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Holland CK, Jez JM. Fidelity in plant hormone modifications catalyzed by Arabidopsis GH3 acyl acid amido synthetases. J Biol Chem 2024; 300:107421. [PMID: 38815865 DOI: 10.1016/j.jbc.2024.107421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases conjugate amino acids to acyl acid hormones to either activate or inactivate the hormone molecule. The largest subgroup of GH3 proteins modify the growth-promoting hormone auxin (indole-3-acetic acid; IAA) with the second largest class activating the defense hormone jasmonic acid (JA). The two-step reaction mechanism of GH3 proteins provides a potential proofreading mechanism to ensure fidelity of hormone modification. Examining pyrophosphate release in the first-half reaction of Arabidopsis GH3 proteins that modify IAA (AtGH3.2/YDK2, AtGH3.5/WES1, AtGH3.17/VAS2), JA (AtGH3.11/JAR1), and other acyl acids (AtGH3.7, AtGH3.12/PBS3) indicates that acyl acid-AMP intermediates are hydrolyzed into acyl acid and AMP in the absence of the amino acid, a typical feature of pre-transfer editing mechanisms. Single-turnover kinetic analysis of AtGH3.2/YDK2 and AtGH3.5/WES1 shows that non-cognate acyl acid-adenylate intermediates are more rapidly hydrolyzed than the cognate IAA-adenylate. In contrast, AtGH3.11/JAR1 only adenylates JA, not IAA. While some of the auxin-conjugating GH3 proteins in Arabidopsis (i.e., AtGH3.5/WES1) accept multiple acyl acid substrates, others, like AtGH3.2/YDK2, are specific for IAA; however, both these proteins share similar active site residues. Biochemical analysis of chimeric variants of AtGH3.2/YDK2 and AtGH3.5/WES1 indicates that the C-terminal domain contributes to selection of cognate acyl acid substrates. These findings suggest that the hydrolysis of non-cognate acyl acid-adenylate intermediates, or proofreading, proceeds via a slowed structural switch that provides a checkpoint for fidelity before the full reaction proceeds.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Williams College, Williamstown, Massachusetts; Department of Biology, Washington University in St Louis, St Louis, Missouri
| | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, Missouri.
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Balbinott N, Margis R. The many faces of lysine acylation in proteins: Phytohormones as unexplored substrates. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111866. [PMID: 37714383 DOI: 10.1016/j.plantsci.2023.111866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Protein post-translational modification (PTM) is a ubiquitous process that occurs in most proteins. Lysine residues containing an ε-amino group are recognized as hotspots for the addition of different chemical groups. Lysine acetylation, extensively studied in histones, serves as an epigenetic hallmark capable of promoting changes in chromatin structure and availability. Acyl groups derived from molecules involved in carbohydrate and lipid metabolisms, such as lactate, succinate and hydroxybutyrate, were identified as lysine modifications of histones and other proteins. Lysine-acyltransferases do not exhibit significant substrate specificity concerning acyl donors. Furthermore, plant hormones harboring acyl groups often form conjugates with free amino acids to regulate their activity and function during plant physiological processes and responses, a process mediated by GH3 enzymes. Besides forming low-molecular weight conjugates, auxins have been shown to covalently modify proteins in bean seeds. Aside from auxins, other phytohormones with acyl groups are unexplored potential substrates for post-translational acylation of proteins. Using MS data searches, we revealed various proteins with lysine residues linked to auxin, abscisic acid, gibberellic acid, jasmonic acid, and salicylic acid. These findings raise compelling questions about the ability of plant hormones harboring carboxyl groups to serve as new candidates for protein acylation and acting in protein PTM and modulation.
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Affiliation(s)
- Natalia Balbinott
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rogerio Margis
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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3
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Yang BX, Li ZX, Liu SS, Yang J, Wang PY, Liu HW, Zhou X, Liu LW, Wu ZB, Yang S. Novel cinnamic acid derivatives as a versatile tool for developing agrochemicals for controlling plant virus and bacterial diseases by enhancing plant defense responses. PEST MANAGEMENT SCIENCE 2023; 79:2556-2570. [PMID: 36864774 DOI: 10.1002/ps.7433] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Plant pathogens have led to large yield and quality losses in crops worldwide. The discovery and study of novel agrochemical alternatives based on the chemical modification of bioactive natural products is a highly efficient approach. Here, two series of novel cinnamic acid derivatives incorporating diverse building blocks with alternative linking patterns were designed and synthesized to identify their antiviral capacity and antibacterial activity. RESULTS The bioassay results demonstrated that most cinnamic acid derivatives had excellent antiviral competence toward tobacco mosaic virus (TMV) in vivo, especially compound A5 (median effective concentration [EC50 ] = 287.7 μg mL-1 ), which had a notable protective effect against TMV when compared with the commercial virucide ribavirin (EC50 = 622.0 μg mL-1 ). In addition, compound A17 had a protective efficiency of 84.3% at 200 μg mL-1 against Xac in plants. Given these outstanding results, the engineered title compounds could be regarded as promising leads for controlling plant virus and bacterial diseases. Preliminary mechanistic studies suggest that compound A5 could enhance the host's defense responses by increasing the activity of defense enzymes and upregulating defense genes, thereby suppressing phytopathogen invasion. CONCLUSION This research lays a foundation for the practical application of cinnamic acid derivatives containing diverse building blocks with alternative linking patterns in pesticide exploration. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Bin-Xin Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Zhen-Xing Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Shuai-Shuai Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Jie Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Pei-Yi Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Hong-Wu Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Li-Wei Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Zhi-Bing Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Song Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
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Brunoni F, Pěnčík A, Žukauskaitė A, Ament A, Kopečná M, Collani S, Kopečný D, Novák O. Amino acid conjugation of oxIAA is a secondary metabolic regulation involved in auxin homeostasis. THE NEW PHYTOLOGIST 2023; 238:2264-2270. [PMID: 36941219 DOI: 10.1111/nph.18887] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 03/11/2023] [Indexed: 05/19/2023]
Affiliation(s)
- Federica Brunoni
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Asta Žukauskaitė
- Department of Chemical Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Anita Ament
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Martina Kopečná
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Silvio Collani
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, SE-90736, Sweden
| | - David Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, Olomouc, CZ-78371, Czech Republic
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Ai G, Huang R, Zhang D, Li M, Li G, Li W, Ahiakpa JK, Wang Y, Hong Z, Zhang J. SlGH3.15, a member of the GH3 gene family, regulates lateral root development and gravitropism response by modulating auxin homeostasis in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111638. [PMID: 36796648 DOI: 10.1016/j.plantsci.2023.111638] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/26/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Multiple Gretchen Hagen 3 (GH3) genes have been implicated in a range of processes in plant growth and development through their roles in maintaining hormonal homeostasis. However, there has only been limited study on the functions of GH3 genes in tomato (Solanum lycopersicum). In this work, we investigated the important function of SlGH3.15, a member of the GH3 gene family in tomato. Overexpression of SlGH3.15 led to severe dwarfism in both the above- and below-ground sections of the plant, accompanied by a substantial decrease in free IAA content and reduction in the expression of SlGH3.9, a paralog of SlGH3.15. Exogenous supply of IAA negatively affected the elongation of the primary root and partially restored the gravitropism defects in SlGH3.15-overexpression lines. While no phenotypic change was observed in the SlGH3.15 RNAi lines, double knockout lines of SlGH3.15 and SlGH3.9 were less sensitive to treatments with the auxin polar transport inhibitor. Overall, these findings revealed important roles of SlGH3.15 in IAA homeostasis and as a negative regulator of free IAA accumulation and lateral root formation in tomato.
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Affiliation(s)
- Guo Ai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Rong Huang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Dedi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Miao Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Guobin Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Wangfang Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - John K Ahiakpa
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yikui Wang
- Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Zhao L, Yang YY, Qu XJ, Ma H, Hu Y, Li HT, Yi TS, Li DZ. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. ANNALS OF BOTANY 2023; 131:199-214. [PMID: 35671385 PMCID: PMC9904356 DOI: 10.1093/aob/mcac062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. METHODS New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. KEY RESULTS Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. CONCLUSIONS Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong 250014, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Lin Q, Gong J, Zhang Z, Meng Z, Wang J, Wang S, Sun J, Gu X, Jin Y, Wu T, yan N, Wang Y, Kai L, Jiang J, Qi S. The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI regulates primary root growth and lateral root elongation. FRONTIERS IN PLANT SCIENCE 2023; 13:1088278. [PMID: 36714693 PMCID: PMC9880472 DOI: 10.3389/fpls.2022.1088278] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
Roots are the main organs through which plants absorb water and nutrients. As the key phytohormone involved in root growth, auxin functions in plant environmental responses by modulating auxin synthesis, distribution and polar transport. The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI can improve root architecture, and tppi1 mutants have significantly shortened primary roots. However, the mechanism underlying the short roots of the tppi1 mutant and the upstream signaling pathway and downstream genes regulated by AtTPPI are unclear. Here, we demonstrated that the AtTPPI gene could promote auxin accumulation in AtTPPI-overexpressing plants. By comparing the transcriptomic data of tppi1 and wild-type roots, we found several upregulations of auxin-related genes, including GH3.3, GH3.9 and GH3.12, may play an important role in the AtTPPI gene-mediated auxin transport signaling pathway, ultimately leading to changes in auxin content and primary root length. Moreover, increased AtTPPI expression can regulate primary root growth and lateral root elongation under different concentration of nitrate conditions. Overall, constitutive expression of AtTPPI increased auxin contents and improved lateral root elongation, constituting a new method for improving the nitrogen utilization efficiency of plants.
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Affiliation(s)
- Qingfang Lin
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jiaxin Gong
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Zhiliang Zhang
- Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zizi Meng
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jianyong Wang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Song Wang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Jing Sun
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Xu Gu
- Technical Services and Sales Department, Zhengzhou Xuanyuan Biotechnology Co. LTD, Zhengzhou, Henan, China
| | - Yuting Jin
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Tong Wu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Nuo yan
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Yuxin Wang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jihong Jiang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Shilian Qi
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
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Chemical inhibition of the auxin inactivation pathway uncovers the roles of metabolic turnover in auxin homeostasis. Proc Natl Acad Sci U S A 2022; 119:e2206869119. [PMID: 35914172 PMCID: PMC9371723 DOI: 10.1073/pnas.2206869119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The phytohormone auxin, indole-3-acetic acid (IAA), plays a prominent role in plant development. Auxin homeostasis is coordinately regulated by auxin synthesis, transport, and inactivation; however, the physiological contribution of auxin inactivation to auxin homeostasis has not been determined. The GH3 IAA-amino acid conjugating enzymes play a central role in auxin inactivation. Chemical inhibition of GH3 proteins in planta is challenging because the inhibition of these enzymes leads to IAA overaccumulation that rapidly induces GH3 expression. Here, we report the characterization of a potent GH3 inhibitor, kakeimide, that selectively targets IAA-conjugating GH3 proteins. Chemical knockdown of the auxin inactivation pathway demonstrates that auxin turnover is very rapid (about 10 min) and indicates that both auxin biosynthesis and inactivation dynamically regulate auxin homeostasis.
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Delfin JC, Kanno Y, Seo M, Kitaoka N, Matsuura H, Tohge T, Shimizu T. AtGH3.10 is another jasmonic acid-amido synthetase in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1082-1096. [PMID: 35247019 DOI: 10.1111/tpj.15724] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Jasmonoyl-isoleucine (JA-Ile) is a key signaling molecule that activates jasmonate-regulated flower development and the wound stress response. For years, JASMONATE RESISTANT1 (JAR1) has been the sole jasmonoyl-amino acid synthetase known to conjugate jasmonic acid (JA) to isoleucine, and the source of persisting JA-Ile in jar1 knockout mutants has remained elusive until now. Here we demonstrate through recombinant enzyme assays and loss-of-function mutant analyses that AtGH3.10 functions as a JA-amido synthetase. Recombinant AtGH3.10 could conjugate JA to isoleucine, alanine, leucine, methionine, and valine. The JA-Ile accumulation in the gh3.10-2 jar1-11 double mutant was nearly eliminated in the leaves and flower buds while its catabolism derivative 12OH-JA-Ile was undetected in the flower buds and unwounded leaves. Residual levels of JA-Ile, JA-Ala, and JA-Val were nonetheless detected in gh3.10-2 jar1-11, suggesting the activities of similar promiscuous enzymes. Upon wounding, the accumulation of JA-Ile and 12OH-JA-Ile and the expression of JA-responsive genes OXOPHYTODIENOIC ACID REDUCTASE3 and JASMONATE ZIM-DOMAIN1 observed in WT, gh3.10-1, and jar1-11 leaves were effectively abolished in gh3.10-2 jar1-11. Additionally, an increased proportion of undeveloped siliques associated with retarded stamen development was observed in gh3.10-2 jar1-11. These findings conclusively show that AtGH3.10 contributes to JA-amino acid biosynthesis and functions partially redundantly with AtJAR1 in sustaining flower development and the wound stress response in Arabidopsis.
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Affiliation(s)
- Jay C Delfin
- Division of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, Japan, 630-0192
| | - Yuri Kanno
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan, 230-0045
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan, 230-0045
| | - Naoki Kitaoka
- Division of Fundamental AgriScience Research, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan, 060-8589
| | - Hideyuki Matsuura
- Division of Fundamental AgriScience Research, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan, 060-8589
| | - Takayuki Tohge
- Division of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, Japan, 630-0192
| | - Takafumi Shimizu
- Division of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, Japan, 630-0192
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Liu CC, Liu YN, Cheng JF, Guo R, Tian L, Wang B. Dual Roles of OsGH3.2 in Modulating Rice Root Morphology and Affecting Arbuscular Mycorrhizal Symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:853435. [PMID: 35481141 PMCID: PMC9037295 DOI: 10.3389/fpls.2022.853435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Several angiosperm GRETCHEN HAGEN 3 (GH3) genes, including tomato SlGH3.4 and rice OsGH3.2 are induced during arbuscular mycorrhizal (AM) symbiosis, but their functions remain largely unclear. Recently, tomato SlGH3.4 was suggested to negatively regulate arbuscule incidence via decreasing auxin levels in colonized cells. In this study, by acquiring rice OsGH3.2pro:β-glucuronidase (GUS) transgenic plants and generating Osgh3.2 mutants via CRISPR/Cas9 technique, the roles of OsGH3.2 in modulating rice root morphology and affecting AM symbiosis were investigated through time course experiments. Unlike SlGH3.4, OsGH3.2 showed asymbiotic expression in rice young lateral roots, and its mutation resulted in a "shallow" root architecture. Such root morphological change was also observed under symbiotic condition and it likely promoted AM fungal colonization, as the mutants exhibited higher colonization levels and arbuscule incidence than wild-type at early stages. Similar to SlGH3.4, OsGH3.2 showed symbiotic expression in cortical cells that have formed mature arbuscules. At late stages of symbiosis, Osgh3.2 mutants showed elongated cortical cells and larger arbuscules than wild-type, indicating elevated auxin level in the colonized cells. Together, these results revealed both asymbiotic and symbiotic roles of OsGH3.2 in modulating rice root architecture and controlling auxin levels in arbusculated cells, which further affected colonization rate and arbuscule phenotype.
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Tang S, Shahriari M, Xiang J, Pasternak T, Igolkina A, Aminizade S, Zhi H, Gao Y, Roodbarkelari F, Sui Y, Jia G, Wu C, Zhang L, Zhao L, Li X, Meshcheryakov G, Samsonova M, Diao X, Palme K, Teale W. The role of AUX1 during lateral root development in the domestication of the model C4 grass Setaria italica. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2021-2034. [PMID: 34940828 DOI: 10.1093/jxb/erab556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from Rubisco. The specialized leaf anatomy required for this separation evolved independently many times. The morphology of C4 root systems is also distinctive and adapted to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture. Using a mutant screen in the C4 model plant Setaria italica, we identify Siaux1-1 and Siaux1-2 as root system architecture mutants. Unlike in S. viridis, AUX1 promotes lateral root development in S. italica. A cell by cell analysis of the Siaux1-1 root apical meristem revealed changes in the distribution of cell volumes in all cell layers and a dependence of the frequency of protophloem and protoxylem strands on SiAUX1. We explore the molecular basis of the role of SiAUX1 in seedling development using an RNAseq analysis of wild-type and Siaux1-1 plants and present novel targets for SiAUX1-dependent gene regulation. Using a selection sweep and haplotype analysis of SiAUX1, we show that Hap-2412TT in the promoter region of SiAUX1 is an allele which is associated with lateral root number and has been strongly selected for during Setaria domestication.
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Affiliation(s)
- Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mojgan Shahriari
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Jishan Xiang
- Academy of Agricultural Sciences/Key Laboratory of Regional Ecological Protection & Agricultural and Animal Husbandry Development, Chifeng University, Chifeng, 024000, Inner Mongolia, China
| | - Taras Pasternak
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Anna Igolkina
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnic University, St. Petersburg, 195259, Russia
| | | | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanzhu Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Farshad Roodbarkelari
- Institute of Biology III, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Yi Sui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuanyin Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Linlin Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xugang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - Georgy Meshcheryakov
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnic University, St. Petersburg, 195259, Russia
| | - Maria Samsonova
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnic University, St. Petersburg, 195259, Russia
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Klaus Palme
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
- Centre of Biological Systems Analysis and BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - William Teale
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
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12
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Jez JM. Connecting primary and specialized metabolism: Amino acid conjugation of phytohormones by GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102194. [PMID: 35219141 DOI: 10.1016/j.pbi.2022.102194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases catalyze the ATP-dependent conjugation of phytohormones with amino acids. Traditionally, GH3 proteins are associated with synthesis of the bioactive jasmonate hormone (+)-7- iso -jasmonoyl-l-isoleucine (JA-Ile) and conjugation of indole-3-acetic acid (IAA) with amino acids that tag the hormone for degradation and/or storage. Modifications of JA and IAA by GH3 acyl acid amido synthetases help maintain phytohormones homeostasis. Recent studies broaden the roles of GH3 proteins to include the regulation of JA biosynthesis; the modification of other auxins (i.e., phenylacetic acid and indole-3-butyric acid); the conjugation of auxinic herbicides, such as 4-dichlorophenoxyacetic acid, 4-(2,4-dichlorophenoxy)butyric acid, and dicamba; and the missing step in the isochorismate pathway for the biosynthesis of salicylic acid. The GH3 protein family joins the growing number of versatile enzyme families that blur the line between primary and specialized metabolism for an increasing range of biology functions.
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Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130 USA.
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13
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Wojtaczka P, Ciarkowska A, Starzynska E, Ostrowski M. The GH3 amidosynthetases family and their role in metabolic crosstalk modulation of plant signaling compounds. PHYTOCHEMISTRY 2022; 194:113039. [PMID: 34861536 DOI: 10.1016/j.phytochem.2021.113039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/15/2021] [Accepted: 11/24/2021] [Indexed: 05/08/2023]
Abstract
The Gretchen Hagen 3 (GH3) genes encoding proteins belonging to the ANL superfamily are widespread in the plant kingdom. The ANL superfamily consists of three groups of adenylating enzymes: aryl- and acyl-CoA synthetases, firefly luciferase, and amino acid-activating adenylation domains of the nonribosomal peptide synthetases (NRPS). GH3s are cytosolic, acidic amidosynthetases of the firefly luciferase group that conjugate auxins, jasmonates, and benzoate derivatives to a wide group of amino acids. In contrast to auxins, which amide conjugates mainly serve as a storage pool of inactive phytohormone or are involved in the hormone degradation process, conjugation of jasmonic acid (JA) results in biologically active phytohormone jasmonyl-isoleucine (JA-Ile). Moreover, GH3s modulate salicylic acid (SA) concentration by conjugation of its precursor, isochorismate. GH3s, as regulators of the phytohormone level, are crucial for normal plant development as well as plant defense response to different abiotic and biotic stress factors. Surprisingly, recent studies indicate that FIN219/JAR1/GH3.11, one of the GH3 proteins, may act not only as an enzyme but is also able to interact with tau-class glutathione S-transferase (GSTU) and constitutive photomorphogenic 1 (COP1) proteins and regulate light and stress signaling pathways. The aim of this work is to summarize our current knowledge of the GH3 family.
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Affiliation(s)
- Patrycja Wojtaczka
- Department of Biochemistry, Nicolaus Copernicus University in Torun, Lwowska 1, 87-100, Torun, Poland
| | - Anna Ciarkowska
- Department of Biochemistry, Nicolaus Copernicus University in Torun, Lwowska 1, 87-100, Torun, Poland
| | - Ewelina Starzynska
- Department of Biochemistry, Nicolaus Copernicus University in Torun, Lwowska 1, 87-100, Torun, Poland
| | - Maciej Ostrowski
- Department of Biochemistry, Nicolaus Copernicus University in Torun, Lwowska 1, 87-100, Torun, Poland.
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14
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Lu S, Wang P, Nai G, Li Y, Su Y, Liang G, Chen B, Mao J. Insight into VvGH3 genes evolutional relationship from monocotyledons and dicotyledons reveals that VvGH3-9 negatively regulates the drought tolerance in transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 172:70-86. [PMID: 35033858 DOI: 10.1016/j.plaphy.2022.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
The Gretchen Hagen3 (GH3) gene family is necessary for growth and development in plants and is regulated by osmotic stress and various hormones. Although it has been reported in many plants, the evolutionary relationship of GH3 in grape has not been systematically analyzed from the perspective of monocotyledonous and dicotyledonous. This study identified and analyzed 188 GH3 genes, which were distinctly divided into 9 subgroups, and found these subgroups have obviously been clustered between monocotyledonous and dicotyledonous. VvGH3-x genes had higher synteny with apple and Arabidopsis than that of rice, and the average Ka/Ks value in monocotyledons was higher than that of dicotyledons. The codon usage index showed that monocotyledons preferred to use G3s, C3s, and GC3s, while dicotyledons preferred to use A3s and T3s. The GH3 genes of grape exhibited different expression patterns in various tissues, different abiotic stresses, and hormonal treatments. The subcellular localization showed that VvGH3-9 was expressed in the nucleus and cytoplasm. Additionally, under 20% PEG treatment, the IAA and ABA contents, relative expression levels of VvGH3-9, relative electrical conductivity (REC), as well as MDA were obviously increased in VvGH3-9 overexpression lines at 72 h. In contrast, compared to WT, the contents of proline and H2O2, the activities of POD, SOD, and CAT, and the relative expression levels of drought responsive genes were significantly decreased in overexpressing lines. Collectively, this study provided helpful insight for the evolution of GH3 genes and presented some possibilities to study the functions of GH3 genes in monocotyledons and dicotyledons.
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Affiliation(s)
- Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ping Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Guojie Nai
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yanmei Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yanli Su
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Guoping Liang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China.
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15
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Guo R, Hu Y, Aoi Y, Hira H, Ge C, Dai X, Kasahara H, Zhao Y. Local conjugation of auxin by the GH3 amido synthetases is required for normal development of roots and flowers in Arabidopsis. Biochem Biophys Res Commun 2022; 589:16-22. [PMID: 34883285 DOI: 10.1016/j.bbrc.2021.11.109] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023]
Abstract
Gretchen Hagen 3 (GH3) amido synthetases conjugate amino acids to a carboxyl group of small molecules including hormones auxin, jasmonate, and salicylic acid. The Arabidopsis genome harbors 19 GH3 genes, whose exact roles in plant development have been difficult to define because of genetic redundancy among the GH3 genes. Here we use CRISPR/Cas9 gene editing technology to delete the Arabidopsis group II GH3 genes, which are able to conjugate indole-3-acetic acid (IAA) to amino acids. We show that plants lacking the eight group II GH3 genes (gh3 octuple mutants) accumulate free IAA and fail to produce IAA-Asp and IAA-Glu conjugates. Consequently, gh3 octuple mutants have extremely short roots, long and dense root hairs, and long hypocotyls. Our characterization of gh3 septuple mutants, which provide sensitized backgrounds, reveals that GH3.17 and GH3.9 play prominent roles in root elongation and seed production, respectively. We show that GH3 functions correlate with their expression patterns, suggesting that local deactivation of auxin also contributes to maintaining auxin homeostasis. Moreover, this work provides a method for elucidating functions of individual members of a gene family, whose members have overlapping functions.
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Affiliation(s)
- Ruipan Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China; Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yun Hu
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yuki Aoi
- Department of Bioregulation and Biointeraction, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8509, Japan
| | - Hayao Hira
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8509, Japan
| | - Chennan Ge
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xinhua Dai
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hiroyuki Kasahara
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, 183-8509, Japan
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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16
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Casanova-Sáez R, Mateo-Bonmatí E, Ljung K. Auxin Metabolism in Plants. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a039867. [PMID: 33431579 PMCID: PMC7919392 DOI: 10.1101/cshperspect.a039867] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism-which comprises biosynthesis, conjugation, and degradation-modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.
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Affiliation(s)
| | | | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
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17
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Jeong J, Park S, Im JH, Yi H. Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene. BMC Genomics 2021; 22:22. [PMID: 33407107 PMCID: PMC7789250 DOI: 10.1186/s12864-020-07345-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/22/2020] [Indexed: 01/07/2023] Open
Abstract
Background The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group III subgroup 6 GH3 genes, and their expression patterns in economically important B. oleracea var. oleracea have not been systematically identified. Results As a first step to understand regulation and molecular functions of Group III subgroup 6 GH3 genes, 34 GH3 genes including four subgroup 6 genes were identified in B. oleracea var. oleracea. Synteny found around subgroup 6 GH3 genes in B. oleracea var. oleracea and Arabidopsis thaliana indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in B. oleracea var. oleracea is not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6 GH3 genes in B. oleracea var. oleracea, only BoGH3.13–1 is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic A. thaliana subgroup 6 GH3 genes. Detailed analyses of promoter activities further showed that BoGH3.13–1 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones. Conclusions Sixty-two base pairs (bp) region (− 340 ~ − 279 bp upstream from start codon) and about 450 bp region (− 1489 to − 1017 bp) in BoGH3.13–1 promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenic Brassica plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07345-9.
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Affiliation(s)
- Jiseong Jeong
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sunhee Park
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jeong Hui Im
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hankuil Yi
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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18
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Xu G, Zhang Y, Li M, Jiao X, Zhou L, Ming Z. Crystal structure of the acyl acid amido synthetase GH3-8 from Oryza sativa. Biochem Biophys Res Commun 2020; 534:266-271. [PMID: 33272567 DOI: 10.1016/j.bbrc.2020.11.098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022]
Abstract
The Gretchen Hagen 3 (GH3) family of acyl acid amido synthetases regulate the levels and activities of plant hormones containing carboxyl groups, thereby modulating diverse physiological responses. While structure-function relationships have been elucidated for dicotyledonous GH3s, the catalytic mechanism of monocotyledonous GH3 remains elusive. Rice (Oryza sativa) is a representative monocot, and its yield is controlled by the natural growth hormone IAA (indole-3-acetic acid). OsGH3-8 is a model GH3 enzyme that conjugates excess IAA to amino acids in an ATP-dependent manner, ensuring auxin homeostasis and regulating disease resistance, growth and development. Here, we report the crystal structure of OsGH3-8 protein in complex with AMP to uncover the molecular and structural basis for the activity of monocotyledonous GH3-8. Structural and sequence comparisons with other GH3 proteins reveal that the AMP/ATP binding sites are highly conserved. Molecular docking studies with IAA, the GH3-inhibitor Adenosine-5'-[2-(1H-indol-3-yl)ethyl]phosphate (AIEP), and Aspartate provide important information for substrate binding and selectivity of OsGH3-8. Moreover, the observation that AIEP nearly occupies the entire binding site for AMP, IAA and amino acid, offers a ready explanation for the inhibitory effect of AIEP. Taken together, the present study provides vital insights into the molecular mechanisms of monocot GH3 function, and will help to shape the future designs of effective inhibitors.
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Affiliation(s)
- Guolyu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, PR China
| | - Yukun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, PR China
| | - Mingyang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, PR China
| | - Xi Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, PR China
| | - Le Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, PR China
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, PR China.
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19
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Tarelkina TV, Novitskaya LL, Galibina NA, Moshchenskaya YL, Nikerova KM, Nikolaeva NN, Sofronova IN, Ivanova DS, Semenova LI. Expression Analysis of Key Auxin Biosynthesis, Transport, and Metabolism Genes of Betula pendula with Special Emphasis on Figured Wood Formation in Karelian Birch. PLANTS 2020; 9:plants9111406. [PMID: 33105649 PMCID: PMC7690449 DOI: 10.3390/plants9111406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/31/2022]
Abstract
Auxin status in woody plants is believed to be a critical factor for the quantity and quality of the wood formed. It has been previously demonstrated that figured wood formation in Karelian birch (Betula pendula Roth var. carelica (Merckl.) Hämet-Ahti) is associated with a reduced auxin level and elevated sugar content in the differentiating xylem, but the molecular mechanisms of the abnormal xylogenesis remained largely unclear. We have identified genes involved in auxin biosynthesis (Yucca), polar auxin transport (PIN) and the conjugation of auxin with amino acids (GH3) and UDP-glucose (UGT84B1) in the B. pendula genome, and analysed their expression in trunk tissues of trees differing in wood structure. Almost all the investigated genes were overexpressed in Karelian birch trunks. Although Yucca genes were overexpressed, trunk tissues in areas developing figured grain had traits of an auxin-deficient phenotype. Overexpression of GH3s and UGT84B1 appears to have a greater effect on figured wood formation. Analysis of promoters of the differentially expressed genes revealed a large number of binding sites with various transcription factors associated with auxin and sugar signalling. These data agree with the hypothesis that anomalous figured wood formation in Karelian birch may be associated with the sugar induction of auxin conjugation.
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20
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Brunoni F, Collani S, Casanova-Sáez R, Šimura J, Karady M, Schmid M, Ljung K, Bellini C. Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis. THE NEW PHYTOLOGIST 2020; 226:1753-1765. [PMID: 32004385 DOI: 10.1111/nph.16463] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Dynamic regulation of the concentration of the natural auxin (IAA) is essential to coordinate most of the physiological and developmental processes and responses to environmental changes. Oxidation of IAA is a major pathway to control auxin concentrations in angiosperms and, along with IAA conjugation, to respond to perturbation of IAA homeostasis. However, these regulatory mechanisms remain poorly investigated in conifers. To reduce this knowledge gap, we investigated the different contributions of the IAA inactivation pathways in conifers. MS-based quantification of IAA metabolites under steady-state conditions and after perturbation was investigated to evaluate IAA homeostasis in conifers. Putative Picea abies GH3 genes (PaGH3) were identified based on a comprehensive phylogenetic analysis including angiosperms and basal land plants. Auxin-inducible PaGH3 genes were identified by expression analysis and their IAA-conjugating activity was explored. Compared to Arabidopsis, oxidative and conjugative pathways differentially contribute to reduce IAA concentrations in conifers. We demonstrated that the oxidation pathway plays a marginal role in controlling IAA homeostasis in spruce. By contrast, an excess of IAA rapidly activates GH3-mediated irreversible conjugation pathways. Taken together, these data indicate that a diversification of IAA inactivation mechanisms evolved specifically in conifers.
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Affiliation(s)
- Federica Brunoni
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University (Umu), 90736, Umeå, Sweden
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Silvio Collani
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University (Umu), 90736, Umeå, Sweden
| | - Rubén Casanova-Sáez
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
| | - Jan Šimura
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
| | - Michal Karady
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
- Departmebt of Chemical Biology and Genetics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, CZ-78371, Olomouc, Czech Republic
| | - Markus Schmid
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University (Umu), 90736, Umeå, Sweden
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
| | - Catherine Bellini
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University (Umu), 90736, Umeå, Sweden
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
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Torrens-Spence MP, Bobokalonova A, Carballo V, Glinkerman CM, Pluskal T, Shen A, Weng JK. PBS3 and EPS1 Complete Salicylic Acid Biosynthesis from Isochorismate in Arabidopsis. MOLECULAR PLANT 2019; 12:1577-1586. [PMID: 31760159 DOI: 10.1016/j.molp.2019.11.005] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 05/20/2023]
Abstract
Salicylic acid (SA) is an important phytohormone mediating both local and systemic defense responses in plants. Despite over half a century of research, how plants biosynthesize SA remains unresolved. In Arabidopsis, a major part of SA is derived from isochorismate, a key intermediate produced by the isochorismate synthase, which is reminiscent of SA biosynthesis in bacteria. Whereas bacteria employ an isochorismate pyruvate lyase (IPL) that catalyzes the turnover of isochorismate to pyruvate and SA, plants do not contain an IPL ortholog and generate SA from isochorismate through an unknown mechanism. Combining genetic and biochemical approaches, we delineated the SA biosynthetic pathway downstream of isochorismate in Arabidopsis. We found that PBS3, a GH3 acyl adenylase-family enzyme important for SA accumulation, catalyzes ATP- and Mg2+-dependent conjugation of L-glutamate primarily to the 8-carboxyl of isochorismate and yields the key SA biosynthetic intermediate, isochorismoyl-glutamate A. Moreover, we discovered that EPS1, a BAHD acyltransferase-family protein with a previously implicated role in SA accumulation upon pathogen attack, harbors a noncanonical active site and an unprecedented isochorismoyl-glutamate A pyruvoyl-glutamate lyase activity that produces SA from the isochorismoyl-glutamate A substrate. Together, PBS3 and EPS1 form a two-step metabolic pathway to produce SA from isochorismate in Arabidopsis, which is distinct from how SA is biosynthesized in bacteria. This study closes a major knowledge gap in plant SA metabolism and would help develop new strategies for engineering disease resistance in crop plants.
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Affiliation(s)
| | - Anastassia Bobokalonova
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Valentina Carballo
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | | | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Amber Shen
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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22
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Pinto RT, Freitas NC, Máximo WPF, Cardoso TB, Prudente DDO, Paiva LV. Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp. BMC Genomics 2019; 20:812. [PMID: 31694532 PMCID: PMC6836404 DOI: 10.1186/s12864-019-6176-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/07/2019] [Indexed: 01/25/2023] Open
Abstract
Background Coffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which leads to management problems regarding the plantations maintenance, harvest and processing of grains. Therefore, an efficient clonal propagation process is required for this species cultivation, which is possible by reaching a scalable and cost-effective somatic embryogenesis protocol. A key process on somatic embryogenesis induction is the auxin homeostasis performed by Gretchen Hagen 3 (GH3) proteins through amino acid conjugation. In this study, the GH3 family members were identified on C. canephora genome, and by performing analysis related to gene and protein structure and transcriptomic profile on embryogenic tissues, we point a GH3 gene as a potential regulator of auxin homeostasis during early somatic embryogenesis in C. arabica plants. Results We have searched within the published C. canephora genome and found 17 GH3 family members. We checked the conserved domains for GH3 proteins and clustered the members in three main groups according to phylogenetic relationships. We identified amino acids sets in four GH3 proteins that are related to acidic amino acid conjugation to auxin, and using a transcription factor (TF) network approach followed by RT-qPCR we analyzed their possible transcriptional regulators and expression profiles in cells with contrasting embryogenic potential in C. arabica. The CaGH3.15 expression pattern is the most correlated with embryogenic potential and with CaBBM, a C. arabica ortholog of a major somatic embryogenesis regulator. Conclusion Therefore, one out of the GH3 members may be influencing on coffee somatic embryogenesis by auxin conjugation with acidic amino acids, which leads to the phytohormone degradation. It is an indicative that this gene can serve as a molecular marker for coffee cells with embryogenic potential and needs to be further studied on how much determinant it is for this process. This work, together with future studies, can support the improvement of coffee clonal propagation through in vitro derived somatic embryos.
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Affiliation(s)
- Renan Terassi Pinto
- Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200000, Brazil
| | | | | | | | | | - Luciano Vilela Paiva
- Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200000, Brazil.
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Gan Z, Fei L, Shan N, Fu Y, Chen J. Identification and Expression Analysis of Gretchen Hagen 3 (GH3) in Kiwifruit ( Actinidia chinensis) During Postharvest Process. PLANTS 2019; 8:plants8110473. [PMID: 31698719 PMCID: PMC6918289 DOI: 10.3390/plants8110473] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/26/2019] [Accepted: 11/05/2019] [Indexed: 11/16/2022]
Abstract
In plants, the Gretchen GH3 (GH3) protein is involved in free auxin (IAA) and amino acid conjugation, thus controlling auxin homeostasis. To date, many GH3 gene families have been identified from different plant species. However, the GH3 gene family in kiwifruit (Actinidia chinensis) has not been reported. In this study, 12 AcGH3 genes were identified, phylogenetic analysis of AtGH3 (Arabidopsis), SlGH3 (Solanum lycopersicum), and AcGH3 provided insights into various orthologous relationships among these proteins, which were categorized into three groups. Expression analysis of AcGH3 genes at different postharvest stages suggested limited or no role for most of the AcGH3 genes at the initiation of fruit ripening. AcGH3.1 was the only gene exhibiting ripening-associated expression. Further study showed that the expression of AcGH3.1 gene was induced by NAA (1-naphthylacetic acid, auxin analogue) and inhibited by 1-MCP (1-methylcyclopropene, ethylene receptor inhibitor), respectively. AcGH3.1 gene silencing inhibited gene expression and delayed fruit softening in kiwifruit. The results indicate that AcGH3.1 may play an important role in the softening process of fruits. Analysis of the AcGH3.1 promoter revealed the presence of many cis-elements related to hormones, light, and drought. The determination of GUS (β-Galactosidase) enzyme activity revealed that promoter activity increased strikingly upon abscisic acid (ABA), ethylene, or NAA treatment, and significantly decreased with salicylic acid (SA) treatment. The present study could help in the identification of GH3 genes and revelation of AcGH3.1 gene function during postharvest stages, which pave the way for further functional verification of the AcGH3.1 gene.
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Affiliation(s)
- Zengyu Gan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang 330045, China; (Z.G.); (L.F.); (Y.F.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Liuying Fei
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang 330045, China; (Z.G.); (L.F.); (Y.F.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Nan Shan
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Yongqi Fu
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang 330045, China; (Z.G.); (L.F.); (Y.F.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Jinyin Chen
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang 330045, China; (Z.G.); (L.F.); (Y.F.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China;
- Pingxiang University, Pingxiang 337055, China
- Correspondence: ; Fax: +86-0791-83813185
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Chai WW, Wang WY, Ma Q, Yin HJ, Hepworth SR, Wang SM. Comparative transcriptome analysis reveals unique genetic adaptations conferring salt tolerance in a xerohalophyte. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:670-683. [PMID: 31064640 DOI: 10.1071/fp18295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
Most studies on salt tolerance in plants have been conducted using glycophytes like Arabidopsis thaliana (L.) Heynh., with limited resistance to salinity. The xerohalophyte Zygophyllum xanthoxylum (Bunge) Engl. is a salt-accumulating desert plant that efficiently transports Na+ into vacuoles to manage salt and exhibits increased growth under salinity conditions, suggesting a unique transcriptional response compared with glycophytes. We used transcriptome profiling by RNA-seq to compare gene expression in roots of Z. xanthoxylum and A. thaliana under 50 mM NaCl treatments. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis suggested that 50 mM NaCl was perceived as a stimulus for Z. xanthoxylum whereas a stress for A. thaliana. Exposure to 50 mM NaCl caused metabolic shifts towards gluconeogenesis to stimulate growth of Z. xanthoxylum, but triggered defensive systems in A. thaliana. Compared with A. thaliana, a vast array of ion transporter genes was induced in Z. xanthoxylum, revealing an active strategy to uptake Na+ and nutrients from the environment. An ascorbate-glutathione scavenging system for reactive oxygen species was also crucial in Z. xanthoxylum, based on high expression of key enzyme genes. Finally, key regulatory genes for the biosynthesis pathways of abscisic acid and gibberellin showed distinct expression patterns between the two species and auxin response genes were more active in Z. xanthoxylum compared with A. thaliana. Our results provide an important framework for understanding unique patterns of gene expression conferring salt resistance in Z. xanthoxylum.
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Affiliation(s)
- Wei-Wei Chai
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China
| | - Wen-Ying Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China
| | - Qing Ma
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China
| | - Hong-Ju Yin
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China
| | - Shelley R Hepworth
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China; and Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
| | - Suo-Min Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China; and Corresponding author.
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25
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Kong W, Zhang Y, Deng X, Li S, Zhang C, Li Y. Comparative Genomic and Transcriptomic Analysis Suggests the Evolutionary Dynamic of GH3 Genes in Gramineae Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:1297. [PMID: 31681387 PMCID: PMC6803601 DOI: 10.3389/fpls.2019.01297] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/18/2019] [Indexed: 05/18/2023]
Abstract
Glycoside hydrolase 3 (GH3) gene family belongs to auxin-responsive gene families and is tightly linked with hormone homeostasis and signaling pathways. However, our knowledge about the evolutionary dynamic of GH3 genes in Gramineae crops is limited. In this study, a comparative genomic and transcriptomic analysis was conducted to study evolutionary patterns and the driving selective forces of GH3 gene family in six representative Gramineae crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa ssp. japonica (Os). A total of 17, 13, 11, 9, 8, and 11 GH3 proteins (GH3s) were identified in Si, Zm, Sb, Hv, Bd, and Os, respectively. Phylogenetic, conserved motif, and gene structural analyses could divide all GH3s into two groups (I and II), and all GH3s consisted of seven orthogroups (Ors) on the basis of Or identification result. We further found that genes in the same Or showed similar sequence and structural features, whereas genes in the same groups exhibited intrinsic differences in exon numbers and intron lengths. These results revealed GH3 genes in the same groups have been differentiated. Obvious differences in total numbers of GH3 genes, Ors, and duplication events among these six tested Gramineae crops reflected lineage-specific expansions and homologous gene loss/gain of GH3 gene family during the evolutionary process. In addition, selective force and expression analyses indicated that all GH3 genes were constrained by strong purifying selection, and GH3 genes in conserved Ors showed higher expression levels than that in unconserved Ors. The current study highlighted different evolutionary patterns of GH3 genes in Gramineae crops resulted from different evolutionary rates and duplication events and provided a vital insight into the functional divergence of GH3 genes.
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Liu J, Moyankova D, Lin CT, Mladenov P, Sun RZ, Djilianov D, Deng X. Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis. BMC PLANT BIOLOGY 2018; 18:351. [PMID: 30541446 PMCID: PMC6291977 DOI: 10.1186/s12870-018-1566-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/22/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Water shortage is a major factor that harms agriculture and ecosystems worldwide. Plants display various levels of tolerance to water deficit, but only resurrection plants can survive full desiccation of their vegetative tissues. Haberlea rhodopensis, an endemic plant of the Balkans, is one of the few resurrection plants found in Europe. We performed transcriptomic analyses of this species under slight, severe and full dehydration and recovery to investigate the dynamics of gene expression and associate them with existing physiological and metabolomics data. RESULTS De novo assembly yielded a total of 142,479 unigenes with an average sequence length of 1034 nt. Among them, 18,110 unigenes were differentially expressed. Hierarchical clustering of all differentially expressed genes resulted in seven clusters of dynamic expression patterns. The most significant expression changes, involving more than 15,000 genes, started at severe dehydration (~ 20% relative water content) and were partially maintained at full desiccation (< 10% relative water content). More than a hundred pathways were enriched and functionally organized in a GO/pathway network at the severe dehydration stage. Transcriptomic changes in key pathways were analyzed and discussed in relation to metabolic processes, signal transduction, quality control of protein and DNA repair in this plant during dehydration and rehydration. CONCLUSION Reprograming of the transcriptome occurs during severe dehydration, resulting in a profound alteration of metabolism toward alternative energy supply, hormone signal transduction, and prevention of DNA/protein damage under very low cellular water content, underlying the observed physiological and metabolic responses and the resurrection behavior of H. rhodopensis.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, 262700 China
| | - Daniela Moyankova
- Abiotic Stress Group, Agrobioinstitute, Agricultural Academy, 1164 Sofia, Bulgaria
| | - Chih-Ta Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Petko Mladenov
- Abiotic Stress Group, Agrobioinstitute, Agricultural Academy, 1164 Sofia, Bulgaria
| | - Run-Ze Sun
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Dimitar Djilianov
- Abiotic Stress Group, Agrobioinstitute, Agricultural Academy, 1164 Sofia, Bulgaria
| | - Xin Deng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
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27
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Yu D, Qanmber G, Lu L, Wang L, Li J, Yang Z, Liu Z, Li Y, Chen Q, Mendu V, Li F, Yang Z. Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture. BMC PLANT BIOLOGY 2018; 18:350. [PMID: 30541440 PMCID: PMC6291927 DOI: 10.1186/s12870-018-1545-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 11/20/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Auxin-induced genes regulate many aspects of plant growth and development. The Gretchen Hagen 3 (GH3) gene family, one of three major early auxin-responsive families, is ubiquitous in the plant kingdom and its members function as regulators in modulating hormonal homeostasis, and stress adaptations. Specific Auxin-amido synthetase activity of GH3 subfamily II genes is reported to reversibly inactivate or fully degrade excess auxin through the formation of amino acid conjugates. Despite these crucial roles, to date, genome-wide analysis of the GH3 gene family has not been reported in cotton. RESULTS We identified a total of 10 GH3 subfamily II genes in G. arboreum, 10 in G. raimondii, and 20 in G. hirsutum, respectively. Bioinformatic analysis showed that cotton GH3 genes are conserved with the established GH3s in plants. Expression pattern analysis based on RNA-seq data and qRT-PCR revealed that 20 GhGH3 genes were differentially expressed in a temporally and spatially specific manner, indicating their diverse functions in growth and development. We further summarized the organization of promoter regulatory elements and monitored their responsiveness to treatment with IAA (indole-3-acetic acid), SA (salicylic acid), GA (gibberellic acid) and BL (brassinolide) by qRT-PCR in roots and stems. These hormones seemed to regulate the expression of GH3 genes in both a positive and a negative manner while certain members likely have higher sensitivity to all four hormones. Further, we tested the expression of GhGH3 genes in the BR-deficient mutant pag1 and the corresponding wild-type (WT) of CCRI24. The altered expression reflected the true responsiveness to BL and further suggested possible reasons, at least in part, responsible for the dramatic dwarf and shriveled phenotypes of pag1. CONCLUSION We comprehensively identified GH3 subfamily II genes in cotton. GhGH3s are differentially expressed in various tissues/organs/stages. Their response to IAA, SA, BL and GA and altered expression in pag1 suggest that some GhGH3 genes might be simultaneously involved in multiple hormone signaling pathways. Taken together, our results suggest that members of the GhGH3 gene family could be possible candidate genes for mechanistic study and applications in cotton fiber development in addition to the reconstruction of plant architecture.
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Affiliation(s)
- Daoqian Yu
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052 China
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Lili Lu
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052 China
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Lingling Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Jie Li
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052 China
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Zhaoen Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052 China
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Zhao Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Yi Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Quanjia Chen
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Venugopal Mendu
- Fiber and Biopolymer Research Institute (FBRI), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA
| | - Fuguang Li
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052 China
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000 China
| | - Zuoren Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Urumqi, 830052 China
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000 China
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Chiu LW, Heckert MJ, You Y, Albanese N, Fenwick T, Siehl DL, Castle LA, Tao Y. Members of the GH3 Family of Proteins Conjugate 2,4-D and Dicamba with Aspartate and Glutamate. PLANT & CELL PHYSIOLOGY 2018; 59:2366-2380. [PMID: 30101323 DOI: 10.1093/pcp/pcy160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 08/01/2018] [Indexed: 06/08/2023]
Abstract
Auxin homeostasis is a highly regulated process that must be maintained to allow auxin to exert critical growth and developmental controls. Auxin conjugase and hydrolase family proteins play important roles in auxin homeostasis through means of storage, activation, inactivation, response inhibition and degradation of auxins in plants. We systematically evaluated 60 GRETCHEN HAGEN3 (GH3) proteins from diverse plant species for amino acid conjugation activity with the known substrates jasmonic acid (JA), IAA and 4-hydroxybenzoate (4-HBA). While our results largely confirm that Group II conjugases prefer IAA, we observed no clear substrate preference among Group III proteins, and only three of 11 Group I proteins showed the expected preference for JA, indicating that sequence similarity does not always predict substrate specificity. Such a sequence-substrate relationship held true when sequence similarity at the acyl acid-binding site was used for grouping. Several GH3 proteins could catalyze formation of the potentially degradation-destined aspartate (Asp) and glutamate (Glu) conjugates of IAA and the synthetic auxins 2,4-D and dicamba. We found that 2,4-D-Asp/Glu conjugates, but not dicamba and IAA conjugates, were hydrolyzed in Arabidopsis and soybean by AtILL5- and AtIAR3-like amidohydrolases, releasing free 2,4-D in plant cells when conjugates were exogenously applied to seedlings. Dicamba-Asp or dicamba-Glu conjugates were not hydrolyzed in vivo in infiltrated plants nor in vitro with recombinant amidohydrolases. These findings could open the door for exploration of a dicamba herbicide tolerance strategy through conjugation.
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Affiliation(s)
- Li-Wei Chiu
- Trait Discovery & Technology, DuPont Pioneer, 4010 Point Eden Way, Hayward, CA, USA
| | - Matthew J Heckert
- Trait Discovery & Technology, DuPont Pioneer, 4010 Point Eden Way, Hayward, CA, USA
| | - You You
- Trait Discovery & Technology, DuPont Pioneer, 4010 Point Eden Way, Hayward, CA, USA
| | - Nicholas Albanese
- Trait Discovery & Technology, DuPont Pioneer, 4010 Point Eden Way, Hayward, CA, USA
| | - Tamara Fenwick
- Trait Discovery & Technology, DuPont Pioneer, 4010 Point Eden Way, Hayward, CA, USA
| | - Daniel L Siehl
- Trait Discovery & Technology, DuPont Pioneer, 4010 Point Eden Way, Hayward, CA, USA
| | - Linda A Castle
- Trait Discovery & Technology, DuPont Pioneer, 4010 Point Eden Way, Hayward, CA, USA
| | - Yumin Tao
- Trait Discovery & Technology, DuPont Pioneer, 4010 Point Eden Way, Hayward, CA, USA
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Zhang C, Zhang L, Wang D, Ma H, Liu B, Shi Z, Ma X, Chen Y, Chen Q. Evolutionary History of the Glycoside Hydrolase 3 (GH3) Family Based on the Sequenced Genomes of 48 Plants and Identification of Jasmonic Acid-Related GH3 Proteins in Solanum tuberosum. Int J Mol Sci 2018; 19:ijms19071850. [PMID: 29937487 PMCID: PMC6073592 DOI: 10.3390/ijms19071850] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/01/2018] [Accepted: 06/19/2018] [Indexed: 12/20/2022] Open
Abstract
Glycoside Hydrolase 3 (GH3) is a phytohormone-responsive family of proteins found in many plant species. These proteins contribute to the biological activity of indolacetic acid (IAA), jasmonic acid (JA), and salicylic acid (SA). They also affect plant growth and developmental processes as well as some types of stress. In this study, GH3 genes were identified in 48 plant species, including algae, mosses, ferns, gymnosperms, and angiosperms. No GH3 representative protein was found in algae, but we identified 4 genes in mosses, 19 in ferns, 7 in gymnosperms, and several in angiosperms. The results showed that GH3 proteins are mainly present in seed plants. Phylogenetic analysis of all GH3 proteins showed three separate clades. Group I was related to JA adenylation, group II was related to IAA adenylation, and group III was separated from group II, but its function was not clear. The structure of the GH3 proteins indicated highly conserved sequences in the plant kingdom. The analysis of JA adenylation in relation to gene expression of GH3 in potato (Solanum tuberosum) showed that StGH3.12 greatly responded to methyl jasmonate (MeJA) treatment. The expression levels of StGH3.1, StGH3.11, and StGH3.12 were higher in the potato flowers, and StGH3.11 expression was also higher in the stolon. Our research revealed the evolution of the GH3 family, which is useful for studying the precise function of GH3 proteins related to JA adenylation in S. tuberosum when the plants are developing and under biotic stress.
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Affiliation(s)
- Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Leilei Zhang
- College of Agronomy, Liaocheng University, Liaocheng 252059, Shandong, China.
| | - Dongdong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Haoli Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Bailin Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Zheng Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xiaohui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Qin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Mackelprang R, Okrent RA, Wildermuth MC. Preference of Arabidopsis thaliana GH3.5 acyl amido synthetase for growth versus defense hormone acyl substrates is dictated by concentration of amino acid substrate aspartate. PHYTOCHEMISTRY 2017; 143:19-28. [PMID: 28743075 DOI: 10.1016/j.phytochem.2017.07.001] [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] [Received: 03/30/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 06/07/2023]
Abstract
The GH3 family of adenylating enzymes conjugate acyl substrates such as the growth hormone indole-3-acetic acid (IAA) to amino acids via a two-step reaction of acyl substrate adenylation followed by amino acid conjugation. Arabidopsis thaliana GH3.5 was previously shown to be unusual in that it could adenylate both IAA and the defense hormone salicylic acid (SA, 2-hydroxybenzoate). Our detailed studies of the kinetics of GH3.5 on a variety of auxin and benzoate substrates provides insight into the acyl preference and reaction mechanism of GH3.5. For example, we found GH3.5 activity on substituted benzoates is not defined by the substitution position as it is for GH3.12/PBS3. Most importantly, we show that GH3.5 strongly prefers Asp as the amino acid conjugate and that the concentration of Asp dictates the functional activity of GH3.5 on IAA vs. SA. Not only is Asp used in amino acid biosynthesis, but it also plays an important role in nitrogen mobilization and in the production of downstream metabolites, including pipecolic acid which propagates defense systemically. During active growth, [IAA] and [Asp] are high and the catalytic efficiency (kcat/Km) of GH3.5 for IAA is 360-fold higher than with SA. GH3.5 is expressed under these conditions and conversion of IAA to inactive IAA-Asp would provide fine spatial and temporal control over local auxin developmental responses. By contrast, [SA] is dramatically elevated in response to (hemi)-biotrophic pathogens which also induce GH3.5 expression. Under these conditions, [Asp] is low and GH3.5 has equal affinity (Km) for SA and IAA with similar catalytic efficiencies. However, the concentration of IAA tends to be very low, well below the Km for IAA. Therefore, GH3.5 catalyzed formation of SA-Asp would occur, fine-tuning localized defensive responses through conversion of active free SA to SA-Asp. Taken together, we show how GH3.5, with dual activity on IAA and SA, can integrate cellular metabolic status via Asp to provide fine control of growth vs. defense outcomes and hormone homeostasis.
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Affiliation(s)
- Rebecca Mackelprang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Rachel A Okrent
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Mary C Wildermuth
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
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Berens ML, Berry HM, Mine A, Argueso CT, Tsuda K. Evolution of Hormone Signaling Networks in Plant Defense. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:401-425. [PMID: 28645231 DOI: 10.1146/annurev-phyto-080516-035544] [Citation(s) in RCA: 277] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Studies with model plants such as Arabidopsis thaliana have revealed that phytohormones are central regulators of plant defense. The intricate network of phytohormone signaling pathways enables plants to activate appropriate and effective defense responses against pathogens as well as to balance defense and growth. The timing of the evolution of most phytohormone signaling pathways seems to coincide with the colonization of land, a likely requirement for plant adaptations to the more variable terrestrial environments, which included the presence of pathogens. In this review, we explore the evolution of defense hormone signaling networks by combining the model plant-based knowledge about molecular components mediating phytohormone signaling and cross talk with available genome information of other plant species. We highlight conserved hubs in hormone cross talk and discuss evolutionary advantages of defense hormone cross talk. Finally, we examine possibilities of engineering hormone cross talk for improvement of plant fitness and crop production.
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Affiliation(s)
- Matthias L Berens
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Hannah M Berry
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Akira Mine
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Cristiana T Argueso
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Kenichi Tsuda
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
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Structural basis of jasmonate-amido synthetase FIN219 in complex with glutathione S-transferase FIP1 during the JA signal regulation. Proc Natl Acad Sci U S A 2017; 114:E1815-E1824. [PMID: 28223489 DOI: 10.1073/pnas.1609980114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Far-red (FR) light-coupled jasmonate (JA) signaling is necessary for plant defense and development. FR insensitive 219 (FIN219) is a member of the Gretchen Hagen 3 (GH3) family of proteins in Arabidopsis and belongs to the adenylate-forming family of enzymes. It directly controls biosynthesis of jasmonoyl-isoleucine in JA-mediated defense responses and interacts with FIN219-interacting protein 1 (FIP1) under FR light conditions. FIN219 and FIP1 are involved in FR light signaling and are regulators of the interplay between light and JA signaling. However, how their interactions affect plant physiological functions remains unclear. Here, we demonstrate the crystal structures of FIN219-FIP1 while binding with substrates at atomic resolution. Our results show an unexpected FIN219 conformation and demonstrate various differences between this protein and other members of the GH3 family. We show that the rotated C-terminal domain of FIN219 alters ATP binding and the core structure of the active site. We further demonstrate that this unique FIN219-FIP1 structure is crucial for increasing FIN219 activity and determines the priority of substrate binding. We suggest that the increased FIN219 activity resulting from the complex form, a conformation for domain switching, allows FIN219 to switch to its high-affinity mode and thereby enhances JA signaling under continuous FR light conditions.
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Fesel PH, Zuccaro A. Dissecting endophytic lifestyle along the parasitism/mutualism continuum in Arabidopsis. Curr Opin Microbiol 2016; 32:103-112. [DOI: 10.1016/j.mib.2016.05.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 11/17/2022]
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Liao D, Chen X, Chen A, Wang H, Liu J, Liu J, Gu M, Sun S, Xu G. The characterization of six auxin-induced tomato GH3 genes uncovers a member, SlGH3.4, strongly responsive to arbuscular mycorrhizal symbiosis. PLANT & CELL PHYSIOLOGY 2015; 56:674-87. [PMID: 25535196 DOI: 10.1093/pcp/pcu212] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 12/16/2014] [Indexed: 05/08/2023]
Abstract
In plants, the GH3 gene family is widely considered to be involved in a broad range of plant physiological processes, through modulation of hormonal homeostasis. Multiple GH3 genes have been functionally characterized in several plant species; however, to date, limited works to study the GH3 genes in tomato have been reported. Here, we characterize the expression and regulatory profiles of six tomato GH3 genes, SlGH3.2, SlGH3.3, SlGH3.4, SlGH3.7, SlGH3.9 and SlGH3.15, in response to different phytohormone applications and arbuscular mycorrhizal (AM) fungal colonization. All six GH3 genes showed inducible responses to external IAA, and three members were significantly up-regulated in response to AM symbiosis. In particular, SlGH3.4, the transcripts of which were barely detectable under normal growth conditions, was strongly activated in the IAA-treated and AM fungal-colonized roots. A comparison of the SlGH3.4 expression in wild-type plants and M161, a mutant with a defect in AM symbiosis, confirmed that SlGH3.4 expression is highly correlated to mycorrhizal colonization. Histochemical staining demonstrated that a 2,258 bp SlGH3.4 promoter fragment could drive β-glucuronidase (GUS) expression strongly in root tips, steles and cortical cells of IAA-treated roots, but predominantly in the fungal-colonized cells of mycorrhizal roots. A truncated 654 bp promoter failed to direct GUS expression in IAA-treated roots, but maintained the symbiosis-induced activity in mycorrhizal roots. In summary, our results suggest that a mycorrhizal signaling pathway that is at least partially independent of the auxin signaling pathway has evolved for the co-regulation of the auxin- and mycorrhiza-activated GH3 genes in plants.
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Affiliation(s)
- Dehua Liao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095, China These authors contributed equally to this work
| | - Xiao Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095, China These authors contributed equally to this work
| | - Aiqun Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095, China
| | - Huimin Wang
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianjian Liu
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Junli Liu
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Mian Gu
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095, China MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
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Cecchini NM, Jung HW, Engle NL, Tschaplinski TJ, Greenberg JT. ALD1 Regulates Basal Immune Components and Early Inducible Defense Responses in Arabidopsis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:455-66. [PMID: 25372120 DOI: 10.1094/mpmi-06-14-0187-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Robust immunity requires basal defense machinery to mediate timely responses and feedback cycles to amplify defenses against potentially spreading infections. AGD2-LIKE DEFENSE RESPONSE PROTEIN 1 (ALD1) is needed for the accumulation of the plant defense signal salicylic acid (SA) during the first hours after infection with the pathogen Pseudomonas syringae and is also upregulated by infection and SA. ALD1 is an aminotransferase with multiple substrates and products in vitro. Pipecolic acid (Pip) is an ALD1-dependent bioactive product induced by P. syringae. Here, we addressed roles of ALD1 in mediating defense amplification as well as the levels and responses of basal defense machinery. ALD1 needs immune components PAD4 and ICS1 (an SA synthesis enzyme) to confer disease resistance, possibly through a transcriptional amplification loop between them. Furthermore, ALD1 affects basal defense by controlling microbial-associated molecular pattern (MAMP) receptor levels and responsiveness. Vascular exudates from uninfected ALD1-overexpressing plants confer local immunity to the wild type and ald1 mutants yet are not enriched for Pip. We infer that, in addition to affecting Pip accumulation, ALD1 produces non-Pip metabolites that play roles in immunity. Thus, distinct metabolite signals controlled by the same enzyme affect basal and early defenses versus later defense responses, respectively.
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Affiliation(s)
- Nicolás M Cecchini
- 1 Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago 60637, U.S.A
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Wang X, Du J, Yao X. Structural and dynamic basis of acid amido synthetase GH3.1: an investigation of substrate selectivity and major active site access channels. MOLECULAR BIOSYSTEMS 2014; 11:809-18. [PMID: 25531425 DOI: 10.1039/c4mb00608a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Auxin/IAA (Indole-3-acetic acid) plays critical roles in many aspects of plant growth and development. Gretchen Hagen 3.1 (GH3.1) enzyme from grapevine (Vitis vinifera) catalyzes the ATP-dependent conjugation of aspartate to IAA suggesting a significant way to modulate levels of cellular auxins/IAA. It is reported that VvGH3.1 prefers IAA as the substrate than 1-naphthaleneacetic acid (NAA) and benzothiazole-2-oxyacetic acid (BTOA), whereas the detailed interaction mechanism of these substrates remains unclear. In this study, based on the recently reported crystal structure of VvGH3.1 and AtGH3.12, the open form of VvGH3.1 was built. Then combined computational techniques including molecular docking, molecular dynamics (MD) simulations, Molecular Mechanics Generalized Born Surface Area and Poisson-Boltzmann Surface Area (MM-GB/PBSA) methods and active site access channel analysis were utilized to investigate the binding mechanism of three substrates, IAA, NAA and BTOA, and dynamic behaviors of GH3.1 induced by substrate binding. The predicted binding free energy is in agreement with the experimental work with an order of IAA < NAA < BTOA. Key residues interacting with three substrates and residues specifically binding to one of them were identified. The strong hydrogen bond interaction formed between IAA and Ser108, Ser339, Gln560 makes it the best substrate over NAA and BTOA. The dynamic behaviors, especially in the dominant access channels of IAA and NAA bound GH3.1, were found to be different from those in the BTOA-GH3.1 system with larger bottleneck radius and shorter length. This study provided novel insight to understand the substrate selectivity mechanism of GH3.1 and also for the rational design of novel auxin-based herbicides and growth regulators.
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Affiliation(s)
- Xue Wang
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao 266109, China.
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38
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Meesters C, Mönig T, Oeljeklaus J, Krahn D, Westfall CS, Hause B, Jez JM, Kaiser M, Kombrink E. A chemical inhibitor of jasmonate signaling targets JAR1 in Arabidopsis thaliana. Nat Chem Biol 2014; 10:830-6. [PMID: 25129030 DOI: 10.1038/nchembio.1591] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/12/2014] [Indexed: 12/11/2022]
Abstract
Jasmonates are lipid-derived plant hormones that regulate plant defenses and numerous developmental processes. Although the biosynthesis and molecular function of the most active form of the hormone, (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile), have been unraveled, it remains poorly understood how the diversity of bioactive jasmonates regulates such a multitude of plant responses. Bioactive analogs have been used as chemical tools to interrogate the diverse and dynamic processes of jasmonate action. By contrast, small molecules impairing jasmonate functions are currently unknown. Here, we report on jarin-1 as what is to our knowledge the first small-molecule inhibitor of jasmonate responses that was identified in a chemical screen using Arabidopsis thaliana. Jarin-1 impairs the activity of JA-Ile synthetase, thereby preventing the synthesis of the active hormone, JA-Ile, whereas closely related enzymes are not affected. Thus, jarin-1 may serve as a useful chemical tool in search for missing regulatory components and further dissection of the complex jasmonate signaling networks.
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Affiliation(s)
- Christian Meesters
- 1] Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany. [2] Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Timon Mönig
- Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Julian Oeljeklaus
- Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Daniel Krahn
- Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Corey S Westfall
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Markus Kaiser
- Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Erich Kombrink
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
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Ayil-Gutiérrez B, Galaz-Ávalos RM, Peña-Cabrera E, Loyola-Vargas VM. Dynamics of the concentration of IAA and some of its conjugates during the induction of somatic embryogenesis in Coffea canephora. PLANT SIGNALING & BEHAVIOR 2013; 8:e26998. [PMID: 24299659 PMCID: PMC4091420 DOI: 10.4161/psb.26998] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 05/18/2023]
Abstract
Most of the somatic embryogenesis (SE) process requires the presence, either before or during the embryogenic process, of at least one exogenous auxin. This exogenous auxin induces the presence of endogenous auxins, which appears to be essential for SE induction. We found that during the preincubation period of SE in Coffea canephora, there is an important increase in both free and conjugated indole-3-acetic acid (IAA), as well as indole-3-butyric acid. This increase is accompanied by an increase in the expression of YUCCA (CcYUC), TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (CcTAA1), and GRETCHEN HAGEN 3 (GH3) genes. On the other hand, most of the IAA compounds decreased during the induction of SE. The results presented in this research suggest that a balance between free IAA and its amide conjugates is necessary to allow the expression of SE-related genes.
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Affiliation(s)
- Benajmín Ayil-Gutiérrez
- Unidad de Bioquímica y Biología Molecular de Plantas; Centro de Investigación Científica de Yucatán; Mérida, Yucatán, México
| | - Rosa María Galaz-Ávalos
- Unidad de Bioquímica y Biología Molecular de Plantas; Centro de Investigación Científica de Yucatán; Mérida, Yucatán, México
| | - Eduardo Peña-Cabrera
- Departamento de Química; Universidad de Guanajuato; Col. Noria Alta S/N, Guanajuato, México
| | - Victor Manuel Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas; Centro de Investigación Científica de Yucatán; Mérida, Yucatán, México
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Round A, Brown E, Marcellin R, Kapp U, Westfall CS, Jez JM, Zubieta C. Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2072-80. [PMID: 24100325 DOI: 10.1107/s0907444913019276] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/11/2013] [Indexed: 01/06/2023]
Abstract
The combination of protein crystallography and small-angle X-ray scattering (SAXS) provides a powerful method to investigate changes in protein conformation. These complementary structural techniques were used to probe the solution structure of the apo and the ligand-bound forms of the Arabidopsis thaliana acyl acid-amido synthetase GH3.12. This enzyme is part of the extensive GH3 family and plays a critical role in the regulation of plant hormones through the formation of amino-acid-conjugated hormone products via an ATP-dependent reaction mechanism. The enzyme adopts two distinct C-terminal domain orientations with `open' and `closed' active sites. Previous studies suggested that ATP only binds in the open orientation. Here, the X-ray crystal structure of GH3.12 is presented in the closed conformation in complex with the nonhydrolysable ATP analogue AMPCPP and the substrate salicylate. Using on-line HPLC purification combined with SAXS measurements, the most likely apo and ATP-bound protein conformations in solution were determined. These studies demonstrate that the C-terminal domain is flexible in the apo form and favours the closed conformation upon ATP binding. In addition, these data illustrate the efficacy of on-line HPLC purification integrated into the SAXS sample-handling environment to reliably monitor small changes in protein conformation through the collection of aggregate-free and highly redundant data.
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Affiliation(s)
- Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France
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Westfall CS, Muehler AM, Jez JM. Enzyme action in the regulation of plant hormone responses. J Biol Chem 2013; 288:19304-11. [PMID: 23709222 DOI: 10.1074/jbc.r113.475160] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plants synthesize a chemically diverse range of hormones that regulate growth, development, and responses to environmental stresses. The major classes of plant hormones are specialized metabolites with exquisitely tailored perception and signaling systems, but equally important are the enzymes that control the dose and exposure to the bioactive forms of these molecules. Here, we review new insights into the role of enzyme families, including the SABATH methyltransferases, the methylesterases, the GH3 acyl acid-amido synthetases, and the hormone peptidyl hydrolases, in controlling the biosynthesis and modifications of plant hormones and how these enzymes contribute to the network of chemical signals responsible for plant growth, development, and environmental adaptation.
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Affiliation(s)
- Corey S Westfall
- Department of Biology, Washington University in St Louis, St Louis, Missouri 63130, USA
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Westfall CS, Zubieta C, Herrmann J, Kapp U, Nanao MH, Jez JM. Structural Basis for Prereceptor Modulation of Plant Hormones by GH3 Proteins. Science 2012; 336:1708-11. [DOI: 10.1126/science.1221863] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Acyl acid amido synthetases of the GH3 family act as critical prereceptor modulators of plant hormone action; however, the molecular basis for their hormone selectivity is unclear. Here, we report the crystal structures of benzoate-specific Arabidopsis thaliana AtGH3.12/PBS3 and jasmonic acid–specific AtGH3.11/JAR1. These structures, combined with biochemical analysis, define features for the conjugation of amino acids to diverse acyl acid substrates and highlight the importance of conformational changes in the carboxyl-terminal domain for catalysis. We also identify residues forming the acyl acid binding site across the GH3 family and residues critical for amino acid recognition. Our results demonstrate how a highly adaptable three-dimensional scaffold is used for the evolution of promiscuous activity across an enzyme family for modulation of plant signaling molecules.
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Böttcher C, Dennis EG, Booker GW, Polyak SW, Boss PK, Davies C. A novel tool for studying auxin-metabolism: the inhibition of grapevine indole-3-acetic acid-amido synthetases by a reaction intermediate analogue. PLoS One 2012; 7:e37632. [PMID: 22649546 PMCID: PMC3359377 DOI: 10.1371/journal.pone.0037632] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 04/27/2012] [Indexed: 02/03/2023] Open
Abstract
An important process for the regulation of auxin levels in plants is the inactivation of indole-3-acetic acid (IAA) by conjugation to amino acids. The conjugation reaction is catalysed by IAA-amido synthetases belonging to the family of GH3 proteins. Genetic approaches to study the biological significance of these enzymes have been hampered by large gene numbers and a high degree of functional redundancy. To overcome these difficulties a chemical approach based on the reaction mechanism of GH3 proteins was employed to design a small molecule inhibitor of IAA-amido synthetase activity. Adenosine-5'-[2-(1H-indol-3-yl)ethyl]phosphate (AIEP) mimics the adenylated intermediate of the IAA-conjugation reaction and was therefore proposed to compete with the binding of MgATP and IAA in the initial stages of catalysis. Two grapevine IAA-amido synthetases with different catalytic properties were chosen to test the inhibitory effects of AIEP in vitro. GH3-1 has previously been implicated in the grape berry ripening process and is restricted to two amino acid substrates, whereas GH3-6 conjugated IAA to 13 amino acids. AIEP is the most potent inhibitor of GH3 enzymes so far described and was shown to be competitive against MgATP and IAA binding to both enzymes with K(i)-values 17-68-fold lower than the respective K(m)-values. AIEP also exhibited in vivo activity in an ex planta test system using young grape berries. Exposure to 5-20 µM of the inhibitor led to decreased levels of the common conjugate IAA-Asp and reduced the accumulation of the corresponding Asp-conjugate upon treatment with a synthetic auxin. AIEP therefore represents a novel chemical probe with which to study IAA-amido synthetase function.
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Kumar R, Agarwal P, Tyagi AK, Sharma AK. Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum). Mol Genet Genomics 2012. [PMID: 22228229 DOI: 10.1007/s00438‐011‐0672‐6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
In plants, auxin-mediated responses are regulated by diverse proteins. One such class of proteins, i.e. GH3, is involved in the conjugation of IAA to amino acids and provides a negative feedback loop to control auxin homoeostasis. In order to have a better understanding of the mechanism of the auxin action, 15 genes encoding GH3 members were identified using existing EST databases of tomato. Their orthologs were identified from tobacco, potato, N. benthemiana, pepper, and petunia. Phylogenetic analysis of AtGH3, SlGH3, and their Solanaceae orthologs provided insights into various orthologous relationships among these proteins. These genes were found to be responsive to a variety of signals including, phytohormones and environmental stresses. Analysis of AuxRE elements in their promoters showed variability in the sequence as well as number of this element. Up-regulation of only 11 SlGH3 genes, in response to exogenous auxin, suggested possible relationship between the diversity in the sequence and number of AuxRE element with the auxin inducibility. Expression analysis of SlGH3 genes in different vegetative and reproductive tissues/stages suggested limited or no role for most of the SlGH3 genes at the initiation of fruit ripening. However, up-regulation of SlGH3-1 and -2 at the onset of fruit ripening indicates that these genes could have a role in fruit ripening. The present study characterizes GH3 gene family of tomato and its evolutionary relationship with members of this family from other Solanaceae species and Arabidopsis. It could help in the identification of GH3 genes and revelation of their function during vegetative/reproductive development stages from other Solanaceae members.
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Affiliation(s)
- Rahul Kumar
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
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Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum). Mol Genet Genomics 2012; 287:221-35. [DOI: 10.1007/s00438-011-0672-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/22/2011] [Indexed: 12/29/2022]
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