51
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Li J, Yang Y, Chai M, Ren M, Yuan J, Yang W, Dong Y, Liu B, Jian Q, Wang S, Peng B, Yuan H, Fan H. Gibberellins modulate local auxin biosynthesis and polar auxin transport by negatively affecting flavonoid biosynthesis in the root tips of rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110545. [PMID: 32771158 DOI: 10.1016/j.plantsci.2020.110545] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/28/2020] [Accepted: 05/30/2020] [Indexed: 05/07/2023]
Abstract
As critical signalling molecules, both gibberellin (GA) and auxin play essential roles in regulating root elongation, and many studies have been shown that auxin influences GA biosynthesis and signalling. However, the mechanism by which GA affects auxin in root elongation is still unknown. In this study, root elongation and DR5-GUS activity were analyzed in rice seedlings. Paclobutrazol-induced short root phenotypes could be partially reversed by co-treatment with IAA, and the inhibition of root elongation caused by naphthylphthalamic acid could be partially reversed when plants were co-treated with GA. DR5-GUS activity was increased in the presence of GA and was reduced at the root tip of paclobutrazol-treated seedlings, indicating that GA could regulate local auxin biosynthesis and polar auxin transport (PAT) in rice root tips. Our RNA-seq analysis showed that GA was involved in the regulation of flavonoid biosynthesis. Flavonoid accumulation level in ks1 root tips was significantly increased and negatively correlated with GA content in GA- and PAC-treated seedlings. GA also rescued the decreased DR5-GUS activity induced by quercetin in rice root tips, confirming that flavonoids act as an intermediary in GA-mediated auxin biosynthesis and PAT. Based on RNA-seq and qPCR analyses, we determined that GA regulates local auxin biosynthesis and polar auxin transport by modulating the expression of OsYUCCA6 and PIN. Our findings provide valuable new insights into the interactions between GA and auxin in the root tips of rice.
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Affiliation(s)
- Jintao Li
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
| | - Yuna Yang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mengmeng Chai
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mengdi Ren
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Jingjia Yuan
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Wenqian Yang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Yu Dong
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - BinWen Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Qingmei Jian
- College of Bioengineering, Jingchu University of Technology, Jingmen, 448000, China
| | - Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Bo Peng
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Hongyu Yuan
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Haiyan Fan
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
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Watanabe M, Walther D, Ueda Y, Kondo K, Ishikawa S, Tohge T, Burgos A, Brotman Y, Fernie AR, Hoefgen R, Wissuwa M. Metabolomic markers and physiological adaptations for high phosphate utilization efficiency in rice. PLANT, CELL & ENVIRONMENT 2020; 43:2066-2079. [PMID: 32361994 DOI: 10.1111/pce.13777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Utilizing phosphate more efficiently is crucial for sustainable crop production. Highly efficient rice (Oryza sativa) cultivars have been identified and this study aims to identify metabolic markers associated with P utilization efficiency (PUE). P deficiency generally reduced leaf P concentrations and CO2 assimilation rates but efficient cultivars were reducing leaf P concentrations further than inefficient ones while maintaining similar CO2 assimilation rates. Adaptive changes in carbon metabolism were detected but equally in efficient and inefficient cultivar groups. Groups furthermore did not differ with respect to partial substitutions of phospholipids by sulfo- and galactolipids. Metabolites significantly more abundant in the efficient group, such as sinapate, benzoate and glucoronate, were related to antioxidant defence and may help alleviating oxidative stress caused by P deficiency. Sugar alcohols ribitol and threitol were another marker metabolite for higher phosphate efficiency as were several amino acids, especially threonine. Since these metabolites are not known to be associated with P deficiency, they may provide novel clues for the selection of more P efficient genotypes. In conclusion, metabolite signatures detected here were not related to phosphate metabolism but rather helped P efficient lines to keep vital processes functional under the adverse conditions of P starvation.
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Affiliation(s)
- Mutsumi Watanabe
- MPI of Molecular Plant Physiology, Potsdam, Germany
- NARA Institute of Science and Technology, Nara, Japan
| | - Dirk Walther
- MPI of Molecular Plant Physiology, Potsdam, Germany
| | - Yoshiaki Ueda
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Katsuhiko Kondo
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Satoru Ishikawa
- National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Takayuki Tohge
- MPI of Molecular Plant Physiology, Potsdam, Germany
- NARA Institute of Science and Technology, Nara, Japan
| | | | | | | | | | - Matthias Wissuwa
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
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53
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Deng M, Zhang X, Luo J, Liu H, Wen W, Luo H, Yan J, Xiao Y. Metabolomics analysis reveals differences in evolution between maize and rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1710-1722. [PMID: 32445406 DOI: 10.1111/tpj.14856] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates. However, it is unclear how evolution contributes to metabolic variation in plants. Here, we investigated the metabolomics data from leaf and seed tissues in maize and rice. Using principal components analysis based on leaf metabolites but not seed metabolites, metabolomics data could be clearly separated for rice Indica and Japonica accessions, while two maize subgroups, temperate and tropical, showed more visible admixture. Rice and maize seed exhibited significant interspecific differences in metabolic variation, while within rice, leaf and seed displayed similar metabolic variations. Among 10 metabolic categories, flavonoids had higher variation in maize than rice, indicating flavonoids are a key constituent of interspecific metabolic divergence. Interestingly, metabolic regulation was also found to be reshaped dramatically from positive to negative correlations, indicative of the differential evolutionary processes in maize and rice. Moreover, perhaps due to this divergence significantly more metabolic interactions were identified in rice than maize. Furthermore, in rice, the leaf was found to harbor much more intense metabolic interactions than the seed. Our result suggests that metabolomes are valuable for tracking evolutionary history, thereby complementing and extending genomic insights concerning which features are responsible for interspecific differentiation in maize and rice.
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Affiliation(s)
- Min Deng
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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54
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Cobos M, Pérez S, Braga J, Vargas-Arana G, Flores L, Paredes JD, Maddox JD, Marapara JL, Castro JC. Nutritional evaluation and human health-promoting potential of compounds biosynthesized by native microalgae from the Peruvian Amazon. World J Microbiol Biotechnol 2020; 36:121. [PMID: 32681243 DOI: 10.1007/s11274-020-02896-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/12/2020] [Indexed: 02/07/2023]
Abstract
A plausible strategy to mitigate socioeconomic problems in the Peruvian Amazon is through the sustainable exploitation of biodiversity resources, such as native microalgae. Several studies worldwide affirm that these microorganisms are excellent sources of higher value products for human nutrition and possess health-promoting biochemicals, but these attributes are unknown for the native microalgae of Peru. Therefore, the aim of this investigation was to evaluate the nutritional and human health-promoting potential of compounds biosynthesized by native microalgae from the Peruvian Amazon. Ten native microalgae strains of the groups cyanobacteria and chlorophyta were cultured in BG-11 medium and their biomass harvested and dried. Standardized methods were then used to determine proximate composition, fatty acids and amino acids composition, antioxidant activity, and total phenolic content. All ten microalgae strains produce primary nutrients, the entire spectrum of essential amino acids, essential fatty acids, and 3 of the 10 microalgae strains produced eisosapentaenoic acid. Additionally, all microalgae strains exhibited antioxidant activities and contained phenolic compounds. In conclusion, native microalgae strains from the Peruvian Amazon analyzed in this study possess the ability to biosynthesize and accumulate several nutrients and compounds with human health-promoting potential.
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Affiliation(s)
- Marianela Cobos
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Iquitos, Peru.
| | - Sheyla Pérez
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Iquitos, Peru
| | - Janeth Braga
- Departamento Académico de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru.,Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Gabriel Vargas-Arana
- Laboratorio de Química de Productos Naturales, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Peru
| | - Leenin Flores
- Laboratorio de Biotecnología Acuática, Instituto del Mar del Perú (IMARPE), Lima, Peru
| | - Jae D Paredes
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Iquitos, Peru
| | - J Dylan Maddox
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Iquitos, Peru.,Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA.,Environmental Sciences, American Public University System, Charles Town, WV, 25414, USA
| | - Jorge L Marapara
- Departamento Académico de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru.,Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru
| | - Juan C Castro
- Departamento Académico de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru. .,Unidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, Peru.
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55
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Tohge T, Scossa F, Wendenburg R, Frasse P, Balbo I, Watanabe M, Alseekh S, Jadhav SS, Delfin JC, Lohse M, Giavalisco P, Usadel B, Zhang Y, Luo J, Bouzayen M, Fernie AR. Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex. MOLECULAR PLANT 2020; 13:1027-1046. [PMID: 32305499 DOI: 10.1016/j.molp.2020.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 02/01/2020] [Accepted: 04/11/2020] [Indexed: 05/10/2023]
Abstract
While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species, those defining specialized metabolism are less well characterized and more highly variable across species. In this study, we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato. For this purpose, GC-MS- and LC-MS-based metabolomics of different tissues of Solanum lycopersicum and wild tomato species were carried out, in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis, and publicly available RNA-sequencing data for annotation of biosynthetic genes. The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism, allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway. The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening. Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via Ardeatina 546 00178 Rome, Italy
| | - Regina Wendenburg
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Pierre Frasse
- Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan 31326, France
| | - Ilse Balbo
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Sagar Sudam Jadhav
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jay C Delfin
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192 Japan
| | - Marc Lohse
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany
| | - Bjoern Usadel
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52056 Aachen, Germany
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Mondher Bouzayen
- Université de Toulouse, INP-ENSA Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan 31326, France
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany; Institute of Plant Systems Biology, 4000 Plovdiv, Bulgaria.
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56
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Elessawy FM, Bazghaleh N, Vandenberg A, Purves RW. Polyphenol profile comparisons of seed coats of five pulse crops using a semi-quantitative liquid chromatography-mass spectrometric method. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:458-471. [PMID: 31869515 DOI: 10.1002/pca.2909] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/22/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Pulse crops are nutritious and therefore widely grown. Pulse seed coats are typically discarded, despite their high content of polyphenols that are known for their antioxidant properties and health benefits. A better understanding of polyphenol diversity and biochemical pathways will ultimately provide insight into how polyphenols are linked to health benefits, which will help to better utilise these seed coats. OBJECTIVES To explore polyphenol profiles among seed coats of diverse genotypes of five pulse crops using a targeted liquid chromatography mass spectrometry (LC-MS) method. METHODS Four genotypes of each of common bean, chickpea, pea, lentil and faba bean seed coats were selected for analysis. Following extraction, polyphenols were quantified using LC-MS. RESULTS An LC-MS method was developed to quantify 98 polyphenols from 13 different classes in 30 min. The low-tannin seed coats had the lowest concentrations of all polyphenols. Chickpea and pea seed coats had the most similar polyphenolic profiles. The black common bean showed the most diverse seed coat polyphenol profile, including several anthocyanins not detected in any of the other seed coats. CONCLUSION The LC-MS method reported herein was used to show polyphenol diversity within several polyphenol classes among the pulse crop seed coats. Detected in all seed coats, flavonols and hydroxybenzoic acids appear well-conserved in the edible Fabaceae. The presence of anthocyanins, flavan-3-ols and proanthocyanins in the coloured seed coats suggests that unique divergent branches were introduced in the flavonoid biosynthetic pathway, possibly in response to environmental stressors.
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Affiliation(s)
- Fatma M Elessawy
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Navid Bazghaleh
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Randy W Purves
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Centre for Veterinary Drug Residues, Canadian Food Inspection Agency, Saskatoon, Saskatchewan, Canada
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57
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Sarkar D, Maranas CD. SNPeffect: identifying functional roles of SNPs using metabolic networks. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:512-531. [PMID: 32167625 PMCID: PMC9328443 DOI: 10.1111/tpj.14746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/20/2020] [Indexed: 05/04/2023]
Abstract
Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.
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Affiliation(s)
- Debolina Sarkar
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
| | - Costas D. Maranas
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
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58
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Li Y, Shan X, Tong L, Wei C, Lu K, Li S, Kimani S, Wang S, Wang L, Gao X. The Conserved and Particular Roles of the R2R3-MYB Regulator FhPAP1 from Freesia hybrida in Flower Anthocyanin Biosynthesis. PLANT & CELL PHYSIOLOGY 2020; 61:1365-1380. [PMID: 32392327 DOI: 10.1093/pcp/pcaa065] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Anthocyanin biosynthesis is mainly controlled by MYB-bHLH-WD40 (MBW) complexes that modulate the expression of anthocyanin biosynthetic genes (ABGs). The MYB regulators involved in anthocyanin biosynthesis arose early during plant evolution and thus might function divergently in different evolutionary lineages. Although the anthocyanin-promoting R2R3-MYB regulators in eudicots have been comprehensively explored, little consensus has been reached about functional discrepancies versus conservation among MYB regulators from different plant lineages. Here, we integrated transcriptome analysis, gene expression profiles, gain-of-function experiments and transient protoplast transfection assays to functionally characterize the monocot Freesia hybrida anthocyanin MYB regulator gene FhPAP1, which showed correlations with late ABGs. FhPAP1 could activate ABGs as well as TT8-clade genes FhTT8L, AtTT8 and NtAN1 when overexpressed in Freesia, Arabidopsis and tobacco, respectively. Consistently, FhPAP1 could interact with FhTT8L and FhTTG1 to form the conserved MBW complex and shared similar target genes with its orthologs from Arabidopsis. Most prominently, FhPAP1 displayed higher transactivation capacity than its homologs in Arabidopsis and tobacco, which was instantiated in its powerful regulation on ABGs. Moreover, we found that FhPAP1 might be the selected gene during the domestication and rapid evolution of the wild Freesia species to generate intensive flower pigmentation. These results showed that while the MBW complex was highly evolutionarily conserved between tested monocot and core eudicot plants, participating MYB regulators showed functional differences in transactivation capacity according to their activation domain and played important roles in the flower coloration domestication and evolution of angiosperms.
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Affiliation(s)
- Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xiaotong Shan
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Linna Tong
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Chao Wei
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Keyu Lu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Shuying Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Shadrack Kimani
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
- Department of Biological and Physical Sciences, Karatina University, P.O. Box 1957, 10101 Karatina, Kenya
| | - Shucai Wang
- School of Life Sciences, Linyi University, Linyi, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
- National Demonstration Center for Experimental Biology Education, Northeast Normal University, Changchun, China
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Wu X, Riaz M, Yan L, Zhang Z, Jiang C. How the cells were injured and the secondary metabolites in the shikimate pathway were changed by boron deficiency in trifoliate orange root. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:630-639. [PMID: 32335386 DOI: 10.1016/j.plaphy.2020.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 05/24/2023]
Abstract
Boron (B) deficiency is frequently observed in citrus orchards as a major cause for loss of productivity and quality. The structural and morphological responses of roots to B deficiency have been reported in some plants. The study was conducted to get novel information about the B-deficient-induced cellular injuries and target secondary metabolites in the shikimate pathway. Fluorescent vital staining, paraffin section, transmission electron microscopy (TEM) and target metabolomics were to investigate the responses of the cell viability and structure, and target aromatic metabolites in the shikimate pathway in B-deficient trifoliate orange roots. Boron deprivation-induced ROS accumulation accelerated the membrane peroxidation, resulting in weakened cell vitality and cell rupture in roots. In addition, B deficiency increased phenylalanine (Phe), tyrosine (Try) in roots, thereby promoting the biosynthesis of salicylic acid, caffeic acid and ferulic acid. B-starvation up-regulated salicylic acid and lignin while reduced 3-indoleacetic acid (IAA) content. These adverse effects might be involved in the structural and morphological changes in B-deficient roots. What is more, the results provide a new insight into the mechanism of B deficiency-induced structural damage and elongation inhibition on roots.
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Affiliation(s)
- Xiuwen Wu
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China; College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan, 410000, PR China
| | - Muhammad Riaz
- Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Lei Yan
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Zhenhua Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan, 410000, PR China
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.
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Wen W, Alseekh S, Fernie AR. Conservation and diversification of flavonoid metabolism in the plant kingdom. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:100-108. [PMID: 32422532 DOI: 10.1016/j.pbi.2020.04.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 05/05/2023]
Abstract
Flavonoids are by far the largest class of polyphenols with huge structural and functional diversity. However, the mystery regarding the exact evolutionary pressures which lead to the amazing diversity in plant flavonoids has yet to be completely uncovered. Here we review recent advances in understanding the conservation and diversification of flavonoid pathway from algae and early land plants to vascular plants including the model plant Arabidopsis and economically important species such as cereals, legumes, and medicinal plants. Studies on the origin and evolution of R2R3-MYB regulatory system demonstrated its highly conserved function of regulating flavonoid production in land plants and this innovation appears to have been crucial in boosting the overall levels of these compounds in land plants. Convergent evolution has occurred as different flavonoids independently which emerged in distant taxa resulting in similar defense and tolerance characteristics against environmental stresses. Future studies on an increasing number of plant species taking advantage of newly developed genomic and metabolite profiling technologies are envisaged to provide comprehensive insight into flavonoid biosynthesis as well as pathway diversification and the underlying evolutionary mechanisms.
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Affiliation(s)
- Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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Saigo T, Wang T, Watanabe M, Tohge T. Diversity of anthocyanin and proanthocyanin biosynthesis in land plants. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:93-99. [PMID: 32387820 DOI: 10.1016/j.pbi.2020.04.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 05/22/2023]
Abstract
Anthocyanins and proanthocyanidins are among the most numerous and widely distributed pigments in land plants. Given that these pigments are the valuable compounds, as stress protectants and health-promoting components because of their potent antioxidant activity, several metabolic engineering approaches focusing on these compounds have been attempted. Currently, the difference in biological functions between flavonoid decorations is focused, because some aglycone decorations were found to be key factors rendering physiological functions against environmental stresses. Therefore, metabolic diversity and functional genomics approaches focusing on anthocyanin decoration should be reconsidered. Additionally, since the production of anthocyanins and proanthocyanidins in plants is often represented in a tissue-specific manner and by stress induction, elucidation of the specific regulatory mechanisms of how these pathways have been evolved, is highly important. Here, we review current knowledge of the diversity of chemical structure and regulators of anthocyanin/proanthocyanin biosynthesis with cross-species comparison to assess metabolic evolution.
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Affiliation(s)
- Tomoki Saigo
- Graduate School of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, 630-0192 Japan
| | - Tong Wang
- Graduate School of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, 630-0192 Japan
| | - Mutsumi Watanabe
- Graduate School of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, 630-0192 Japan
| | - Takayuki Tohge
- Graduate School of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, 630-0192 Japan.
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Calumpang CLF, Saigo T, Watanabe M, Tohge T. Cross-Species Comparison of Fruit-Metabolomics to Elucidate Metabolic Regulation of Fruit Polyphenolics Among Solanaceous Crops. Metabolites 2020; 10:E209. [PMID: 32438728 PMCID: PMC7281770 DOI: 10.3390/metabo10050209] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/03/2020] [Accepted: 05/14/2020] [Indexed: 11/24/2022] Open
Abstract
Many solanaceous crops are an important part of the human daily diet. Fruit polyphenolics are plant specialized metabolites that are recognized for their human health benefits and their defensive role against plant abiotic and biotic stressors. Flavonoids and chlorogenates are the major polyphenolic compounds found in solanaceous fruits that vary in quantity, physiological function, and structural diversity among and within plant species. Despite their biological significance, the elucidation of metabolic shifts of polyphenols during fruit ripening in different fruit tissues, has not yet been well-characterized in solanaceous crops, especially at a cross-species and cross-cultivar level. Here, we performed a cross-species comparison of fruit-metabolomics to elucidate the metabolic regulation of fruit polyphenolics from three representative crops of Solanaceae (tomato, eggplant, and pepper), and a cross-cultivar comparison among different pepper cultivars (Capsicum annuum cv.) using liquid chromatography-mass spectrometry (LC-MS). We observed a metabolic trade-off between hydroxycinnamates and flavonoids in pungent pepper and anthocyanin-type pepper cultivars and identified metabolic signatures of fruit polyphenolics in each species from each different tissue-type and fruit ripening stage. Our results provide additional information for metabolomics-assisted crop improvement of solanaceous fruits towards their improved nutritive properties and enhanced stress tolerance.
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Affiliation(s)
| | | | | | - Takayuki Tohge
- Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan; (C.L.F.C.); (T.S.); (M.W.)
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63
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Tohge T, Fernie AR. Co-Regulation of Clustered and Neo-Functionalized Genes in Plant-Specialized Metabolism. PLANTS (BASEL, SWITZERLAND) 2020; 9:E622. [PMID: 32414181 PMCID: PMC7285293 DOI: 10.3390/plants9050622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 01/20/2023]
Abstract
Current findings of neighboring genes involved in plant specialized metabolism provide the genomic signatures of metabolic evolution. Two such genomic features, namely, (i) metabolic gene cluster and (ii) neo-functionalization of tandem gene duplications, represent key factors corresponding to the creation of metabolic diversity of plant specialized metabolism. So far, several terpenoid and alkaloid biosynthetic genes have been characterized with gene clusters in some plants. On the other hand, some modification genes involved in flavonoid and glucosinolate biosynthesis were found to arise via gene neo-functionalization. Although the occurrence of both types of metabolic evolution are different, the neighboring genes are generally regulated by the same or related regulation factors. Therefore, the translation-based approaches associated with genomics, and transcriptomics are able to be employed for functional genomics focusing on plant secondary metabolism. Here, we present a survey of the current understanding of neighboring genes involved in plant secondary metabolism. Additionally, a genomic overview of neighboring genes of four model plants and transcriptional co-expression network neighboring genes to detect metabolic gene clusters in Arabidopsis is provided. Finally, the insights functional genomics have provided concerning the evolution and mechanistic regulation of both the formation and operation of metabolic neighboring clusters is discussed.
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Affiliation(s)
- Takayuki Tohge
- Graduate School of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma 630-0192, Japan
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Wang J, Ma X, Yang J, Hui Y, She J, Tian T, Li Z, Xu W, Gao Z, Su Z, Zhao H. Coexpression Analysis Reveals Dynamic Modules Regulating the Growth and Development of Cirri in the Rattans ( Calamus simplicifolius and Daemonorops jenkinsiana). Front Genet 2020; 11:378. [PMID: 32477399 PMCID: PMC7236543 DOI: 10.3389/fgene.2020.00378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/27/2020] [Indexed: 01/01/2023] Open
Abstract
Rattan is regarded as one of the major non-timber forest products, second only to wood and bamboo, worldwide. Although the published genomes of Calamus simplicifolius and Daemonorops jenkinsiana have facilitated genome-wide gene functional analyses, coexpression networks (CENs) provide more comprehensive and complete annotations of gene function at the transcriptome level. Thus, we analyzed the CENs of the two rattans, C. simplicifolius and D. jenkinsiana, by integrating the genome sequences and analyzing in-house transcriptome data from different development stages of their cirri using a well-developed strategy. A total of 3,504 and 3,027 functional modules were identified in C. simplicifolius and D. jenkinsiana, respectively, based on a combination of CENs, gene family classification, and function enrichment tools. These modules covered the major developmental processes, including photosynthesis, lignin biosynthesis, flavonoid biosynthesis, and phenylpropanoid biosynthesis. Reference annotations were refined using CENs and functional modules. Moreover, we obtained novel insights into the regulation of cirrus growth and development in rattans. Furthermore, Rattan-NET (http://rattan.bamboogdb.org/), an online database with analysis tools for gene set enrichment analysis, module enrichment, network comparison analysis, and cis-element analysis, was constructed for the easy analysis of gene function and regulation modules involved in the growth and development of cirri in rattans.
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Affiliation(s)
- Jiongliang Wang
- State Forestry and Grassland Administration/Beijing Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiaotong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yanan Hui
- State Forestry and Grassland Administration/Beijing Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Jiajie She
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tian Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhongqiu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhimin Gao
- State Forestry and Grassland Administration/Beijing Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hansheng Zhao
- State Forestry and Grassland Administration/Beijing Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
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65
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Fernández-Marín B, Nadal M, Gago J, Fernie AR, López-Pozo M, Artetxe U, García-Plazaola JI, Verhoeven A. Born to revive: molecular and physiological mechanisms of double tolerance in a paleotropical and resurrection plant. THE NEW PHYTOLOGIST 2020; 226:741-759. [PMID: 32017123 DOI: 10.1111/nph.16464] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/20/2020] [Indexed: 05/24/2023]
Abstract
Resurrection plants recover physiological functions after complete desiccation. Almost all of them are native to tropical warm environments. However, the Gesneriaceae include four genera, remnant of the past palaeotropical flora, which inhabit temperate mountains. One of these species is additionally freezing-tolerant: Ramonda myconi. We hypothesise that this species has been able to persist in a colder climate thanks to some resurrection-linked traits. To disentangle the physiological mechanisms underpinning multistress tolerance to desiccation and freezing, we conducted an exhaustive seasonal assessment of photosynthesis (gas exchange, limitations to partitioning, photochemistry and galactolipids) and primary metabolism (through metabolomics) in two natural populations at different elevations. R. myconi displayed low rates of photosynthesis, largely due to mesophyll limitation. However, plants were photosynthetically active throughout the year, excluding a reversible desiccation period. Common responses to desiccation and low temperature involved chloroplast protection: enhanced thermal energy dissipation, higher carotenoid to Chl ratio and de-epoxidation of the xanthophyll cycle. As specific responses, antioxidants and secondary metabolic routes rose upon desiccation, while putrescine, proline and a variety of sugars rose in winter. The data suggest conserved mechanisms to cope with photo-oxidation during desiccation and cold events, while additional metabolic mechanisms may have evolved as specific adaptations to cold during recent glaciations.
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Affiliation(s)
- Beatriz Fernández-Marín
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
- Department of Botany, Ecology and Plant Physiology, University of La Laguna (ULL), Tenerife, 38200, Spain
| | - Miquel Nadal
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears (UIB), Instituto de Agroecología y Economía del Agua (INAGEA), ctra. Valldemossa km 7.5, Palma de Mallorca, 07122, Spain
| | - Jorge Gago
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears (UIB), Instituto de Agroecología y Economía del Agua (INAGEA), ctra. Valldemossa km 7.5, Palma de Mallorca, 07122, Spain
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Marina López-Pozo
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Unai Artetxe
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - José Ignacio García-Plazaola
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Amy Verhoeven
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
- Biology Department (OWS352), University of St Thomas, 2115 Summit Ave., St Paul, MN, USA
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66
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Ziv C, Kumar D, Sela N, Itkin M, Malitsky S, Schaffer AA, Prusky DB. Sugar-regulated susceptibility of tomato fruit to Colletotrichum and Penicillium requires differential mechanisms of pathogenicity and fruit responses. Environ Microbiol 2020; 22:2870-2891. [PMID: 32323444 DOI: 10.1111/1462-2920.15031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 12/22/2022]
Abstract
Colletotrichum gloeosporioides and Penicillium expansum cause postharvest diseases in tropical and deciduous fruit. During colonization, C. gloeosporioides and P. expansum secrete ammonia in hosts with low sugar content (LowSC) and gluconic acid in hosts with high sugar content (HighSC), respectively, as a mechanism to modulate enhanced pathogenicity. We studied the pathogens interactions with tomato lines of similar genetic background but differing in their sugar content. Colletotrichum gloeosporioides showed enhanced colonization of the LowSC line with differential expression response of 15% of its genes including enhanced relative expression of glycosyl hydrolases, glucanase and MFS-transporter genes. Enhanced colonization of P. expansum occurred in the HighSC line, accompanied by an increase in carbohydrate metabolic processes mainly phosphoenolpyruvate carboxykinase, and only 4% of differentially expressed genes. Gene response of the two host lines strongly differed depending on the sugar level. Limited colonization of HighSC line by C. gloeosporioides was accompanied by a marked alteration of gene expression compared the LowSC response to the same pathogen; while colonization by P. expansum resulted in a similar response of the two different hosts. We suggest that this differential pattern of fungal/host responses may be the basis for the differential of host range of both pathogens in nature.
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Affiliation(s)
- Carmit Ziv
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Dilip Kumar
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Maxim Itkin
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sergey Malitsky
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Arthur A Schaffer
- Department of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
| | - Dov B Prusky
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion, 7505101, Israel
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67
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Zhao J, Li P, Xia T, Wan X. Exploring plant metabolic genomics: chemical diversity, metabolic complexity in the biosynthesis and transport of specialized metabolites with the tea plant as a model. Crit Rev Biotechnol 2020; 40:667-688. [PMID: 32321331 DOI: 10.1080/07388551.2020.1752617] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The diversity and complexity of secondary metabolites in tea plants contribute substantially to the popularity of tea, by determining tea flavors and their numerous health benefits. The most significant characteristics of tea plants are that they concentrate the complex plant secondary metabolites into one leaf: flavonoids, alkaloids, theanine, volatiles, and saponins. Many fundamental questions regarding tea plant secondary metabolism remain unanswered. This includes how tea plants accumulate high levels of monomeric galloylated catechins, unlike the polymerized flavan-3-ols in most other plants, as well as how they are evolved to selectively synthesize theanine and caffeine, and how tea plants properly transport and store these cytotoxic products and then reuse them in defense. Tea plants coordinate many metabolic pathways that simultaneously take place in young tea leaves in response to both developmental and environmental cues. With the available genome sequences of tea plants and high-throughput metabolomic tools as great platforms, it is of particular interest to launch metabolic genomics studies using tea plants as a model system. Plant metabolic genomics are to investigate all aspects of plant secondary metabolism at the genetic, genome, and molecular levels. This includes plant domestication and adaptation, divergence and convergence of secondary metaboloic pathways. The biosynthesis, transport, storage, and transcriptional regulation mechanisms of all metabolites are of core interest in the plant as a whole. This review highlights relevant contexts of metabolic genomics, outstanding questions, and strategies for answering them, with aim to guide future research for genetic improvement of nutrition quality for healthier plant foods.
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Affiliation(s)
- Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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68
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Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie A, Tohge T, Mutwil M. Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots. THE PLANT CELL 2020; 32:853-870. [PMID: 31988262 PMCID: PMC7145505 DOI: 10.1105/tpc.19.00780] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 05/20/2023]
Abstract
Selaginella moellendorffii is a representative of the lycophyte lineage that is studied to understand the evolution of land plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, only a few studies have investigated the expression and transcriptional coordination of Selaginella genes, precluding us from understanding the evolution of the transcriptional programs behind these traits. We present a gene expression atlas comprising all major organs, tissue types, and the diurnal gene expression profiles for S. moellendorffii We show that the transcriptional gene module responsible for the biosynthesis of lignocellulose evolved in the ancestor of vascular plants and pinpoint the duplication and subfunctionalization events that generated multiple gene modules involved in the biosynthesis of various cell wall types. We demonstrate how secondary metabolism is transcriptionally coordinated and integrated with other cellular pathways. Finally, we identify root-specific genes and show that the evolution of roots did not coincide with an increased appearance of gene families, suggesting that the development of new organs does not coincide with increased fixation of new gene functions. Our updated database at conekt.plant.tools represents a valuable resource for studying the evolution of genes, gene families, transcriptomes, and functional gene modules in the Archaeplastida kingdom.
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Affiliation(s)
- Camilla Ferrari
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Devendra Shivhare
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Bjoern Oest Hansen
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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69
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Wang P, Luo Y, Huang J, Gao S, Zhu G, Dang Z, Gai J, Yang M, Zhu M, Zhang H, Ye X, Gao A, Tan X, Wang S, Wu S, Cahoon EB, Bai B, Zhao Z, Li Q, Wei J, Chen H, Luo R, Gong D, Tang K, Zhang B, Ni Z, Huang G, Hu S, Chen Y. The genome evolution and domestication of tropical fruit mango. Genome Biol 2020; 21:60. [PMID: 32143734 PMCID: PMC7059373 DOI: 10.1186/s13059-020-01959-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
Background Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces.
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Affiliation(s)
- Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
| | - Yingfeng Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jianfeng Huang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Guopeng Zhu
- School of Landscape and Horticulture, Hainan University, Haikou, 570208, Hainan, China
| | - Zhiguo Dang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Jiangtao Gai
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Meng Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Min Zhu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Huangkai Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Aiping Gao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Xinyu Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Sen Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Shuangyang Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Edgar B Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Beibei Bai
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.,School of Landscape and Horticulture, Hainan University, Haikou, 570208, Hainan, China
| | - Zhichang Zhao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Qian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Junya Wei
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Huarui Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Ruixiong Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China
| | - Deyong Gong
- Guizhou Subtropical Crops Research Institute, Xingyi, Qianxinan, Guzhou, 562400, China
| | - Kexuan Tang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bing Zhang
- Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhangguang Ni
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, 678005, Yunnan, China
| | - Guodi Huang
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, Guangxi, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China. .,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China. .,School of Landscape and Horticulture, Hainan University, Haikou, 570208, Hainan, China.
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Limones-Mendez M, Dugrand-Judek A, Villard C, Coqueret V, Froelicher Y, Bourgaud F, Olry A, Hehn A. Convergent evolution leading to the appearance of furanocoumarins in citrus plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110392. [PMID: 32005397 DOI: 10.1016/j.plantsci.2019.110392] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 06/10/2023]
Abstract
Furanocoumarins are defense molecules mainly described in four plant families that are phylogenetically distant. Molecular characterization of the biosynthetic pathway has been started for many years in Apiaceae and Rutaceae. The results obtained thus far in Apiaceae indicated a major role of cytochromes P450 (P450s) in the CYP71 family. In the present work, we describe the importance of another subfamily of P450s, CYP82D, identified by using a deep analysis of the citrus (Rutaceae) genome and microarray database. CYP82D64 is able to hydroxylate xanthotoxin to generate 5-OH-xanthotoxin. Minor and limited amino acid changes in the CYP82D64 coding sequence between Citrus paradisi and Citrus hystrix provide the enzyme in the latter with the ability to hydroxylate herniarin, but with low efficiency. The kinetic constants of the enzyme are consistent with those of other enzymes of this type in plants and indicate that it may be the physiological substrate. The activity of the enzyme is identical to that of CYP71AZ6 identified in parsnip, showing possible evolutionary convergence between these two families of plants. It is highly possible that these molecules are derived from the synthesis of ubiquitous coumarins throughout the plant kingdom.
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Affiliation(s)
| | | | - Cloé Villard
- Université de Lorraine, INRA, LAE, F54000, Nancy, France
| | | | | | - Frédéric Bourgaud
- Plant Advanced Technologies SA, F-54500, Vandœuvre-lès-Nancy, France
| | - Alexandre Olry
- Université de Lorraine, INRA, LAE, F54000, Nancy, France
| | - Alain Hehn
- Université de Lorraine, INRA, LAE, F54000, Nancy, France.
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71
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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72
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Davies KM, Jibran R, Zhou Y, Albert NW, Brummell DA, Jordan BR, Bowman JL, Schwinn KE. The Evolution of Flavonoid Biosynthesis: A Bryophyte Perspective. FRONTIERS IN PLANT SCIENCE 2020; 11:7. [PMID: 32117358 PMCID: PMC7010833 DOI: 10.3389/fpls.2020.00007] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/07/2020] [Indexed: 05/04/2023]
Abstract
The flavonoid pathway is one of the best characterized specialized metabolite pathways of plants. In angiosperms, the flavonoids have varied roles in assisting with tolerance to abiotic stress and are also key for signaling to pollinators and seed dispersal agents. The pathway is thought to be specific to land plants and to have arisen during the period of land colonization around 550-470 million years ago. In this review we consider current knowledge of the flavonoid pathway in the bryophytes, consisting of the liverworts, hornworts, and mosses. The pathway is less characterized for bryophytes than angiosperms, and the first genetic and molecular studies on bryophytes are finding both commonalities and significant differences in flavonoid biosynthesis and pathway regulation between angiosperms and bryophytes. This includes biosynthetic pathway branches specific to each plant group and the apparent complete absence of flavonoids from the hornworts.
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Affiliation(s)
- Kevin M. Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Yanfei Zhou
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - David A. Brummell
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Brian R. Jordan
- Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Kathy E. Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
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73
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Lansing H, Doering L, Fischer K, Baune MC, Schaewen AV. Analysis of potential redundancy among Arabidopsis 6-phosphogluconolactonase isoforms in peroxisomes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:823-836. [PMID: 31641750 DOI: 10.1093/jxb/erz473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/10/2019] [Indexed: 05/21/2023]
Abstract
Recent work revealed that PGD2, an Arabidopsis 6-phosphogluconate dehydrogenase (6-PGD) catalysing the third step of the oxidative pentose-phosphate pathway (OPPP) in peroxisomes, is essential during fertilization. Earlier studies on the second step, catalysed by PGL3, a dually targeted Arabidopsis 6-phosphogluconolactonase (6-PGL), reported the importance of OPPP reactions in plastids but their irrelevance in peroxisomes. Assuming redundancy of 6-PGL activity in peroxisomes, we examined the sequences of other higher plant enzymes. In tomato, there exist two 6-PGL isoforms with the strong PTS1 motif SKL. However, their analysis revealed problems regarding peroxisomal targeting: reporter-PGL detection in peroxisomes required construct modification, which was also applied to the Arabidopsis isoforms. The relative contribution of PGL3 versus PGL5 during fertilization was assessed by mutant crosses. Reduced transmission ratios were found for pgl3-1 (T-DNA-eliminated PTS1) and also for knock-out allele pgl5-2. The prominent role of PGL3 showed as compromised growth of pgl3-1 seedlings on sucrose and higher activity of mutant PGL3-1 versus PGL5 using purified recombinant proteins. Evidence for PTS1-independent uptake was found for PGL3-1 and other Arabidopsis PGL isoforms, indicating that peroxisome import may be supported by a piggybacking mechanism. Thus, multiple redundancy at the level of the second OPPP step in peroxisomes explains the occurrence of pgl3-1 mutant plants.
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Affiliation(s)
- Hannes Lansing
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
| | - Lennart Doering
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
| | - Kerstin Fischer
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
| | - Marie-Christin Baune
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
| | - Antje Von Schaewen
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
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Zeng X, Yuan H, Dong X, Peng M, Jing X, Xu Q, Tang T, Wang Y, Zha S, Gao M, Li C, Shu C, Wei Z, Qimei W, Basang Y, Dunzhu J, Li Z, Bai L, Shi J, Zheng Z, Yu S, Fernie AR, Luo J, Nyima T. Genome-wide Dissection of Co-selected UV-B Responsive Pathways in the UV-B Adaptation of Qingke. MOLECULAR PLANT 2020; 13:112-127. [PMID: 31669581 DOI: 10.1016/j.molp.2019.10.009] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/16/2019] [Accepted: 10/15/2019] [Indexed: 05/03/2023]
Abstract
Qingke (Tibetan hulless barley) has long been cultivated and exposed to long-term and strong UV-B radiation on the Tibetan Plateau, which renders it an ideal species for elucidating novel UV-B responsive mechanisms in plants. Here we report a comprehensive metabolite profiling and metabolite-based genome-wide association study (mGWAS) using 196 diverse qingke and barley accessions. Our results demonstrated both constitutive and induced accumulation, and common genetic regulation, of metabolites from different branches of the phenylpropanoid pathway that are involved in UV-B protection. A total of 90 significant mGWAS loci for these metabolites were identified in barley-qingke differentiation regions, and a number of high-level metabolite trait alleles were found to be significantly enriched in qingke, suggesting co-selection of various phenylpropanoids. Upon dissecting the entire phenylpropanoid pathway, we identified some key determinants controlling natural variation of phenylpropanoid content, including three novel proteins, a flavone C-pentosyltransferase, a tyramine hydroxycinnamoyl acyltransferase, and a MYB transcription factor. Our study, furthermore, demonstrated co-selection of both constitutive and induced phenylpropanoids for UV-B protection in qingke.
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Affiliation(s)
- Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Xuekui Dong
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; VIB-UGent Center for Plant Systems Biology, Ghent University, Technologiepark-Zwijnaarde, 71, 9052 Ghent, Belgium
| | - Xinyu Jing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qijun Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Tang Tang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Sang Zha
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Meng Gao
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Congzhi Li
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Chujin Shu
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Zexiu Wei
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Agricultural Resources and Environment Research Institute, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Wangmu Qimei
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yuzhen Basang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Jiabu Dunzhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Zeqing Li
- Wuhan Igenebook Biotechnology Co., Ltd., Wuhan, China
| | - Lijun Bai
- Chengdu Life Baseline Technology Co., Ltd, Chengdu, 610041, China
| | - Jian Shi
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Zhigang Zheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 144776, Germany
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; College of Tropical Crops, Hainan University, Haikou, Hainan 572208, China.
| | - Tashi Nyima
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China; Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China.
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Zhu J, Xu Q, Zhao S, Xia X, Yan X, An Y, Mi X, Guo L, Samarina L, Wei C. Comprehensive co-expression analysis provides novel insights into temporal variation of flavonoids in fresh leaves of the tea plant (Camellia sinensis). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110306. [PMID: 31779914 DOI: 10.1016/j.plantsci.2019.110306] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 05/18/2023]
Abstract
Flavonoids are the major class of characteristic secondary compounds in Camellia sinensis that affect quality of tea. However, the temporal variation and the underlying regulatory mechanism of flavonoid biosynthesis during different growth months require a further investigation. Here, we combined analyses of the metabolomics and transcriptomics to tea leaves freshly collected during five different months for a comprehensive understanding of flavonoid metabolism regulation in tea plants. Through loading plot analysis, significant changes in the contents of metabolites during growing months were discovered, and further co-expression and association analysis indicated that one flavone glycoside (naringenin-7-O-glucoside) and two flavonol glycosides (quercetin-3-O-galactoside and kaemferol-3-O-(6″-O-p-courmaroyl)-glucoside) were evaluated as growth markers, which may explain the high bitterness and astringency of August teas; additionally, the high levels of two flavan-3-ols (gallocatechin and catechin gallate) may contribute to the flavor formation of April tea. Meanwhile, multiple flavonoid-related structural genes, MYB and bHLH transcription factors exhibit specific expression patterns to modulate the biosynthesis of these key flavonoids. A co-expression regulatory sub-network was constructed based on profiles of differentially expressed genes; one CsbHLH and six transcription factors (three CsbHLHs and three CsMYBs) exhibited negative and positive roles in the regulation of flavonoid biosynthetic genes, respectively. Taken together, our results provide new insights into the regulation of principle flavonoids for unique flavor of tea regulated by many flavonoid-related structural genes and transcription factors during different growth months.
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Affiliation(s)
- Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Qingshan Xu
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shiqi Zhao
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Xiaomei Yan
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Lingxiao Guo
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Lidiia Samarina
- Russian Research Institute of Floriculture and Subtropical Crops, 354002 Yana Fabritsiusa st. 2/28, Sochi, Russian Federation
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China.
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Liu YY, Chen XR, Wang JP, Cui WQ, Xing XX, Chen XY, Ding WY, God'spower BO, Eliphaz N, Sun MQ, Li YH. Transcriptomic analysis reveals flavonoid biosynthesis of Syringa oblata Lindl. in response to different light intensity. BMC PLANT BIOLOGY 2019; 19:487. [PMID: 31711412 PMCID: PMC6849326 DOI: 10.1186/s12870-019-2100-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/25/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Hazy weather significantly increase air pollution and affect light intensity which may also affect medicinal plants growth. Syringa oblata Lindl. (S. oblata), an effective anti-biofilm medicinal plants, is also vulnerable to changes in plant photoperiods and other abiotic stress responses. Rutin, one of the flavonoids, is the main bioactive ingredient in S. oblata that inhibits Streptococcus suis biofilm formation. Thus, the present study aims to explore the biosynthesis and molecular basis of flavonoids in S. oblata in response to different light intensity. RESULTS In this study, it was shown that compared with natural (Z0) and 25% ~ 35% (Z2) light intensities, the rutin content of S. oblata under 50% ~ 60% (Z1) light intensity increased significantly. In addition, an integrated analysis of metabolome and transcriptome was performed using light intensity stress conditions from two kinds of light intensities which S. oblata was subjected to: Z0 and Z1. The results revealed that differential metabolites and genes were mainly related to the flavonoid biosynthetic pathway. We found out that 13 putative structural genes and a transcription factor bHLH were significantly up-regulated in Z1. Among them, integration analysis showed that 3 putative structural genes including 4CL1, CYP73A and CYP75B1 significantly up-regulated the rutin biosynthesis, suggesting that these putative genes may be involved in regulating the flavonoid biosynthetic pathway, thereby making them key target genes in the whole metabolic process. CONCLUSIONS The present study provided helpful information to search for the novel putative genes that are potential targets for S. oblata in response to light intensity.
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Affiliation(s)
- Yan-Yan Liu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xing-Ru Chen
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Jin-Peng Wang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Wen-Qiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xiao-Xu Xing
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xue-Ying Chen
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Wen-Ya Ding
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Bello-Onaghise God'spower
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Nsabimana Eliphaz
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Meng-Qing Sun
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yan-Hua Li
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China.
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China.
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Gao J, Shen L, Yuan J, Zheng H, Su Q, Yang W, Zhang L, Nnaemeka VE, Sun J, Ke L, Sun Y. Functional analysis of GhCHS, GhANR and GhLAR in colored fiber formation of Gossypium hirsutum L. BMC PLANT BIOLOGY 2019; 19:455. [PMID: 31664897 PMCID: PMC6819470 DOI: 10.1186/s12870-019-2065-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/02/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND The formation of natural colored fibers mainly results from the accumulation of different anthocyanidins and their derivatives in the fibers of Gossypium hirsutum L. Chalcone synthase (CHS) is the first committed enzyme of flavonoid biosynthesis, and anthocyanidins are transported into fiber cells after biosynthesis mainly by Anthocyanidin reductase (ANR) and Leucoanthocyanidin reductase (LAR) to present diverse colors with distinct stability. The biochemical and molecular mechanism of pigment formation in natural colored cotton fiber is not clear. RESULTS The three key genes of GhCHS, GhANR and GhLAR were predominantly expressed in the developing fibers of colored cotton. In the GhCHSi, GhANRi and GhLARi transgenic cottons, the expression levels of GhCHS, GhANR and GhLAR significantly decreased in the developing cotton fiber, negatively correlated with the content of anthocyanidins and the color depth of cotton fiber. In colored cotton Zongxu1 (ZX1) and the GhCHSi, GhANRi and GhLARi transgenic lines of ZX1, HZ and ZH, the anthocyanidin contents of the leaves, cotton kernels, the mixture of fiber and seedcoat were all changed and positively correlated with the fiber color. CONCLUSION The three genes of GhCHS, GhANR and GhLAR were predominantly expressed early in developing colored cotton fibers and identified to be a key genes of cotton fiber color formation. The expression levels of the three genes affected the anthocyanidin contents and fiber color depth. So the three genes played a crucial part in cotton fiber color formation and has important significant to improve natural colored cotton quality and create new colored cotton germplasm resources by genetic engineering.
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Affiliation(s)
- Jianfang Gao
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Li Shen
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Jingli Yuan
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Hongli Zheng
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Quansheng Su
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Weiguang Yang
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Liqing Zhang
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Vitalis Ekene Nnaemeka
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Jie Sun
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China
| | - Liping Ke
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
| | - Yuqiang Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016 Zhejiang China
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Maeda HA. Harnessing evolutionary diversification of primary metabolism for plant synthetic biology. J Biol Chem 2019; 294:16549-16566. [PMID: 31558606 DOI: 10.1074/jbc.rev119.006132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Plants produce numerous natural products that are essential to both plant and human physiology. Recent identification of genes and enzymes involved in their biosynthesis now provides exciting opportunities to reconstruct plant natural product pathways in heterologous systems through synthetic biology. The use of plant chassis, although still in infancy, can take advantage of plant cells' inherent capacity to synthesize and store various phytochemicals. Also, large-scale plant biomass production systems, driven by photosynthetic energy production and carbon fixation, could be harnessed for industrial-scale production of natural products. However, little is known about which plants could serve as ideal hosts and how to optimize plant primary metabolism to efficiently provide precursors for the synthesis of desirable downstream natural products or specialized (secondary) metabolites. Although primary metabolism is generally assumed to be conserved, unlike the highly-diversified specialized metabolism, primary metabolic pathways and enzymes can differ between microbes and plants and also among different plants, especially at the interface between primary and specialized metabolisms. This review highlights examples of the diversity in plant primary metabolism and discusses how we can utilize these variations in plant synthetic biology. I propose that understanding the evolutionary, biochemical, genetic, and molecular bases of primary metabolic diversity could provide rational strategies for identifying suitable plant hosts and for further optimizing primary metabolism for sizable production of natural and bio-based products in plants.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
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79
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Djami-Tchatchou AT, Matsaunyane LBT, Ntushelo K. Gene expression responses of tomato inoculated with Pectobacterium carotovorum subsp. carotovorum. Microbiologyopen 2019; 8:e911. [PMID: 31536683 PMCID: PMC6925151 DOI: 10.1002/mbo3.911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/12/2019] [Accepted: 06/30/2019] [Indexed: 12/28/2022] Open
Abstract
Defense responses of tomato (Solanum lycopersicum L.) against attack by Pectobacterium carotovorum subsp. carotovorum (Pcc), the causal agent of soft rot diseases, were studied. The expression of some tomato defense genes were evaluated by real‐time PCR quantification analysis, 24 and 72 hr after actively growing tomato plants were inoculated with Pcc. These included: MYB transcriptor factor, ethylene response element‐binding protein, suppressor of the G2 allele of Skp1, cytochrome P450, small Sar1 GTPase, hydroxycinnamoyl‐CoA:quinate hydroxycinnamoyl transferase, pathogenesis‐related protein 1a, endo‐1,3‐beta‐glucanase, chitinase, proteinase inhibitor, defensin, CC‐NBS‐LRR resistance protein, and phenylalanine ammonia lyase. The results showed dynamic transcriptomic changes, with transcripts exhibiting different expression kinetics at 24 and 72 hr to confer resistance to tomato against Pcc infection.
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Affiliation(s)
- Arnaud T Djami-Tchatchou
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Florida, South Africa
| | | | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Florida, South Africa
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80
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Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, Coppens F, Vandepoele K. PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res 2019; 46:D1190-D1196. [PMID: 29069403 PMCID: PMC5753339 DOI: 10.1093/nar/gkx1002] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/12/2017] [Indexed: 11/14/2022] Open
Abstract
PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.
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Affiliation(s)
- Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tim Diels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | | | | | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria 0028, South Africa
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
- To whom correspondence should be addressed. Tel: +32 9 331 3822; Fax: +32 9 331 3809;
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Li Z, Chen Y, Meesapyodsuk D, Qiu X. The Biosynthetic Pathway of Major Avenanthramides in Oat. Metabolites 2019; 9:metabo9080163. [PMID: 31394723 PMCID: PMC6724135 DOI: 10.3390/metabo9080163] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/17/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
Avenanthramides are a group of N-cinnamoylanthranilic acids, with health-promoting properties mainly found in oat (Avena sativa L.). However, the biosynthetic mechanism for the main three types of avenanthramides (Avn-A, Avn-B and Avn-C) is not completely understood. In the present study, we report molecular identification and functional characterization of three different types of genes from oat encoding 4-coumarate-CoA ligase (4CL), hydroxycinnamoyl-CoA:hydroxyanthranilate N-hydroxycinnamoyl transferase (HHT) and a caffeoyl-CoA O-methyltransferase (CCoAOMT) enzymes, all involved in the biosynthesis of these avenanthramides. In vitro enzymatic assays using the proteins expressed in Escherichia coli showed that oat 4CL could convert p-coumaric acid, caffeic acid and ferulic acid to their CoA thioesters. Oat HHTs were only responsible for the biosynthesis of Avn-A and Avn-C using hydroxyanthranilic acid as an acyl acceptor and p-coumaroyl-CoA and caffeoyl-CoA as an acyl donor, respectively. Avn-B was synthesized by a CCoAOMT enzyme through the methylation of Avn-C. Collectively, these results have elucidated the molecular mechanisms for the biosynthesis of three major avenanthramides in vitro and paved the way for metabolic engineering of the biosynthetic pathway in heterologous systems to produce nutraceutically important compounds and make possible genetic improvement of this nutritional trait in oat through marker-assisted breeding.
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Affiliation(s)
- Zhiyong Li
- Department of Food & Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Yi Chen
- Department of Food & Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Dauenpen Meesapyodsuk
- Department of Food & Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Xiao Qiu
- Department of Food & Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
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82
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Carella P, Gogleva A, Hoey DJ, Bridgen AJ, Stolze SC, Nakagami H, Schornack S. Conserved Biochemical Defenses Underpin Host Responses to Oomycete Infection in an Early-Divergent Land Plant Lineage. Curr Biol 2019; 29:2282-2294.e5. [PMID: 31303485 DOI: 10.1016/j.cub.2019.05.078] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/28/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022]
Abstract
The expansion of plants onto land necessitated the evolution of robust defense strategies to protect against a wide array of microbial invaders. Whereas host responses to microbial colonization are extensively explored in evolutionarily young land plant lineages such as angiosperms, we know relatively little about plant-pathogen interactions in early-diverging land plants thought to better represent the ancestral state. Here, we define the transcriptional and proteomic response of the early-divergent liverwort Marchantia polymorpha to infection with the oomycete pathogen Phytophthora palmivora. We uncover a robust molecular response to oomycete colonization in Marchantia that consists of conserved land plant gene families. Direct macroevolutionary comparisons of host infection responses in Marchantia and the model angiosperm Nicotiana benthamiana further reveal a shared set of orthologous microbe-responsive genes that include members of the phenylpropanoid metabolic pathway. In addition, we identify a role for the Marchantia R2R3-MYB transcription factor MpMyb14 in activating phenylpropanoid (flavonoid) biosynthesis during oomycete infection. Mpmyb14 mutants infected with P. palmivora fail to activate phenylpropanoid biosynthesis gene expression and display enhanced disease susceptibility compared to wild-type plants. Conversely, the ectopic induction of MpMyb14 led to the accumulation of anthocyanin-like pigments and dramatically enhanced liverwort resistance to P. palmivora infection. Collectively, our results demonstrate that the Marchantia response to oomycete infection displays evolutionarily conserved features indicative of an ancestral pathogen deterrence strategy centered on phenylpropanoid-mediated biochemical defenses.
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Affiliation(s)
- Philip Carella
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Anna Gogleva
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - David John Hoey
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Anthony John Bridgen
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Sara Christina Stolze
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg, Cologne 50829, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg, Cologne 50829, Germany
| | - Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK; Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 EA3, UK.
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83
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Labarrere B, Prinzing A, Dorey T, Chesneau E, Hennion F. Variations of Secondary Metabolites among Natural Populations of Sub-Antarctic Ranunculus Species Suggest Functional Redundancy and Versatility. PLANTS (BASEL, SWITZERLAND) 2019; 8:E234. [PMID: 31331007 PMCID: PMC6681328 DOI: 10.3390/plants8070234] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/28/2019] [Accepted: 07/16/2019] [Indexed: 11/25/2022]
Abstract
Plants produce a high diversity of metabolites which help them sustain environmental stresses and are involved in local adaptation. However, shaped by both the genome and the environment, the patterns of variation of the metabolome in nature are difficult to decipher. Few studies have explored the relative parts of geographical region versus environment or phenotype in metabolomic variability within species and none have discussed a possible effect of the region on the correlations between metabolites and environments or phenotypes. In three sub-Antarctic Ranunculus species, we examined the role of region in metabolite differences and in the relationship between individual compounds and environmental conditions or phenotypic traits. Populations of three Ranunculus species were sampled across similar environmental gradients in two distinct geographical regions in îles Kerguelen. Two metabolite classes were studied, amines (quantified by high-performance liquid chromatography and fluorescence spectrophotometry) and flavonols (quantified by ultra-high-performance liquid chromatography with triple quadrupole mass spectrometry). Depending on regions, the same environment or the same trait may be related to different metabolites, suggesting metabolite redundancy within species. In several cases, a given metabolite showed different or even opposite relations with the same environmental condition or the same trait across the two regions, suggesting metabolite versatility within species. Our results suggest that metabolites may be functionally redundant and versatile within species, both in their response to environments and in their relation with the phenotype. These findings open new perspectives for understanding evolutionary responses of plants to environmental changes.
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Affiliation(s)
- Bastien Labarrere
- UMR 6553 ECOBIO, Université de Rennes 1, OSUR, CNRS, Av du Général Leclerc, F-35042 Rennes, France
| | - Andreas Prinzing
- UMR 6553 ECOBIO, Université de Rennes 1, OSUR, CNRS, Av du Général Leclerc, F-35042 Rennes, France
| | - Thomas Dorey
- Institut für Systematische und Evolutionäre Botanik, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Emeline Chesneau
- UMR 6553 ECOBIO, Université de Rennes 1, OSUR, CNRS, Av du Général Leclerc, F-35042 Rennes, France
| | - Françoise Hennion
- UMR 6553 ECOBIO, Université de Rennes 1, OSUR, CNRS, Av du Général Leclerc, F-35042 Rennes, France.
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84
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Zhan X, Shen Q, Chen J, Yang P, Wang X, Hong Y. Rice sulfoquinovosyltransferase SQD2.1 mediates flavonoid glycosylation and enhances tolerance to osmotic stress. PLANT, CELL & ENVIRONMENT 2019; 42:2215-2230. [PMID: 30942482 DOI: 10.1111/pce.13554] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 05/07/2023]
Abstract
Sulfoquinovosyltransferase 2 (SQD2) catalyses the final step in the sulfoquinovosyldiacylglycerol (SQDG) biosynthetic pathway. It is involved in the phosphate starvation response. Here, we show that rice SQD2.1 has dual activities catalysing SQDG synthesis and flavonoid glycosylation. SQD2.1 null mutants (sqd2.1) in rice had decreased levels of glycosidic flavonoids, particularly apigenin 7-O-glucoside (A7G), whereas these metabolites were increased in rice plants overexpressing SQD2.1. The sqd2.1 mutants and SQD2.1 overexpressing lines showed reduced and enhanced, respectively, tolerance to salinity and drought. Treating the sqd2.1 mutants with A7G decreased oxidative damage and restored stress tolerance to the wild-type levels. These findings demonstrate that SQD2.1 has a novel function in the glycosylation of flavonoids that is required for osmotic stress tolerance in rice. The novel activity of SQD2.1 in the production of glycosidic flavonoids improves scavenging of reactive oxygen species and protects against excessive oxidation.
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Affiliation(s)
- Xinqiao Zhan
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingwen Shen
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Chen
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pei Yang
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, St. Louis, Missouri, 63121
- Donald Danforth plant Science Center, St. Louis, Missouri, 63132
| | - Yueyun Hong
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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86
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Zeb N, Rashid MH, Mubarak MQE, Ghafoor S, de Visser SP. Flavonol biosynthesis by nonheme iron dioxygenases: A computational study into the structure and mechanism. J Inorg Biochem 2019; 198:110728. [PMID: 31203088 DOI: 10.1016/j.jinorgbio.2019.110728] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
Plants produce flavonol compounds for vital functions regarding plant growth, fruit and flower colouring as well as fruit ripening processes. Several of these biosynthesis steps are stereo- and regioselective and are being carried out by nonheme iron enzymes. Using density functional theory calculations on a large active site model complex of flavanone-3β-hydroxylase (FHT), we established the mechanism for conversion of naringenin to its dihydroflavonol, which is a key step in the mechanism of flavonol biosynthesis. The reaction starts with dioxygen binding to the iron(II) centre and a reaction with α-ketoglutarate co-substrate gives succinate, an iron(IV)-oxo species and CO2 with large exothermicity and small reaction barriers. The rate-determining reaction step in the mechanism; however, is hydrogen atom abstraction of an aliphatic CH bond by the iron(IV)-oxo species. We identify a large kinetic isotope effect for the replacement of the transferring hydrogen atom by deuterium. In a final step the OH and substrate radicals combine to form the alcohol product with a barrier of several kcal mol-1. We show that the latter is the result of geometric constraints in the active site pocket. Furthermore, the calculations show that a weak tertiary CH bond is shielded from the iron(IV)-oxo species in the substrate binding position and therefore the enzyme is able to activate a stronger CH bond. As such, the flavanone-3β-hydroxylase enzyme reacts regioselectively with one specific CH bond of naringenin by avoiding activation of weaker bonds through tight substrate and oxidant positioning.
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Affiliation(s)
- Neelam Zeb
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom; National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad H Rashid
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - M Qadri E Mubarak
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sidra Ghafoor
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom; Department of Chemistry, Government College University Faisalabad, Jhang Road, 3800 Faisalabad, Pakistan
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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87
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Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant Ferula assafoetida. G3-GENES GENOMES GENETICS 2019; 9:807-816. [PMID: 30679248 PMCID: PMC6404600 DOI: 10.1534/g3.118.200852] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ferula assafoetida is a medicinal plant of the Apiaceae family that has traditionally been used for its therapeutic value. Particularly, terpenoid and phenylpropanoid metabolites, major components of the root-derived oleo-gum-resin, exhibit anti-inflammatory and cytotoxic activities, thus offering a resource for potential therapeutic lead compounds. However, genes and enzymes for terpenoid and coumarin-type phenylpropanoid metabolism have thus far remained uncharacterized in F. assafoetida. Comparative de novo transcriptome analysis of roots, leaves, stems, and flowers was combined with computational annotation to identify candidate genes with probable roles in terpenoid and coumarin biosynthesis. Gene network analysis showed a high abundance of predicted terpenoid- and phenylpropanoid-metabolic pathway genes in flowers. These findings offer a deeper insight into natural product biosynthesis in F. assafoetida and provide genomic resources for exploiting the medicinal potential of this rare plant.
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Perez de Souza L, Scossa F, Proost S, Bitocchi E, Papa R, Tohge T, Fernie AR. Multi-tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1132-1153. [PMID: 30480348 PMCID: PMC6850281 DOI: 10.1111/tpj.14178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/15/2018] [Accepted: 11/23/2018] [Indexed: 05/02/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important legume species with a rich natural diversity of landraces that originated from the wild forms following multiple independent domestication events. After the publication of its genome, several resources for this relevant crop have been made available. A comprehensive characterization of specialized metabolism in P. vulgaris, however, is still lacking. In this study, we used a metabolomics approach based on liquid chromatography-mass spectrometry to dissect the chemical composition at a tissue-specific level in several accessions of common bean belonging to different gene pools. Using a combination of literature search, mass spectral interpretation, 13 C-labeling, and correlation analyses, we were able to assign chemical classes and/or putative structures for approximately 39% of all measured metabolites. Additionally, we integrated this information with transcriptomics data and phylogenetic inference from multiple legume species to reconstruct the possible metabolic pathways and identify sets of candidate genes involved in the biosynthesis of specialized metabolites. A particular focus was given to flavonoids, triterpenoid saponins and hydroxycinnamates, as they represent metabolites involved in important ecological interactions and they are also associated with several health-promoting benefits when integrated into the human diet. The data are presented here in the form of an accessible resource that we hope will set grounds for further studies on specialized metabolism in legumes.
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Affiliation(s)
| | - Federico Scossa
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Consiglio per la ricerca in agricoltura e l′analisi dell′economia agrariaCREA‐OFAVia di Fioranello 5200134RomeItaly
| | - Sebastian Proost
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Takayuki Tohge
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Graduate School of Biological SciencesNara Institute of Science and TechnologyIkoma, Nara630‐0192Japan
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
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89
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Fàbregas N, Fernie AR. The metabolic response to drought. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1077-1085. [PMID: 30726961 DOI: 10.1093/jxb/ery437] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/28/2018] [Indexed: 05/23/2023]
Abstract
Metabolic regulation is one of the main mechanisms involved in the maintenance of cell osmotic potential under abiotic stress. To date, metabolite profiling approaches have been extensively used to characterize the molecular responses to abiotic stress in many plant species. However, studies revealing the specific metabolic responses of plants exposed to water-deficit stress remain limited. Here, we review the most recent developments that advance our understanding of the metabolic response to drought stress in Arabidopsis and rice. We provide an updated schematic overview of the specific metabolic signature of wild-type plants in response to drought.
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Affiliation(s)
- Norma Fàbregas
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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90
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Maeda HA. Evolutionary Diversification of Primary Metabolism and Its Contribution to Plant Chemical Diversity. FRONTIERS IN PLANT SCIENCE 2019; 10:881. [PMID: 31354760 PMCID: PMC6635470 DOI: 10.3389/fpls.2019.00881] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/20/2019] [Indexed: 05/05/2023]
Abstract
Plants produce a diverse array of lineage-specific specialized (secondary) metabolites, which are synthesized from primary metabolites. Plant specialized metabolites play crucial roles in plant adaptation as well as in human nutrition and medicine. Unlike well-documented diversification of plant specialized metabolic enzymes, primary metabolism that provides essential compounds for cellular homeostasis is under strong selection pressure and generally assumed to be conserved across the plant kingdom. Yet, some alterations in primary metabolic pathways have been reported in plants. The biosynthetic pathways of certain amino acids and lipids have been altered in specific plant lineages. Also, two alternative pathways exist in plants for synthesizing primary precursors of the two major classes of plant specialized metabolites, terpenoids and phenylpropanoids. Such primary metabolic diversities likely underlie major evolutionary changes in plant metabolism and chemical diversity by acting as enabling or associated traits for the evolution of specialized metabolic pathways.
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91
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Fang C, Fernie AR, Luo J. Exploring the Diversity of Plant Metabolism. TRENDS IN PLANT SCIENCE 2019; 24:83-98. [PMID: 30297176 DOI: 10.1016/j.tplants.2018.09.006] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 05/23/2023]
Abstract
Plants produce a huge array of metabolites, far more than those produced by most other organisms. Unraveling this diversity and its underlying genetic variation has attracted increasing research attention. Post-genomic profiling platforms have enabled the marriage and mining of the enormous amount of phenotypic and genetic diversity. We review here achievements to date and challenges remaining that are associated with plant metabolic research using multi-omic strategies. We focus mainly on strategies adopted in investigating the diversity of plant metabolism and its underlying features. Recent advances in linking metabotypes with phenotypic and genotypic traits are also discussed. Taken together, we conclude that exploring the diversity of metabolism could provide new insights into plant evolution and domestication.
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Affiliation(s)
- Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 144776, Germany; Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570288, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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92
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Ghasemi S, Kumleh HH, Kordrostami M. Changes in the expression of some genes involved in the biosynthesis of secondary metabolites in Cuminum cyminum L. under UV stress. PROTOPLASMA 2019; 256:279-290. [PMID: 30083789 DOI: 10.1007/s00709-018-1297-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 07/29/2018] [Indexed: 05/08/2023]
Abstract
Biotic and abiotic stresses cause special defense reactions in plant organs, which after a series of reactions, these stresses produce secondary metabolites. The effect of ultraviolet radiation on the expression of key genes involved in the biosynthesis of secondary metabolites (Phenylalanine ammonia lyase (PAL), Hydroxymethylglutaryl-CoA reductase (HMG-CoA reductase), GPP synthases, Deoxyribonino heptulosinate 7-phosphate synthase (DAHP), and Deoxy Xylose Phosphate Synthase (DXS)), and the association of these genes with different amounts of secondary metabolites (phenol, terpene, flavonoids, anthocyanins, alkaloids, lycopene, and beta-carotene) was investigated in this study. The results of this study showed that the application of UV-B stress significantly increased the expression of GPPs, HMG-CoA reductase, DXS, DAHPs, and PAL genes compared to the control plants. The expression of two key genes involved in the biosynthesis of phenylpropanoids, including DAHPs and PAL, increased with UV-B stress, and the highest expression was related to the PAL gene. The results revealed that UV-B stress caused a significant increase in total levels of terpenoids, phenols, flavonoids, anthocyanins, alkaloids, beta-carotene, and lycopene. The highest relative expression of all genes was obtained in treatment A (UV-B radiation for 1 h), while in treatment B (UV-B radiation for 2 h), no significant changes were observed in the expression of the genes.
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Affiliation(s)
- Sepideh Ghasemi
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, P.O. Box 41635-1314, Rasht, Iran
| | - Hassan Hassani Kumleh
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, P.O. Box 41635-1314, Rasht, Iran.
| | - Mojtaba Kordrostami
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, P.O. Box 41635-1314, Rasht, Iran
- Rice Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran
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93
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Yonekura-Sakakibara K, Higashi Y, Nakabayashi R. The Origin and Evolution of Plant Flavonoid Metabolism. FRONTIERS IN PLANT SCIENCE 2019; 10:943. [PMID: 31428108 PMCID: PMC6688129 DOI: 10.3389/fpls.2019.00943] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/08/2019] [Indexed: 05/18/2023]
Abstract
During their evolution, plants have acquired the ability to produce a huge variety of compounds. Unlike the specialized metabolites that accumulate in limited numbers of species, flavonoids are widely distributed in the plant kingdom. Therefore, a detailed analysis of flavonoid metabolism in genomics and metabolomics is an ideal way to investigate how plants have developed their unique metabolic pathways during the process of evolution. More comprehensive and precise metabolite profiling integrated with genomic information are helpful to emerge unexpected gene functions and/or pathways. The distribution of flavonoids and their biosynthetic genes in the plant kingdom suggests that flavonoid biosynthetic pathways evolved through a series of steps. The enzymes that form the flavonoid scaffold structures probably first appeared by recruitment of enzymes from primary metabolic pathways, and later, enzymes that belong to superfamilies such as 2-oxoglutarate-dependent dioxygenase, cytochrome P450, and short-chain dehydrogenase/reductase modified and varied the structures. It is widely accepted that the first two enzymes in flavonoid biosynthesis, chalcone synthase, and chalcone isomerase, were derived from common ancestors with enzymes in lipid metabolism. Later enzymes acquired their function by gene duplication and the subsequent acquisition of new functions. In this review, we describe the recent progress in metabolomics technologies for flavonoids and the evolution of flavonoid skeleton biosynthetic enzymes to understand the complicate evolutionary traits of flavonoid metabolism in plant kingdom.
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94
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Schimmel BCJ, Alba JM, Wybouw N, Glas JJ, Meijer TT, Schuurink RC, Kant MR. Distinct Signatures of Host Defense Suppression by Plant-Feeding Mites. Int J Mol Sci 2018; 19:E3265. [PMID: 30347842 PMCID: PMC6214137 DOI: 10.3390/ijms19103265] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/12/2018] [Accepted: 10/14/2018] [Indexed: 01/09/2023] Open
Abstract
Tomato plants are attacked by diverse herbivorous arthropods, including by cell-content-feeding mites, such as the extreme generalist Tetranychus urticae and specialists like Tetranychus evansi and Aculops lycopersici. Mite feeding induces plant defense responses that reduce mite performance. However, T. evansi and A. lycopersici suppress plant defenses via poorly understood mechanisms and, consequently, maintain a high performance on tomato. On a shared host, T. urticae can be facilitated by either of the specialist mites, likely due to the suppression of plant defenses. To better understand defense suppression and indirect plant-mediated interactions between herbivorous mites, we used gene-expression microarrays to analyze the transcriptomic changes in tomato after attack by either a single mite species (T. urticae, T. evansi, A. lycopersici) or two species simultaneously (T. urticae plus T. evansi or T. urticae plus A. lycopersici). Additionally, we assessed mite-induced changes in defense-associated phytohormones using LC-MS/MS. Compared to non-infested controls, jasmonates (JAs) and salicylate (SA) accumulated to higher amounts upon all mite-infestation treatments, but the response was attenuated after single infestations with defense-suppressors. Strikingly, whereas 8 to 10% of tomato genes were differentially expressed upon single infestations with T. urticae or A. lycopersici, respectively, only 0.1% was altered in T. evansi-infested plants. Transcriptome analysis of dual-infested leaves revealed that A. lycopersici primarily suppressed T. urticae-induced JA defenses, while T. evansi dampened T. urticae-triggered host responses on a transcriptome-wide scale. The latter suggests that T. evansi not solely down-regulates plant gene expression, but rather directs it back towards housekeeping levels. Our results provide valuable new insights into the mechanisms underlying host defense suppression and the plant-mediated facilitation of competing herbivores.
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Affiliation(s)
- Bernardus C J Schimmel
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands.
| | - Juan M Alba
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands.
| | - Nicky Wybouw
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands.
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium.
| | - Joris J Glas
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands.
| | - Tomas T Meijer
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands.
| | - Robert C Schuurink
- Department of Plant Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, P.O. Box 94215, 1090 GE Amsterdam, The Netherlands.
| | - Merijn R Kant
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands.
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95
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Reyes-Rivera J, Soto-Hernández M, Canché-Escamilla G, Terrazas T. Structural Characterization of Lignin in Four Cacti Wood: Implications of Lignification in the Growth Form and Succulence. FRONTIERS IN PLANT SCIENCE 2018; 9:1518. [PMID: 30386367 PMCID: PMC6199501 DOI: 10.3389/fpls.2018.01518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/27/2018] [Indexed: 05/24/2023]
Abstract
Wood lignin composition strongly depends on anatomical features and it has been used as a marker for characterizing major plant groups. Wood heterogeneity in Cactaceae is involved in evolutionary and adaptive processes within this group; moreover, it is highly correlated to the species growth form. Here we studied the lignin structure from different types of woods in four Cactaceae species with different stem morphologies (Pereskia lychnidiflora, tree/fibrous wood; Opuntia streptacantha and Pilosocereus chrysacanthus, tree/succulent fibrous wood; Ferocactus hamatacanthus, cylindrical stem/dimorphic wood) in order to determine their relationship with the wood anatomy in an evolutionary-adaptive context. Dioxane lignin was isolated and analyzed by pyrolysis coupled with gas chromatography and mass spectrometry (Py-GC/MS), two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR) and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). The main linkages are the β-O-4' ether (67-85%), the β-β' resinol (10-26%) and the β-5' and α-O-4' linkages of the phenylcoumaran structures (≤7%). Spirodienone structures have a considerable abundance (5%) in the dimorphic wood of F. hamatacanthus. In addition, low contents (≤3%) of α,β-diaryl ether, α-oxidized β-O-4' ether and dibenzodioxocin structures were found. The sinapyl- and coniferyl acetates are not part of the wood lignin in any of the studied species. The low (≤5%) γ-acetylation in the F. hamatacanthus and P. chrysacanthus wood lignin is here interpreted as an evidence of a high specialization of the wood elements in the conduction/storage of water. The lignin of the studied Cactaceae is composed predominantly of guaiacyl and syringyl units (S/G: 0.9-16.4). High abundance of syringyl units (62-94%) in three of the four species is considered as a defense mechanism against oxidative agents, it is a very conspicuous trait in the most succulent species with dimorphic wood. Furthermore, it is also associated with ferulates and the herein called γ-acetylated guaiacyl-syringaresinol complexes acting as nucleation sites for lignification and as cross-links between lignin and carbohydrates at the wide-band tracheid-fiber junctions.
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Affiliation(s)
- Jorge Reyes-Rivera
- Programa de Botánica, Colegio de Postgraduados en Ciencias Agrícolas, Texcoco, Estado de México, Mexico
| | - Marcos Soto-Hernández
- Programa de Botánica, Colegio de Postgraduados en Ciencias Agrícolas, Texcoco, Estado de México, Mexico
| | | | - Teresa Terrazas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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96
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Dai F, Wang Z, Li Z, Luo G, Wang Y, Tang C. Transcriptomic and proteomic analyses of mulberry (Morus atropurpurea) fruit response to Ciboria carunculoides. J Proteomics 2018; 193:142-153. [PMID: 30315889 DOI: 10.1016/j.jprot.2018.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 09/09/2018] [Accepted: 10/09/2018] [Indexed: 01/09/2023]
Abstract
The aim of this work was to gain insights into the molecular mechanisms and dynamics of the mulberry (Morus atropurpurea) fruit response to Ciboria carunculoides infection. A transcriptomic and proteomic study was carried out based on RNA sequencing and isobaric tags for relative and absolute quantification analysis, respectively. These data were then validated using quantitative real-time PCR and multiple reaction monitoring assays. Comparative analyses revealed that 9.0% of the transcriptome and 20.8% of the proteome were differentially regulated after C. carunculoides infection at the early stage (stage 1) and middle stage (stage 2), but correlation analysis revealed that only 145 genes were differentially regulated at both the transcriptome and proteome levels. The combined transcriptome and proteome analysis showed that plant hormone signal transduction, calcium-mediated defense signaling, transcription factors, and secondary metabolites were stimulated, whereas photosynthesis and cellular growth-related metabolism were suppressed after C. carunculoides infection. These finding provide theoretical foundation for disease resistance breeding of C. carunculoides. BIOLOGICAL SIGNIFICANCE: Ciboria carunculoides is a major fungal pathogen that infects mulberry fruit, leading to extensive damage and productivity loss. Despite this major impact, the mulberry fruit response to C. carunculoides infection has yet to be characterized. This study provides the first system-wide datasets with which to examine changes in the transcriptome and proteome after C. carunculoides infection in mulberry fruit. The results showed that plant hormone signal transduction, calcium-mediated defense signaling, and other pathways were stimulated, whereas photosynthesis and cellular growth-related metabolism were suppressed by C. carunculoides. These results will lead to a better understanding of the molecular mechanisms triggered in mulberry fruit in response to C. carunculoides infection and will provide new molecular targets for regulating defense responses to fungal pathogens in berry fruits.
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Affiliation(s)
- Fanwei Dai
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, China; Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China
| | - Zhenjiang Wang
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, China; Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China
| | - Zhiyi Li
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guoqing Luo
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, China; Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China
| | - Yi Wang
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Cuiming Tang
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, China; Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China.
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97
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Trinh CS, Jeong CY, Lee WJ, Truong HA, Chung N, Han J, Hong SW, Lee H. Paenibacillus pabuli strain P7S promotes plant growth and induces anthocyanin accumulation in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:264-272. [PMID: 29906776 DOI: 10.1016/j.plaphy.2018.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 05/23/2023]
Abstract
In this study, a novel plant growth-promoting rhizobacteria (PGPR), the bacterial strain Paenibacillus pabuli P7S (PP7S), showed promising plant growth-promoting effects. Furthermore, it induced anthocyanin accumulation in Arabidopsis. When co-cultivated with PP7S, there was a significant increase in anthocyanin content and biomass of Arabidopsis seedlings compared with those of the control. The quantitative reverse transcription-polymerase chain reaction analysis revealed higher expression of many key genes regulating anthocyanin and flavonoid biosynthesis pathways in PP7S-treated seedlings when compared with that of the control. Furthermore, higher expression of pathogen-related genes and microbe-associated molecular pattern genes was also observed in response to PP7S, indicating that the PGPR triggered the induced systemic response (ISR) in A. thaliana. These results suggest that PP7S promotes plant growth in A. thaliana and increases anthocyanin biosynthesis by triggering specific ISRs in plant.
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Affiliation(s)
- Cao Son Trinh
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Chan Young Jeong
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea; Odus R&D Center, 262 Daecheong-Ro, Samseong-myeon Eumseong-Gun, Chungcheongbuk-Do 369-830, Republic of Korea
| | - Won Je Lee
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Hai An Truong
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Namhyun Chung
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Juhyeong Han
- Odus R&D Center, 262 Daecheong-Ro, Samseong-myeon Eumseong-Gun, Chungcheongbuk-Do 369-830, Republic of Korea
| | - Suk-Whan Hong
- Department of Molecular Biotechnology, College of Agriculture and Life Sciences, Bioenergy Research Center, Chonnam National University, Gwangju, Republic of Korea
| | - Hojoung Lee
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, Republic of Korea.
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98
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Deng Y, Li C, Li H, Lu S. Identification and Characterization of Flavonoid Biosynthetic Enzyme Genes in Salvia miltiorrhiza (Lamiaceae). Molecules 2018; 23:E1467. [PMID: 29914175 PMCID: PMC6099592 DOI: 10.3390/molecules23061467] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Flavonoids are a class of important secondary metabolites with a broad spectrum of pharmacological functions. Salviamiltiorrhiza Bunge (Danshen) is a well-known traditional Chinese medicinal herb with a broad diversity of flavonoids. However, flavonoid biosynthetic enzyme genes have not been systematically and comprehensively analyzed in S.miltiorrhiza. Through genome-wide prediction and molecular cloning, twenty six flavonoid biosynthesis-related gene candidates were identified, of which twenty are novel. They belong to nine families potentially encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavone synthase (FNS), flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), flavonol synthase (FLS), dihydroflavonol 4-reductase (DFR), and anthocyanidin synthase (ANS), respectively. Analysis of intron/exon structures, features of deduced proteins and phylogenetic relationships revealed the conservation and divergence of S.miltiorrhiza flavonoid biosynthesis-related proteins and their homologs from other plant species. These genes showed tissue-specific expression patterns and differentially responded to MeJA treatment. Through comprehensive and systematic analysis, fourteen genes most likely to encode flavonoid biosynthetic enzymes were identified. The results provide valuable information for understanding the biosynthetic pathway of flavonoids in medicinal plants.
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Affiliation(s)
- Yuxing Deng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151 Malianwa North Road, Haidian District, Beijing 100193, China.
| | - Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151 Malianwa North Road, Haidian District, Beijing 100193, China.
| | - Heqin Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151 Malianwa North Road, Haidian District, Beijing 100193, China.
- College of Agronomy, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao 266109, China.
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No.151 Malianwa North Road, Haidian District, Beijing 100193, China.
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99
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Shi H, Liu G, Wei Y, Chan Z. The zinc-finger transcription factor ZAT6 is essential for hydrogen peroxide induction of anthocyanin synthesis in Arabidopsis. PLANT MOLECULAR BIOLOGY 2018; 97:165-176. [PMID: 29675814 DOI: 10.1007/s11103-018-0730-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/16/2018] [Indexed: 05/20/2023]
Abstract
The accumulation of flavonoids is activated by various abiotic stresses, and the induction of reactive oxygen species (ROS) especially hydrogen peroxide (H2O2) is a general response to abiotic stress in plants. However, the direct link between flavonoids and H2O2 and underlying mechanism remain elusive. In this study, we found that the concentrations of anthocyanin and flavonoids were significantly induced by H2O2 treatment. Furthermore, we found that the transcript level of ZINC FINGER of ARABIDOPSIS THALIANA 6 (ZAT6) was significantly activated after exogenous H2O2 treatment, and modulation of AtZAT6 expression positively affected the concentrations of both anthocyanin and total flavonoids. Notably, exogenous H2O2-induced anthocyanin synthesis was largely alleviated in AtZAT6 knockdown plants, but showed higher level in AtZAT6 overexpressing plants. AtZAT6 directly activated the expressions of TT5, TT7, TT3, TT18, MYB12, and MYB111 through binding to their promoters with TACAAT elements of these genes, and the activation of MYB12 and MYB111 up-regulated the expressions of TT4 and TT6. Taken together, this study indicates that AtZAT6 plays important role in H2O2-activated anthocyanin synthesis, via directly binding to the promoters of several genes that involved in anthocyanin synthesis.
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Affiliation(s)
- Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Zhulong Chan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
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100
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Tohge T, Borghi M, Fernie AR. The natural variance of the Arabidopsis floral secondary metabolites. Sci Data 2018; 5:180051. [PMID: 29611844 PMCID: PMC5881409 DOI: 10.1038/sdata.2018.51] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/07/2018] [Indexed: 12/15/2022] Open
Abstract
Application of mass spectrometry-based metabolomics enables the detection of genotype-related natural variance in metabolism. Differences in secondary metabolite composition of flowers of 64 Arabidopsis thaliana (Arabidopsis) natural accessions, representing a considerable portion of the natural variation in this species are presented. The raw metabolomic data of the accessions and reference extracts derived from flavonoid knockout mutants have been deposited in the MetaboLights database. Additionally, summary tables of floral secondary metabolite data are presented in this article to enable efficient re-use of the dataset either in metabolomics cross-study comparisons or correlation-based integrative analysis of other metabolomic and phenotypic features such as transcripts, proteins and growth and flowering related phenotypes.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Monica Borghi
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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