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Prešern U, Goličnik M. Enzyme Databases in the Era of Omics and Artificial Intelligence. Int J Mol Sci 2023; 24:16918. [PMID: 38069254 PMCID: PMC10707154 DOI: 10.3390/ijms242316918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Enzyme research is important for the development of various scientific fields such as medicine and biotechnology. Enzyme databases facilitate this research by providing a wide range of information relevant to research planning and data analysis. Over the years, various databases that cover different aspects of enzyme biology (e.g., kinetic parameters, enzyme occurrence, and reaction mechanisms) have been developed. Most of the databases are curated manually, which improves reliability of the information; however, such curation cannot keep pace with the exponential growth in published data. Lack of data standardization is another obstacle for data extraction and analysis. Improving machine readability of databases is especially important in the light of recent advances in deep learning algorithms that require big training datasets. This review provides information regarding the current state of enzyme databases, especially in relation to the ever-increasing amount of generated research data and recent advancements in artificial intelligence algorithms. Furthermore, it describes several enzyme databases, providing the reader with necessary information for their use.
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Affiliation(s)
| | - Marko Goličnik
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia;
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Chakraborty P, Biswas A, Dey S, Bhattacharjee T, Chakrabarty S. Cytochrome P450 Gene Families: Role in Plant Secondary Metabolites Production and Plant Defense. J Xenobiot 2023; 13:402-423. [PMID: 37606423 PMCID: PMC10443375 DOI: 10.3390/jox13030026] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
Cytochrome P450s (CYPs) are the most prominent family of enzymes involved in NADPH- and O2-dependent hydroxylation processes throughout all spheres of life. CYPs are crucial for the detoxification of xenobiotics in plants, insects, and other organisms. In addition to performing this function, CYPs serve as flexible catalysts and are essential for producing secondary metabolites, antioxidants, and phytohormones in higher plants. Numerous biotic and abiotic stresses frequently affect the growth and development of plants. They cause a dramatic decrease in crop yield and a deterioration in crop quality. Plants protect themselves against these stresses through different mechanisms, which are accomplished by the active participation of CYPs in several biosynthetic and detoxifying pathways. There are immense potentialities for using CYPs as a candidate for developing agricultural crop species resistant to biotic and abiotic stressors. This review provides an overview of the plant CYP families and their functions to plant secondary metabolite production and defense against different biotic and abiotic stresses.
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Affiliation(s)
- Panchali Chakraborty
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA;
| | - Ashok Biswas
- Annual Bast Fiber Breeding Laboratory, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
- Department of Horticulture, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Susmita Dey
- Annual Bast Fiber Breeding Laboratory, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
- Department of Plant Pathology and Seed Science, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tuli Bhattacharjee
- Department of Chemistry, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Swapan Chakrabarty
- College of Forest Resources and Environmental Sciences, Michigan Technological University, Houghton, MI 49931, USA
- College of Computing, Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
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Li X, Wang L, Li W, Zhang X, Zhang Y, Dong S, Song X, Zhao J, Chen M, Yuan X. Genome-Wide Identification and Expression Profiling of Cytochrome P450 Monooxygenase Superfamily in Foxtail Millet. Int J Mol Sci 2023; 24:11053. [PMID: 37446233 DOI: 10.3390/ijms241311053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
The cytochrome P450 monooxygenases (CYP450) are the largest enzyme family in plant metabolism and widely involved in the biosynthesis of primary and secondary metabolites. Foxtail millet (Setaria italica (L.) P. Beauv) can respond to abiotic stress through a highly complex polygene regulatory network, in which the SiCYP450 family is also involved. Although the CYP450 superfamily has been systematically studied in a few species, the research on the CYP450 superfamily in foxtail millet has not been completed. In this study, three hundred and thirty-one SiCYP450 genes were identified in the foxtail millet genome by bioinformatics methods, which were divided into four groups, including forty-six subgroups. One hundred and sixteen genes were distributed in thirty-three tandem duplicated gene clusters. Chromosome mapping showed that SiCYP450 was distributed on seven chromosomes. In the SiCYP450 family of foxtail millet, 20 conserved motifs were identified. Cis-acting elements in the promoter region of SiCYP450 genes showed that hormone response elements were found in all SiCYP450 genes. Of the three hundred and thirty-one SiCYP450 genes, nine genes were colinear with the Arabidopsis thaliana genes. Two hundred SiCYP450 genes were colinear with the Setaria viridis genes, including two hundred and forty-five gene duplication events. The expression profiles of SiCYP450 genes in different organs and developmental stages showed that SiCYP450 was preferentially expressed in specific tissues, and many tissue-specific genes were identified, such as SiCYP75B6, SiCYP96A7, SiCYP71A55, SiCYP71A61, and SiCYP71A62 in the root, SiCYP78A1 and SiCYP94D9 in leaves, and SiCYP78A6 in the ear. The RT-PCR data showed that SiCYP450 could respond to abiotic stresses, ABA, and herbicides in foxtail millet. Among them, the expression levels of SiCYP709B4, SiCYP71A11, SiCYP71A14, SiCYP78A1, SiCYP94C3, and SiCYP94C4 were significantly increased under the treatment of mesotrione, florasulam, nicosulfuron, fluroxypyr, and sethoxydim, indicating that the same gene might respond to multiple herbicides. The results of this study will help reveal the biological functions of the SiCYP450 family in development regulation and stress response and provide a basis for molecular breeding of foxtail millet.
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Affiliation(s)
- Xiaorui Li
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Linlin Wang
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Weidong Li
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Xin Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Yujia Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Shuqi Dong
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Xi'e Song
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Juan Zhao
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Mingxun Chen
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiangyang Yuan
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
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Casey A, Dolan L. Genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with herbicide resistance evolved before the origin of land plants. PLoS One 2023; 18:e0273594. [PMID: 36800395 PMCID: PMC9937507 DOI: 10.1371/journal.pone.0273594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Cytochrome P450 (CYP) monooxygenases and glutathione S-transferases (GST) are enzymes that catalyse chemical modifications of a range of organic compounds. Herbicide resistance has been associated with higher levels of CYP and GST gene expression in some herbicide-resistant weed populations compared to sensitive populations of the same species. By comparing the protein sequences of 9 representative species of the Archaeplastida-the lineage which includes red algae, glaucophyte algae, chlorophyte algae, and streptophytes-and generating phylogenetic trees, we identified the CYP and GST proteins that existed in the common ancestor of the Archaeplastida. All CYP clans and all but one land plant GST classes present in land plants evolved before the divergence of streptophyte algae and land plants from their last common ancestor. We also demonstrate that there are more genes encoding CYP and GST proteins in land plants than in algae. The larger numbers of genes among land plants largely results from gene duplications in CYP clans 71, 72, and 85 and in the GST phi and tau classes [1,2]. Enzymes that either metabolise herbicides or confer herbicide resistance belong to CYP clans 71 and 72 and the GST phi and tau classes. Most CYP proteins that have been shown to confer herbicide resistance are members of the CYP81 family from clan 71. These results demonstrate that the clan and class diversity in extant plant CYP and GST proteins had evolved before the divergence of land plants and streptophyte algae from a last common ancestor estimated to be between 515 and 474 million years ago. Then, early in embryophyte evolution during the Palaeozoic, gene duplication in four of the twelve CYP clans, and in two of the fourteen GST classes, led to the large numbers of CYP and GST proteins found in extant land plants. It is among the genes of CYP clans 71 and 72 and GST classes phi and tau that alleles conferring herbicide resistance evolved in the last fifty years.
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Affiliation(s)
- Alexandra Casey
- Gregor Mendel Institute, Vienna, Austria
- Department of Plant Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Liam Dolan
- Gregor Mendel Institute, Vienna, Austria
- Department of Plant Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
- * E-mail:
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Julca I, Tan QW, Mutwil M. Toward kingdom-wide analyses of gene expression. TRENDS IN PLANT SCIENCE 2023; 28:235-249. [PMID: 36344371 DOI: 10.1016/j.tplants.2022.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Gene expression data for Archaeplastida are accumulating exponentially, with more than 300 000 RNA-sequencing (RNA-seq) experiments available for hundreds of species. The gene expression data stem from thousands of experiments that capture gene expression in various organs, tissues, cell types, (a)biotic perturbations, and genotypes. Advances in software tools make it possible to process all these data in a matter of weeks on modern office computers, giving us the possibility to study gene expression in a kingdom-wide manner for the first time. We discuss how the expression data can be accessed and processed and outline analyses that take advantage of cross-species analyses, allowing us to generate powerful and robust hypotheses about gene function and evolution.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Marszalek-Zenczak M, Satyr A, Wojciechowski P, Zenczak M, Sobieszczanska P, Brzezinski K, Iefimenko T, Figlerowicz M, Zmienko A. Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members. FRONTIERS IN PLANT SCIENCE 2023; 14:1104303. [PMID: 36778696 PMCID: PMC9909608 DOI: 10.3389/fpls.2023.1104303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity.
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Affiliation(s)
| | - Anastasiia Satyr
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Faculty of Computing and Telecommunications, Poznan University of Technology, Poznan, Poland
| | - Michal Zenczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Tetiana Iefimenko
- Department of Biology, National University of Kyiv-Mohyla Academy, Kyiv, Ukraine
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Sandoval-Ibáñez O, Rolo D, Ghandour R, Hertle AP, Armarego-Marriott T, Sampathkumar A, Zoschke R, Bock R. De-etiolation-induced protein 1 (DEIP1) mediates assembly of the cytochrome b 6f complex in Arabidopsis. Nat Commun 2022; 13:4045. [PMID: 35831297 PMCID: PMC9279372 DOI: 10.1038/s41467-022-31758-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/01/2022] [Indexed: 11/26/2022] Open
Abstract
The conversion of light energy to chemical energy by photosynthesis requires the concerted action of large protein complexes in the thylakoid membrane. Recent work has provided fundamental insights into the three-dimensional structure of these complexes, but how they are assembled from hundreds of parts remains poorly understood. Particularly little is known about the biogenesis of the cytochrome b6f complex (Cytb6f), the redox-coupling complex that interconnects the two photosystems. Here we report the identification of a factor that guides the assembly of Cytb6f in thylakoids of chloroplasts. The protein, DE-ETIOLATION-INDUCED PROTEIN 1 (DEIP1), resides in the thylakoid membrane and is essential for photoautotrophic growth. Knock-out mutants show a specific loss of Cytb6f, and are defective in complex assembly. We demonstrate that DEIP1 interacts with the two cytochrome subunits of the complex, PetA and PetB, and mediates the assembly of intermediates in Cytb6f biogenesis. The identification of DEIP1 provides an entry point into the study of the assembly pathway of a crucial complex in photosynthetic electron transfer. The Cytb6f complex is a multi-subunit enzyme that couples the two photosystems during the light reactions of photosynthesis. Here the authors show that the thylakoid-localized DEIP1 protein interacts with the PetA and PetB subunits, and is essential for Cytb6f complex assembly in Arabidopsis.
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Affiliation(s)
- Omar Sandoval-Ibáñez
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - David Rolo
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rabea Ghandour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alexander P Hertle
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Tegan Armarego-Marriott
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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Tian F, Han C, Chen X, Wu X, Mi J, Wan X, Liu Q, He F, Chen L, Yang H, Zhong Y, Qian Z, Zhang F. PscCYP716A1-Mediated Brassinolide Biosynthesis Increases Cadmium Tolerance and Enrichment in Poplar. FRONTIERS IN PLANT SCIENCE 2022; 13:919682. [PMID: 35865284 PMCID: PMC9294640 DOI: 10.3389/fpls.2022.919682] [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: 04/13/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd), as one of the heavy metals with biological poisonousness, seriously suppresses plant growth and does harm to human health. Hence, phytoremediation was proposed to mitigate the negative effects from Cd and restore contaminated soil. However, the internal mechanisms of detoxification of Cd used in phytoremediation are not completely revealed. In this study, we cloned the cytochrome P450 gene PscCYP716A1 from hybrid poplar "Chuanxiang No. 1" and found that the PscCYP716A1 was transcriptionally upregulated by Cd stress and downregulated by the exogenous brassinolide (BR). Meanwhile, PscCYP716A1 significantly promoted the poplar growth and enhanced the Cd accumulation in poplar. Compared to wild-type poplars, overexpressed PscCYP716A1 lines produced higher levels of endogenous BR and showed a stronger tolerance to Cd, which revealed that PscCYP716A1 may reduce the oxidative stress damage induced by Cd stress through accelerating BR synthesis. In general, PscCYP716A1 has a potential superiority in regulating the plant's tolerance to Cd stress, which will provide a scientific basis and a new type of gene-modified poplar for Cd-pollution remediation.
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Affiliation(s)
- Feifei Tian
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Chengyu Han
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoxi Chen
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Xiaolu Wu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jiaxuan Mi
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Xueqin Wan
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Qinglin Liu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Fang He
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Lianghua Chen
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Hanbo Yang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Yu Zhong
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Zongliang Qian
- Forestry and Grassland Bureau of Ganzi Prefecture, Kangding, China
| | - Fan Zhang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
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Negisho K, Shibru S, Matros A, Pillen K, Ordon F, Wehner G. Association Mapping of Drought Tolerance Indices in Ethiopian Durum Wheat ( Triticum turgidum ssp. durum). FRONTIERS IN PLANT SCIENCE 2022; 13:838088. [PMID: 35693182 PMCID: PMC9178276 DOI: 10.3389/fpls.2022.838088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Ethiopia is a major producer of durum wheat in sub-Saharan Africa. However, its production is prone to drought stress as it is fully dependent on rain, which is erratic and unpredictable. This study aimed to detect marker-trait associations (MTAs) and quantitative trait loci (QTLs) related to indices. Six drought tolerance indices, i.e., drought susceptibility index (DSI), geometric mean productivity (GMP), relative drought index (RDI), stress tolerance index (STI), tolerance index (TOL), and yield stability index (YSI) were calculated from least-square means (lsmeans) of grain yield (GY) and traits significantly (p < 0.001) correlated with grain yield (GY) under field drought stress (FDS) and field non-stress (FNS) conditions. GY, days to grain filling (DGF), soil plant analysis development (SPAD) chlorophyll meter, seeds per spike (SPS), harvest index (HI), and thousand kernel weight (TKW) were used to calculate DSI, GMP, RDI, STI, TOL, and YSI drought indices. Accessions, DW084, DW082, DZ004, C037, and DW092 were selected as the top five drought-tolerant based on DSI, RDI, TOL, and YSI combined ranking. Similarly, C010, DW033, DW080, DW124-2, and C011 were selected as stable accessions based on GMP and STI combined ranking. A total of 184 MTAs were detected linked with drought indices at -log10p ≥ 4.0,79 of which were significant at a false discovery rate (FDR) of 5%. Based on the linkage disequilibrium (LD, r 2 ≥ 0.2), six of the MTAs with a positive effect on GY-GMP were detected on chromosomes 2B, 3B, 4A, 5B, and 6B, explaining 14.72, 10.07, 26.61, 21.16, 21.91, and 22.21% of the phenotypic variance, respectively. The 184 MTAs were clustered into 102 QTLs. Chromosomes 1A, 2B, and 7A are QTL hotspots with 11 QTLs each. These chromosomes play a key role in drought tolerance and respective QTL may be exploited by marker-assisted selection for improving drought stress tolerance in wheat.
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Affiliation(s)
- Kefyalew Negisho
- National Agricultural Biotechnology Research Center, Ethiopian Institute of Agricultural Research (EIAR), Holeta, Ethiopia
| | - Surafel Shibru
- Melkassa Research Center, Ethiopian Institute of Agricultural Research (EIAR), Melkassa, Ethiopia
| | - Andrea Matros
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University, Halle, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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Wu F, Zhou Y, Shen Y, Sun Z, Li L, Li T. Linking Multi-Omics to Wheat Resistance Types to Fusarium Head Blight to Reveal the Underlying Mechanisms. Int J Mol Sci 2022; 23:ijms23042280. [PMID: 35216395 PMCID: PMC8880642 DOI: 10.3390/ijms23042280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 02/05/2023] Open
Abstract
Fusarium head blight (FHB) caused by Fusarium graminearum is a worldwide disease which has destructive effects on wheat production, resulting in severe yield reduction and quality deterioration, while FHB-infected wheat grains are toxic to people and animals due to accumulation of fungal toxins. Although impressive progress towards understanding host resistance has been achieved, our knowledge of the mechanism underlying host resistance is still quite limited due to the complexity of wheat-pathogen interactions. In recent years, disease epidemics, the resistance germplasms and components, the genetic mechanism of FHB, and disease management and control, etc., have been well reviewed. However, the resistance mechanism of FHB is quite complex with Type I, II to V resistances. In this review, we focus on the potential resistance mechanisms by linking different resistance types to multi-omics and emphasize the pathways or genes that may play significant roles in the different types of resistance. Deciphering the complicated mechanism of FHB resistance types in wheat at the integral levels based on multi-omics may help discover the genes or pathways that are critical for different FHB resistance, which could then be utilized and manipulated to improve FHB resistance in wheat breeding programs by using transgenic approaches, gene editing, or marker assisted selection strategies.
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11
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Cai Z, Wang C, Chen C, Zou L, Yin S, Liu S, Yuan J, Wu N, Liu X. Comparative transcriptome analysis reveals variations of bioactive constituents in Lonicera japonica flowers under salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 173:87-96. [PMID: 35114506 DOI: 10.1016/j.plaphy.2022.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 05/25/2023]
Abstract
Lonicera japonica flowers (LJF) is a traditional Chinese medicine packed with phenols constituents and widely used in the treatments of various diseases throughout the world. However, there is still very little known on how LJF identifies and resists salt stress. Here in, we systematically investigated the effect of salt on the phenotypic, metabolite, and transcriptomic in LJF. During long term stress (35 days), 1055 differential expression genes (DEGs) involved in the biosynthesis of secondary metabolites were screened through transcriptome analysis, among which the candidate genes and pathways involved in phenols biosynthesis were highlighted; and performed by phylogenetic tree analysis and multiple nucleotide sequence alignment. Ninety compounds were identified and their relative levels were compared between the control and stressed groups based on the LC-MS analysis, Putative biosynthesis networks of phenolic acid and flavonoid were con-structed with structural DEGs. Strikingly, the expression patterns of structural DEGs were mostly consistent with the variations of phenols under salt stress. Notably, the upregulation of UDP-glycosyl transferases under salt stress indicated post-modification of glycosyl transferases may participate in downstream flavonoids synthesis. This study reveals the relationships of the gene regulation and the phenols biosynthesis in LJF under salt stress, paving the way for the use of gene-specific expression to improve the yield of biocomponent.
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Affiliation(s)
- Zhichen Cai
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Chengcheng Wang
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Cuihua Chen
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Lisi Zou
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shengxin Yin
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shengjin Liu
- Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Jiahuan Yuan
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Nan Wu
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xunhong Liu
- Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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Rolli E, de Zélicourt A, Alzubaidy H, Karampelias M, Parween S, Rayapuram N, Han B, Froehlich K, Abulfaraj AA, Alhoraibi H, Mariappan K, Andrés-Barrao C, Colcombet J, Hirt H. The Lys-motif receptor LYK4 mediates Enterobacter sp. SA187 triggered salt tolerance in Arabidopsis thaliana. Environ Microbiol 2021; 24:223-239. [PMID: 34951090 PMCID: PMC9304150 DOI: 10.1111/1462-2920.15839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/27/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022]
Abstract
Root endophytes establish beneficial interactions with plants, improving holobiont resilience and fitness, but how plant immunity accommodates beneficial microbes is poorly understood. The multi-stress tolerance-inducing endophyte Enterobacter sp. SA187 triggers a canonical immune response in Arabidopsis only at high bacterial dosage (>108 CFUs ml-1 ), suggesting that SA187 is able to evade or suppress the plant defence system at lower titres. Although SA187 flagellin epitopes are recognized by the FLS2 receptor, SA187-triggered salt tolerance functions independently of the FLS2 system. In contrast, overexpression of the chitin receptor components LYK4 and LYK5 compromised the beneficial effect of SA187 on Arabidopsis, while it was enhanced in lyk4 mutant plants. Transcriptome analysis revealed that the role of LYK4 is intertwined with a function in remodelling defence responses with growth and root developmental processes. LYK4 interferes with modification of plant ethylene homeostasis by Enterobacter SA187 to boost salt stress resistance. Collectively, these results contribute to unlock the crosstalk between components of the plant immune system and beneficial microbes and point to a new role for the Lys-motif receptor LYK4 in beneficial plant-microbe interaction.
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Affiliation(s)
- Eleonora Rolli
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Axel de Zélicourt
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Hanin Alzubaidy
- DARWIN21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael Karampelias
- DARWIN21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sabiha Parween
- DARWIN21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Naganand Rayapuram
- DARWIN21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Baoda Han
- DARWIN21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Katja Froehlich
- DARWIN21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aala A Abulfaraj
- Department of Biological Sciences, Science and Arts College, Rabigh Campus, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hanna Alhoraibi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kiruthiga Mariappan
- DARWIN21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Cristina Andrés-Barrao
- DARWIN21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jean Colcombet
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Heribert Hirt
- DARWIN21, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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13
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Pineau E, Sauveplane V, Grienenberger E, Bassard JE, Beisson F, Pinot F. CYP77B1 a fatty acid epoxygenase specific to flowering plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 307:110905. [PMID: 33902861 DOI: 10.1016/j.plantsci.2021.110905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/17/2021] [Accepted: 04/02/2021] [Indexed: 05/02/2023]
Abstract
Contrary to animals, little is known in plants about enzymes able to produce fatty acid epoxides. In our attempt to find and characterize a new fatty acid epoxygenase in Arabidopsis thaliana, data mining brought our attention on CYP77B1. Modification of the N-terminus was necessary to get enzymatic activity after heterologous expression in yeast. The common plant fatty acid C18:2 was converted into the diol 12,13-dihydroxy-octadec-cis-9-enoic acid when incubated with microsomes of yeast expressing modified CYP77B1 and AtEH1, a soluble epoxide hydrolase. This diol originated from the hydrolysis by AtEH1 of the epoxide 12,13-epoxy-octadec-cis-9-enoic acid produced by CYP77B1. A spatio-temporal study of CYP77B1 expression performed with RT-qPCR revealed the highest level of transcripts in flower bud while, in open flower, the enzyme was mainly present in pistil. CYP77B1 promoter-driven GUS expression confirmed reporter activities in pistil and also in stamens and petals. In silico co-regulation data led us to hypothesize that CYP77B1 could be involved in cutin synthesis but when flower cutin of loss-of-function mutants cyp77b1 was analyzed, no difference was found compared to cutin of wild type plants. Phylogenetic analysis showed that CYP77B1 is strictly conserved in flowering plants, suggesting a specific function in this lineage.
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Affiliation(s)
- Emmanuelle Pineau
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
| | - Vincent Sauveplane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
| | - Etienne Grienenberger
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
| | - Jean-Etienne Bassard
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
| | - Frédéric Beisson
- Institut de Biosciences et Biotechnologies d'Aix-Marseille, CEA, CNRS, Aix Marseille Université, UMR 7265, CEA Cadarache, F-13108, Saint-Paul-lez-Durance, France.
| | - Franck Pinot
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
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14
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Schnabel A, Cotinguiba F, Athmer B, Vogt T. Piper nigrum CYP719A37 Catalyzes the Decisive Methylenedioxy Bridge Formation in Piperine Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2021; 10:128. [PMID: 33435446 PMCID: PMC7826766 DOI: 10.3390/plants10010128] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/16/2022]
Abstract
Black pepper (Piper nigrum) is among the world's most popular spices. Its pungent principle, piperine, has already been identified 200 years ago, yet the biosynthesis of piperine in black pepper remains largely enigmatic. In this report we analyzed the characteristic methylenedioxy bridge formation of the aromatic part of piperine by a combination of RNA-sequencing, functional expression in yeast, and LC-MS based analysis of substrate and product profiles. We identified a single cytochrome P450 transcript, specifically expressed in black pepper immature fruits. The corresponding gene was functionally expressed in yeast (Saccharomyces cerevisiae) and characterized for substrate specificity with a series of putative aromatic precursors with an aromatic vanilloid structure. Methylenedioxy bridge formation was only detected when feruperic acid (5-(4-hydroxy-3-methoxyphenyl)-2,4-pentadienoic acid) was used as a substrate, and the corresponding product was identified as piperic acid. Two alternative precursors, ferulic acid and feruperine, were not accepted. Our data provide experimental evidence that formation of the piperine methylenedioxy bridge takes place in young black pepper fruits after a currently hypothetical chain elongation of ferulic acid and before the formation of the amide bond. The partially characterized enzyme was classified as CYP719A37 and is discussed in terms of specificity, storage, and phylogenetic origin of CYP719 catalyzed reactions in magnoliids and eudicots.
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Affiliation(s)
- Arianne Schnabel
- Leibniz Institute of Plant Biochemistry, Department Cell and Metabolic Biology, Weinberg 3, D-06120 Halle (Saale), Germany; (A.S.); (B.A.)
| | - Fernando Cotinguiba
- Instituto de Pesquisas de Produtos Naturais (IPPN), Universidade Federal do Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro/RJ, Brazil;
| | - Benedikt Athmer
- Leibniz Institute of Plant Biochemistry, Department Cell and Metabolic Biology, Weinberg 3, D-06120 Halle (Saale), Germany; (A.S.); (B.A.)
| | - Thomas Vogt
- Leibniz Institute of Plant Biochemistry, Department Cell and Metabolic Biology, Weinberg 3, D-06120 Halle (Saale), Germany; (A.S.); (B.A.)
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15
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Wang J, Nan N, Shi L, Li N, Huang S, Zhang A, Liu Y, Guo P, Liu B, Xu ZY. Arabidopsis BRCA1 represses RRTF1-mediated ROS production and ROS-responsive gene expression under dehydration stress. THE NEW PHYTOLOGIST 2020; 228:1591-1610. [PMID: 32621388 DOI: 10.1111/nph.16786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Reactive oxygen species (ROS) act as important secondary messengers in abscisic acid (ABA) signaling and induce stomatal closure under dehydration stress. The breast cancer susceptibility gene 1 (BRCA1), an important tumor suppressor in animals, functions primarily in the maintenance of genome integrity in animals and plants. However, whether and how the plant BRCA1 regulates intracellular ROS homeostasis in guard cells under dehydration stress remains unknown. Here, we found that Arabidopsis atbrca1 loss-of-function mutants showed dehydration stress tolerance. This stress tolerant phenotype of atbrca1 was a result of ABA- and ROS-induced stomatal closure, which was enhanced in atbrca1 mutants compared with the wild-type. AtBRCA1 downregulated the expression of ROS-responsive and marker genes. Notably, these genes were also the targets of the AP2/ERF transcriptional activator RRTF1/ERF109. Under normal conditions, AtBRCA1 physically interacted with RRTF1 and inhibited its binding to the GCC-box-like sequence in target gene promoters. Under dehydration stress, the expression of AtBRCA1 was dramatically reduced and that of RRTF1 was activated, thus inducing the expression of ROS-responsive genes. Overall, our study reveals a novel molecular function of AtBRCA1 in the transcriptional regulation of intracellular ROS homeostasis under dehydration stress.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Nan Nan
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lulu Shi
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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16
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Hale B, Phipps C, Rao N, Wijeratne A, Phillips GC. Differential Expression Profiling Reveals Stress-Induced Cell Fate Divergence in Soybean Microspores. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1510. [PMID: 33171842 PMCID: PMC7695151 DOI: 10.3390/plants9111510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 01/01/2023]
Abstract
Stress-induced microspore embryogenesis is a widely employed method to achieve homozygosity in plant breeding programs. However, the molecular mechanisms that govern gametophyte de- and redifferentiation are understood poorly. In this study, RNA-Seq was used to evaluate global changes across the microspore transcriptome of soybean (Glycine max [L.] Merrill) as a consequence of pretreatment low-temperature stress. Expression analysis revealed more than 20,000 differentially expressed genes between treated and control microspore populations. Functional enrichment illustrated that many of these genes (e.g., those encoding heat shock proteins and cytochrome P450s) were upregulated to maintain cellular homeostasis through the mitigation of oxidative damage. Moreover, transcripts corresponding to saccharide metabolism, vacuolar transport, and other pollen-related developmental processes were drastically downregulated among treated microspores. Temperature stress also triggered cell wall modification and cell proliferation-characteristics that implied putative commitment to an embryonic pathway. These findings collectively demonstrate that pretreatment cold stress induces soybean microspore reprogramming through suppression of the gametophytic program while concomitantly driving sporophytic development.
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Affiliation(s)
- Brett Hale
- College of Science and Mathematics, Arkansas State University, Jonesboro, AR 72467-1080, USA;
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
| | - Callie Phipps
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
| | - Naina Rao
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
| | - Asela Wijeratne
- College of Science and Mathematics, Arkansas State University, Jonesboro, AR 72467-1080, USA;
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
| | - Gregory C. Phillips
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR 72467-0639, USA; (C.P.); (N.R.); (G.C.P.)
- College of Agriculture, Arkansas State University, Jonesboro, AR 72467-1080, USA
- Agricultural Experiment Station, University of Arkansas System Division of Agriculture, Jonesboro, AR 72467-2340, USA
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17
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Rastogi S, Satapathy S, Shah S, Mytrai, Prakash H. In silico identification of cytochrome P450s involved in Ocimum tenuiflorum subjected to four abiotic stresses. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Analyses of functional conservation and divergence reveal requirement of bHLH010/089/091 for pollen development at elevated temperature in Arabidopsis. J Genet Genomics 2020; 47:477-492. [DOI: 10.1016/j.jgg.2020.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 01/03/2023]
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19
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Wu Y, Wang T, Xin Y, Wang G, Xu LA. Overexpression of the GbF3' H1 Gene Enhanced the Epigallocatechin, Gallocatechin, and Catechin Contents in Transgenic Populus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:998-1006. [PMID: 31910001 DOI: 10.1021/acs.jafc.9b07008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ginkgo biloba L. leaves are a flavonoid resource for the pharmaceutical industry. The flavonoid 3'-hydroxylase (F3'H) is a key enzyme in the flavonoid biosynthesis pathway. However, the role of F3'H in flavonoid biosynthesis and metabolism is unclear. In this study, we characterized and functionally analyzed the ginkgo F3'H gene GbF3'H1 that encodes a protein of 520 amino acids. Expression profiling showed that GbF3'H1 was highly expressed in the leaves of ginkgo in September. Subcellular localization showed that GbF3'H1 occurred predominately in the cytoplasm. Transgenic poplars overexpressing GbF3'H1 had more red pigmentation in leaves than did wild-type (WT) plants. Furthermore, the concentrations of epigallocatechin, gallocatechin, and catechin in the downstream products synthesized by flavonoids were significantly higher in the transgenic plants than in the WT plants. These results indicate that the overexpression of GbF3'H1 enhances flavonoid production in transgenic plants and provides new insights into flavonoid biosynthesis and metabolism.
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Affiliation(s)
- Yaqiong Wu
- Co-Innovation Center for Sustainable Forestry in Southern China , Nanjing Forestry University , 159 Longpan Road , Nanjing 210037 , China
- Department of Forest and Conservation Sciences, Faculty of Forestry , The University of British Columbia , Vancouver V6T 1Z4 , Canada
| | - Tongli Wang
- Department of Forest and Conservation Sciences, Faculty of Forestry , The University of British Columbia , Vancouver V6T 1Z4 , Canada
| | - Yue Xin
- Co-Innovation Center for Sustainable Forestry in Southern China , Nanjing Forestry University , 159 Longpan Road , Nanjing 210037 , China
| | - Guibin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China , Nanjing Forestry University , 159 Longpan Road , Nanjing 210037 , China
| | - Li-An Xu
- Co-Innovation Center for Sustainable Forestry in Southern China , Nanjing Forestry University , 159 Longpan Road , Nanjing 210037 , China
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20
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Boachon B, Burdloff Y, Ruan JX, Rojo R, Junker RR, Vincent B, Nicolè F, Bringel F, Lesot A, Henry L, Bassard JE, Mathieu S, Allouche L, Kaplan I, Dudareva N, Vuilleumier S, Miesch L, André F, Navrot N, Chen XY, Werck-Reichhart D. A Promiscuous CYP706A3 Reduces Terpene Volatile Emission from Arabidopsis Flowers, Affecting Florivores and the Floral Microbiome. THE PLANT CELL 2019; 31:2947-2972. [PMID: 31628167 PMCID: PMC6925022 DOI: 10.1105/tpc.19.00320] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/06/2019] [Accepted: 10/16/2019] [Indexed: 05/15/2023]
Abstract
Flowers are essential but vulnerable plant organs, exposed to pollinators and florivores; however, flower chemical defenses are rarely investigated. We show here that two clustered terpene synthase and cytochrome P450 encoding genes (TPS11 and CYP706A3) on chromosome 5 of Arabidopsis (Arabidopsis thaliana) are tightly coexpressed in floral tissues, upon anthesis and during floral bud development. TPS11 was previously reported to generate a blend of sesquiterpenes. By heterologous coexpression of TPS11 and CYP706A3 in yeast (Saccharomyces cerevisiae) and Nicotiana benthamiana, we demonstrate that CYP706A3 is active on TPS11 products and also further oxidizes its own primary oxidation products. Analysis of headspace and soluble metabolites in cyp706a3 and 35S:CYP706A3 mutants indicate that CYP706A3-mediated metabolism largely suppresses sesquiterpene and most monoterpene emissions from opening flowers, and generates terpene oxides that are retained in floral tissues. In flower buds, the combined expression of TPS11 and CYP706A3 also suppresses volatile emissions and generates soluble sesquiterpene oxides. Florivory assays with the Brassicaceae specialist Plutella xylostella demonstrate that insect larvae avoid feeding on buds expressing CYP706A3 and accumulating terpene oxides. Composition of the floral microbiome appears also to be modulated by CYP706A3 expression. TPS11 and CYP706A3 simultaneously evolved within Brassicaceae and form the most versatile functional gene cluster described in higher plants so far.plantcell;31/12/2947/FX1F1fx1.
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Affiliation(s)
- Benoît Boachon
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 2357, Université de Strasbourg, 67084 Strasbourg, France
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- University of Lyon, UJM-Saint-Etienne, CNRS, BVpam Formation de Recherche en Evolution 3727, 42000 Saint-Etienne, France
| | - Yannick Burdloff
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Ju-Xin Ruan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
- Plant Science Research Center, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Rakotoharisoa Rojo
- Institute for Integrative Biology of the Cell (I2BC), iBiTec-S/SBSM, Commissariat à l'Energie Atomique, CNRS, Université Paris Sud, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Robert R Junker
- Evolutionary Ecology of Plants, Department Biodiversity of Plants, Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Bruno Vincent
- Plateforme d'Analyses pour la Chimie, GDS 3648, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Florence Nicolè
- University of Lyon, UJM-Saint-Etienne, CNRS, BVpam Formation de Recherche en Evolution 3727, 42000 Saint-Etienne, France
| | - Françoise Bringel
- Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR 7156 CNRS, 67000 Strasbourg, France
| | - Agnès Lesot
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Laura Henry
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Jean-Etienne Bassard
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Sandrine Mathieu
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Lionel Allouche
- Evolutionary Ecology of Plants, Department Biodiversity of Plants, Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Ian Kaplan
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Stéphane Vuilleumier
- Plateforme d'Analyses pour la Chimie, GDS 3648, CNRS, Université de Strasbourg, 67000 Strasbourg, France
- Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR 7156 CNRS, 67000 Strasbourg, France
| | - Laurence Miesch
- Equipe de Synthèse Organique et Phytochimie, Institut de Chimie, Unité Mixte de Recherche 7177, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - François André
- Institute for Integrative Biology of the Cell (I2BC), iBiTec-S/SBSM, Commissariat à l'Energie Atomique, CNRS, Université Paris Sud, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Nicolas Navrot
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 2357, Université de Strasbourg, 67084 Strasbourg, France
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
- Plant Science Research Center, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Danièle Werck-Reichhart
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Unité Propre de Recherche 2357, Université de Strasbourg, 67084 Strasbourg, France
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21
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Vogt T. Unusual spermine-conjugated hydroxycinnamic acids on pollen: function and evolutionary advantage. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5311-5315. [PMID: 30476279 PMCID: PMC6255709 DOI: 10.1093/jxb/ery359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Thomas Vogt
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, Halle (Saale), Germany
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22
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Kawade K, Li Y, Koga H, Sawada Y, Okamoto M, Kuwahara A, Tsukaya H, Hirai MY. The cytochrome P450 CYP77A4 is involved in auxin-mediated patterning of the Arabidopsis thaliana embryo. Development 2018; 145:145/17/dev168369. [PMID: 30213790 DOI: 10.1242/dev.168369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/30/2018] [Indexed: 12/30/2022]
Abstract
Metabolism often plays an important role in developmental control, in addition to supporting basal physiological requirements. However, our understanding of this interaction remains limited. Here, we performed quantitative phenome analysis of Arabidopsis thaliana cytochrome P450 mutants to identify a novel interaction between development and metabolism. We found that cyp77a4 mutants exhibit specific defects in cotyledon development, including asymmetric positioning and cup-shaped morphology, which could be rescued by introducing the CYP77A4 gene. Microscopy revealed that the abnormal patterning was detected at least from the 8-cell stage of the cyp77a4 embryos. We next analysed auxin distribution in mutant embryos, as the phenotypes resembled those of auxin-related mutants. We found that the auxin response pattern was severely perturbed in the cyp77a4 embryos owing to an aberrant distribution of the auxin efflux carrier PIN1. CYP77A4 intracellularly localised to the endoplasmic reticulum, which is consistent with the notion that this enzyme acts as an epoxidase of unsaturated fatty acids in the microsomal fraction. We propose that the CYP77A4-dependent metabolic pathway is an essential element for the establishment of polarity in plant embryos.
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Affiliation(s)
- Kensuke Kawade
- Okazaki Institute for Integrative Bioscience, 5-1, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan .,National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yimeng Li
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Koga
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mami Okamoto
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ayuko Kuwahara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hirokazu Tsukaya
- Okazaki Institute for Integrative Bioscience, 5-1, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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Davoodi Mastakani F, Pagheh G, Rashidi Monfared S, Shams-Bakhsh M. Identification and expression analysis of a microRNA cluster derived from pre-ribosomal RNA in Papaver somniferum L. and Papaver bracteatum L. PLoS One 2018; 13:e0199673. [PMID: 30067748 PMCID: PMC6070170 DOI: 10.1371/journal.pone.0199673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 06/12/2018] [Indexed: 11/19/2022] Open
Abstract
Opium poppy (Papaver somniferum L.) is one of the ancient medical crops, which produces several important alkaloids such as morphine, noscapine, sanguinarine and codeine. MicroRNAs are endogenous non-coding RNAs that play important regulatory roles in plant diverse biological processes. Many plant miRNAs are encoded as single transcriptional units, in contrast to animal miRNAs, which are often clustered. Herein, using computational approaches, a total of 22 miRNA precursors were identified, which five of them were located as a clustered in pre-ribosomal RNA. Afterward, the transcript level of the precursor and the mature of clustered miRNAs in two species of the Papaveraceae family, i.e. P. somniferum L. and P. bracteatum L, were quantified by RT-PCR. With respect to obtained results, these clustered miRNAs were expressed differentially in different tissues of these species. Moreover, using target prediction and Gene Ontology (GO)-based on functional classification indicated that these miRNAs might play crucial roles in various biological processes as well as metabolic pathways. In this study, we discovered the clustered miRNA derived from pre-rRNA, which may shed some light on the importance of miRNAs in the plant kingdom.
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Affiliation(s)
- Farshad Davoodi Mastakani
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Gabriel Pagheh
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sajad Rashidi Monfared
- Department of Agricultural Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Masoud Shams-Bakhsh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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24
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He H, Van Breusegem F, Mhamdi A. Redox-dependent control of nuclear transcription in plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3359-3372. [PMID: 29659979 DOI: 10.1093/jxb/ery130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/27/2018] [Indexed: 05/03/2023]
Abstract
Redox-dependent regulatory networks are affected by altered cellular or extracellular levels of reactive oxygen species (ROS). Perturbations of ROS production and scavenging homeostasis have a considerable impact on the nuclear transcriptome. While the regulatory mechanisms by which ROS modulate gene transcription in prokaryotes, lower eukaryotes, and mammalian cells are well established, new insights into the mechanism underlying redox control of gene expression in plants have only recently been known. In this review, we aim to provide an overview of the current knowledge on how ROS and thiol-dependent transcriptional regulatory networks are controlled. We assess the impact of redox perturbations and oxidative stress on transcriptome adjustments using cat2 mutants as a model system and discuss how redox homeostasis can modify the various parts of the transcriptional machinery.
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Affiliation(s)
- Huaming He
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Amna Mhamdi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
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25
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Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO. A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals. Front Mol Biosci 2018; 5:29. [PMID: 29682508 PMCID: PMC5897657 DOI: 10.3389/fmolb.2018.00029] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Penelope J. Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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26
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Wei K, Chen H. Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice. BMC Genomics 2018; 19:35. [PMID: 29320982 PMCID: PMC5764023 DOI: 10.1186/s12864-017-4425-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 12/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cytochrome P450 monooxygenases (CYP450, CYP, P450) catalyze numerous monooxygenation/hydroxylation reactions in biochemical pathways. Although CYP superfamily has been systematically studied in a few species, the genome-scale research about it in rice has not been done. RESULTS In this study, a total of 355 CYPs encoded by 326 genes were identified in japonica genome. The OsCYP genes are classified into 10 clans including 45 families according to phylogenetic analysis. More than half of the genes are distributed in 53 tandem duplicated gene clusters. Intron-exon structure of OsCYPs exhibits highly conserved and specificity within a family, and divergences of duplicate genes in gene structure result in non-functionalization, neo-functionalization or sub-functionalization. Selection pressure analysis showed that rice CYPs are under purifying selection. The microarray data analysis shows that some genes are tissue-specific expression, such as OsCYP710A5 and OsCYP71X14 in endosperm, OsCYP99A3 and OsCYP78A16 in root and OsCYP93G2 and OsCYP97D7 in leaf. Analysis of RNA-seq data derived from rice leaf developmental gradient indicates that some OsCYPs exhibit zone-specific expression patterns. OsCYP87C2, OsCYP96B5, OsCYP96B8 and OsCYP84A5 were specifically expressed in leaf base and transitional zone. The transcripts of lineages II and IV-1 members were highly abundant in maturing zone. Eighty three OsCYPs are differentially expressed in response to drought stress, of which OsCYP51G3, OsCYP709C9, OsCYP709C5, OsCYP81A6, OsCYP72A18 and OsCYP704A5 are strongly induced and OsCYP78A16, OsCYP89C9 and OsCYP704A5 are down-regulated significantly, and some of the results were validated by qPCR. And 23 up-regulated and 17 down-regulated genes are specific to Osbhlh148 mutation under drought stress. Compared to those in wild type, the changes in transcript levels of several genes are slight in the mutant, such as OsCYP51G3, OsCYP94C2, OsCYP709C9 and OsCYP709C5. CONCLUSION The whole-genomic analysis of rice P450 superfamily provides a clue to understanding biological function of OsCYPs in development regulation and drought stress response, and is helpful to rice molecular breeding.
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, 36 Xian-Qian-Zhi Street, Zhangzhou, Fujian, 363000, China.
| | - Huiqin Chen
- School of Biological Sciences and Biotechnology, Minnan Normal University, 36 Xian-Qian-Zhi Street, Zhangzhou, Fujian, 363000, China.
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27
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Li S, Chen Y, Zhu X, Wang Y, Jung KH, Chen L, Xuan Y, Duan Y. The transcriptomic changes of Huipizhi Heidou (Glycine max), a nematode-resistant black soybean during Heterodera glycines race 3 infection. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:96-104. [PMID: 29169106 DOI: 10.1016/j.jplph.2017.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 05/07/2023]
Abstract
Glycine max (soybean) is an extremely important crop, representing a major source of oil and protein for human beings. Heterodera glycines (soybean cyst nematode, SCN) infection severely reduces soybean production; therefore, protecting soybean from SCN has become an issue for breeders. Black soybean has exhibited a different grade of resistance to SCN. However, the underlying mechanism of Huipizhi Heidou resistance against SCN remains elusive. The Huipizhi Heidou (ZDD2315) and race 3 of Heterodera glycines were chosen to study the mechanism of resistance via examination of transcriptomic changes. After 5, 10, and 15days of SCN infection, whole roots were sampled for RNA extraction, and uninfected samples were simultaneously collected as a control. 740, 1413, and 4925 genes were isolated by padj (p-value adjusted)<0.05 after 5, 10, and 15days of the infection, respectively, and 225 differentially expressed genes were overlapped at all the time points. We found that the differentially expressed genes (DEGs) at 5, 10, and 15days after infection were involved in various biological function categories; in particular, induced genes were enriched in defense response, hormone mediated signaling process, and response to stress. To verify the pathways observed in the GO and KEGG enrichment results, effects of hormonal signaling in cyst-nematode infection were further examined via treatment with IAA (indo-3-acetic acid), salicylic acid (SA), gibberellic acid (GA), jasmonic acid (JA), and ethephon, a precursor of ethylene. The results indicate that five hormones led to a significant reduction of J2 number in the roots of Huipizhi Heidou and Liaodou15, representing SCN-resistant and susceptible lines, respectively. Taken together, our analyses are aimed at understanding the resistance mechanism of Huipizhi Heidou against the SCN race 3 via the dissection of transcriptomic changes upon J2 infection. The data presented here will help further research on the basis of soybean and cyst-nematode interaction.
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Affiliation(s)
- Shuang Li
- College of Plant Protection, Shenyang Agricultural University, 110866,Shenyang, China.
| | - Yu Chen
- College of Plant Protection, Shenyang Agricultural University, 110866,Shenyang, China
| | - Xiaofeng Zhu
- College of Plant Protection, Shenyang Agricultural University, 110866,Shenyang, China
| | - Yuanyuan Wang
- College of Biology science and technology, Shenyang Agricultural University, 110866, Shenyang, China
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Lijie Chen
- College of Plant Protection, Shenyang Agricultural University, 110866,Shenyang, China
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University, 110866,Shenyang, China.
| | - Yuxi Duan
- College of Plant Protection, Shenyang Agricultural University, 110866,Shenyang, China.
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28
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Zhou K, Long L, Sun Q, Wang W, Gao W, Chu Z, Cai C, Mo J, Cheng J, Zhang X, Liu Y, Du X, Miao C, Shi Y, Yuan Y, Zhang X, Cai Y. Molecular characterisation and functional analysis of a cytochrome P450 gene in cotton. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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29
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Pineau E, Xu L, Renault H, Trolet A, Navrot N, Ullmann P, Légeret B, Verdier G, Beisson F, Pinot F. Arabidopsis thaliana EPOXIDE HYDROLASE1 (AtEH1) is a cytosolic epoxide hydrolase involved in the synthesis of poly-hydroxylated cutin monomers. THE NEW PHYTOLOGIST 2017; 215:173-186. [PMID: 28497532 DOI: 10.1111/nph.14590] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
Epoxide hydrolases (EHs) are present in all living organisms. They have been extensively characterized in mammals; however, their biological functions in plants have not been demonstrated. Based on in silico analysis, we identified AtEH1 (At3g05600), a putative Arabidopsis thaliana epoxide hydrolase possibly involved in cutin monomer synthesis. We expressed AtEH1 in yeast and studied its localization in vivo. We also analyzed the composition of cutin from A. thaliana lines in which this gene was knocked out. Incubation of recombinant AtEH1 with epoxy fatty acids confirmed its capacity to hydrolyze epoxides of C18 fatty acids into vicinal diols. Transfection of Nicotiana benthamiana leaves with constructs expressing AtEH1 fused to enhanced green fluorescent protein (EGFP) indicated that AtEH1 is localized in the cytosol. Analysis of cutin monomers in loss-of-function Ateh1-1 and Ateh1-2 mutants showed an accumulation of 18-hydroxy-9,10-epoxyoctadecenoic acid and a concomitant decrease in corresponding vicinal diols in leaf and seed cutin. Compared with wild-type seeds, Ateh1 seeds showed delayed germination under osmotic stress conditions and increased seed coat permeability to tetrazolium red. This work reports a physiological role for a plant EH and identifies AtEH1 as a new member of the complex machinery involved in cutin synthesis.
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Affiliation(s)
- Emmanuelle Pineau
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000, Strasbourg, France
| | - Lin Xu
- Institute of Biosciences and Biotechnologies, CEA-CNRS-Aix Marseille Université, UMR 7265, LB3M, F-13108, Cadarache, France
| | - Hugues Renault
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000, Strasbourg, France
| | - Adrien Trolet
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000, Strasbourg, France
| | - Nicolas Navrot
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000, Strasbourg, France
| | - Pascaline Ullmann
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000, Strasbourg, France
| | - Bertrand Légeret
- Institute of Biosciences and Biotechnologies, CEA-CNRS-Aix Marseille Université, UMR 7265, LB3M, F-13108, Cadarache, France
| | - Gaëtan Verdier
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000, Strasbourg, France
| | - Fred Beisson
- Institute of Biosciences and Biotechnologies, CEA-CNRS-Aix Marseille Université, UMR 7265, LB3M, F-13108, Cadarache, France
| | - Franck Pinot
- Université de Strasbourg, CNRS, IBMP UPR 2357, F-67000, Strasbourg, France
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30
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Wisecaver JH, Borowsky AT, Tzin V, Jander G, Kliebenstein DJ, Rokas A. A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants. THE PLANT CELL 2017; 29:944-959. [PMID: 28408660 PMCID: PMC5466033 DOI: 10.1105/tpc.17.00009] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/12/2017] [Accepted: 04/09/2017] [Indexed: 05/20/2023]
Abstract
Plants produce diverse specialized metabolites (SMs), but the genes responsible for their production and regulation remain largely unknown, hindering efforts to tap plant pharmacopeia. Given that genes comprising SM pathways exhibit environmentally dependent coregulation, we hypothesized that genes within a SM pathway would form tight associations (modules) with each other in coexpression networks, facilitating their identification. To evaluate this hypothesis, we used 10 global coexpression data sets, each a meta-analysis of hundreds to thousands of experiments, across eight plant species to identify hundreds of coexpressed gene modules per data set. In support of our hypothesis, 15.3 to 52.6% of modules contained two or more known SM biosynthetic genes, and module genes were enriched in SM functions. Moreover, modules recovered many experimentally validated SM pathways, including all six known to form biosynthetic gene clusters (BGCs). In contrast, bioinformatically predicted BGCs (i.e., those lacking an associated metabolite) were no more coexpressed than the null distribution for neighboring genes. These results suggest that most predicted plant BGCs are not genuine SM pathways and argue that BGCs are not a hallmark of plant specialized metabolism. We submit that global gene coexpression is a rich, largely untapped resource for discovering the genetic basis and architecture of plant natural products.
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Affiliation(s)
- Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Alexander T Borowsky
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institute for Desert Research, Ben Gurion University, Sede-Boqer Campus 84990, Israel
| | - Georg Jander
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California-Davis, Davis, California 95616
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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31
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Ruprecht C, Vaid N, Proost S, Persson S, Mutwil M. Beyond Genomics: Studying Evolution with Gene Coexpression Networks. TRENDS IN PLANT SCIENCE 2017; 22:298-307. [PMID: 28126286 DOI: 10.1016/j.tplants.2016.12.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/06/2016] [Accepted: 12/22/2016] [Indexed: 05/08/2023]
Abstract
Understanding how genomes change as organisms become more complex is a central question in evolution. Molecular evolutionary studies typically correlate the appearance of genes and gene families with the emergence of biological pathways and morphological features. While such approaches are of great importance to understand how organisms evolve, they are also limited, as functionally related genes work together in contexts of dynamic gene networks. Since functionally related genes are often transcriptionally coregulated, gene coexpression networks present a resource to study the evolution of biological pathways. In this opinion article, we discuss recent developments in this field and how coexpression analyses can be merged with existing genomic approaches to transfer functional knowledge between species to study the appearance or extension of pathways.
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Affiliation(s)
- Colin Ruprecht
- Max-Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Neha Vaid
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Sebastian Proost
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Staffan Persson
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; ARC Centre of Excellence in Plant Cell Walls, School of Biosciences, University of Melbourne,Parkville, VIC 3010, Australia
| | - Marek Mutwil
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany.
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32
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Ihsan MZ, Ahmad SJN, Shah ZH, Rehman HM, Aslam Z, Ahuja I, Bones AM, Ahmad JN. Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:233. [PMID: 28289422 PMCID: PMC5326801 DOI: 10.3389/fpls.2017.00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/07/2017] [Indexed: 05/29/2023]
Abstract
The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.
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Affiliation(s)
- Muhammad Z. Ihsan
- Cholistan Institute of Desert Studies, The Islamia University BahawalpurBahawalpur, Pakistan
| | - Samina J. N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, Faculty of Meteorology, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Hafiz M. Rehman
- Department of Electronic and Biomedical Engineering, Chonnam National UniversityGwangju, South Korea
| | - Zubair Aslam
- Department of Agronomy, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Ishita Ahuja
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Atle M. Bones
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Jam N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
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Abstract
Plants, like other eukaryotes, have evolved complex mechanisms to coordinate gene expression during development, environmental response, and cellular homeostasis. Transcription factors (TFs), accompanied by basic cofactors and posttranscriptional regulators, are key players in gene-regulatory networks (GRNs). The coordinated control of gene activity is achieved by the interplay of these factors and by physical interactions between TFs and DNA. Here, we will briefly outline recent technological progress made to elucidate GRNs in plants. We will focus on techniques that allow us to characterize physical interactions in GRNs in plants and to analyze their regulatory consequences. Targeted manipulation allows us to test the relevance of specific gene-regulatory interactions. The combination of genome-wide experimental approaches with mathematical modeling allows us to get deeper insights into key-regulatory interactions and combinatorial control of important processes in plants.
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Affiliation(s)
- Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Dijun Chen
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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34
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Ghosh S. Triterpene Structural Diversification by Plant Cytochrome P450 Enzymes. FRONTIERS IN PLANT SCIENCE 2017; 8:1886. [PMID: 29170672 PMCID: PMC5684119 DOI: 10.3389/fpls.2017.01886] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 10/18/2017] [Indexed: 05/06/2023]
Abstract
Cytochrome P450 monooxygenases (P450s) represent the largest enzyme family of the plant metabolism. Plants typically devote about 1% of the protein-coding genes for the P450s to execute primary metabolism and also to perform species-specific specialized functions including metabolism of the triterpenes, isoprene-derived 30-carbon compounds. Triterpenes constitute a large and structurally diverse class of natural products with various industrial and pharmaceutical applications. P450-catalyzed structural modification is crucial for the diversification and functionalization of the triterpene scaffolds. In recent times, a remarkable progress has been made in understanding the function of the P450s in plant triterpene metabolism. So far, ∼80 P450s are assigned biochemical functions related to the plant triterpene metabolism. The members of the subfamilies CYP51G, CYP85A, CYP90B-D, CYP710A, CYP724B, and CYP734A are generally conserved across the plant kingdom to take part in plant primary metabolism related to the biosynthesis of essential sterols and steroid hormones. However, the members of the subfamilies CYP51H, CYP71A,D, CYP72A, CYP81Q, CYP87D, CYP88D,L, CYP93E, CYP705A, CYP708A, and CYP716A,C,E,S,U,Y are required for the metabolism of the specialized triterpenes that might perform species-specific functions including chemical defense toward specialized pathogens. Moreover, a recent advancement in high-throughput sequencing of the transcriptomes and genomes has resulted in identification of a large number of candidate P450s from diverse plant species. Assigning biochemical functions to these P450s will be of interest to extend our knowledge on triterpene metabolism in diverse plant species and also for the sustainable production of valuable phytochemicals.
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Du H, Ran F, Dong HL, Wen J, Li JN, Liang Z. Genome-Wide Analysis, Classification, Evolution, and Expression Analysis of the Cytochrome P450 93 Family in Land Plants. PLoS One 2016; 11:e0165020. [PMID: 27760179 PMCID: PMC5070762 DOI: 10.1371/journal.pone.0165020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/05/2016] [Indexed: 01/09/2023] Open
Abstract
Cytochrome P450 93 family (CYP93) belonging to the cytochrome P450 superfamily plays important roles in diverse plant processes. However, no previous studies have investigated the evolution and expression of the members of this family. In this study, we performed comprehensive genome-wide analysis to identify CYP93 genes in 60 green plants. In all, 214 CYP93 proteins were identified; they were specifically found in flowering plants and could be classified into ten subfamilies-CYP93A-K, with the last two being identified first. CYP93A is the ancestor that was derived in flowering plants, and the remaining showed lineage-specific distribution-CYP93B and CYP93C are present in dicots; CYP93F is distributed only in Poaceae; CYP93G and CYP93J are monocot-specific; CYP93E is unique to legumes; CYP93H and CYP93K are only found in Aquilegia coerulea, and CYP93D is Brassicaceae-specific. Each subfamily generally has conserved gene numbers, structures, and characteristics, indicating functional conservation during evolution. Synonymous nucleotide substitution (dN/dS) analysis showed that CYP93 genes are under strong negative selection. Comparative expression analyses of CYP93 genes in dicots and monocots revealed that they are preferentially expressed in the roots and tend to be induced by biotic and/or abiotic stresses, in accordance with their well-known functions in plant secondary biosynthesis.
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Affiliation(s)
- Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Feng Ran
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Hong-Li Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jia-Na Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Zhe Liang
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Singapore
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Rasool S, Mohamed R. Plant cytochrome P450s: nomenclature and involvement in natural product biosynthesis. PROTOPLASMA 2016; 253:1197-209. [PMID: 26364028 DOI: 10.1007/s00709-015-0884-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/31/2015] [Indexed: 05/10/2023]
Abstract
Cytochrome P450s constitute the largest family of enzymatic proteins in plants acting on various endogenous and xenobiotic molecules. They are monooxygenases that insert one oxygen atom into inert hydrophobic molecules to make them more reactive and hydro-soluble. Besides for physiological functions, the extremely versatile cytochrome P450 biocatalysts are highly demanded in the fields of biotechnology, medicine, and phytoremediation. The nature of reactions catalyzed by P450s is irreversible, which makes these enzymes attractions in the evolution of plant metabolic pathways. P450s are prime targets in metabolic engineering approaches for improving plant defense against insects and pathogens and for production of secondary metabolites such as the anti-neoplastic drugs taxol or indole alkaloids. The emerging examples of P450 involvement in natural product synthesis in traditional medicinal plant species are becoming increasingly interesting, as they provide new alternatives to modern medicines. In view of the divergent roles of P450s, we review their classification and nomenclature, functions and evolution, role in biosynthesis of secondary metabolites, and use as tools in pharmacology.
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Affiliation(s)
- Saiema Rasool
- Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Rozi Mohamed
- Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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Sun X, Sun C, Li Z, Hu Q, Han L, Luo H. AsHSP17, a creeping bentgrass small heat shock protein modulates plant photosynthesis and ABA-dependent and independent signalling to attenuate plant response to abiotic stress. PLANT, CELL & ENVIRONMENT 2016; 39:1320-37. [PMID: 26610288 DOI: 10.1111/pce.12683] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 11/16/2015] [Indexed: 05/20/2023]
Abstract
Heat shock proteins (HSPs) are molecular chaperones that accumulate in response to heat and other abiotic stressors. Small HSPs (sHSPs) belong to the most ubiquitous HSP subgroup with molecular weights ranging from 12 to 42 kDa. We have cloned a new sHSP gene, AsHSP17 from creeping bentgrass (Agrostis stolonifera) and studied its role in plant response to environmental stress. AsHSP17 encodes a protein of 17 kDa. Its expression was strongly induced by heat in both leaf and root tissues, and by salt and abscisic acid (ABA) in roots. Transgenic Arabidopsis plants constitutively expressing AsHSP17 exhibited enhanced sensitivity to heat and salt stress accompanied by reduced leaf chlorophyll content and decreased photosynthesis under both normal and stressed conditions compared to wild type. Overexpression of AsHSP17 also led to hypersensitivity to exogenous ABA and salinity during germination and post-germinative growth. Gene expression analysis indicated that AsHSP17 modulates expression of photosynthesis-related genes and regulates ABA biosynthesis, metabolism and ABA signalling as well as ABA-independent stress signalling. Our results suggest that AsHSP17 may function as a protein chaperone to negatively regulate plant responses to adverse environmental stresses through modulating photosynthesis and ABA-dependent and independent signalling pathways.
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Affiliation(s)
- Xinbo Sun
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
- Key Laboratory of Crop Growth Regulation of Hebei Province, Agricultural University of Hebei, Baoding, 071001, China
| | - Chunyu Sun
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Zhigang Li
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Qian Hu
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Liebao Han
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China
| | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
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Guo J, Ma X, Cai Y, Ma Y, Zhan Z, Zhou YJ, Liu W, Guan M, Yang J, Cui G, Kang L, Yang L, Shen Y, Tang J, Lin H, Ma X, Jin B, Liu Z, Peters RJ, Zhao ZK, Huang L. Cytochrome P450 promiscuity leads to a bifurcating biosynthetic pathway for tanshinones. THE NEW PHYTOLOGIST 2016; 210:525-34. [PMID: 26682704 PMCID: PMC4930649 DOI: 10.1111/nph.13790] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 10/29/2015] [Indexed: 05/21/2023]
Abstract
Cytochromes P450 (CYPs) play a key role in generating the structural diversity of terpenoids, the largest group of plant natural products. However, functional characterization of CYPs has been challenging because of the expansive families found in plant genomes, diverse reactivity and inaccessibility of their substrates and products. Here we present the characterization of two CYPs, CYP76AH3 and CYP76AK1, which act sequentially to form a bifurcating pathway for the biosynthesis of tanshinones, the oxygenated diterpenoids from the Chinese medicinal plant Danshen (Salvia miltiorrhiza). These CYPs had similar transcription profiles to that of the known gene responsible for tanshinone production in elicited Danshen hairy roots. Biochemical and RNA interference studies demonstrated that both CYPs are promiscuous. CYP76AH3 oxidizes ferruginol at two different carbon centers, and CYP76AK1 hydroxylates C-20 of two of the resulting intermediates. Together, these convert ferruginol into 11,20-dihydroxy ferruginol and 11,20-dihydroxy sugiol en route to tanshinones. Moreover, we demonstrated the utility of these CYPs by engineering yeast for heterologous production of six oxygenated diterpenoids, which in turn enabled structural characterization of three novel compounds produced by CYP-mediated oxidation. Our results highlight the incorporation of multiple CYPs into diterpenoid metabolic engineering, and a continuing trend of CYP promiscuity generating complex networks in terpenoid biosynthesis.
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Affiliation(s)
- Juan Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Xiaohui Ma
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P.R. China
| | - Yuan Cai
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, P.R. China
| | - Ying Ma
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Zhilai Zhan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, P.R. China
| | - Wujun Liu
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, P.R. China
| | - Mengxin Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Jian Yang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Guanghong Cui
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Liping Kang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Lei Yang
- Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai 201602, P.R. China
| | - Ye Shen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Jinfu Tang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Huixin Lin
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Xiaojing Ma
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Baolong Jin
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Zongbao K. Zhao
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, P.R. China
- Corresponding authors: Luqi Huang, Tel: 86-10-84044340. , Zongbao K. Zhao, Tel: 86-411-84379211.
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
- Corresponding authors: Luqi Huang, Tel: 86-10-84044340. , Zongbao K. Zhao, Tel: 86-411-84379211.
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Terol J, Tadeo F, Ventimilla D, Talon M. An RNA-Seq-based reference transcriptome for Citrus. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:938-50. [PMID: 26261026 DOI: 10.1111/pbi.12447] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/04/2015] [Accepted: 07/01/2015] [Indexed: 05/20/2023]
Abstract
Previous RNA-Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA-Seq analysis, obtained from 12 Citrus species: C. medica, C. aurantifolia, C. limon, C. bergamia, C. clementina, C. deliciosa, C. reshni, C. maxima, C. paradisi, C. aurantium, C. sinensis and Poncirus trifoliata. Four different organs were analysed: root, phloem, leaf and flower. A total of 3421 million Illumina reads were produced and mapped against the reference C. clementina genome sequence. Transcript discovery pipeline revealed 3326 new genes, the number of genes with alternative splicing was increased to 19,739, and a total of 73,797 transcripts were identified. Differential expression studies between the four tissues showed that gene expression is overall related to the physiological function of the specific organs above any other variable. Variants discovery analysis revealed the presence of indels and SNPs in genes associated with fruit quality and productivity. Pivotal pathways in citrus such as those of flavonoids, flavonols, ethylene and auxin were also analysed in detail.
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Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Francisco Tadeo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Daniel Ventimilla
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
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Ruprecht C, Mendrinna A, Tohge T, Sampathkumar A, Klie S, Fernie AR, Nikoloski Z, Persson S, Mutwil M. FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants. PLANT PHYSIOLOGY 2016; 170:1878-94. [PMID: 26754669 PMCID: PMC4775111 DOI: 10.1104/pp.15.01281] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/07/2016] [Indexed: 05/07/2023]
Abstract
Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression networks have indicated that, not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce, and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one-third of the genes of a plant's genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in coexpression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen- and root-specific cell wall modules that multiplied to confer tip growth in pollen tubes and root hairs, respectively. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html.
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Affiliation(s)
- Colin Ruprecht
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Amelie Mendrinna
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Takayuki Tohge
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Arun Sampathkumar
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Sebastian Klie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Zoran Nikoloski
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Staffan Persson
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Marek Mutwil
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
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Ilc T, Parage C, Boachon B, Navrot N, Werck-Reichhart D. Monoterpenol Oxidative Metabolism: Role in Plant Adaptation and Potential Applications. FRONTIERS IN PLANT SCIENCE 2016; 7:509. [PMID: 27200002 PMCID: PMC4844611 DOI: 10.3389/fpls.2016.00509] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/31/2016] [Indexed: 05/20/2023]
Abstract
Plants use monoterpenols as precursors for the production of functionally and structurally diverse molecules, which are key players in interactions with other organisms such as pollinators, flower visitors, herbivores, fungal, or microbial pathogens. For humans, many of these monoterpenol derivatives are economically important because of their pharmaceutical, nutraceutical, flavor, or fragrance applications. The biosynthesis of these derivatives is to a large extent catalyzed by enzymes from the cytochrome P450 superfamily. Here we review the knowledge on monoterpenol oxidative metabolism in plants with special focus on recent elucidations of oxidation steps leading to diverse linalool and geraniol derivatives. We evaluate the common features between oxidation pathways of these two monoterpenols, such as involvement of the CYP76 family, and highlight the differences. Finally, we discuss the missing steps and other open questions in the biosynthesis of oxygenated monoterpenol derivatives.
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Fragkostefanakis S, Simm S, Paul P, Bublak D, Scharf KD, Schleiff E. Chaperone network composition in Solanum lycopersicum explored by transcriptome profiling and microarray meta-analysis. PLANT, CELL & ENVIRONMENT 2015; 38:693-709. [PMID: 25124075 DOI: 10.1111/pce.12426] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 08/05/2014] [Indexed: 05/28/2023]
Abstract
Heat shock proteins (Hsps) are molecular chaperones primarily involved in maintenance of protein homeostasis. Their function has been best characterized in heat stress (HS) response during which Hsps are transcriptionally controlled by HS transcription factors (Hsfs). The role of Hsfs and Hsps in HS response in tomato was initially examined by transcriptome analysis using the massive analysis of cDNA ends (MACE) method. Approximately 9.6% of all genes expressed in leaves are enhanced in response to HS, including a subset of Hsfs and Hsps. The underlying Hsp-Hsf networks with potential functions in stress responses or developmental processes were further explored by meta-analysis of existing microarray datasets. We identified clusters with differential transcript profiles with respect to abiotic stresses, plant organs and developmental stages. The composition of two clusters points towards two major chaperone networks. One cluster consisted of constitutively expressed plastidial chaperones and other genes involved in chloroplast protein homeostasis. The second cluster represents genes strongly induced by heat, drought and salinity stress, including HsfA2 and many stress-inducible chaperones, but also potential targets of HsfA2 not related to protein homeostasis. This observation attributes a central regulatory role to HsfA2 in controlling different aspects of abiotic stress response and tolerance in tomato.
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Affiliation(s)
- Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt/Main, Germany; Cluster of Excellence Frankfurt, Goethe University, 60438, Frankfurt/Main, Germany
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Vahabi K, Sherameti I, Bakshi M, Mrozinska A, Ludwig A, Reichelt M, Oelmüller R. The interaction of Arabidopsis with Piriformospora indica shifts from initial transient stress induced by fungus-released chemical mediators to a mutualistic interaction after physical contact of the two symbionts. BMC PLANT BIOLOGY 2015; 15:58. [PMID: 25849363 PMCID: PMC4384353 DOI: 10.1186/s12870-015-0419-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/08/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of many plant species including Arabidopsis thaliana. The symbiotic interaction promotes plant performance, growth and resistance/tolerance against abiotic and biotic stress. RESULTS We demonstrate that exudated compounds from the fungus activate stress and defense responses in the Arabidopsis roots and shoots before the two partners are in physical contact. They induce stomata closure, stimulate reactive oxygen species (ROS) production, stress-related phytohormone accumulation and activate defense and stress genes in the roots and/or shoots. Once a physical contact is established, the stomata re-open, ROS and phytohormone levels decline, and the number and expression level of defense/stress-related genes decreases. CONCLUSIONS We propose that exudated compounds from P. indica induce stress and defense responses in the host. Root colonization results in the down-regulation of defense responses and the activation of genes involved in promoting plant growth, metabolism and performance.
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Affiliation(s)
- Khabat Vahabi
- />Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Irena Sherameti
- />Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Madhunita Bakshi
- />Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Anna Mrozinska
- />Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Anatoli Ludwig
- />Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Michael Reichelt
- />Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Ralf Oelmüller
- />Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
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Investigation of terpene diversification across multiple sequenced plant genomes. Proc Natl Acad Sci U S A 2014; 112:E81-8. [PMID: 25502595 DOI: 10.1073/pnas.1419547112] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Plants produce an array of specialized metabolites, including chemicals that are important as medicines, flavors, fragrances, pigments and insecticides. The vast majority of this metabolic diversity is untapped. Here we take a systematic approach toward dissecting genetic components of plant specialized metabolism. Focusing on the terpenes, the largest class of plant natural products, we investigate the basis of terpene diversity through analysis of multiple sequenced plant genomes. The primary drivers of terpene diversification are terpenoid synthase (TS) "signature" enzymes (which generate scaffold diversity), and cytochromes P450 (CYPs), which modify and further diversify these scaffolds, so paving the way for further downstream modifications. Our systematic search of sequenced plant genomes for all TS and CYP genes reveals that distinct TS/CYP gene pairs are found together far more commonly than would be expected by chance, and that certain TS/CYP pairings predominate, providing signals for key events that are likely to have shaped terpene diversity. We recover TS/CYP gene pairs for previously characterized terpene metabolic gene clusters and demonstrate new functional pairing of TSs and CYPs within previously uncharacterized clusters. Unexpectedly, we find evidence for different mechanisms of pathway assembly in eudicots and monocots; in the former, microsyntenic blocks of TS/CYP gene pairs duplicate and provide templates for the evolution of new pathways, whereas in the latter, new pathways arise by mixing and matching of individual TS and CYP genes through dynamic genome rearrangements. This is, to our knowledge, the first documented observation of the unique pattern of TS and CYP assembly in eudicots and monocots.
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Melloul M, Iraqi D, El Alaoui M, Erba G, Alaoui S, Ibriz M, Elfahime E. Identification of Differentially Expressed Genes by
cDNA-AFLP Technique in Response to Drought Stress
in Triticum durum. Food Technol Biotechnol 2014; 52:479-488. [PMID: 27904321 PMCID: PMC5079143 DOI: 10.17113/ftb.52.04.14.3701] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/12/2014] [Indexed: 12/27/2022] Open
Abstract
Drought is the single largest abiotic stress factor leading to reduced crop yields. The identification of differentially expressed genes and the understanding of their functions in environmentally stressful conditions are essential to improve drought tolerance. Transcriptomics is a powerful approach for the global analysis of molecular mechanisms under abiotic stress. To identify genes that are important for drought tolerance, we analyzed mRNA populations from untreated and drought-stressed leaves of Triticum durum by cDNA- -amplified fragment length polymorphism (cDNA-AFLP) technique. Overall, 76 transcript- -derived fragments corresponding to differentially induced transcripts were successfully sequenced. Most of the transcripts identified here, using basic local alignment search tool (BLAST) database, were genes belonging to different functional categories related to metabolism, energy, cellular biosynthesis, cell defense, signal transduction, transcription regulation, protein degradation and transport. The expression patterns of these genes were confirmed by quantitative reverse transcriptase real-time polymerase chain reaction (qRT- -PCR) based on ten selected genes representing different patterns. These results could facilitate the understanding of cellular mechanisms involving groups of genes that act in coordination in response to stimuli of water deficit. The identification of novel stress-responsive genes will provide useful data that could help develop breeding strategies aimed at improving durum wheat tolerance to field stress.
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Affiliation(s)
- Marouane Melloul
- Genetic and Biometry Laboratory, Faculty of Sciences, University Ibn Tofail, BP 133,
14000 Kenitra, Morocco
- Functional Genomic Platform, Technical Unit (UATRS), National Center for Scientific and Technical Research (CNRST), Angle Allal Fassi, Avenue des FAR, Hay Riad, BP 8027, 10102 Rabat, Morocco
| | - Driss Iraqi
- National Institute of Agronomical Research, Avenue de la Victoire, BP 415, Rabat, Morocco
| | - MyAbdelaziz El Alaoui
- Genetic and Biometry Laboratory, Faculty of Sciences, University Ibn Tofail, BP 133,
14000 Kenitra, Morocco
- Functional Genomic Platform, Technical Unit (UATRS), National Center for Scientific and Technical Research (CNRST), Angle Allal Fassi, Avenue des FAR, Hay Riad, BP 8027, 10102 Rabat, Morocco
| | - Gilles Erba
- Labgene Scientific Instruments, Athens Building, Business Park, 74160 Archamps, France
| | - Sanaa Alaoui
- Functional Genomic Platform, Technical Unit (UATRS), National Center for Scientific and Technical Research (CNRST), Angle Allal Fassi, Avenue des FAR, Hay Riad, BP 8027, 10102 Rabat, Morocco
| | - Mohammed Ibriz
- Genetic and Biometry Laboratory, Faculty of Sciences, University Ibn Tofail, BP 133,
14000 Kenitra, Morocco
| | - Elmostafa Elfahime
- Functional Genomic Platform, Technical Unit (UATRS), National Center for Scientific and Technical Research (CNRST), Angle Allal Fassi, Avenue des FAR, Hay Riad, BP 8027, 10102 Rabat, Morocco
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Rana S, Bhat WW, Dhar N, Pandith SA, Razdan S, Vishwakarma R, Lattoo SK. Molecular characterization of two A-type P450s, WsCYP98A and WsCYP76A from Withania somnifera (L.) Dunal: expression analysis and withanolide accumulation in response to exogenous elicitations. BMC Biotechnol 2014; 14:89. [PMID: 25416924 PMCID: PMC4247701 DOI: 10.1186/s12896-014-0089-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 10/06/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Pharmacological investigations position withanolides as important bioactive molecules demanding their enhanced production. Therefore, one of the pivotal aims has been to gain knowledge about complete biosynthesis of withanolides in terms of enzymatic and regulatory genes of the pathway. However, the pathway remains elusive at the molecular level. P450s monooxygenases play a crucial role in secondary metabolism and predominantly help in functionalizing molecule core structures including withanolides. RESULTS In an endeavor towards identification and characterization of different P450s, we here describe molecular cloning, characterization and expression analysis of two A-type P450s, WsCYP98A and WsCYP76A from Withania somnifera. Full length cDNAs of WsCYP98A and WsCYP76A have open reading frames of 1536 and 1545 bp encoding 511 (58.0 kDa) and 515 (58.7 kDa) amino acid residues, respectively. Entire coding sequences of WsCYP98A and WsCYP76A cDNAs were expressed in Escherichia coli BL21 (DE3) using pGEX4T-2 expression vector. Quantitative real-time PCR analysis indicated that both genes express widely in leaves, stalks, roots, flowers and berries with higher expression levels of WsCYP98A in stalks while WsCYP76A transcript levels were more obvious in roots. Further, transcript profiling after methyl jasmonate, salicylic acid, and gibberellic acid elicitations displayed differential transcriptional regulation of WsCYP98A and WsCYP76A. Copious transcript levels of both P450s correlated positively with the higher production of withanolides. CONCLUSIONS Two A-types P450 WsCYP98A and WsCYP76A were isolated, sequenced and heterologously expressed in E. coli. Both P450s are spatially regulated at transcript level showing differential tissue specificity. Exogenous elicitors acted as both positive and negative regulators of mRNA transcripts. Methyl jasmonate and salicylic acid resulted in copious expression of WsCYP98A and WsCYP76A. Enhanced mRNA levels also corroborated well with the increased accumulation of withanolides in response to elicitations. The empirical findings suggest that elicitors possibly incite defence or stress responses of the plant by triggering higher accumulation of withanolides.
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Affiliation(s)
- Satiander Rana
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Tawi-180001, India.
| | - Wajid Waheed Bhat
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Tawi-180001, India.
| | - Niha Dhar
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Tawi-180001, India.
| | - Shahzad A Pandith
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Tawi-180001, India.
| | - Sumeer Razdan
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Tawi-180001, India.
| | - Ram Vishwakarma
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Tawi-180001, India.
| | - Surrinder K Lattoo
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Tawi-180001, India.
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Blée E, Boachon B, Burcklen M, Le Guédard M, Hanano A, Heintz D, Ehlting J, Herrfurth C, Feussner I, Bessoule JJ. The reductase activity of the Arabidopsis caleosin RESPONSIVE TO DESSICATION20 mediates gibberellin-dependent flowering time, abscisic acid sensitivity, and tolerance to oxidative stress. PLANT PHYSIOLOGY 2014; 166:109-24. [PMID: 25056921 PMCID: PMC4149700 DOI: 10.1104/pp.114.245316] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/22/2014] [Indexed: 05/20/2023]
Abstract
Contrasting with the wealth of information available on the multiple roles of jasmonates in plant development and defense, knowledge about the functions and the biosynthesis of hydroxylated oxylipins remains scarce. By expressing the caleosin RESPONSIVE TO DESSICATION20 (RD20) in Saccharomyces cerevisiae, we show that the recombinant protein possesses an unusual peroxygenase activity with restricted specificity toward hydroperoxides of unsaturated fatty acid. Accordingly, Arabidopsis (Arabidopsis thaliana) plants overexpressing RD20 accumulate the product 13-hydroxy-9,11,15-octadecatrienoic acid, a linolenate-derived hydroxide. These plants exhibit elevated levels of reactive oxygen species (ROS) associated with early gibberellin-dependent flowering and abscisic acid hypersensitivity at seed germination. These phenotypes are dependent on the presence of active RD20, since they are abolished in the rd20 null mutant and in lines overexpressing RD20, in which peroxygenase was inactivated by a point mutation of a catalytic histidine residue. RD20 also confers tolerance against stress induced by Paraquat, Rose Bengal, heavy metal, and the synthetic auxins 1-naphthaleneacetic acid and 2,4-dichlorophenoxyacetic acid. Under oxidative stress, 13-hydroxy-9,11,15-octadecatrienoic acid still accumulates in RD20-overexpressing lines, but this lipid oxidation is associated with reduced ROS levels, minor cell death, and delayed floral transition. A model is discussed where the interplay between fatty acid hydroxides generated by RD20 and ROS is counteracted by ethylene during development in unstressed environments.
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Affiliation(s)
- Elizabeth Blée
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
| | - Benoît Boachon
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
| | - Michel Burcklen
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
| | - Marina Le Guédard
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
| | - Abdulsamie Hanano
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
| | - Jürgen Ehlting
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
| | - Cornelia Herrfurth
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
| | - Ivo Feussner
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
| | - Jean-Jacques Bessoule
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357-Université de Strasbourg, 67083 Strasbourg cedex, France (E.B., B.B., M.B., A.H., D.H., J.E.)Laboratoire de Biogénèse Membranaire, Bâtiment A3-Institut National de la Recherche Agronomique Bordeaux Aquitaine, 33140 Villenave d'Ornon, France (M.L.G., J.-J.B.); andGeorg-August-University, Albrecht-von-Haller Institute, Department of Plant Biochemistry, 37077 Goettingen, Germany (C.H., I.F.)
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Gaquerel E, Gulati J, Baldwin IT. Revealing insect herbivory-induced phenolamide metabolism: from single genes to metabolic network plasticity analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:679-92. [PMID: 24617849 PMCID: PMC5140026 DOI: 10.1111/tpj.12503] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/20/2014] [Accepted: 03/03/2014] [Indexed: 05/18/2023]
Abstract
The phenylpropanoid metabolic space comprises a network of interconnected metabolic branches that contribute to the biosynthesis of a large array of compounds with functions in plant development and stress adaptation. During biotic challenges, such as insect attack, a major rewiring of gene networks associated with phenylpropanoid metabolism is observed. This rapid reconfiguration of gene expression allows prioritized production of metabolites that help the plant solve ecological problems. Phenolamides are a group of phenolic derivatives that originate from diversion of hydroxycinnamoyl acids from the main phenylpropanoid pathway after N-acyltransferase-dependent conjugation to polyamines or aryl monoamines. These structurally diverse metabolites are abundant in the reproductive organs of many plants, and have recently been shown to play roles as induced defenses in vegetative tissues. In the wild tobacco, Nicotiana attenuata, in which herbivory-induced regulation of these metabolites has been studied, rapid elevations of the levels of phenolamides that function as induced defenses result from a multi-hormonal signaling network that re-shapes connected metabolic pathways. In this review, we summarize recent findings in the regulation of phenolamides obtained by mass spectrometry-based metabolomics profiling, and outline a conceptual framework for gene discovery in this pathway. We also introduce a multifactorial approach that is useful in deciphering metabolic pathway reorganizations among tissues in response to stress.
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Affiliation(s)
- Emmanuel Gaquerel
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
- Center for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360,69120 Heidelberg, Germany
| | - Jyotasana Gulati
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
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Zhang T, Zhao X, Wang W, Huang L, Liu X, Zong Y, Zhu L, Yang D, Fu B, Li Z. Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum. PLANT MOLECULAR BIOLOGY 2014; 84:315-27. [PMID: 24104862 DOI: 10.1007/s11103-013-0135-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 09/23/2013] [Indexed: 05/25/2023]
Abstract
Transcriptomic data for Sorghum propinquum, the wild-type sorghum, are limited in public databases. S. propinquum has a subterranean rhizome and transcriptome data will help in understanding the molecular mechanisms underlying rhizome formation. We sequenced the transcriptome of S. propinquum aerial-shoot and rhizome using an Illumina platform. More than 70 % of the genes in the S. propinquum genome were expressed in aerial-shoot and rhizome. The expression patterns of 1963 and 599 genes, including transcription factors, were specific or enriched in aerial-shoot and rhizome respectively, indicating their possible roles in physiological processes in these tissues. Comparative analysis revealed several cis-elements, ACGT box, GCCAC, GATC and TGACG box, which showed significantly higher abundance in aerial-shoot-specific genes. In rhizome-specific genes MYB and ROOTMOTIFTAPOX1 motifs, and 10 promoter and cytokinin-responsive elements were highly enriched. Of the S. propinquum genes, 27.9 % were identified as alternatively spliced and about 60 % of the alternative splicing (AS) events were tissue-specific, suggesting that AS played a crucial role in determining tissue-specific cellular function. The transcriptome data, especially the co-localized rhizome-enriched expressed transcripts that mapped to the publicly available rhizome-related quantitative trait loci, will contribute to gene discovery in S. propinquum and to functional studies of the sorghum genome. Deep transcriptome sequencing revealed a clear difference in the expression patterns of genes between aerial-shoot and rhizome in S. propinquum. This data set provides essential information for future studies into the molecular genetic mechanisms involved in rhizome formation.
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Affiliation(s)
- Ting Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun St., Beijing, 100081, China
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Krokida A, Delis C, Geisler K, Garagounis C, Tsikou D, Peña-Rodríguez LM, Katsarou D, Field B, Osbourn AE, Papadopoulou KK. A metabolic gene cluster in Lotus japonicus discloses novel enzyme functions and products in triterpene biosynthesis. THE NEW PHYTOLOGIST 2013; 200:675-690. [PMID: 23909862 DOI: 10.1111/nph.12414] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/20/2013] [Indexed: 05/03/2023]
Abstract
Genes for triterpene biosynthetic pathways exist as metabolic gene clusters in oat and Arabidopsis thaliana plants. We characterized the presence of an analogous gene cluster in the model legume Lotus japonicus. In the genomic regions flanking the oxidosqualene cyclase AMY2 gene, genes for two different classes of cytochrome P450 and a gene predicted to encode a reductase were identified. Functional characterization of the cluster genes was pursued by heterologous expression in Nicotiana benthamiana. The gene expression pattern was studied under different developmental and environmental conditions. The physiological role of the gene cluster in nodulation and plant development was studied in knockdown experiments. A novel triterpene structure, dihydrolupeol, was produced by AMY2. A new plant cytochrome P450, CYP71D353, which catalyses the formation of 20-hydroxybetulinic acid in a sequential three-step oxidation of 20-hydroxylupeol was characterized. The genes within the cluster are highly co-expressed during root and nodule development, in hormone-treated plants and under various environmental stresses. A transcriptional gene silencing mechanism that appears to be involved in the regulation of the cluster genes was also revealed. A tightly co-regulated cluster of functionally related genes is involved in legume triterpene biosynthesis, with a possible role in plant development.
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Affiliation(s)
- Afrodite Krokida
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Costas Delis
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Katrin Geisler
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Constantine Garagounis
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Daniela Tsikou
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Luis M Peña-Rodríguez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Dimitra Katsarou
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
| | - Ben Field
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Anne E Osbourn
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Aeolou Str., Larisa, 41221, Greece
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