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Guan J, Zhu J, Liu H, Yang H, Zhong S, Chen W, Yi X, Chen C, Tan F, Shen J, Luo P. Arogenate dehydratase isoforms strategically deregulate phenylalanine biosynthesis in Akebia trifoliata. Int J Biol Macromol 2024; 271:132587. [PMID: 38788880 DOI: 10.1016/j.ijbiomac.2024.132587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/01/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Arogenate dehydratase (ADT) is key for phenylalanine (Phe) biosynthesis in plants. To examine ADT components and function in Akebia trifoliata, a representative of Ranunculaceae, we first identified eight ADTs (AktADT1-8, encoding sequences varying from 1032 to 1962 bp) in the A. trifoliata reference genome and five proteins (AktADT1, AktADT4, AktADT7, AktADT8 and AktADT8s) with moonlighting prephenate dehydratase (PDT) activity and Km values varying from 0.43 to 2.17 mM. Structurally, two basic residue combinations (Val314/Ala317 and Ala314/Val317) in the PAC domain are essential for the moonlighting PDT activity of ADTs. Functionally, AktADT4 and AktADT8 successfully restored the wild-type phenotype of pha2, a knockout mutant of Saccharomyces cerevisiae. In addition, AktADTs are ubiquitously expressed, but their expression levels are tissue specific, and the half maximal inhibitory concentration (IC50) of Phe for AktADTs ranged from 49.81 to 331.17 μM. Both AktADT4 and AktADT8 and AktADT8s localized to chloroplast stromules and the cytosol, respectively, while the remaining AktADTs localized to the chloroplast stroma. These findings suggest that various strategies exist for regulating Phe biosynthesis in A. trifoliata. This provides a reasonable explanation for the high Phe content and insights for further genetic improvement of the edible fruits of A. trifoliata.
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Affiliation(s)
- Ju Guan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China; Cuisine Science Key Laboratory of Sichuan Province, Sichuan Tourism University, Chengdu 611130, China
| | - Jun Zhu
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Hao Liu
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China; Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu 611130, China
| | - Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Wei Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China; Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu 611130, China
| | - Xiaoxiao Yi
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Jinliang Shen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, Sichuan, China.
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Li X, Liu Y, Hu W, Yin B, Liang B, Li Z, Zhang X, Xu J, Zhou S. Integrative physiological, metabolomic, and transcriptomic analysis reveals the drought responses of two apple rootstock cultivars. BMC PLANT BIOLOGY 2024; 24:219. [PMID: 38532379 DOI: 10.1186/s12870-024-04902-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Drought is considered the main environmental factor restricting apple production and thus the development of the apple industry. Rootstocks play an important role in enhancing the drought tolerance of apple plants. Studies of the physiology have demonstrated that 'ZC9-3' is a strong drought-resistant rootstock, whereas 'Jizhen-2' is a weak drought-resistant rootstock. However, the metabolites in these two apple rootstock varieties that respond to drought stress have not yet been characterized, and the molecular mechanisms underlying their responses to drought stress remain unclear. RESULTS In this study, the physiological and molecular mechanisms underlying differences in the drought resistance of 'Jizhen-2' (drought-sensitive) and 'ZC9-3' (drought-resistant) apple rootstocks were explored. Under drought stress, the relative water content of the leaves was maintained at higher levels in 'ZC9-3' than in 'Jizhen-2', and the photosynthetic, antioxidant, and osmoregulatory capacities of 'ZC9-3' were stronger than those of 'Jizhen-2'. Metabolome analysis revealed a total of 95 and 156 differentially accumulated metabolites in 'Jizhen-2' and 'ZC9-3' under drought stress, respectively. The up-regulated metabolites in the two cultivars were mainly amino acids and derivatives. Transcriptome analysis revealed that there were more differentially expressed genes and transcription factors in 'ZC9-3' than in 'Jizhen-2' throughout the drought treatment. Metabolomic and transcriptomic analysis revealed that amino acid biosynthesis pathways play key roles in mediating drought resistance in apple rootstocks. A total of 13 metabolites, including L-α-aminoadipate, L-homoserine, L-threonine, L-isoleucine, L-valine, L-leucine, (2S)-2-isopropylmalate, anthranilate, L-tryptophan, L-phenylalanine, L-tyrosine, L-glutamate, and L-proline, play an important role in the difference in drought resistance between 'ZC9-3' and 'Jizhen-2'. In addition, 13 genes encoding O-acetylserine-(thiol)-lyase, S-adenosylmethionine synthetase, ketol-acid isomeroreductase, dihydroxyacid dehydratase, isopropylmalate isomerase, branched-chain aminotransferase, pyruvate kinase, 3-dehydroquinate dehydratase/shikimate 5-dehydrogenase, N-acetylglutamate-5-P-reductase, and pyrroline-5-carboxylate synthetase positively regulate the response of 'ZC9-3' to drought stress. CONCLUSIONS This study enhances our understanding of the response of apple rootstocks to drought stress at the physiological, metabolic, and transcriptional levels and provides key insights that will aid the cultivation of drought-resistant apple rootstock cultivars. Especially, it identifies key metabolites and genes underlying the drought resistance of apple rootstocks.
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Affiliation(s)
- Xiaohan Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Yitong Liu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Wei Hu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Baoying Yin
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Bowen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Zhongyong Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Xueying Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Jizhong Xu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China.
| | - Shasha Zhou
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China.
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Clayton EJ, Islam NS, Pannunzio K, Kuflu K, Sirjani R, Kohalmi SE, Dhaubhadel S. Soybean AROGENATE DEHYDRATASES (GmADTs): involvement in the cytosolic isoflavonoid metabolon or trans-organelle continuity? FRONTIERS IN PLANT SCIENCE 2024; 15:1307489. [PMID: 38322824 PMCID: PMC10845154 DOI: 10.3389/fpls.2024.1307489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Soybean (Glycine max) produces a class of phenylalanine (Phe) derived specialized metabolites, isoflavonoids. Isoflavonoids are unique to legumes and are involved in defense responses in planta, and they are also necessary for nodule formation with nitrogen-fixing bacteria. Since Phe is a precursor of isoflavonoids, it stands to reason that the synthesis of Phe is coordinated with isoflavonoid production. Two putative AROGENATE DEHYDRATASE (ADT) isoforms were previously co-purified with the soybean isoflavonoid metabolon anchor ISOFLAVONE SYNTHASE2 (GmIFS2), however the GmADT family had not been characterized. Here, we present the identification of the nine member GmADT family. We determined that the GmADTs share sequences required for enzymatic activity and allosteric regulation with other characterized plant ADTs. Furthermore, the GmADTs are differentially expressed, and multiple members have dual substrate specificity, also acting as PREPHENATE DEHYDRATASES. All GmADT isoforms were detected in the stromules of chloroplasts, and they all interact with GmIFS2 in the cytosol. In addition, GmADT12A interacts with multiple other isoflavonoid metabolon members. These data substantiate the involvement of GmADT isoforms in the isoflavonoid metabolon.
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Affiliation(s)
- Emily J. Clayton
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Nishat S. Islam
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Kelsey Pannunzio
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kuflom Kuflu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ramtin Sirjani
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Susanne E. Kohalmi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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Tong Y, Yi SC, Liu SY, Xu L, Qiu ZX, Zeng DQ, Tang WW. Bruceine D may affect the phenylpropanoid biosynthesis by acting on ADTs thus inhibiting Bidens pilosa L. seed germination. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113943. [PMID: 35999761 DOI: 10.1016/j.ecoenv.2022.113943] [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: 12/24/2021] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Bruceine D is a natural quassinoid, which was successfully isolated in our research group from the residue of Brucea javanica (L.) seeds. Our previous research showed that Bruceine D prevented Bidens pilosa L. seed germination by suppressing the activity of key enzymes and the expression levels of key genes involved in the phenylpropanoid biosynthesis pathway. In this study, integrated analyses of non-targeted metabolomic and transcriptomic were performed. A total of 356 different accumulated metabolites (DAMs) were identified, and KEGG pathway analyses revealed that most of these DAMs were involved in phenylpropanoid biosynthesis. The decreased expression of ADTs and content of L-phenylalanine implicates that Bruceine D may suppress the downstream phenylpropanoid biosynthesis pathway by disrupting primary metabolism, that is, the phenylalanine biosynthesis pathway, thus inhibiting the final products, resulting in the interruption of B. pilosa seed germination. These results suggest that Bruceine D may inhibit the B. pilosa seed germination by suppressing phenylpropanoid biosynthesis through acting on ADTs.
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Affiliation(s)
- Yao Tong
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Shan-Chi Yi
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Shu-Yu Liu
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Lin Xu
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Zhuo-Xun Qiu
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Dong-Qiang Zeng
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Wen-Wei Tang
- Guangxi Key Laboratory of Agrio-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China.
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Chakraborty A, Mahajan S, Jaiswal SK, Sharma VK. Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. Commun Biol 2021; 4:1193. [PMID: 34654884 PMCID: PMC8521574 DOI: 10.1038/s42003-021-02720-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 08/13/2021] [Indexed: 12/28/2022] Open
Abstract
Curcuma longa, or turmeric, is traditionally known for its immense medicinal properties and has diverse therapeutic applications. However, the absence of a reference genome sequence is a limiting factor in understanding the genomic basis of the origin of its medicinal properties. In this study, we present the draft genome sequence of C. longa, belonging to Zingiberaceae plant family, constructed using 10x Genomics linked reads and Oxford Nanopore long reads. For comprehensive gene set prediction and for insights into its gene expression, transcriptome sequencing of leaf tissue was also performed. The draft genome assembly had a size of 1.02 Gbp with ~70% repetitive sequences, and contained 50,401 coding gene sequences. The phylogenetic position of C. longa was resolved through a comprehensive genome-wide analysis including 16 other plant species. Using 5,388 orthogroups, the comparative evolutionary analysis performed across 17 species including C. longa revealed evolution in genes associated with secondary metabolism, plant phytohormones signaling, and various biotic and abiotic stress tolerance responses. These mechanisms are crucial for perennial and rhizomatous plants such as C. longa for defense and environmental stress tolerance via production of secondary metabolites, which are associated with the wide range of medicinal properties in C. longa.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shubham K Jaiswal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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Hixson KK, Marques JV, Wendler JP, McDermott JE, Weitz KK, Clauss TR, Monroe ME, Moore RJ, Brown J, Lipton MS, Bell CJ, Paša-Tolić L, Davin LB, Lewis NG. New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:664250. [PMID: 34113365 PMCID: PMC8185232 DOI: 10.3389/fpls.2021.664250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Multiple Arabidopsis arogenate dehydratase (ADT) knock-out (KO) mutants, with phenotypes having variable lignin levels (up to circa 70% reduction), were studied to investigate how differential reductions in ADTs perturb its overall plant systems biology. Integrated "omics" analyses (metabolome, transcriptome, and proteome) of wild type (WT), single and multiple ADT KO lines were conducted. Transcriptome and proteome data were collapsed into gene ortholog (GO) data, with this allowing for enzymatic reaction and metabolome cross-comparisons to uncover dominant or likely metabolic biosynthesis reactions affected. Network analysis of enzymes-highly correlated to stem lignin levels-deduced the involvement of novel putative lignin related proteins or processes. These included those associated with ribosomes, the spliceosome, mRNA transport, aminoacyl tRNA biosynthesis, and phosphorylation. While prior work helped explain lignin biosynthesis regulation at the transcriptional level, our data here provide support for a new hypothesis that there are additional post-transcriptional and translational level processes that need to be considered. These findings are anticipated to lead to development of more accurate depictions of lignin/phenylpropanoid biosynthesis models in situ, with new protein targets identified for further biochemical analysis and/or plant bioengineering. Additionally, using KEGG defined functional categorization of proteomics and transcriptomics analyses, we detected significant changes to glucosinolate, α-linolenic acid, nitrogen, carotenoid, aromatic amino acid, phenylpropanoid, and photosynthesis-related metabolic pathways in ADT KO mutants. Metabolomics results also revealed that putative carotenoid and galactolipid levels were generally increased in amount, whereas many glucosinolates and phenylpropanoids (including flavonoids and lignans) were decreased in the KO mutants.
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Affiliation(s)
- Kim K. Hixson
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joaquim V. Marques
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Jason P. Wendler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jason E. McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Karl K. Weitz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Therese R. Clauss
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Matthew E. Monroe
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ronald J. Moore
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joseph Brown
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Mary S. Lipton
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Callum J. Bell
- National Center for Genome Resources, Santa Fe, NM, United States
| | - Ljiljana Paša-Tolić
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Laurence B. Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Norman G. Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
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Lynch JH, Dudareva N. Aromatic Amino Acids: A Complex Network Ripe for Future Exploration. TRENDS IN PLANT SCIENCE 2020; 25:670-681. [PMID: 32526172 DOI: 10.1016/j.tplants.2020.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 05/28/2023]
Abstract
In plants, high carbon flux is committed to the biosynthesis of phenylalanine, tyrosine, and tryptophan, owing to their roles not only in the production of proteins, but also as precursors to thousands of primary and specialized metabolites. The core plastidial pathways that supply the majority of aromatic amino acids (AAAs) have previously been described in detail. More recently, the discovery of cytosolic enzymes contributing to overall AAA biosynthesis, as well as the identification of intracellular transporters and the continuing elucidation of transcriptional and post-transcriptional regulatory mechanisms, have revealed the complexity of this intercompartmental metabolic network. Here, we review the latest breakthroughs in AAA production and use the newest findings to highlight both longstanding and newly developed questions.
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Affiliation(s)
- Joseph H Lynch
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN 47907-2063, USA
| | - Natalia Dudareva
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
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Perkowski MC, Warpeha KM. Phenylalanine roles in the seed-to-seedling stage: Not just an amino acid. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110223. [PMID: 31623788 DOI: 10.1016/j.plantsci.2019.110223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Phenylalanine is an aromatic amino acid that provides the carbon skeleton for the phenylpropanoid pathway, making many diverse chemicals used for structure, defense, and yet undiscovered functions. The identification of the arogenate dehydratase (ADT) enzymes in the genetic model Arabidopsis thaliana provided a platform to explore the roles of phenylalanine in all stages of life: germination, in the seed-to-seedling transition stage, organelle function, and in generation of defense mechanisms, enabling further studies in other plants. From the literature, data indicate that phenylalanine produced by ADT may have direct roles in organellar and tissue development. Recent studies implicate ADTs in cell division and protection from Reactive Oxygen Species, and in signaling and growth. Research in phenylalanine and subsequent phenylpropanoids also point to a role of phenylalanine as a purveyor of C and N nutrients. The understanding of phenylalanine action in plant cells is enhanced by recent research on phenylalanine in animal cells.
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Affiliation(s)
- Mark C Perkowski
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Katherine M Warpeha
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States.
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de Oliveira MVV, Jin X, Chen X, Griffith D, Batchu S, Maeda HA. Imbalance of tyrosine by modulating TyrA arogenate dehydrogenases impacts growth and development of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:901-922. [PMID: 30457178 DOI: 10.1111/tpj.14169] [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: 10/06/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
l-Tyrosine is an essential aromatic amino acid required for the synthesis of proteins and a diverse array of plant natural products; however, little is known on how the levels of tyrosine are controlled in planta and linked to overall growth and development. Most plants synthesize tyrosine by TyrA arogenate dehydrogenases, which are strongly feedback-inhibited by tyrosine and encoded by TyrA1 and TyrA2 genes in Arabidopsis thaliana. While TyrA enzymes have been extensively characterized at biochemical levels, their in planta functions remain uncertain. Here we found that TyrA1 suppression reduces seed yield due to impaired anther dehiscence, whereas TyrA2 knockout leads to slow growth with reticulate leaves. The tyra2 mutant phenotypes were exacerbated by TyrA1 suppression and rescued by the expression of TyrA2, TyrA1 or tyrosine feeding. Low-light conditions synchronized the tyra2 and wild-type growth, and ameliorated the tyra2 leaf reticulation. After shifting to normal light, tyra2 transiently decreased tyrosine and subsequently increased aspartate before the appearance of the leaf phenotypes. Overexpression of the deregulated TyrA enzymes led to hyper-accumulation of tyrosine, which was also accompanied by elevated aspartate and reticulate leaves. These results revealed that TyrA1 and TyrA2 have distinct and overlapping functions in flower and leaf development, respectively, and that imbalance of tyrosine, caused by altered TyrA activity and regulation, impacts growth and development of Arabidopsis. The findings provide critical bases for improving the production of tyrosine and its derived natural products, and further elucidating the coordinated metabolic and physiological processes to maintain tyrosine levels in plants.
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Affiliation(s)
- Marcos V V de Oliveira
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Xing Jin
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Xuan Chen
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Daniel Griffith
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Sai Batchu
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
- Department of Biology, The College of New Jersey, Biology Building, 2000 Pennington Road, Ewing, NJ, 08628, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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Schenck CA, Maeda HA. Tyrosine biosynthesis, metabolism, and catabolism in plants. PHYTOCHEMISTRY 2018; 149:82-102. [PMID: 29477627 DOI: 10.1016/j.phytochem.2018.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/26/2018] [Accepted: 02/02/2018] [Indexed: 05/22/2023]
Abstract
L-Tyrosine (Tyr) is an aromatic amino acid (AAA) required for protein synthesis in all organisms, but synthesized de novo only in plants and microorganisms. In plants, Tyr also serves as a precursor of numerous specialized metabolites that have diverse physiological roles as electron carriers, antioxidants, attractants, and defense compounds. Some of these Tyr-derived plant natural products are also used in human medicine and nutrition (e.g. morphine and vitamin E). While the Tyr biosynthesis and catabolic pathways have been extensively studied in microbes and animals, respectively, those of plants have received much less attention until recently. Accumulating evidence suggest that the Tyr biosynthetic pathways differ between microbes and plants and even within the plant kingdom, likely to support the production of lineage-specific plant specialized metabolites derived from Tyr. The interspecies variations of plant Tyr pathway enzymes can now be used to enhance the production of Tyr and Tyr-derived compounds in plants and other synthetic biology platforms.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Bross CD, Howes TR, Abolhassani Rad S, Kljakic O, Kohalmi SE. Subcellular localization of Arabidopsis arogenate dehydratases suggests novel and non-enzymatic roles. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1425-1440. [PMID: 28338876 PMCID: PMC5444438 DOI: 10.1093/jxb/erx024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Arogenate dehydratases (ADTs) catalyze the final step in phenylalanine biosynthesis in plants. The Arabidopsis thaliana genome encodes a family of six ADTs capable of decarboxylating/dehydrating arogenate into phenylalanine. Using cyan fluorescent protein (CFP)-tagged proteins, the subcellular localization patterns of all six A. thaliana ADTs were investigated in intact Nicotiana benthamiana and A. thaliana leaf cells. We show that A. thaliana ADTs localize to stroma and stromules (stroma-filled tubules) of chloroplasts. This localization pattern is consistent with the enzymatic function of ADTs as many enzymes required for amino acid biosynthesis are primarily localized to chloroplasts, and stromules are thought to increase metabolite transport from chloroplasts to other cellular compartments. Furthermore, we provide evidence that ADTs have additional, non-enzymatic roles. ADT2 localizes in a ring around the equatorial plane of chloroplasts or to a chloroplast pole, which suggests that ADT2 is a component of the chloroplast division machinery. In addition to chloroplasts, ADT5 was also found in nuclei, again suggesting a non-enzymatic role for ADT5. We also show evidence that ADT5 is transported to the nucleus via stromules. We propose that ADT2 and ADT5 are moonlighting proteins that play an enzymatic role in phenylalanine biosynthesis and a second role in chloroplast division or transcriptional regulation, respectively.
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Affiliation(s)
- Crystal D Bross
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
| | - Travis R Howes
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
| | - Sara Abolhassani Rad
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
| | - Ornela Kljakic
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
| | - Susanne E Kohalmi
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
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12
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Chen Q, Man C, Li D, Tan H, Xie Y, Huang J. Arogenate Dehydratase Isoforms Differentially Regulate Anthocyanin Biosynthesis in Arabidopsis thaliana. MOLECULAR PLANT 2016; 9:1609-1619. [PMID: 27720844 DOI: 10.1016/j.molp.2016.09.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/24/2016] [Accepted: 09/26/2016] [Indexed: 05/24/2023]
Abstract
Anthocyanins, a group of L-phenylalanine (Phe)-derived flavonoids, have been demonstrated to play important roles in plant stress resistance and interactions between plants and insects. Although the anthocyanin biosynthetic pathway and its regulatory mechanisms have been extensively studied, it remains unclear whether the level of Phe supply affects anthocyanin biosynthesis. Here, we investigated the roles of arogenate dehydratases (ADTs), the key enzymes that catalyze the conversion of arogenate into Phe, in sucrose-induced anthocyanin biosynthesis in Arabidopsis. Genetic analysis showed that all six ADT isoforms function redundantly in anthocyanin biosynthesis but have differential contributions. ADT2 contributes the most to anthocyanin accumulation, followed by ADT1 and ADT3, and ADT4-ADT6. We found that anthocyanin content is positively correlated with the levels of Phe and sucrose-induced ADT transcripts in seedlings. Consistently, addition of Phe to the medium could dramatically increase anthocyanin content in the wild-type plants and rescue the phenotype of the adt1 adt3 double mutant regarding the anthocyanin accumulation. Moreover, transgenic plants overexpressing ADT4, which appears to be less sensitive to Phe than overexpression of ADT2, hyperaccumulate Phe and produce elevated level of anthocyanins. Taken together, our results suggest that the level of Phe is an important regulatory factor for sustaining anthocyanin biosynthesis.
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Affiliation(s)
- Qingbo Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Cong Man
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Danning Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Huijuan Tan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Ye Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Jirong Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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Miao L, Zhang L, Raboanatahiry N, Lu G, Zhang X, Xiang J, Gan J, Fu C, Li M. Transcriptome Analysis of Stem and Globally Comparison with Other Tissues in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1403. [PMID: 27708656 PMCID: PMC5030298 DOI: 10.3389/fpls.2016.01403] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/02/2016] [Indexed: 05/25/2023]
Abstract
Brassica napus is one of the most important oilseed crops in the world. However, there is currently no enough stem transcriptome information and comparative transcriptome analysis of different tissues, which impedes further functional genomics research on B. napus. In this study, the stem transcriptome of B. napus was characterized by RNA-seq technology. Approximately 13.4 Gb high-quality clean reads with an average length of 100 bp were generated and used for comparative transcriptome analysis with the existing transcriptome sequencing data of roots, leaves, flower buds, and immature embryos of B. napus. All the transcripts were annotated against GO and KEGG databases. The common genes in five tissues, differentially expressed genes (DEGs) of the common genes between stems and other tissues, and tissue-specific genes were detected, and the main biochemical activities and pathways implying the common genes, DEGs and tissue-specific genes were investigated. Accordingly, the common transcription factors (TFs) in the five tissues and tissue-specific TFs were identified, and a TFs-based regulation network between TFs and the target genes involved in 'Phenylpropanoid biosynthesis' pathway were constructed to show several important TFs and key nodes in the regulation process. Collectively, this study not only provided an available stem transcriptome resource in B. napus, but also revealed valuable comparative transcriptome information of five tissues of B. napus for future investigation on specific processes, functions and pathways.
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Affiliation(s)
- Liyun Miao
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Libin Zhang
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Nadia Raboanatahiry
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Guangyuan Lu
- Oil Crops Research Institute, Chinese Academy of Agricultural SciencesWuhan, China
| | - Xuekun Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural SciencesWuhan, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Chunhua Fu
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- School of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
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Mazzei P, Vinale F, Woo SL, Pascale A, Lorito M, Piccolo A. Metabolomics by Proton High-Resolution Magic-Angle-Spinning Nuclear Magnetic Resonance of Tomato Plants Treated with Two Secondary Metabolites Isolated from Trichoderma. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3538-45. [PMID: 27088924 DOI: 10.1021/acs.jafc.6b00801] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Trichoderma fungi release 6-pentyl-2H-pyran-2-one (1) and harzianic acid (2) secondary metabolites to improve plant growth and health protection. We isolated metabolites 1 and 2 from Trichoderma strains, whose different concentrations were used to treat seeds of Solanum lycopersicum. The metabolic profile in the resulting 15 day old tomato leaves was studied by high-resolution magic-angle-spinning nuclear magnetic resonance (HRMAS NMR) spectroscopy directly on the whole samples without any preliminary extraction. Principal component analysis (PCA) of HRMAS NMR showed significantly enhanced acetylcholine and γ-aminobutyric acid (GABA) content accompanied by variable amount of amino acids in samples treated with both Trichoderma secondary metabolites. Seed germination rates, seedling fresh weight, and the metabolome of tomato leaves were also dependent upon doses of metabolites 1 and 2 treatments. HRMAS NMR spectroscopy was proven to represent a rapid and reliable technique for evaluating specific changes in the metabolome of plant leaves and calibrating the best concentration of bioactive compounds required to stimulate plant growth.
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Affiliation(s)
- Pierluigi Mazzei
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Francesco Vinale
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche (CNR) , Via Università 133, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Sheridan Lois Woo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche (CNR) , Via Università 133, 80055 Portici, Città Metropolitana di Napoli, Italy
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Alberto Pascale
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Matteo Lorito
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche (CNR) , Via Università 133, 80055 Portici, Città Metropolitana di Napoli, Italy
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
| | - Alessandro Piccolo
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II , Via Università 100, 80055 Portici, Città Metropolitana di Napoli, Italy
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Dastmalchi M, Bernards MA, Dhaubhadel S. Twin anchors of the soybean isoflavonoid metabolon: evidence for tethering of the complex to the endoplasmic reticulum by IFS and C4H. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:689-706. [PMID: 26856401 DOI: 10.1111/tpj.13137] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/26/2016] [Accepted: 02/01/2016] [Indexed: 05/02/2023]
Abstract
Isoflavonoids are specialized plant metabolites, almost exclusive to legumes, and their biosynthesis forms a branch of the diverse phenylpropanoid pathway. Plant metabolism may be coordinated at many levels, including formation of protein complexes, or 'metabolons', which represent the molecular level of organization. Here, we have confirmed the existence of the long-postulated isoflavonoid metabolon by identifying elements of the complex, their subcellular localizations and their interactions. Isoflavone synthase (IFS) and cinnamate 4-hydroxylase (C4H) have been shown to be tandem P450 enzymes that are anchored in the ER, interacting with soluble enzymes of the phenylpropanoid and isoflavonoid pathways (chalcone synthase, chalcone reductase and chalcone isomerase). The soluble enzymes of these pathways, whether localized to the cytoplasm or nucleus, are tethered to the ER through interaction with these P450s. The complex is also held together by interactions between the soluble elements. We provide evidence for IFS interaction with upstream and non-consecutive enzymes. The existence of such a protein complex suggests a possible mechanism for flux of metabolites into the isoflavonoid pathway. Further, through interaction studies, we identified several candidates that are associated with GmIFS2, an isoform of IFS, in soybean hairy roots. This list provides additional candidates for various biosynthetic and structural elements that are involved in isoflavonoid production. Our interaction studies provide valuable information about isoform specificity among isoflavonoid enzymes, which may guide future engineering of the pathway in legumes or help overcome bottlenecks in heterologous expression.
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Affiliation(s)
- Mehran Dastmalchi
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
| | - Mark A Bernards
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Sangeeta Dhaubhadel
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
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16
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Schenck CA, Chen S, Siehl DL, Maeda HA. Non-plastidic, tyrosine-insensitive prephenate dehydrogenases from legumes. Nat Chem Biol 2015; 11:52-7. [PMID: 25402771 DOI: 10.1038/nchembio.1693] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/19/2014] [Indexed: 11/09/2022]
Abstract
L-Tyrosine (Tyr) and its plant-derived natural products are essential in both plants and humans. In plants, Tyr is generally assumed to be synthesized in the plastids via arogenate dehydrogenase (TyrA(a), also known also ADH), which is strictly inhibited by L-Tyr. Using phylogenetic and expression analyses, together with recombinant enzyme and endogenous activity assays, we identified prephenate dehydrogenases (TyrA(p)s, also known as PDHs) from two legumes, Glycine max (soybean) and Medicago truncatula. The identified PDHs were phylogenetically distinct from canonical plant ADH enzymes, preferred prephenate to arogenate substrate, localized outside of the plastids and were not inhibited by L-Tyr. The results provide molecular evidence for the diversification of primary metabolic Tyr pathway via an alternative cytosolic PDH pathway in plants.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Siyu Chen
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
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17
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Amiour N, Imbaud S, Clément G, Agier N, Zivy M, Valot B, Balliau T, Quilleré I, Tercé-Laforgue T, Dargel-Graffin C, Hirel B. An integrated "omics" approach to the characterization of maize (Zea mays L.) mutants deficient in the expression of two genes encoding cytosolic glutamine synthetase. BMC Genomics 2014; 15:1005. [PMID: 25410248 PMCID: PMC4247748 DOI: 10.1186/1471-2164-15-1005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 11/04/2014] [Indexed: 11/21/2022] Open
Abstract
Background To identify the key elements controlling grain production in maize, it is essential to have an integrated view of the responses to alterations in the main steps of nitrogen assimilation by modification of gene expression. Two maize mutant lines (gln1.3 and gln1.4), deficient in two genes encoding cytosolic glutamine synthetase, a key enzyme involved in nitrogen assimilation, were previously characterized by a reduction of kernel size in the gln1.4 mutant and by a reduction of kernel number in the gln1.3 mutant. In this work, the differences in leaf gene transcripts, proteins and metabolite accumulation in gln1.3 and gln1.4 mutants were studied at two key stages of plant development, in order to identify putative candidate genes, proteins and metabolic pathways contributing on one hand to the control of plant development and on the other to grain production. Results The most interesting finding in this study is that a number of key plant processes were altered in the gln1.3 and gln1.4 mutants, including a number of major biological processes such as carbon metabolism and transport, cell wall metabolism, and several metabolic pathways and stress responsive and regulatory elements. We also found that the two mutants share common or specific characteristics across at least two or even three of the “omics” considered at the vegetative stage of plant development, or during the grain filling period. Conclusions This is the first comprehensive molecular and physiological characterization of two cytosolic glutamine synthetase maize mutants using a combined transcriptomic, proteomic and metabolomic approach. We find that the integration of the three “omics” procedures is not straight forward, since developmental and mutant-specific levels of regulation seem to occur from gene expression to metabolite accumulation. However, their potential use is discussed with a view to improving our understanding of nitrogen assimilation and partitioning and its impact on grain production. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1005) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bertrand Hirel
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), Centre de Versailles-Grignon, Unité Mixte de Recherche 1318 INRA-Agro-ParisTech, Equipe de Recherche Labellisée, Centre National de la Recherche Scientifique 3559, RD10, F-78026 Versailles, Cedex, France.
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18
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Camargo ELO, Nascimento LC, Soler M, Salazar MM, Lepikson-Neto J, Marques WL, Alves A, Teixeira PJPL, Mieczkowski P, Carazzolle MF, Martinez Y, Deckmann AC, Rodrigues JC, Grima-Pettenati J, Pereira GAG. Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus. BMC PLANT BIOLOGY 2014; 14:256. [PMID: 25260963 PMCID: PMC4189757 DOI: 10.1186/s12870-014-0256-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/20/2014] [Indexed: 05/07/2023]
Abstract
BACKGROUND Nitrogen (N) is a main nutrient required for tree growth and biomass accumulation. In this study, we analyzed the effects of contrasting nitrogen fertilization treatments on the phenotypes of fast growing Eucalyptus hybrids (E. urophylla x E. grandis) with a special focus on xylem secondary cell walls and global gene expression patterns. RESULTS Histological observations of the xylem secondary cell walls further confirmed by chemical analyses showed that lignin was reduced by luxuriant fertilization, whereas a consistent lignin deposition was observed in trees grown in N-limiting conditions. Also, the syringyl/guaiacyl (S/G) ratio was significantly lower in luxuriant nitrogen samples. Deep sequencing RNAseq analyses allowed us to identify a high number of differentially expressed genes (1,469) between contrasting N treatments. This number is dramatically higher than those obtained in similar studies performed in poplar but using microarrays. Remarkably, all the genes involved the general phenylpropanoid metabolism and lignin pathway were found to be down-regulated in response to high N availability. These findings further confirmed by RT-qPCR are in agreement with the reduced amount of lignin in xylem secondary cell walls of these plants. CONCLUSIONS This work enabled us to identify, at the whole genome level, xylem genes differentially regulated by N availability, some of which are involved in the environmental control of xylogenesis. It further illustrates that N fertilization can be used to alter the quantity and quality of lignocellulosic biomass in Eucalyptus, offering exciting prospects for the pulp and paper industry and for the use of short coppices plantations to produce second generation biofuels.
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Affiliation(s)
- Eduardo Leal Oliveira Camargo
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
- />Laboratoire de Recherche en Sciences Végétales, UMR 5546: CNRS - Université de Toulouse III (UPS), Auzeville, BP 42617, F-31326 Castanet-Tolosan, France
| | - Leandro Costa Nascimento
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Marçal Soler
- />Laboratoire de Recherche en Sciences Végétales, UMR 5546: CNRS - Université de Toulouse III (UPS), Auzeville, BP 42617, F-31326 Castanet-Tolosan, France
| | - Marcela Mendes Salazar
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Jorge Lepikson-Neto
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Wesley Leoricy Marques
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Ana Alves
- />Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Group, Tapada da Ajuda, Lisboa, Portugal
- />Centro de Estudos Florestais, Tapada da Ajuda, Lisboa, Portugal
| | - Paulo José Pereira Lima Teixeira
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | | | - Marcelo Falsarella Carazzolle
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Yves Martinez
- />Fédération de Recherche “Agrobiosciences, Interactions et Biodiversité”, 24 Chemin de borde rouge, BP 42617, 31326 Castanet-Tolosan, France
| | - Ana Carolina Deckmann
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - José Carlos Rodrigues
- />Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Group, Tapada da Ajuda, Lisboa, Portugal
- />Centro de Estudos Florestais, Tapada da Ajuda, Lisboa, Portugal
| | - Jacqueline Grima-Pettenati
- />Laboratoire de Recherche en Sciences Végétales, UMR 5546: CNRS - Université de Toulouse III (UPS), Auzeville, BP 42617, F-31326 Castanet-Tolosan, France
| | - Gonçalo Amarante Guimarães Pereira
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
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