 10.3390/microorganisms10061168] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023] Open
Abstract
B vitamins act as coenzymes in a myriad of cellular reactions. These include energy production, methyl donor generation, neurotransmitter synthesis, and immune functions. Due to the ubiquitous roles of these vitamins, their deficiencies significantly affect the host’s metabolism. Recently, novel roles of B vitamins in the homeostasis of gut microbial ecology and intestinal health continue to be unravelled. This review focuses on the functional roles and biosynthesis of B vitamins and how these vitamins influence the growth and proliferation of the gut microbiota. We have identified the gut bacteria that can produce vitamins, and their biosynthetic mechanisms are presented. The effects of B vitamin deficiencies on intestinal morphology, inflammation, and its effects on intestinal disorders are also discussed.
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7
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Wu J, Yan X, Weng P, Chen G, Wu Z. Homology- and cross-resistance of Lactobacillus plantarum to acid and osmotic stress and the influence of induction conditions on its proliferation by RNA-Seq. J Basic Microbiol 2021; 61:576-590. [PMID: 33945164 DOI: 10.1002/jobm.202100051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/23/2021] [Accepted: 04/18/2021] [Indexed: 12/27/2022]
Abstract
In this study, homology- and cross-resistance of Lactobacillus plantarum L1 and Lactobacillus plantarum L2 to acid and osmotic stress were investigated. Meanwhile, its proliferation mechanism was demonstrated by transcriptomic analysis using RNA sequencing. We found that the homologous-resistance and cross-resistance of L. plantarum L1 and L. plantarum L2 increased after acid and osmotic induction treatment by lactic acid and sodium lactate solution in advance, and the survival rate of live bacteria was improved. In addition, the count of viable bacteria of L. plantarum L2 significantly increased cultivated at a pH 5.0 with a 15% sodium lactate sublethal treatment, compared with the control group. Further study revealed that genes related to membrane transport, amino acid metabolism, nucleotide metabolism, and cell growth were significantly upregulated. These findings will contribute to promote high-density cell culture of starter cultures production in the fermented food industry.
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Affiliation(s)
- Jingyi Wu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Xu Yan
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Peifang Weng
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Gong Chen
- Sichuan Food Fermentation Industry Research and Design Institute, Chengdu, Sichuan, China
| | - Zufang Wu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
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8
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Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa. Int J Mol Sci 2021; 22:ijms22073477. [PMID: 33801727 PMCID: PMC8036860 DOI: 10.3390/ijms22073477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/26/2023] Open
Abstract
Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.
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Lu C, Liu Y, Li J, Liu L, Du G. Engineering of Biosynthesis Pathway and NADPH Supply for Improved L-5-Methyltetrahydrofolate Production by Lactococcus lactis. J Microbiol Biotechnol 2021; 31:154-162. [PMID: 31893598 PMCID: PMC9705839 DOI: 10.4014/jmb.1910.10069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/17/2019] [Indexed: 12/15/2022]
Abstract
L-5-methyltetrahydrofolate (5-MTHF) is one of the biological active forms of folate, which is widely used as a nutraceutical. However, low yield and serious pollution associated with the chemical synthesis of 5-MTHF hampers its sustainable supply. In this study, 5-MTHF production was improved by engineering the 5-MTHF biosynthesis pathway and NADPH supply in Lactococcus lactis for developing a green and sustainable biosynthesis approach. Specifically, overexpressing the key rate-limiting enzyme methylenetetrahydrofolate reductase led to intracellular 5-MTHF accumulation, reaching 18 μg/l. Next, 5-MTHF synthesis was further enhanced by combinatorial overexpression of 5-MTHF synthesis pathway enzymes with methylenetetrahydrofolate reductase, resulting in 1.7-fold enhancement. The folate supply pathway was strengthened by expressing folE encoding GTP cyclohydrolase I, which increased 5-MTHF production 2.4-fold to 72 μg/l. Furthermore, glucose-6-phosphate dehydrogenase was overexpressed to improve the redox cofactor NADPH supply for 5-MTHF biosynthesis, which led to a 60% increase in intracellular NADPH and a 35% increase in 5-MTHF production (97 μg/l). To reduce formation of the by-product 5-formyltetrahydrofolate, overexpression of 5-formyltetrahydrofolate cyclo-ligase converted 5-formyltetrahydrofolate to 5,10-methyltetrahydrofolate, which enhanced the 5-MTHF titer to 132 μg/l. Finally, combinatorial addition of folate precursors to the fermentation medium boosted 5-MTHF production, reaching 300 μg/l. To the best of our knowledge, this titer is the highest achieved by L. lactis. This study lays the foundation for further engineering of L. lactis for efficient 5-MTHF biosynthesis.
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Affiliation(s)
- Chuanchuan Lu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China,Corresponding authors Y.Liu Phone: +86-510-85197117 Fax: +86-510-85918309 E-mail:
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 2422, P.R. China,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 141, P.R. China,G.Du Phone: +86-510-85918309 Fax: +86-510-85918309 E-mail:
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10
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Grabsztunowicz M, Rokka A, Farooq I, Aro EM, Mulo P. Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria. BMC PLANT BIOLOGY 2020; 20:413. [PMID: 32887556 PMCID: PMC7650296 DOI: 10.1186/s12870-020-02635-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/30/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Non-photosynthetic plastids of plants are known to be involved in a range of metabolic and biosynthetic reactions, even if they have been difficult to study due to their small size and lack of color. The morphology of root plastids is heterogeneous and also the plastid size, density and subcellular distribution varies depending on the cell type and developmental stage, and therefore the functional features have remained obscure. Although the root plastid proteome is likely to reveal specific functional features, Arabidopsis thaliana root plastid proteome has not been studied to date. RESULTS In the present study, we separated Arabidopsis root protein fraction enriched with plastids and mitochondria by 2D-PAGE and identified 84 plastid-targeted and 77 mitochondrion-targeted proteins using LC-MS/MS. The most prevalent root plastid protein categories represented amino acid biosynthesis, carbohydrate metabolism and lipid biosynthesis pathways, while the enzymes involved in starch and sucrose metabolism were not detected. Mitochondrion-targeted proteins were classified mainly into the energetics category. CONCLUSIONS This is the first study presenting gel-based map of Arabidopsis thaliana root plastid and mitochondrial proteome. Our findings suggest that Arabidopsis root plastids have broad biosynthetic capacity, and that they do not play a major role in a long-term storage of carbohydrates. The proteomic map provides a tool for further studies to compare changes in the proteome, e.g. in response to environmental cues, and emphasizes the role of root plastids in nitrogen and sulfur metabolism as well as in amino acid and fatty acid biosynthesis. The results enable taking a first step towards an integrated view of root plastid/mitochondrial proteome and metabolic functions in Arabidopsis thaliana roots.
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Affiliation(s)
| | - Anne Rokka
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Irum Farooq
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland
| | - Paula Mulo
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland.
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11
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Woortman DV, Fuchs T, Striegel L, Fuchs M, Weber N, Brück TB, Rychlik M. Microalgae a Superior Source of Folates: Quantification of Folates in Halophile Microalgae by Stable Isotope Dilution Assay. Front Bioeng Biotechnol 2020; 7:481. [PMID: 32039182 PMCID: PMC6985443 DOI: 10.3389/fbioe.2019.00481] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/23/2019] [Indexed: 12/24/2022] Open
Abstract
A multitude of human nutritional supplements based on Chlorella vulgaris biomass has recently been introduced to the specialty food market. In this study, an analysis of total folate contents in Chlorella sp. and a series of marine microalgae was conducted to evaluate folate content in alternative algae-based food production strains. For the first time, total folate content and vitamer distribution in microalgae were analyzed by stable isotope dilution assay (SIDA) using LC-MS/MS, which has demonstrated its superiority with respect to folate quantification. Consistently, high folate contents were detected in all examined microalgae samples. High folate concentrations of 3,460 ± 134 μg/100 g dry biomass were detected in freshly cultivated Chlorella vulgaris, notably also in other well-researched microalgae strains. To that end, the highest folate content currently documented for any algae sample was measured in the marine microalgae Picochlorum sp. isolate with values of 6,470 ± 167 μg/100 g dry biomass. This calls for alternative products based on other algae biomass. Our data indicate that freshwater and marine microalgae provide extremely high concentrations of folates, which warrant further studies on the regulation of pteroylpolyglutamates in algae as well as on bioaccessibility, absorption, and retention in humans.
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Affiliation(s)
- Dirk Volker Woortman
- Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Tobias Fuchs
- Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Lisa Striegel
- Chair of Analytical Food Chemistry, Technical University of Munich, Freising, Germany
| | - Monika Fuchs
- Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Nadine Weber
- Chair of Analytical Food Chemistry, Technical University of Munich, Freising, Germany
| | - Thomas B. Brück
- Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Michael Rychlik
- Chair of Analytical Food Chemistry, Technical University of Munich, Freising, Germany
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
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12
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Cao X, Du B, Han F, Zhou Y, Ren J, Wang W, Chen Z, Zhang Y. Crystal Structure of the Chloroplastic Glutamine Phosphoribosylpyrophosphate Amidotransferase GPRAT2 From Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:157. [PMID: 32174940 PMCID: PMC7056826 DOI: 10.3389/fpls.2020.00157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/31/2020] [Indexed: 05/03/2023]
Abstract
Chloroplastic glutamine phosphoribosylpyrophosphate amidotransferase (GPRATase) catalyzes the first committed step of de novo purine biosynthesis in Arabidopsis thaliana, and DAS734 is a direct and specific inhibitor of AtGPRAT, with phytotoxic effects similar to the leaf beaching phenotypes of known AtGPRAT genetic mutants, especially cia1 and atd2. However, the structure of AtGPRAT and the inhibition mode of DAS734 still remain poorly understood. In this study, we solved the structure of AtGPRAT2, which revealed structural differences between AtGPRAT2 and bacterial enzymes. Kinetics assay demonstrated that DAS734 behaves as a competitive inhibitor for the substrate phosphoribosyl pyrophosphate (PRPP) of AtGPRAT2. Docking studies showed that DAS734 forms electrostatic interactions with R264 and hydrophobic interactions with several residues, which was verified by binding assays. Collectively, our study provides important insights into the inhibition mechanism of DAS734 to AtGPRAT2 and sheds light on future studies into further development of more potent herbicides targeting Arabidopsis GPRATases.
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Affiliation(s)
- Xueli Cao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Bowen Du
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Fengjiao Han
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Yu Zhou
- Department of Computational Chemistry, National Institute of Biological Sciences, Beijing, China
| | - Junhui Ren
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Wenhe Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Zeliang Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
- *Correspondence: Yi Zhang,
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13
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Hutinet G, Kot W, Cui L, Hillebrand R, Balamkundu S, Gnanakalai S, Neelakandan R, Carstens AB, Fa Lui C, Tremblay D, Jacobs-Sera D, Sassanfar M, Lee YJ, Weigele P, Moineau S, Hatfull GF, Dedon PC, Hansen LH, de Crécy-Lagard V. 7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat Commun 2019; 10:5442. [PMID: 31784519 PMCID: PMC6884629 DOI: 10.1038/s41467-019-13384-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, was recently detected in genomic DNA of Enterobacteria phage 9g and was proposed to protect phage DNA from a wide variety of restriction enzymes. In this study, we identify three additional 2'-deoxy-7-deazaguanine modifications, which are all intermediates of the same pathway, in viruses: 2'-deoxy-7-amido-7-deazaguanine (dADG), 2'-deoxy-7-cyano-7-deazaguanine (dPreQ0) and 2'-deoxy-7- aminomethyl-7-deazaguanine (dPreQ1). We identify 180 phages or archaeal viruses that encode at least one of the enzymes of this pathway with an overrepresentation (60%) of viruses potentially infecting pathogenic microbial hosts. Genetic studies with the Escherichia phage CAjan show that DpdA is essential to insert the 7-deazaguanine base in phage genomic DNA and that 2'-deoxy-7-deazaguanine modifications protect phage DNA from host restriction enzymes.
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Affiliation(s)
- Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Roman Hillebrand
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Nitto Denko Avecia, 125 Fortune Boulevard, Milford, MA, 01757, USA
| | - Seetharamsingh Balamkundu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Shanmugavel Gnanakalai
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Ramesh Neelakandan
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | | | - Chuan Fa Lui
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Denise Tremblay
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Mandana Sassanfar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Peter Weigele
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Sylvain Moineau
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Graham F Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
- University of Florida, Genetics Institute, Gainesville, Florida, 32610, USA.
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14
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Liang Q, Wang K, Liu X, Riaz B, Jiang L, Wan X, Ye X, Zhang C. Improved folate accumulation in genetically modified maize and wheat. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1539-1551. [PMID: 30753561 PMCID: PMC6411382 DOI: 10.1093/jxb/ery453] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/13/2018] [Indexed: 05/10/2023]
Abstract
Folates are indispensable co-factors for one-carbon metabolism in all organisms. In humans, suboptimal folate intake results in serious disorders. One promising strategy for improving human folate status is to enhance folate levels in food crops by metabolic engineering. In this study, we cloned two GmGCHI (GTP cyclohydrolase I) genes (Gm8gGCHI and Gm3gGCHI) and one GmADCS (aminodeoxychorismate synthase) gene from soybean, which are responsible for synthesizing the folate precursors pterin and p-aminobenzoate, respectively. We initially confirmed their functions in transgenic Arabidopsis plants and found that Gm8gGCHI increased pterin and folate production more than Gm3gGCHI did. We then co-expressed Gm8gGCHI and GmADCS driven by endosperm-specific promoters in maize and wheat, two major staple crops, to boost their folate metabolic flux. A 4.2-fold and 2.3-fold increase in folate levels were observed in transgenic maize and wheat grains, respectively. To optimize wheat folate enhancement, codon-optimized Gm8gGCHI and tomato LeADCS genes under the control of a wheat endosperm-specific glutenin promoter (1Dx5) were co-transformed. This yielded a 5.6-fold increase in folate in transgenic wheat grains (Gm8gGCHI+/LeADCS+). This two-gene co-expression strategy therefore has the potential to greatly enhance folate levels in maize and wheat, thus improving their nutritional value.
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Affiliation(s)
- Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoning Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bisma Riaz
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xing Wan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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15
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Tabatabaei I, Dal Bosco C, Bednarska M, Ruf S, Meurer J, Bock R. A highly efficient sulfadiazine selection system for the generation of transgenic plants and algae. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:638-649. [PMID: 30144344 PMCID: PMC6381783 DOI: 10.1111/pbi.13004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/17/2018] [Indexed: 05/02/2023]
Abstract
The genetic transformation of plant cells is critically dependent on the availability of efficient selectable marker gene. Sulfonamides are herbicides that, by inhibiting the folic acid biosynthetic pathway, suppress the growth of untransformed cells. Sulfonamide resistance genes that were previously developed as selectable markers for plant transformation were based on the assumption that, in plants, the folic acid biosynthetic pathway resides in the chloroplast compartment. Consequently, the Sul resistance protein, a herbicide-insensitive dihydropteroate synthase, was targeted to the chloroplast. Although these vectors produce transgenic plants, the transformation efficiencies are low compared to other markers. Here, we show that this inefficiency is due to the erroneous assumption that the folic acid pathway is located in chloroplasts. When the RbcS transit peptide was replaced by a transit peptide for protein import into mitochondria, the compartment where folic acid biosynthesis takes place in yeast, much higher resistance to sulfonamide and much higher transformation efficiencies are obtained, suggesting that current sul vectors are likely to function due to low-level mistargeting of the resistance protein to mitochondria. We constructed a series of optimized transformation vectors and demonstrate that they produce transgenic events at very high frequency in both the seed plant tobacco and the green alga Chlamydomonas reinhardtii. Co-transformation experiments in tobacco revealed that sul is even superior to nptII, the currently most efficient selectable marker gene, and thus provides an attractive marker for the high-throughput genetic transformation of plants and algae.
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Affiliation(s)
- Iman Tabatabaei
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Cristina Dal Bosco
- Department für Biologie ILudwig‐Maximilians‐Universität MünchenMünchenGermany
- Present address:
Pioneer Hi‐Bred Northern Europe Service Division GmbHEschbachGermany
| | - Marta Bednarska
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Stephanie Ruf
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Jörg Meurer
- Department für Biologie ILudwig‐Maximilians‐Universität MünchenMünchenGermany
| | - Ralph Bock
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
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16
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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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17
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Bodnar JL, Fitch S, Rosati A, Zhong J. The folA gene from the Rickettsia endosymbiont of Ixodes pacificus encodes a functional dihydrofolate reductase enzyme. Ticks Tick Borne Dis 2017; 9:443-449. [PMID: 29284564 DOI: 10.1016/j.ttbdis.2017.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 12/07/2017] [Accepted: 12/16/2017] [Indexed: 11/24/2022]
Abstract
Although nonpathogenic bacterial endosymbionts have been shown to contribute to their arthropod host's fitness by supplying them with essential vitamins and amino acids, little is known about the nutritional basis for the symbiotic relationship of endosymbionts in ticks. Our lab has previously reported that Rickettsia species phylotype G021 in Ixodes pacificus carries all five genes for de novo folate synthesis, and that these genes are monophyletic with homologs from other Rickettsia species. In this study, the rickettsial folate synthesis folA gene, coding for dihydrofolate reductase, was PCR amplified, cloned into an expression vector, and overexpressed in E. coli. Bioinformatic analysis identified that the FolA protein of phylotype G021 has the conserved DHFR domain, NADP binding sites, and substrate binding sites of bacterial dihydrofolate reductase. SDS-PAGE results showed that recombinant rickettsial FolA protein was overexpressed in BL21(DE3) E. coli in its soluble form. Affinity chromatography was used to purify the protein, and in vitro enzyme assays were performed to assess the biochemical activity of dihydrofolate reductase. The specific activity of recombinant FolA from phylotype G021 was determined to be 16.1 U/mg. This study has revealed that Rickettsia species phylotype G021 of I. pacificus is capable of producing a functional enzyme of the folate biosynthesis pathway, addressing the nutritional interactions behind the symbiosis between Rickettsia species phylotype G021 and its host.
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Affiliation(s)
- James L Bodnar
- Department of Biological Sciences, Humboldt State University, 1 Harpst Street, Arcata, CA, 95521, USA.
| | - Sergio Fitch
- Department of Biological Sciences, Humboldt State University, 1 Harpst Street, Arcata, CA, 95521, USA.
| | - Allison Rosati
- Department of Biological Sciences, Humboldt State University, 1 Harpst Street, Arcata, CA, 95521, USA.
| | - Jianmin Zhong
- Department of Biological Sciences, Humboldt State University, 1 Harpst Street, Arcata, CA, 95521, USA.
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18
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Sirota TV, Lyamina NE, Weisfeld LI. The Antioxidant properties of para-Aminobenzoic acid and its sodium salt. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917050219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Xie W, Perry G, Martin CJ, Shim YS, Navabi A, Pauls KP. Molecular characterization of dihydroneopterin aldolase and aminodeoxychorismate synthase in common bean—genes coding for enzymes in the folate synthesis pathway. Genome 2017; 60:588-600. [DOI: 10.1139/gen-2016-0227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Common beans (Phaseolus vulgaris) are excellent sources of dietary folates, but different varieties contain different amounts of these compounds. Genes coding for dihydroneopterin aldolase (DHNA) and aminodeoxychorismate synthase (ADCS) of the folate synthesis pathway were characterized by PCR amplification, BAC clone sequencing, and whole genome sequencing. All DHNA and ADCS genes in the Mesoamerican cultivar OAC Rex were isolated and compared with those genes in the genome of Andean genotype G19833. Both genotypes have two functional DHNA genes and one pseudo gene. PvDHNA1 and PvDHNA2 proteins have similar secondary structures and conserved residues as DHNA homologs in Staphylococcus aureus and Arabidopsis. Sequence analysis and synteny mapping indicated that PvDHNA1 might be a duplicated and transposed copy of PvDHNA2. There is only one ADCS gene (PvADCS) identified in the bean genome and it is identical in OAC Rex and G19833. PvADCS has the conserved motifs required for catalytic activity similar to other plant ADCS homologs. DHNA and ADCS gene-specific markers were developed, mapped, and compared to their physical locations on chromosomes 1 and 7, respectively. The gene-specific markers developed in this study should be useful for detection and selection of varieties with enhanced folate contents in bean breeding programs.
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Affiliation(s)
- Weilong Xie
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - Gregory Perry
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - C. Joe Martin
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - Youn-Seb Shim
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - Alireza Navabi
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - K. Peter Pauls
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
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20
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Watanabe S, Ohtani Y, Tatsukami Y, Aoki W, Amemiya T, Sukekiyo Y, Kubokawa S, Ueda M. Folate Biofortification in Hydroponically Cultivated Spinach by the Addition of Phenylalanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4605-4610. [PMID: 28548831 DOI: 10.1021/acs.jafc.7b01375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Folate is an important vitamin mainly ingested from vegetables, and folate deficiency causes various health problems. Recently, several studies demonstrated folate biofortification in plants or food crops by metabolic engineering through genetic modifications. However, the production and sales of genetically modified foods are under strict regulation. Here, we developed a new approach to achieve folate biofortification in spinach (Spinacia oleracea) without genetic modification. We hydroponically cultivated spinach with the addition of three candidate compounds expected to fortify folate. As a result of liquid chromatography tandem mass spectrometry analysis, we found that the addition of phenylalanine increased the folate content up to 2.0-fold (306 μg in 100 g of fresh spinach), representing 76.5% of the recommended daily allowance for adults. By measuring the intermediates of folate biosynthesis, we revealed that phenylalanine activated folate biosynthesis in spinach by increasing the levels of pteridine and p-aminobenzoic acid. Our approach is a promising and practical approach to cultivate nutrient-enriched vegetables.
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Affiliation(s)
- Sho Watanabe
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuta Ohtani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
| | - Yohei Tatsukami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
- Japan Society for the Promotion of Science , Sakyo-ku, Kyoto 606-8502, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center , Shimogyo-ku, Kyoto 600-8813, Japan
| | - Takashi Amemiya
- Mitsubishi Plastic, Inc. , Chiyoda-ku, Tokyo 100-8252, Japan
| | | | | | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Sakyo-ku, Kyoto 606-8502, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center , Shimogyo-ku, Kyoto 600-8813, Japan
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21
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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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Keshari D, Singh KS, Sharma R, Yadav S, Singh SK. MSMEG_5684 down-regulation in Mycobacterium smegmatis affects its permeability, survival under stress and persistence. Tuberculosis (Edinb) 2017; 103:61-70. [PMID: 28237035 DOI: 10.1016/j.tube.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/06/2017] [Accepted: 01/17/2017] [Indexed: 11/16/2022]
Abstract
The Mycobacterium tuberculosis (Mtb) genome sequence and annotation details have been available for a long time; however physiological relevance of many ORFs remains poorly described. Mtb is a pathogenic strain; hence, surrogate strains such as Mycobacterium bovis BCG and Mycobacterium smegmatis (Msmeg) have also been studied to gain an understanding of mycobacterial physiology and metabolism. The Mycobacterium smegmatis mc2 155 ORF MSMEG_5684 is annotated as a part of serine biosynthetic pathway, however, its physiological significance remains to be established experimentally. To understand the relevance of SerC for Msmeg physiology we developed a recombinant Mycobacterium smegmatis with SerC knockdown (KD) and also complemented it with serC over-expressing construct (KDC). The KD showed reduced growth compared to wild-type (WT) and complemented strain on glycerol as carbon source. The growth of KD was restored after supplementation of serine. The survival studies with WT and KD under oxidative, nitrosative and detergent stresses showed increased susceptibility of KD. The KD also showed increased susceptibility to antimycobacterial agents and poor ability for in vitro persistence. Also, the serC transcript profiling showed increased expression under stress. The complementation studies with Msmeg serC showed growth restoration of E. coli-ΔserC in minimal medium.
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Affiliation(s)
- Deepa Keshari
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Kumar Sachin Singh
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Rishabh Sharma
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Shailendra Yadav
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Sudheer Kumar Singh
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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23
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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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24
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Yue H, Liang Q, Zhang W, Cao Z, Tan G, Zhang C, Wang B. A Monoclonal Antibody-Based Enzyme-Linked Immunosorbent Assay for 5-Formyltetrahydrofolate Detection in Maize Kernels. FOOD ANAL METHOD 2016. [DOI: 10.1007/s12161-016-0503-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Yang Z, Shang Z, Wang L, Lu Q, Wen X, Chi W, Zhang L, Lu C. Purine biosynthetic enzyme ATase2 is involved in the regulation of early chloroplast development and chloroplast gene expression in Arabidopsis. PHOTOSYNTHESIS RESEARCH 2015; 126:285-300. [PMID: 25837856 DOI: 10.1007/s11120-015-0131-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/24/2015] [Indexed: 05/14/2023]
Abstract
To investigate the molecular mechanism of chloroplast biogenesis and development, we characterized an Arabidopsis mutant (dg169, delayed greening 169) which showed growth retardation and delayed greening phenotype in leaves. Newly emerged chlorotic leaves recovered gradually with leaf development in the mutant, and the mature leaves showed similar phenotype to those of wild-typewild-type plants. Compared with wild-type, the chloroplasts were oval-shaped and smaller and the thylakoid membranes were less abundant in yellow section of young leaves of dg169. In addition, the functions of photosystem II (PSII) and photosystem I (PSI) were also impaired. Furthermore, the amount of core subunits of PSII and PSI, as well as PSII and PSI complexes reduced in yellow section of young leaves of dg169. Map-based positional cloning identified that phenotype of dg169 was attributed to a point mutation of ATase2 which converts the conserved Ile-155 residue to Asn. ATase2 catalyzes the first step of de novo purine biosynthesis. This mutation resulted in impaired purine synthesis and a significant decrease in ATP, ADP, GTP and GDP contents. The analysis of ATase2-GFP protein fusion showed that ATase2 was localized to nucleoid of chloroplasts. Our results further demonstrated that the levels of PEP-dependent transcripts in yellow section of young leaves of dg169 were decreased while NEP-dependent and both PEP- and NEP-dependent transcripts and chloroplast DNA replications were increased. The results in this study suggest that ATase2 plays an essential role in early chloroplast development through maintaining PEP function.
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Affiliation(s)
- Zhipan Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zengzhen Shang
- 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
| | - Lei 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
| | - Qingtao Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaogang Wen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Congming Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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26
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Lian T, Guo W, Chen M, Li J, Liang Q, Liu F, Meng H, Xu B, Chen J, Zhang C, Jiang L. Genome-wide identification and transcriptional analysis of folate metabolism-related genes in maize kernels. BMC PLANT BIOLOGY 2015; 15:204. [PMID: 26283542 PMCID: PMC4539672 DOI: 10.1186/s12870-015-0578-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/23/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND Maize is a major staple food crop globally and contains various concentrations of vitamins. Folates are essential water-soluble B-vitamins that play an important role as one-carbon (C1) donors and acceptors in organisms. To gain an understanding of folate metabolism in maize, we performed an intensive in silico analysis to screen for genes involved in folate metabolism using publicly available databases, followed by examination of the transcript expression patterns and profiling of the folate derivatives in the kernels of two maize inbred lines. RESULTS A total of 36 candidate genes corresponding to 16 folate metabolism-related enzymes were identified. The maize genome contains all the enzymes required for folate and C1 metabolism, characterized by highly conserved functional domains across all the other species investigated. Phylogenetic analysis revealed that these enzymes in maize are conserved throughout evolution and have a high level of similarity with those in sorghum and millet. The LC-MS analyses of two maize inbred lines demonstrated that 5-methyltetrahydrofolate was the major form of folate derivative in young seeds, while 5-formyltetrahydrofolate in mature seeds. Most of the genes involved in folate and C1 metabolism exhibited similar transcriptional expression patterns between these two maize lines, with the highest transcript abundance detected on day after pollination (DAP) 6 and the decreased transcript abundance on DAP 12 and 18. Compared with the seeds on DAP 30, 5-methyltetrahydrofolate was decreased and 5-formyltetrahydrofolate was increased sharply in the mature dry seeds. CONCLUSIONS The enzymes involved in folate and C1 metabolism are conserved between maize and other plant species. Folate and C1 metabolism is active in young developing maize seeds at transcriptional levels.
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Affiliation(s)
- Tong Lian
- 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.
| | - Maoran Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| | - Jinglai Li
- Beijing Institute of Pharmacology and Toxicology, Beijing, People's Republic of China.
| | - Qiuju Liang
- 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.
| | - Fang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| | - Hongyan Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| | - Bosi Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| | - Jinfeng Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
- Southwest University of Science and Technology, Mianyang, 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.
| | - 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.
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Lambret-Frotté J, de Almeida LCS, de Moura SM, Souza FLF, Linhares FS, Alves-Ferreira M. Validating Internal Control Genes for the Accurate Normalization of qPCR Expression Analysis of the Novel Model Plant Setaria viridis. PLoS One 2015; 10:e0135006. [PMID: 26247784 PMCID: PMC4527663 DOI: 10.1371/journal.pone.0135006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/15/2015] [Indexed: 01/10/2023] Open
Abstract
Employing reference genes to normalize the data generated with quantitative PCR (qPCR) can increase the accuracy and reliability of this method. Previous results have shown that no single housekeeping gene can be universally applied to all experiments. Thus, the identification of a suitable reference gene represents a critical step of any qPCR analysis. Setaria viridis has recently been proposed as a model system for the study of Panicoid grasses, a crop family of major agronomic importance. Therefore, this paper aims to identify suitable S. viridis reference genes that can enhance the analysis of gene expression in this novel model plant. The first aim of this study was the identification of a suitable RNA extraction method that could retrieve a high quality and yield of RNA. After this, two distinct algorithms were used to assess the gene expression of fifteen different candidate genes in eighteen different samples, which were divided into two major datasets, the developmental and the leaf gradient. The best-ranked pair of reference genes from the developmental dataset included genes that encoded a phosphoglucomutase and a folylpolyglutamate synthase; genes that encoded a cullin and the same phosphoglucomutase as above were the most stable genes in the leaf gradient dataset. Additionally, the expression pattern of two target genes, a SvAP3/PI MADS-box transcription factor and the carbon-fixation enzyme PEPC, were assessed to illustrate the reliability of the chosen reference genes. This study has shown that novel reference genes may perform better than traditional housekeeping genes, a phenomenon which has been previously reported. These results illustrate the importance of carefully validating reference gene candidates for each experimental set before employing them as universal standards. Additionally, the robustness of the expression of the target genes may increase the utility of S. viridis as a model for Panicoid grasses.
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Affiliation(s)
- Julia Lambret-Frotté
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | | | - Stéfanie M. de Moura
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | - Flavio L. F. Souza
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | - Francisco S. Linhares
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | - Marcio Alves-Ferreira
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
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28
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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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29
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de Crécy-Lagard V. Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. Comput Struct Biotechnol J 2014; 10:41-50. [PMID: 25210598 PMCID: PMC4151868 DOI: 10.1016/j.csbj.2014.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The availability of thousands of sequenced genomes has revealed the diversity of biochemical solutions to similar chemical problems. Even for molecules at the heart of metabolism, such as cofactors, the pathway enzymes first discovered in model organisms like Escherichia coli or Saccharomyces cerevisiae are often not universally conserved. Tetrahydrofolate (THF) (or its close relative tetrahydromethanopterin) is a universal and essential C1-carrier that most microbes and plants synthesize de novo. The THF biosynthesis pathway and enzymes are, however, not universal and alternate solutions are found for most steps, making this pathway a challenge to annotate automatically in many genomes. Comparing THF pathway reconstructions and functional annotations of a chosen set of folate synthesis genes in specific prokaryotes revealed the strengths and weaknesses of different microbial annotation platforms. This analysis revealed that most current platforms fail in metabolic reconstruction of variant pathways. However, all the pieces are in place to quickly correct these deficiencies if the different databases were built on each other's strengths.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science and Genetics Institute, University of Florida, Gainesville, FL, United States
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30
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Leston S, Nunes M, Viegas I, Nebot C, Cepeda A, Pardal MÂ, Ramos F. The influence of sulfathiazole on the macroalgae Ulva lactuca. CHEMOSPHERE 2014; 100:105-110. [PMID: 24393561 DOI: 10.1016/j.chemosphere.2013.12.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 12/09/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
Sulfonamides (SA) are a class of antibiotics routinely found in environmental matrices and therefore their role as contaminants should be investigated in non-target organisms. With this purpose the present experimental work has evaluated the exposure of the chlorophycean Ulva lactuca L. to sulfathiazole (STZ), a SA drug commonly used in aquaculture, at two concentrations representing prophylactic (25 μg mL(-1)) and therapeutic (50 μg mL(-1)) administrations. Results showed that STZ exhibits high stability in seawater with only 18% degradation over the 5d assay at both dosages tested. Also, macroalgae demonstrated an efficient uptake capacity with constant internal concentrations after 24h regardless of the external solutions and thus should be considered as a bioindicator species in risk assessment. Both STZ concentrations induced a slight inhibition of the macroalgae growth after 96 h.
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Affiliation(s)
- Sara Leston
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Apartado 3046, 3001-401 Coimbra, Portugal; CEF - Center for Pharmaceutical Studies, Health Sciences Campus, Pharmacy Faculty, University of Coimbra, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal.
| | - Margarida Nunes
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Apartado 3046, 3001-401 Coimbra, Portugal; CEF - Center for Pharmaceutical Studies, Health Sciences Campus, Pharmacy Faculty, University of Coimbra, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
| | - Ivan Viegas
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Apartado 3046, 3001-401 Coimbra, Portugal; CNC - Centre for Neurosciences and Cell Biology, Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Carolina Nebot
- Departamento de Nutrición y Bromatología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo 27002, Spain
| | - Alberto Cepeda
- Departamento de Nutrición y Bromatología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo 27002, Spain
| | - Miguel Ângelo Pardal
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Apartado 3046, 3001-401 Coimbra, Portugal
| | - Fernando Ramos
- CEF - Center for Pharmaceutical Studies, Health Sciences Campus, Pharmacy Faculty, University of Coimbra, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
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Para-aminobenzoic acid (PABA) synthase enhances thermotolerance of mushroom Agaricus bisporus. PLoS One 2014; 9:e91298. [PMID: 24614118 PMCID: PMC3948851 DOI: 10.1371/journal.pone.0091298] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 02/11/2014] [Indexed: 12/03/2022] Open
Abstract
Most mushrooms are thermo-sensitive to temperatures over 23°C, which greatly restricts their agricultural cultivation. Understanding mushroom’s innate heat-tolerance mechanisms may facilitate genetic improvements of their thermotolerance. Agaricus bisporus strain 02 is a relatively thermotolerant mushroom strain, while strain 8213 is quite thermo-sensitive. Here, we compared their responses at proteomic level to heat treatment at 33°C. We identified 73 proteins that are differentially expressed between 02 and 8213 or induced upon heat stress in strain 02 itself, 48 of which with a known identity. Among them, 4 proteins are constitutively more highly expressed in 02 than 8213; and they can be further upregulated in response to heat stress in 02, but not in 8213. One protein is encoded by the para-aminobenzoic acid (PABA) synthase gene Pabs, which has been shown to scavenge the reactive oxygen species in vitro. Pabs mRNA and its chemical product PABA show similar heat stress induction pattern as PABA synthase protein and are more abundant in 02, indicating transcriptional level upregulation of Pabs upon heat stress. A specific inhibitor of PABA synthesis impaired thermotolerance of 02, while exogenous PABA or transgenic overexpression of 02 derived PABA synthase enhanced thermotolerance of 8213. Furthermore, compared to 8213, 02 accumulated less H2O2 but more defense-related proteins (e.g., HSPs and Chitinase) under heat stress. Together, these results demonstrate a role of PABA in enhancing mushroom thermotolerance by removing H2O2 and elevating defense-related proteins.
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32
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Cândido EDS, Fernandes GDR, de Alencar SA, Cardoso MHES, Lima SMDF, Miranda VDJ, Porto WF, Nolasco DO, de Oliveira-Júnior NG, Barbosa AEADD, Pogue RE, Rezende TMB, Dias SC, Franco OL. Shedding some light over the floral metabolism by arum lily (Zantedeschia aethiopica) spathe de novo transcriptome assembly. PLoS One 2014; 9:e90487. [PMID: 24614014 PMCID: PMC3948674 DOI: 10.1371/journal.pone.0090487] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 02/01/2014] [Indexed: 01/19/2023] Open
Abstract
Zantedeschia aethiopica is an evergreen perennial plant cultivated worldwide and commonly used for ornamental and medicinal purposes including the treatment of bacterial infections. However, the current understanding of molecular and physiological mechanisms in this plant is limited, in comparison to other non-model plants. In order to improve understanding of the biology of this botanical species, RNA-Seq technology was used for transcriptome assembly and characterization. Following Z. aethiopica spathe tissue RNA extraction, high-throughput RNA sequencing was performed with the aim of obtaining both abundant and rare transcript data. Functional profiling based on KEGG Orthology (KO) analysis highlighted contigs that were involved predominantly in genetic information (37%) and metabolism (34%) processes. Predicted proteins involved in the plant circadian system, hormone signal transduction, secondary metabolism and basal immunity are described here. In silico screening of the transcriptome data set for antimicrobial peptide (AMP) –encoding sequences was also carried out and three lipid transfer proteins (LTP) were identified as potential AMPs involved in plant defense. Spathe predicted protein maps were drawn, and suggested that major plant efforts are expended in guaranteeing the maintenance of cell homeostasis, characterized by high investment in carbohydrate, amino acid and energy metabolism as well as in genetic information.
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Affiliation(s)
- Elizabete de Souza Cândido
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Gabriel da Rocha Fernandes
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Sérgio Amorim de Alencar
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Marlon Henrique e Silva Cardoso
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Stella Maris de Freitas Lima
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Vívian de Jesus Miranda
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - William Farias Porto
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Diego Oliveira Nolasco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Curso de Física, Universidade Católica de Brasília, Brasília - DF, Brazil
| | - Nelson Gomes de Oliveira-Júnior
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Programa de Pós-Graduação em Biologia Animal, Universidade de Brasília, Brasília-DF, Brazil
| | - Aulus Estevão Anjos de Deus Barbosa
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Robert Edward Pogue
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Taia Maria Berto Rezende
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Curso de Odontologia, Universidade Católica de Brasília, Brasília - DF, Brazil
| | - Simoni Campos Dias
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Octávio Luiz Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
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Benstein RM, Ludewig K, Wulfert S, Wittek S, Gigolashvili T, Frerigmann H, Gierth M, Flügge UI, Krueger S. Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis. THE PLANT CELL 2013; 25:5011-29. [PMID: 24368794 PMCID: PMC3904002 DOI: 10.1105/tpc.113.118992] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/26/2013] [Accepted: 12/06/2013] [Indexed: 05/17/2023]
Abstract
In plants, two independent serine biosynthetic pathways, the photorespiratory and glycolytic phosphoserine (PS) pathways, have been postulated. Although the photorespiratory pathway is well characterized, little information is available on the function of the PS pathway in plants. Here, we present a detailed characterization of phosphoglycerate dehydrogenases (PGDHs) as components of the PS pathway in Arabidopsis thaliana. All PGDHs localize to plastids and possess similar kinetic properties, but they differ with respect to their sensitivity to serine feedback inhibition. Furthermore, analysis of pgdh1 and phosphoserine phosphatase mutants revealed an embryo-lethal phenotype and PGDH1-silenced lines were inhibited in growth. Metabolic analyses of PGDH1-silenced lines grown under ambient and high CO2 conditions indicate a direct link between PS biosynthesis and ammonium assimilation. In addition, we obtained several lines of evidence for an interconnection between PS and tryptophan biosynthesis, because the expression of PGDH1 and phosphoserine aminotransferase1 is regulated by MYB51 and MYB34, two activators of tryptophan biosynthesis. Moreover, the concentration of tryptophan-derived glucosinolates and auxin were reduced in PGDH1-silenced plants. In essence, our results provide evidence for a vital function of PS biosynthesis for plant development and metabolism.
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Abstract
Mechanisms postulated to link folate and B12 metabolism with cancer, including genome-wide hypomethylation, gene-specific promoter hypermethylation, and DNA uracil misincorporation, have been observed in prostate tumor cells. However, epidemiological studies of prostate cancer risk, based on dietary intakes and blood levels of folate and vitamin B12 and on folate-pathway gene variants, have generated contradictory findings. In a meta-analysis, circulating concentrations of B12 (seven studies, OR = 1.10; 95% CI 1.01, 1.19; P = 0.002) and (in cohort studies) folate (five studies, OR = 1.18; 95% CI 1.00, 1.40; P = 0.02) were positively associated with an increased risk of prostate cancer. Homocysteine was not associated with risk of prostate cancer (four studies, OR = 0.91; 95% CI 0.69, 1.19; P = 0.5). In a meta-analysis of folate-pathway polymorphisms, MTR 2756A > G (eight studies, OR = 1.06; 95% CI 1.00, 1.12; P = 0.06) and SHMT1 1420C > T (two studies, OR = 1.11; 95% CI 1.00, 1.22; P = 0.05) were positively associated with prostate cancer risk. There were no effects due to any other polymorphisms, including MTHFR 677C > T (12 studies, OR = 1.04; 95% CI 0.97, 1.12; P = 0.3). The positive association of circulating B12 with an increased risk of prostate cancer could be explained by reverse causality. However, given current controversies over mandatory B12 fortification, further research to eliminate a causal role of B12 in prostate cancer initiation and/or progression is required. Meta-analysis does not entirely rule out a positive association of circulating folate with increased prostate cancer risk. As with B12, even a weak positive association would be a significant public health issue, given the high prevalence of prostate cancer and concerns about the potential harms versus benefits of mandatory folic acid fortification.
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Thomas DB, McGoverin CM, McGraw KJ, James HF, Madden O. Vibrational spectroscopic analyses of unique yellow feather pigments (spheniscins) in penguins. J R Soc Interface 2013; 10:20121065. [PMID: 23516063 DOI: 10.1098/rsif.2012.1065] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many animals extract, synthesize and refine chemicals for colour display, where a range of compounds and structures can produce a diverse colour palette. Feather colours, for example, span the visible spectrum and mostly result from pigments in five chemical classes (carotenoids, melanins, porphyrins, psittacofulvins and metal oxides). However, the pigment that generates the yellow colour of penguin feathers appears to represent a sixth, poorly characterized class of feather pigments. This pigment class, here termed 'spheniscin', is displayed by half of the living penguin genera; the larger and richer colour displays of the pigment are highly attractive. Using Raman and mid-infrared spectroscopies, we analysed yellow feathers from two penguin species (king penguin, Aptenodytes patagonicus; macaroni penguin, Eudyptes chrysolophus) to further characterize spheniscin pigments. The Raman spectrum of spheniscin is distinct from spectra of other feather pigments and exhibits 17 distinctive spectral bands between 300 and 1700 cm(-1). Spectral bands from the yellow pigment are assigned to aromatically bound carbon atoms, and to skeletal modes in an aromatic, heterocyclic ring. It has been suggested that the penguin pigment is a pterin compound; Raman spectra from yellow penguin feathers are broadly consistent with previously reported pterin spectra, although we have not matched it to any known compound. Raman spectroscopy can provide a rapid and non-destructive method for surveying the distribution of different classes of feather pigments in the avian family tree, and for correlating the chemistry of spheniscin with compounds analysed elsewhere. We suggest that the sixth class of feather pigments may have evolved in a stem-lineage penguin and endowed modern penguins with a costly plumage trait that appears to be chemically unique among birds.
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Affiliation(s)
- Daniel B Thomas
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
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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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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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Barberis CL, Carranza CS, Chiacchiera SM, Magnoli CE. Influence of herbicide glyphosate on growth and aflatoxin B1 production by Aspergillus section Flavi strains isolated from soil on in vitro assay. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2013; 48:1070-9. [PMID: 24007484 DOI: 10.1080/03601234.2013.824223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The effect of six glyphosate concentrations on growth rate and aflatoxin B1 (AFB1) production by Aspergillus section Flavi strains under different water activity (aW) on maize-based medium was investigated. In general, the lag phase decreased as glyphosate concentration increased and all the strains showed the same behavior at the different conditions tested. The glyphosate increased significantly the growth of all Aspergillus section Flavi strains in different percentages with respect to control depending on pesticide concentration. At 5.0 and 10 mM this fact was more evident; however significant differences between both concentrations were not observed in most strains. Aflatoxin B1 production did not show noticeable differences among different pesticide concentrations assayed at all aW in both strains. This study has shown that these Aspergillus flavus and A. parasiticus strains are able to grow effectively and produce aflatoxins in high nutrient status media over a range of glyphosate concentrations under different water activity conditions.
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Affiliation(s)
- Carla L Barberis
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico, Químicas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, Argentina
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Crops that feed the world 8: Potato: are the trends of increased global production sustainable? Food Secur 2012. [DOI: 10.1007/s12571-012-0220-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Farnham MW, Lester GE, Hassell R. Collard, mustard and turnip greens: Effects of genotypes and leaf position on concentrations of ascorbic acid, folate, β-carotene, lutein and phylloquinone. J Food Compost Anal 2012. [DOI: 10.1016/j.jfca.2012.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Walsh CT, Haynes SW, Ames BD. Aminobenzoates as building blocks for natural productassembly lines. Nat Prod Rep 2012; 29:37-59. [DOI: 10.1039/c1np00072a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kube M, Mitrovic J, Duduk B, Rabus R, Seemüller E. Current view on phytoplasma genomes and encoded metabolism. ScientificWorldJournal 2011; 2012:185942. [PMID: 22550465 PMCID: PMC3322544 DOI: 10.1100/2012/185942] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 11/20/2011] [Indexed: 11/21/2022] Open
Abstract
Phytoplasmas are specialised bacteria that are obligate parasites of plant phloem tissue and insects. These bacteria have resisted all attempts of cell-free cultivation. Genome research is of particular importance to analyse the genetic endowment of such bacteria. Here we review the gene content of the four completely sequenced ‘Candidatus Phytoplasma' genomes that include those of ‘Ca. P. asteris' strains OY-M and AY-WB, ‘Ca. P. australiense,' and ‘Ca. P. mali'. These genomes are characterized by chromosome condensation resulting in sizes below 900 kb and a G + C content of less than 28%. Evolutionary adaption of the phytoplasmas to nutrient-rich environments resulted in losses of genetic modules and increased host dependency highlighted by the transport systems and limited metabolic repertoire. On the other hand, duplication and integration events enlarged the chromosomes and contribute to genome instability. Present differences in the content of membrane and secreted proteins reflect the host adaptation in the phytoplasma strains. General differences are obvious between different phylogenetic subgroups. ‘Ca. P. mali' is separated from the other strains by its deviating chromosome organization, the genetic repertoire for recombination and excision repair of nucleotides or the loss of the complete energy-yielding part of the glycolysis. Apart from these differences, comparative analysis exemplified that all four phytoplasmas are likely to encode an alternative pathway to generate pyruvate and ATP.
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Affiliation(s)
- Michael Kube
- Department of Crop and Animal Sciences, Humboldt-University of Berlin, Lentzeallee 55/57, 14195 Berlin, Germany.
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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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Rossi M, Amaretti A, Raimondi S. Folate production by probiotic bacteria. Nutrients 2011; 3:118-34. [PMID: 22254078 PMCID: PMC3257725 DOI: 10.3390/nu3010118] [Citation(s) in RCA: 368] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 12/24/2010] [Accepted: 01/17/2011] [Indexed: 12/14/2022] Open
Abstract
Probiotic bacteria, mostly belonging to the genera Lactobacillus and Bifidobacterium, confer a number of health benefits to the host, including vitamin production. With the aim to produce folate-enriched fermented products and/or develop probiotic supplements that accomplish folate biosynthesis in vivo within the colon, bifidobacteria and lactobacilli have been extensively studied for their capability to produce this vitamin. On the basis of physiological studies and genome analysis, wild-type lactobacilli cannot synthesize folate, generally require it for growth, and provide a negative contribution to folate levels in fermented dairy products. Lactobacillus plantarum constitutes an exception among lactobacilli, since it is capable of folate production in presence of para-aminobenzoic acid (pABA) and deserves to be used in animal trials to validate its ability to produce the vitamin in vivo. On the other hand, several folate-producing strains have been selected within the genus Bifidobacterium, with a great variability in the extent of vitamin released in the medium. Most of them belong to the species B. adolescentis and B. pseudocatenulatum, but few folate producing strains are found in the other species as well. Rats fed a probiotic formulation of folate-producing bifidobacteria exhibited increased plasma folate level, confirming that the vitamin is produced in vivo and absorbed. In a human trial, the same supplement raised folate concentration in feces. The use of folate-producing probiotic strains can be regarded as a new perspective in the specific use of probiotics. They could more efficiently confer protection against inflammation and cancer, both exerting the beneficial effects of probiotics and preventing the folate deficiency that is associated with premalignant changes in the colonic epithelia.
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Affiliation(s)
- Maddalena Rossi
- Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183, Modena 41100, Italy.
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Weber APM, Linka N. Connecting the plastid: transporters of the plastid envelope and their role in linking plastidial with cytosolic metabolism. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 62:53-77. [PMID: 21526967 DOI: 10.1146/annurev-arplant-042110-103903] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plastids have a multitude of functions in eukaryotic cells, ranging from photosynthesis to storage, and a role in essential biosynthetic pathways. All plastids are of either primary or higher-order endosymbiotic origin. That is, either a photosynthetic cyanobacterium was integrated into a mitochondriate eukaryotic host cell (primary endosymbiosis) or a plastid-bearing eukaryotic cell merged with another eukaryotic cell (secondary or higher-order endosymbioses), thereby passing on the plastid between various eukaryotic lineages. For all of these endosymbioses to become functional, it was essential to establish metabolic connections between organelle and host cell. Here, we review the present understanding of metabolite exchange between plastids and the surrounding cytosol in the context of the endosymbiotic origin of plastids in various eukaryotic lineages. We show that only a small number of transporters that can be traced down to the primary endosymbiotic event are conserved between plastids of diverse origins.
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Affiliation(s)
- Andreas P M Weber
- Institute of Plant Biochemistry, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf, Germany.
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Read M, Müller IB, Mitchell SL, Sims PFG, Hyde JE. Dynamic subcellular localization of isoforms of the folate pathway enzyme serine hydroxymethyltransferase (SHMT) through the erythrocytic cycle of Plasmodium falciparum. Malar J 2010; 9:351. [PMID: 21129192 PMCID: PMC3014972 DOI: 10.1186/1475-2875-9-351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 12/03/2010] [Indexed: 11/10/2022] Open
Abstract
Background The folate pathway enzyme serine hydroxymethyltransferase (SHMT) converts serine to glycine and 5,10-methylenetetrahydrofolate and is essential for the acquisition of one-carbon units for subsequent transfer reactions. 5,10-methylenetetrahydrofolate is used by thymidylate synthase to convert dUMP to dTMP for DNA synthesis. In Plasmodium falciparum an enzymatically functional SHMT (PfSHMTc) and a related, apparently inactive isoform (PfSHMTm) are found, encoded by different genes. Here, patterns of localization of the two isoforms during the parasite erythrocytic cycle are investigated. Methods Polyclonal antibodies were raised to PfSHMTc and PfSHMTm, and, together with specific markers for the mitochondrion and apicoplast, were employed in quantitative confocal fluorescence microscopy of blood-stage parasites. Results As well as the expected cytoplasmic occupancy of PfSHMTc during all stages, localization into the mitochondrion and apicoplast occurred in a stage-specific manner. Although early trophozoites lacked visible organellar PfSHMTc, a significant percentage of parasites showed such fluorescence during the mid-to-late trophozoite and schizont stages. In the case of the mitochondrion, the majority of parasites in these stages at any given time showed no marked PfSHMTc fluorescence, suggesting that its occupancy of this organelle is of limited duration. PfSHMTm showed a distinctly more pronounced mitochondrial location through most of the erythrocytic cycle and GFP-tagging of its N-terminal region confirmed the predicted presence of a mitochondrial signal sequence. Within the apicoplast, a majority of mitotic schizonts showed a marked concentration of PfSHMTc, whose localization in this organelle was less restricted than for the mitochondrion and persisted from the late trophozoite to the post-mitotic stages. PfSHMTm showed a broadly similar distribution across the cycle, but with a distinctive punctate accumulation towards the ends of elongating apicoplasts. In very late post-mitotic schizonts, both PfSHMTc and PfSHMTm were concentrated in the central region of the parasite that becomes the residual body on erythrocyte lysis and merozoite release. Conclusions Both PfSHMTc and PfSHMTm show dynamic, stage-dependent localization among the different compartments of the parasite and sequence analysis suggests they may also reversibly associate with each other, a factor that may be critical to folate cofactor function, given the apparent lack of enzymic activity of PfSHMTm.
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Affiliation(s)
- Martin Read
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Mehrshahi P, Gonzalez-Jorge S, Akhtar TA, Ward JL, Santoyo-Castelazo A, Marcus SE, Lara-Núñez A, Ravanel S, Hawkins ND, Beale MH, Barrett DA, Knox JP, Gregory JF, Hanson AD, Bennett MJ, Dellapenna D. Functional analysis of folate polyglutamylation and its essential role in plant metabolism and development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:267-79. [PMID: 21070407 DOI: 10.1111/j.1365-313x.2010.04336.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cellular folates function as co-enzymes in one-carbon metabolism and are predominantly decorated with a polyglutamate tail that enhances co-enzyme affinity, subcellular compartmentation and stability. Polyglutamylation is catalysed by folylpolyglutamate synthetases (FPGSs) that are specified by three genes in Arabidopsis, FPGS1, 2 and 3, which reportedly encode plastidic, mitochondrial and cytosolic isoforms, respectively. A mutational approach was used to probe the functional importance of folate polyglutamylation in one-carbon metabolism and development. Biochemical analysis of single FPGS loss-of-function mutants established that folate polyglutamylation is essential for organellar and whole-plant folate homeostasis. However, polyglutamylated folates were still detectable, albeit at lower levels, in organelles isolated from the corresponding isozyme knockout lines, e.g. in plastids and mitochondria of the fpgs1 (plastidial) and fpgs2 (mitochondrial) mutants. This result is surprising given the purported single-compartment targeting of each FPGS isozyme. These results indicate redundancy in compartmentalised FPGS activity, which in turn explains the lack of anticipated phenotypic defects for the single FPGS mutants. In agreement with this hypothesis, fpgs1 fpgs2 double mutants were embryo-lethal, fpgs2 fpgs3 mutants exhibited seedling lethality, and fpgs1 fpgs3 mutants were dwarfed with reduced fertility. These phenotypic, metabolic and genetic observations are consistent with targeting of one or more FPGS isozymes to multiple organelles. These data confirm the importance of polyglutamylation in folate compartmentation, folate homeostasis and folate-dependent metabolic processes, including photorespiration, methionine and pantothenate biosynthesis.
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Affiliation(s)
- Payam Mehrshahi
- Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA.
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Abstract
Due to the presence of plastids, eukaryotic photosynthetic cells represent the most highly compartmentalized eukaryotic cells. This high degree of compartmentation requires the transport of solutes across intracellular membrane systems by specific membrane transporters. In this review, we summarize the recent progress on functionally characterized intracellular plant membrane transporters and we link transporter functions to Arabidopsis gene identifiers and to the transporter classification system. In addition, we outline challenges in further elucidating the plant membrane permeome and we provide an outline of novel approaches for the functional characterization of membrane transporters.
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Affiliation(s)
- Nicole Linka
- Institute of Plant Biochemistry, Heinrich-Heine Universität Düsseldorf, Geb. 26.03.01, Universitätsstrasse 1, Düsseldorf, Germany
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Raichaudhuri A, Peng M, Naponelli V, Chen S, Sánchez-Fernández R, Gu H, Gregory JF, Hanson AD, Rea PA. Plant Vacuolar ATP-binding Cassette Transporters That Translocate Folates and Antifolates in Vitro and Contribute to Antifolate Tolerance in Vivo. J Biol Chem 2009; 284:8449-60. [PMID: 19136566 PMCID: PMC2659203 DOI: 10.1074/jbc.m808632200] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 01/05/2009] [Indexed: 02/01/2023] Open
Abstract
The vacuoles of pea (Pisum sativum) leaves and red beet (Beta vulgaris) storage root are major sites for the intracellular compartmentation of folates. In the light of these findings and preliminary experiments indicating that some plant multidrug resistance-associated protein (MRP) subfamily ATP-binding cassette transporters are able to transport compounds of this type, the Arabidopsis thaliana vacuolar MRP, AtMRP1 (AtABCC1), and its functional equivalent(s) in vacuolar membrane vesicles purified from red beet storage root were studied. In so doing, it has been determined that heterologously expressed AtMRP1 and its equivalents in red beet vacuolar membranes are not only competent in the transport of glutathione conjugates but also folate monoglutamates and antifolates as exemplified by pteroyl-l-glutamic acid and methotrexate (MTX), respectively. In agreement with the results of these in vitro transport measurements, analyses of atmrp1 T-DNA insertion mutants of Arabidopsis ecotypes Wassilewskia and Columbia disclose an MTX-hypersensitive phenotype. atmrp1 knock-out mutants are more sensitive than wild-type plants to growth retardation by nanomolar concentrations of MTX, and this is associated with impaired vacuolar antifolate sequestration. The vacuoles of protoplasts isolated from the leaves of Wassilewskia atmrp1 mutants accumulate 50% less [(3)H]MTX than the vacuoles of protoplasts from wild-type plants when incubated in media containing nanomolar concentrations of this antifolate, and vacuolar membrane-enriched vesicles purified from the mutant catalyze MgATP-dependent [(3)H]MTX uptake at only 40% of the capacity of the equivalent membrane fraction from wild-type plants. AtMRP1 and its counterparts in other plant species therefore have the potential for participating in the vacuolar accumulation of folates and related compounds.
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Affiliation(s)
- Ayan Raichaudhuri
- Plant Science Institute, Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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