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Yuan J, Zhang X, Zhang X, Sun Y, Liu C, Li S, Yu Y, Zhang C, Jin S, Wang M, Xiang J, Li F. An ancient whole-genome duplication in barnacles contributes to their diversification and intertidal sessile life adaptation. J Adv Res 2024; 62:91-103. [PMID: 37734567 DOI: 10.1016/j.jare.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023] Open
Abstract
INTRODUCTION Whole-genome duplication (WGD) is one of the most sudden and dramatic events rarely reported in invertebrates, but its occurrence can lead to physiological, morphological, and behavioral diversification. WGD has also never been reported in barnacles, which is one of the most unique groups of crustaceans with extremely speciallized morphology (calcareous shells) and habits (intertidal sessile lifestyle). OBJECTIVES To investigate whether WGD has occurred in barnacles and examine its potential role in driving the adaptive evolution and diversification of barnacles. METHODS Based on a newly sequenced and assembled chromosome-level barnacle genome, a novel WGD event has been identified in barnacles through a comprehensive analysis of interchromosomal synteny, the Hox gene cluster, and synonymous substitution distribution. RESULTS We provide ample evidences for WGD in the barnacle genomes. Comparative genomic analysis indicates that this WGD event predates the divergence of Thoracicalcarea, occurring more than 247 million years ago. The retained ohnologs from the WGD are primarily enriched in various pathways related to environmental information processing, shedding light on the adaptive evolution and diversification of intertidal sessile lifestyle. In addition, transcriptomic analyses show that most of these ohnologs were differentially expressed following the ebb of tide. And the cytochrome P450 ohnologs with differential expression patterns are subject to subfunctionalization and/or neofunctionalization for intertidal adaptation. Besides WGD, parallel evolution underlying intertidal adaptation has also occurred in barnacles. CONCLUSION This study revealed an ancient WGD event in the barnacle genomes, which is potentially associated with the origin and diversification of thoracican barnacles, and may have contributed to the adaptive evolution of their intertidal sessile lifestyle.
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Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yamin Sun
- Research Center for Functional Genomics and Biochip, Tianjin 300457, China
| | - Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chengsong Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Songjun Jin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Min Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China.
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Huang Y, Zhai L, Chai X, Liu Y, Lv J, Pi Y, Gao B, Wang X, Wu T, Zhang X, Han Z, Wang Y. Bacillus B2 promotes root growth and enhances phosphorus absorption in apple rootstocks by affecting MhMYB15. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38924231 DOI: 10.1111/tpj.16893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/13/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Due to the chelation of phosphorus in the soil, it becomes unavailable for plant growth and development. The mechanisms by which phosphorus-solubilizing bacteria activate immobilized phosphorus to promote the growth and development of woody plants, as well as the intrinsic molecular mechanisms, are not clear. Through the analysis of microbial communities in the rhizosphere 16S V3-V4 and a homologous gene encoding microbial alkaline phosphomonoesterase (phoD) in phosphate-efficient (PE) and phosphate-inefficient apple rootstocks, it was found that PE significantly enriched beneficial rhizobacteria. The best phosphorus-solubilizing bacteria, Bacillus sp. strain 7DB1 (B2), was isolated, purified, and identified from the rhizosphere soil of PE rootstocks. Incubating with Bacillus B2 into the rhizosphere of apple rootstocks significantly increased the soluble phosphorus and flavonoid content in the rhizosphere soil. Simultaneously, this process stimulates the root development of the rootstocks and enhances plant phosphorus uptake. After root transcriptome sequencing, candidate transcription factor MhMYB15, responsive to Bacillus B2, was identified through heatmap and co-expression network analysis. Yeast one-hybrid, electrophoretic mobility shift assay, and LUC assay confirmed that MhMYB15 can directly bind to the promoter regions of downstream functional genes, including chalcone synthase MhCHS2 and phosphate transporter MhPHT1;15. Transgenic experiments with MhMYB15 revealed that RNAi-MhMYB15 silenced lines failed to induce an increase in flavonoid content and phosphorus levels in the roots under the treatment of Bacillus B2, and plant growth was slower than the control. In conclusion, MhMYB15 actively responds to Bacillus B2, regulating the accumulation of flavonoids and the uptake of phosphorus, thereby influencing plant growth and development.
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Affiliation(s)
- Yimei Huang
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Longmei Zhai
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Xiaofen Chai
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Yao Liu
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Jiahong Lv
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Ying Pi
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Beibei Gao
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Xiaona Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
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Fiesel PD, Kerwin RE, Daniel Jones A, Last RL. Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.05.542877. [PMID: 37333341 PMCID: PMC10274652 DOI: 10.1101/2023.06.05.542877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by AcylSugar AcylTransferases from sugars and acyl-coenzyme A esters. Published research revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars were analyzed across a small fraction of the >1200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of the Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the Clade II species Solanum melongena (brinjal eggplant) led to the identification of eight unusual structures with inositol or inositol glycoside cores, and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the S. melongena AcylSugar AcylTransferase 3-Like 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.
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Affiliation(s)
- Paul D. Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
| | - Rachel E. Kerwin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
| | - A. Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823 USA
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Ricardo F, Veríssimo AC, Maciel E, Domingues MR, Calado R. Fatty Acid Profiling as a Tool for Fostering the Traceability of the Halophyte Plant Salicornia ramosissima and Contributing to Its Nutritional Valorization. PLANTS (BASEL, SWITZERLAND) 2024; 13:545. [PMID: 38498533 PMCID: PMC10891689 DOI: 10.3390/plants13040545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 03/20/2024]
Abstract
Salicornia ramosissima, commonly known as glasswort or sea asparagus, is a halophyte plant cultivated for human consumption that is often referred to as a sea vegetable rich in health-promoting n-3 fatty acids (FAs). Yet, the effect of abiotic conditions, such as salinity and temperature, on the FA profile of S. ramosissima remains largely unknown. These factors can potentially shape its nutritional composition and yield unique fatty acid signatures that can reveal its geographical origin. In this context, samples of S. ramosissima were collected from four different locations along the coastline of mainland Portugal and their FAs were profiled through gas chromatography-mass spectrometry. The lipid extracts displayed a high content of essential FAs, such as 18:2n-6 and 18:3n-3. In addition to an epoxide fatty acid exclusively identified in samples from the Mondego estuary, the relative abundance of FAs varied between origin sites, revealing that FA profiles can be used as site-specific lipid fingerprints. This study highlights the role of abiotic conditions on the nutritional profile of S. ramosissima and establishes FA profiling as a potential avenue to trace the geographic origin of this halophyte plant. Overall, the present approach can make origin certification possible, safeguard quality, and enhance consumers' trust in novel foods.
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Affiliation(s)
- Fernando Ricardo
- Laboratório para a Inovação e Sustentabilidade dos Recursos Biológicos Marinhos (ECOMARE), Centro de Estudos do Ambiente e do Mar (CESAM), Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana Carolina Veríssimo
- Centro de Estudos do Ambiente e do Mar (CESAM), Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (A.C.V.); (E.M.)
- Laboratório Associado para a Química Verde (LAQV-REQUIMTE), Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Elisabete Maciel
- Centro de Estudos do Ambiente e do Mar (CESAM), Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (A.C.V.); (E.M.)
| | - Maria Rosário Domingues
- Centro de Estudos do Ambiente e do Mar (CESAM), Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (A.C.V.); (E.M.)
- Centro de Espetrometria de Massa, Laboratório Associado para a Química Verde (LAQV-REQUIMTE), Departamento de Química, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ricardo Calado
- Laboratório para a Inovação e Sustentabilidade dos Recursos Biológicos Marinhos (ECOMARE), Centro de Estudos do Ambiente e do Mar (CESAM), Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Wei L, Yang C, John Martin JJ, Li R, Zhou L, Cheng S, Cao H, Liu X. Metabonomics and Transcriptomic Analysis of Free Fatty Acid Synthesis in Seedless and Tenera Oil Palm. Int J Mol Sci 2024; 25:1686. [PMID: 38338979 PMCID: PMC10855455 DOI: 10.3390/ijms25031686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Oil palm, a tropical woody oil crop, is widely used in food, cosmetics, and pharmaceuticals due to its high production efficiency and economic value. Palm oil is rich in free fatty acids, polyphenols, vitamin E, and other nutrients, which are beneficial for human health when consumed appropriately. Therefore, investigating the dynamic changes in free fatty acid content at different stages of development and hypothesizing the influence of regulatory genes on free fatty acid metabolism is crucial for improving palm oil quality and accelerating industry growth. LC-MS/MS is used to analyze the composition and content of free fatty acids in the flesh after 95 days (MS1 and MT1), 125 days (MS2 and MT2), and 185 days (MS3 and MT3) of Seedless (MS) and Tenera (MT) oil palm species fruit pollination. RNA-Seq was used to analyze the expression of genes regulating free fatty acid synthesis and accumulation, with differences in genes and metabolites mapped to the KEGG pathway map using the KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis method. A metabolomics study identified 17 types of saturated and 13 types of unsaturated free fatty acids during the development of MS and MT. Transcriptomic research revealed that 10,804 significantly different expression genes were acquired in the set differential gene threshold between MS and MT. The results showed that FabB was positively correlated with the contents of three main free fatty acids (stearic acid, myristate acid, and palmitic acid) and negatively correlated with the contents of free palmitic acid in the flesh of MS and MT. ACSL and FATB were positively correlated with the contents of three main free fatty acids and negatively correlated with free myristate acid. The study reveals that the expression of key enzyme genes, FabB and FabF, may improve the synthesis of free myristate in oil palm flesh, while FabF, ACSL, and FATB genes may facilitate the production of free palmitoleic acid. These genes may also promote the synthesis of free stearic acid and palmitoleic acid in oil palm flesh. However, the FabB gene may inhibit stearic acid synthesis, while ACSL and FATB genes may hinder myristate acid production. This study provides a theoretical basis for improving palm oil quality.
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Affiliation(s)
- Lu Wei
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
- School of Horticulture, Hainan University, Haikou 570228, China
| | - Cheng Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Jerome Jeyakumar John Martin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Rui Li
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Shuanghong Cheng
- College of Tropical Crops, Yunnan Agricultural University, Pu’er 665000, China;
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Xiaoyu Liu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
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Yadav M, Panwar R, Rustagi A, Chakraborty A, Roy A, Singh IK, Singh A. Comprehensive and evolutionary analysis of Spodoptera litura-inducible Cytochrome P450 monooxygenase gene family in Glycine max elucidate their role in defense. FRONTIERS IN PLANT SCIENCE 2023; 14:1221526. [PMID: 38023937 PMCID: PMC10654349 DOI: 10.3389/fpls.2023.1221526] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023]
Abstract
Plants being sessile organisms and lacking both circulating phagocytic cells and somatic adaptive immune response, have thrived on various defense mechanisms to fend off insect pests and invasion of pathogens. CYP450s are the versatile enzymes, which thwart plants against insect pests by ubiquitous biosynthesis of phytohormones, antioxidants, and secondary metabolites, utilizing them as feeding deterrents and direct toxins. Therefore, a comprehensive analysis of biotic stress-responsive CYPs from Glycine max was performed to ascertain their function against S. litura-infestation. Phylogenetic analysis and evolutionary studies on conserved domains and motifs disclosed the evolutionary correspondence of these GmCYPs with already characterized members of the CYP450 superfamily and close relatedness to Medicago truncatula. These GmCYPs were mapped on 13 chromosomes; they possess 1-8 exons; they have evolved due to duplication and are localized in endoplasmic reticulumn. Further, identification of methyl-jasmonate, salicylic acid, defense responsive and flavonoid biosynthesis regulating cis-acting elements, their interaction with biotic stress regulating proteins and their differential expression in diverse types of tissues, and during herbivory, depicted their responsiveness to biotic stress. Three-dimensional homology modelling of GmCYPs, docking with heme cofactor required for their catalytic activity and enzyme-substrate interactions were performed to understand the functional mechanism of their action. Moreover, to gain insight into their involvement in plant defense, gene expression analysis was evaluated, which revealed differential expression of 11 GmCYPs upon S. litura-infestation, 12 GmCYPs on wounding while foliar spray of ethylene, methyl-jasmonate and salicylic acid differentially regulated 11 GmCYPs, 6 GmCYPs, and 10 GmCYPs respectively. Our study comprehensively analysed the underlying mechanism of GmCYPs function during S. litura-infestation, which can be further utilized for functional characterization to develop new strategies for enhancing soybean resistance to insect pests.
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Affiliation(s)
- Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
| | - Ruby Panwar
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Anjana Rustagi
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Amrita Chakraborty
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Amit Roy
- Forest Molecular Entomology Lab, EXTEMIT-K, EVA 4.0, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Department of Botany, Gargi College, University of Delhi, Delhi, India
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
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Cunha E, Silva M, Chaves I, Demirci H, Lagoa DR, Lima D, Rocha M, Rocha I, Dias O. The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS Comput Biol 2023; 19:e1011499. [PMID: 37729340 PMCID: PMC10545120 DOI: 10.1371/journal.pcbi.1011499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/02/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
Over the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behaviour at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871). The metabolic model comprises 7871 genes, 6231 reactions, and 6481 metabolites across eight compartments. Transcriptomics data was integrated into the model to obtain tissue-specific models for the leaf, inner bark, and phellogen, with specific biomass compositions. The tissue-specific models were merged into a diel multi-tissue metabolic model to predict interactions among the three tissues at the light and dark phases. The metabolic models were also used to analyse the pathways associated with the synthesis of suberin monomers, namely the acyl-lipids, phenylpropanoids, isoprenoids, and flavonoids production. The models developed in this work provide a systematic overview of the metabolism of Q. suber, including its secondary metabolism pathways and cork formation.
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Affiliation(s)
- Emanuel Cunha
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
| | - Miguel Silva
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
| | - Inês Chaves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, Oeiras, Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Huseyin Demirci
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
- SnT/University of Luxembourg, Luxembourg
| | | | - Diogo Lima
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga, Guimarães, Portugal
| | - Isabel Rocha
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, Oeiras, Portugal
| | - Oscar Dias
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga, Guimarães, Portugal
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Chakraborty P, Biswas A, Dey S, Bhattacharjee T, Chakrabarty S. Cytochrome P450 Gene Families: Role in Plant Secondary Metabolites Production and Plant Defense. J Xenobiot 2023; 13:402-423. [PMID: 37606423 PMCID: PMC10443375 DOI: 10.3390/jox13030026] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
Cytochrome P450s (CYPs) are the most prominent family of enzymes involved in NADPH- and O2-dependent hydroxylation processes throughout all spheres of life. CYPs are crucial for the detoxification of xenobiotics in plants, insects, and other organisms. In addition to performing this function, CYPs serve as flexible catalysts and are essential for producing secondary metabolites, antioxidants, and phytohormones in higher plants. Numerous biotic and abiotic stresses frequently affect the growth and development of plants. They cause a dramatic decrease in crop yield and a deterioration in crop quality. Plants protect themselves against these stresses through different mechanisms, which are accomplished by the active participation of CYPs in several biosynthetic and detoxifying pathways. There are immense potentialities for using CYPs as a candidate for developing agricultural crop species resistant to biotic and abiotic stressors. This review provides an overview of the plant CYP families and their functions to plant secondary metabolite production and defense against different biotic and abiotic stresses.
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Affiliation(s)
- Panchali Chakraborty
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA;
| | - Ashok Biswas
- Annual Bast Fiber Breeding Laboratory, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
- Department of Horticulture, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Susmita Dey
- Annual Bast Fiber Breeding Laboratory, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
- Department of Plant Pathology and Seed Science, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tuli Bhattacharjee
- Department of Chemistry, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Swapan Chakrabarty
- College of Forest Resources and Environmental Sciences, Michigan Technological University, Houghton, MI 49931, USA
- College of Computing, Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
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9
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Das A, Begum K, Akhtar S, Ahmed R, Tamuli P, Kulkarni R, Banu S. Genome-wide investigation of Cytochrome P450 superfamily of Aquilaria agallocha: Association with terpenoids and phenylpropanoids biosynthesis. Int J Biol Macromol 2023; 234:123758. [PMID: 36812976 DOI: 10.1016/j.ijbiomac.2023.123758] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 01/12/2023] [Accepted: 02/11/2023] [Indexed: 02/22/2023]
Abstract
Agarwood is a dark resinous wood, produced when Aquilaria tree responds to wounding and microbial infection resulting in the accumulation of fragrant metabolites. Sesquiterpenoids and 2-(2-phenylethyl) chromones are the major phytochemicals in agarwood and Cytochrome P450s (CYPs) are one of the important enzymes in the biosynthesis of these fragrant chemicals. Thus, understanding the repertoire of CYP superfamily in Aquilaria can not only give insights into the fundamentals of agarwood formation, but can also provide a tool for the overproduction of the aroma chemicals. Therefore, current study was designed to investigate CYPs of an agarwood producing plant, Aquilaria agallocha. We identified 136 CYP genes from A. agallocha genome (AaCYPs) and classified them into 8 clans and 38 families. The promoter regions had stress and hormone-related cis-regulatory elements which indicate their participation in the stress response. Duplication and synteny analysis revealed segmental and tandem duplicated and evolutionary related CYP members in other plants. Potential members involved in the biosynthesis of sesquiterpenoids and phenylpropanoids were identified and found to be upregulated in methyl jasmonate-induced callus and infected Aquilaria trees by real-time quantitative PCR analyses. This study highlights the possible involvement of AaCYPs in agarwood resin development and their complex regulation during stress exposure.
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Affiliation(s)
- Ankur Das
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Khaleda Begum
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Suraiya Akhtar
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Raja Ahmed
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | | | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 411042, India
| | - Sofia Banu
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India.
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10
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Zhang J, Liu ZY, Zhang YF, Zhang C, Li X, Liu X, Wang CL. PpyMYB144 transcriptionally regulates pear fruit skin russeting by activating the cytochrome P450 gene PpyCYP86B1. PLANTA 2023; 257:69. [PMID: 36854938 DOI: 10.1007/s00425-023-04102-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
PpyMYB144 directly activates the promoter of PpyCYP86B1, promotes the synthesis of α, ω-diacids, and involves in pear fruit skin russeting. Russeting is an economically important surface disorder in pear (Pyrus pyrifolia) fruit. Previous research has demonstrated that suberin is the pivotal chemical component contributing to pear fruit skin russeting, and fruit bagging treatment effectively reduces the amount of suberin of fruits, and thereby reduces the russeting phenotype. However, the mechanisms of pear fruit skin russeting remain largely unclear, particularly the transcriptional regulation. Here, we dissected suberin concentration and composition of pear fruits along fruit development and confirmed that α, ω-diacids are the predominant constituents in russeted pear fruit skins. Two cytochrome P450 monooxygenase (CYP) family genes (PpyCYP86A1 and PpyCYP86B1) and nine MYB genes were isolated from pear fruit. Expressions of PpyCYP86A1, PpyCYP86B1, and five MYB genes (PpyMYB34, PpyMYB138, PpyMYB138-like, PpyMYB139, and PpyMYB144) were up-regulated during fruit russeting and showed significant correlations with the changes of α, ω-diacids. In addition, dual-luciferase assays indicated that PpyMYB144 could trans-activate the promoter of PpyCYP86B1, and the activation was abolished by motif mutagenesis of AC element on the PpyCYP86B1 promoter. Further, Agrobacterium-mediated transient expression of PpyCYP86B1 and PpyMYB144 in pear fruits induced the deposition of aliphatic suberin. Thus, PpyMYB144 is a novel direct activator of PpyCYP86B1 and contributes to pear fruit skin russeting.
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Affiliation(s)
- Jing Zhang
- College of Horticulture and Landscape Architecture, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, People's Republic of China
| | - Zi-Yu Liu
- College of Horticulture and Landscape Architecture, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, People's Republic of China
| | - Yi-Fan Zhang
- College of Horticulture and Landscape Architecture, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, People's Republic of China
| | - Chen Zhang
- College of Horticulture and Landscape Architecture, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, People's Republic of China
| | - Xi Li
- College of Horticulture and Landscape Architecture, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, People's Republic of China
| | - Xiao Liu
- College of Horticulture and Landscape Architecture, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, People's Republic of China
| | - Chun-Lei Wang
- College of Horticulture and Landscape Architecture, International Research Laboratory of Agriculture and Agri-Product Safety, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, People's Republic of China.
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11
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Teixeira RT. Cork Development: What Lies Within. PLANTS (BASEL, SWITZERLAND) 2022; 11:2671. [PMID: 36297695 PMCID: PMC9611905 DOI: 10.3390/plants11202671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/16/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
The cork layer present in all dicotyledonous plant species with radial growth is the result of the phellogen activity, a secondary meristem that produces phellem (cork) to the outside and phelloderm inwards. These three different tissues form the periderm, an efficient protective tissue working as a barrier against external factors such as environmental aggressions and pathogen attacks. The protective function offered by cork cells is mainly due to the abundance of suberin in their cell walls. Chemically, suberin is a complex aliphatic network of long chain fatty acids and alcohols with glycerol together with aromatic units. In most woody species growing in temperate climates, the first periderm is replaced by a new functional periderm upon a few years after being formed. One exception to this bark development can be found in cork oak (Quercus suber) which display a single periderm that grows continuously. Quercus suber stands by its thick cork layer development with continuous seasonal growth. Cork raw material has been exploited by man for centuries, especially in Portugal and Spain. Nowadays, its applications have widened vastly, from the most known product, stoppers, to purses or insulating materials used in so many industries, such as construction and car production. Research on how cork develops, and the effect environmental factors on cork oak trees is extremely important to maintain production of good-quality cork, and, by maintaining cork oak stands wealthy, we are preserving a very important ecosystem both by its biodiversity and its vital social and economic role in areas already showing a population declination.
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Affiliation(s)
- Rita Teresa Teixeira
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
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12
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Kaashyap M, Kaur S, Ford R, Edwards D, Siddique KH, Varshney RK, Mantri N. Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non-polyadenylated flower lncRNAs in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1402-1416. [PMID: 35395125 PMCID: PMC9241372 DOI: 10.1111/pbi.13822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/26/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Salinity severely affects the yield of chickpea. Understanding the role of lncRNAs can shed light on chickpea salt tolerance mechanisms. However, because lncRNAs are encoded by multiple sites within the genome, their classification to reveal functional versatility at the transcriptional and the post-transcriptional levels is challenging. To address this, we deep sequenced 24 salt-challenged flower transcriptomes from two parental genotypes of a RIL population that significantly differ in salt tolerance ability. The transcriptomes for the first time included 12 polyadenylated and 12 non-polyadenylated RNA libraries to a sequencing depth of ~50 million reads. The ab initio transcriptome assembly comprised ~34 082 transcripts from three biological replicates of salt-tolerant (JG11) and salt-sensitive (ICCV2) flowers. A total of 9419 lncRNAs responding to salt stress were identified, 2345 of which were novel lncRNAs specific to chickpea. The expression of poly(A+) lncRNAs and naturally antisense transcribed RNAs suggest their role in post-transcriptional modification and gene silencing. Notably, 178 differentially expressed lncRNAs were induced in the tolerant genotype but repressed in the sensitive genotype. Co-expression network analysis revealed that the induced lncRNAs interacted with the FLOWERING LOCUS (FLC), chromatin remodelling and DNA methylation genes, thus inducing flowering during salt stress. Furthermore, 26 lncRNAs showed homology with reported lncRNAs such as COOLAIR, IPS1 and AT4, thus confirming the role of chickpea lncRNAs in controlling flowering time as a crucial salt tolerance mechanism in tolerant chickpea genotype. These robust set of differentially expressed lncRNAs provide a deeper insight into the regulatory mechanisms controlled by lncRNAs under salt stress.
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Affiliation(s)
- Mayank Kaashyap
- The Pangenomics LabSchool of ScienceRMIT UniversityMelbourneVICAustralia
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Sukhjiwan Kaur
- Department of Economic DevelopmentJobs, Transport and ResourcesAgriBioCentre for AgriBioscienceMelbourneVICAustralia
| | - Rebecca Ford
- School of Environment and ScienceGriffith UniversityNathanQLDAustralia
| | - David Edwards
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | | | - Rajeev K. Varshney
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruTelanganaIndia
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWAAustralia
| | - Nitin Mantri
- The Pangenomics LabSchool of ScienceRMIT UniversityMelbourneVICAustralia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
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13
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Santos P, Busta L, Yim WC, Cahoon EB, Kosma DK. Structural diversity, biosynthesis, and function of plant falcarin-type polyacetylenic lipids. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2889-2904. [PMID: 35560192 DOI: 10.1093/jxb/erac006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/10/2022] [Indexed: 06/15/2023]
Abstract
The polyacetylenic lipids falcarinol, falcarindiol, and associated derivatives, termed falcarins, have a widespread taxonomical distribution in the plant kingdom and have received increasing interest for their demonstrated health-promoting properties as anti-cancer and anti-inflammatory agents. These fatty acid-derived compounds are also linked to plant pathogen resistance through their potent antimicrobial properties. Falcarin-type polyacetylenes, which contain two conjugated triple bonds, are derived from structural modifications of the common fatty acid oleic acid. In the past half century, much progress has been made in understanding the structural diversity of falcarins in the plant kingdom, whereas limited progress has been made on elucidating falcarin function in plant-pathogen interactions. More recently, an understanding of the biosynthetic machinery underlying falcarin biosynthesis has emerged. This review provides a concise summary of the current state of knowledge on falcarin structural diversity, biosynthesis, and plant defense properties. We also present major unanswered questions about falcarin biosynthesis and function.
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Affiliation(s)
- Patrícia Santos
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Edgar B Cahoon
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
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14
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Liu J, Dong L, Duan R, Hu L, Zhao Y, Zhang L, Wang X. Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:876371. [PMID: 35646018 PMCID: PMC9134122 DOI: 10.3389/fpls.2022.876371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is one of the most important crops, which produces about 25% of the world's edible oil. The nutritional value of soybean oil depends mostly on the relative contents of three unsaturated fatty acids (UFAs), i.e., oleic acid, linoleic acid (LA), and linolenic acid. However, the biosynthetic mechanism of UFAs remains largely unknown, and there are few studies on RNA-seq analysis of developing seeds. To identify the candidate genes and related pathways involved in the regulation of UFA contents during seed development in soybean, two soybean lines with different UFA profiles were selected from 314 cultivars and landraces originated from Southern China, and RNA-seq analysis was performed in soybean seeds at three developmental stages. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a series of genes and pathways related to fatty acid metabolism were identified, and 40 days after flowering (DAF) was found to be the crucial period in the formation of UFA profiles. Further, weighted gene co-expression network analysis identified three modules with six genes whose functions were highly associated with the contents of oleic and LA. The detailed functional investigation of the networks and hub genes could further improve the understanding of the underlying molecular mechanism of UFA contents and might provide some ideas for the improvement in fatty acids profiles in soybean.
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Affiliation(s)
- Junqi Liu
- School of Agriculture, Yunnan University, Kunming, China
| | - Liang Dong
- School of Agriculture, Yunnan University, Kunming, China
| | - Runqing Duan
- School of Agriculture, Yunnan University, Kunming, China
| | - Li Hu
- School of Agriculture, Yunnan University, Kunming, China
| | - Yinyue Zhao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Liang Zhang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xianzhi Wang
- School of Agriculture, Yunnan University, Kunming, China
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15
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Yang J, Li H, Ma R, Chang Y, Qin X, Xu J, Fu Y. Genome-wide transcriptome analysis and characterization of the cytochrome P450 flavonoid biosynthesis genes in pigeon pea (Cajanus cajan). PLANTA 2022; 255:120. [PMID: 35538269 DOI: 10.1007/s00425-022-03896-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
226 CcCYP450 genes were identified at the genomic level and were classified into 45 clades based on phylogenetic analysis. CcCYP75B165 gene was found that might play important roles in the biosynthesis of flavonoids in pigeon pea, and was significantly induced by methyl jasmonate (MeJA). The cytochrome P450 mono-oxygenase (CYP450) superfamily plays a key role in the flavonoid biosynthesis pathway and resists different kinds of stresses. Several CYP450 genes have been identified to be involved in the biosynthesis of crop protection agents. However, the CcCYP450 genes from pigeon pea have not been identified. Here, 226 CcCYP450 genes were identified at the genomic level by analysing the gene structure, distribution on chromosomes, gene duplication, and conserved motifs and were classified into 45 clades based on phylogenetic analysis. RNA-seq analysis revealed clear details of CcCYP450 genes that varied with time of MeJA (methyl jasmonate) induction. Among them, six CcCYP450 subfamily genes were found that might play important roles in the biosynthesis of flavonoids in pigeon pea. The overexpression of CcCYP75B165 in pigeon pea significantly induced the accumulation of genistin and downregulated the contents of cajaninstilbene acid, apigenin, isovitexin, and genistein and the expression of flavonoid synthase genes. This study provides theoretical guidance and plant genetic resources for cultivating new pigeon pea varieties with high flavonoid contents and exploring the molecular mechanisms of the biosynthesis of flavonoids under MeJA treatment.
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Affiliation(s)
- Jie Yang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Hongquan Li
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Ruijin Ma
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Yuanhang Chang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Xiangyu Qin
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Jian Xu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, China
| | - Yujie Fu
- College of Forestry, Beijing Forestry University, Beijing, 100083, China.
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Price CL, Warrilow AGS, Rolley NJ, Parker JE, Thoss V, Kelly DE, Corcionivoschi N, Kelly SL. Cytochrome P450 168A1 from Pseudomonas aeruginosa is involved in the hydroxylation of biologically relevant fatty acids. PLoS One 2022; 17:e0265227. [PMID: 35312722 PMCID: PMC8936499 DOI: 10.1371/journal.pone.0265227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 02/24/2022] [Indexed: 11/26/2022] Open
Abstract
The cytochrome P450 CYP168A1 from Pseudomonas aeruginosa was cloned and expressed in Escherichia coli followed by purification and characterization of function. CYP168A1 is a fatty acid hydroxylase that hydroxylates saturated fatty acids, including myristic (0.30 min-1), palmitic (1.61 min-1) and stearic acids (1.24 min-1), at both the ω-1- and ω-2-positions. However, CYP168A1 only hydroxylates unsaturated fatty acids, including palmitoleic (0.38 min-1), oleic (1.28 min-1) and linoleic acids (0.35 min-1), at the ω-1-position. CYP168A1 exhibited a catalytic preference for palmitic, oleic and stearic acids as substrates in keeping with the phosphatidylcholine-rich environment deep in the lung that is colonized by P. aeruginosa.
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Affiliation(s)
- Claire L. Price
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Andrew G. S. Warrilow
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Nicola J. Rolley
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Josie E. Parker
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Vera Thoss
- Plant Chemistry Group, School of Chemistry, Bangor University, Bangor, Gwynedd, Wales, United Kingdom
| | - Diane E. Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
| | - Nicolae Corcionivoschi
- Agri-Food and Biosciences Institute, Veterinary Science Division, Bacteriology Branch, Stoney Road, Stormont, Belfast, Northern Ireland, United Kingdom
- Faculty of Bioengineering of Animal Resources, Banat University of Agricultural Sciences and Veterinary Medicine, King Michael I of Romania, Timisoara, Romania
| | - Steven L. Kelly
- Centre for Cytochrome P450 Biodiversity, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales, United Kingdom
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17
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Overexpression of the Panax ginseng CYP703 Alters Cutin Composition of Reproductive Tissues in Arabidopsis. PLANTS 2022; 11:plants11030383. [PMID: 35161364 PMCID: PMC8839735 DOI: 10.3390/plants11030383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/16/2022]
Abstract
Cytochrome P450 (CYP) catalyzes a wide variety of monooxygenation reactions in plant primary and secondary metabolisms. Land plants contain CYP703, belonging to the CYP71 clan, which catalyzes the biochemical pathway of fatty acid hydroxylation, especially in male reproductive tissues. Korean/Asian ginseng (Panax ginseng Meyer) has been regarded as one of important medicinal plant for a long time, however the molecular mechanism is less known on its development. In this study, we identified and characterized a CYP703A gene in P. ginseng (PgCYP703A4), regarding reproductive development. PgCYP703A4 shared a high-sequence identity (81–83%) with predicted amino acid as CYP703 in Dancus carota, Pistacia vera, and Camellia sinensis as well as 76% of amino acid sequence identity with reported CYP703 in Arabidopsis thaliana and 75% with Oryza sativa. Amino acid alignment and phylogenetic comparison of P. ginseng with higher plants and known A. thaliana members clearly distinguish the CYP703 members, each containing the AATDTS oxygen binding motif and PERH as a clade signature. The expression of PgCYP704B1 was only detected in P. ginseng flower buds, particularly in meiotic cells and the tapetum layer of developing anther, indicating the conserved role on male reproduction with At- and Os- CYP703. To acquire the clue of function, we transformed the PgCYP703A4 in A. thaliana. Independent overexpressing lines (PgCYP703A4ox) increased silique size and seed number, and altered the contents of fatty acids composition of cutin monomer in the siliques. Our results indicate that PgCYP703A4 is involved in fatty acid hydroxylation which affects cutin production and fruit size.
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18
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Tente E, Ereful N, Rodriguez AC, Grant P, O'Sullivan DM, Boyd LA, Gordon A. Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot. BMC PLANT BIOLOGY 2021; 21:316. [PMID: 34215204 PMCID: PMC8252325 DOI: 10.1186/s12870-021-03086-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/07/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Ergot, caused by the fungal pathogen Claviceps purpurea, infects the female flowers of a range of cereal crops, including wheat. To understand the interaction between C. purpurea and hexaploid wheat we undertook an extensive examination of the reprogramming of the wheat transcriptome in response to C. purpurea infection through floral tissues (i.e. the stigma, transmitting and base ovule tissues of the ovary) and over time. RESULTS C. purpurea hyphae were observed to have grown into and down the stigma at 24 h (H) after inoculation. By 48H hyphae had grown through the transmitting tissue into the base, while by 72H hyphae had surrounded the ovule. By 5 days (D) the ovule had been replaced by fungal tissue. Differential gene expression was first observed at 1H in the stigma tissue. Many of the wheat genes differentially transcribed in response to C. purpurea infection were associated with plant hormones and included the ethylene (ET), auxin, cytokinin, gibberellic acid (GA), salicylic acid and jasmonic acid (JA) biosynthetic and signaling pathways. Hormone-associated genes were first detected in the stigma and base tissues at 24H, but not in the transmitting tissue. Genes associated with GA and JA pathways were seen in the stigma at 24H, while JA and ET-associated genes were identified in the base at 24H. In addition, several defence-related genes were differential expressed in response to C. purpurea infection, including antifungal proteins, endocytosis/exocytosis-related proteins, NBS-LRR class proteins, genes involved in programmed cell death, receptor protein kinases and transcription factors. Of particular interest was the identification of differential expression of wheat genes in the base tissue well before the appearance of fungal hyphae, suggesting that a mobile signal, either pathogen or plant-derived, is delivered to the base prior to colonisation. CONCLUSIONS Multiple host hormone biosynthesis and signalling pathways were significantly perturbed from an early stage in the wheat - C. purpurea interaction. Differential gene expression at the base of the ovary, ahead of arrival of the pathogen, indicated the potential presence of a long-distance signal modifying host gene expression.
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Affiliation(s)
- Eleni Tente
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Nelzo Ereful
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- Philippine Genome Center, Plant Physiology Laboratory, Institute of Plant Breeding, University of the Philippines, Los Baños, Laguna, The Philippines
| | | | - Paul Grant
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
- Present Address: Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK
| | - Lesley A Boyd
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
| | - Anna Gordon
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
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19
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Krishnamurthy P, Vishal B, Bhal A, Kumar PP. WRKY9 transcription factor regulates cytochrome P450 genes CYP94B3 and CYP86B1, leading to increased root suberin and salt tolerance in Arabidopsis. PHYSIOLOGIA PLANTARUM 2021; 172:1673-1687. [PMID: 33619745 DOI: 10.1111/ppl.13371] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/08/2021] [Accepted: 02/12/2021] [Indexed: 05/27/2023]
Abstract
Salinity affects crop productivity worldwide and mangroves growing under high salinity exhibit adaptations such as enhanced root apoplastic barrier to survive under such conditions. We have identified two cytochrome P450 family genes, AoCYP94B3 and AoCYP86B1 from the mangrove tree Avicennia officinalis and characterized them using atcyp94b3 and atcyp86b1, which are mutants of their putative Arabidopsis orthologs and the corresponding complemented lines with A. officinalis genes. CYP94B3 and CYP86B1 transcripts were induced upon salt treatment in the roots of both A. officinalis and Arabidopsis. Both AoCYP94B3 and AoCYP86B1 were localized to the endoplasmic reticulum. Heterologous expression of 35S::AoCYP94B3 and 35S::AoCYP86B1 in their respective Arabidopsis mutants (atcyp94b3 and atcyp86b1) increased the salt tolerance of the transgenic seedlings by reducing the amount of Na+ accumulation in the shoots. Moreover, the reduced root suberin phenotype of atcyp94b3 was rescued in the 35S::AoCYP94B3;atcyp94b3 transgenic Arabidopsis seedlings. Gas-chromatography and mass spectrometry analyses showed that the amount of suberin monomers (C-16 ω-hydroxy acids, C-16 α, ω-dicarboxylic acids and C-20 eicosanol) were increased in the roots of 35S::AoCYP94B3;atcyp94b3 Arabidopsis seedlings. Using chromatin immunoprecipitation and electrophoretic mobility shift assays, we identified AtWRKY9 as the upstream regulator of AtCYP94B3 and AtCYP86B1 in Arabidopsis. In addition, atwrky9 showed suppressed expression of AtCYP94B3 and AtCYP86B1 transcripts, and reduced suberin in the roots. These results show that AtWRKY9 controls suberin deposition by regulating AtCYP94B3 and AtCYP86B1, leading to salt tolerance. Our data can be used for generating salt-tolerant crop plants in the future.
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Affiliation(s)
- Pannaga Krishnamurthy
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute (NERI), National University of Singapore, Singapore, Singapore
| | - Bhushan Vishal
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Amrit Bhal
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Prakash P Kumar
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute (NERI), National University of Singapore, Singapore, Singapore
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20
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Gao J, Chen T, Jiang C, Wang T, Huang O, Zhang X, Liu J. Comparative anatomical and transcriptomic analyses of the color variation of leaves in Aquilaria sinensis. PeerJ 2021; 9:e11586. [PMID: 34221719 PMCID: PMC8231315 DOI: 10.7717/peerj.11586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 05/20/2021] [Indexed: 11/20/2022] Open
Abstract
Color variation in plant tissues is a common phenomenon accompanied with a series of biological changes. In this study, a special-phenotype Aquilaria sinensis (GS) with color variation of leaf was firstly reported, and DNA barcode sequences showed GS samples could not be discriminated clearly with the normal A. sinensis sample (NS), which suggested that the variety was not the cause of the GS formation. To reveal the characteristics of GS compared to NS, the anatomical and transcriptome sequencing studies were carried out. In microscopic observation, the leaves of golden-vein-leaf sample (LGS) and normal-vein-leaf sample (LNS) showed significant differences including the area of the included phloem in midrib and the thickness parameters of palisade and spongy tissues; the stems of golden-vein-leaf sample (SGS) and normal-vein-leaf sample (SNS) were also different in many aspects such as the area of vessels and included phloem. In addition, the structure of chloroplast was more complete in the midrib of LNS than that of LGS, and some particles suspected as virus were found through transmission electron microscope as well. Genes upregulated in LGS in contrast with LNS were mainly enriched in photosynthesis. As for stems, most of the genes upregulated in SGS compared to SNS were involved in translation and metabolism processes. The pathways about photosynthesis and chlorophyll metabolism as well as some important transcription factors may explain the molecular mechanism of the unique phenotypes of leaves and the genes related to suberin biosynthesis may result in the difference of stems. In addition, the genes about defense response especially biotic stress associated with numerous pathogenesis-related (PR) genes upregulated in LGS compared to LNS indicated that the pathogen may be the internal factor. Taken together, our results reveal the macro- and micro-phenotype variations as well as gene expression profiles between GS and NS, which could provide valuable clues for elucidating the mechanism of the color variation of Aquilaria.
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Affiliation(s)
- Jiaqi Gao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Tong Chen
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tielin Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ou Huang
- Guangdong Shangzhengtang Group Co., Ltd, Dongguan, China
| | - Xiang Zhang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Juan Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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21
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Pineau E, Sauveplane V, Grienenberger E, Bassard JE, Beisson F, Pinot F. CYP77B1 a fatty acid epoxygenase specific to flowering plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 307:110905. [PMID: 33902861 DOI: 10.1016/j.plantsci.2021.110905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/17/2021] [Accepted: 04/02/2021] [Indexed: 05/02/2023]
Abstract
Contrary to animals, little is known in plants about enzymes able to produce fatty acid epoxides. In our attempt to find and characterize a new fatty acid epoxygenase in Arabidopsis thaliana, data mining brought our attention on CYP77B1. Modification of the N-terminus was necessary to get enzymatic activity after heterologous expression in yeast. The common plant fatty acid C18:2 was converted into the diol 12,13-dihydroxy-octadec-cis-9-enoic acid when incubated with microsomes of yeast expressing modified CYP77B1 and AtEH1, a soluble epoxide hydrolase. This diol originated from the hydrolysis by AtEH1 of the epoxide 12,13-epoxy-octadec-cis-9-enoic acid produced by CYP77B1. A spatio-temporal study of CYP77B1 expression performed with RT-qPCR revealed the highest level of transcripts in flower bud while, in open flower, the enzyme was mainly present in pistil. CYP77B1 promoter-driven GUS expression confirmed reporter activities in pistil and also in stamens and petals. In silico co-regulation data led us to hypothesize that CYP77B1 could be involved in cutin synthesis but when flower cutin of loss-of-function mutants cyp77b1 was analyzed, no difference was found compared to cutin of wild type plants. Phylogenetic analysis showed that CYP77B1 is strictly conserved in flowering plants, suggesting a specific function in this lineage.
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Affiliation(s)
- Emmanuelle Pineau
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
| | - Vincent Sauveplane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
| | - Etienne Grienenberger
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
| | - Jean-Etienne Bassard
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
| | - Frédéric Beisson
- Institut de Biosciences et Biotechnologies d'Aix-Marseille, CEA, CNRS, Aix Marseille Université, UMR 7265, CEA Cadarache, F-13108, Saint-Paul-lez-Durance, France.
| | - Franck Pinot
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
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22
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Gao G, Wu J, Li B, Jiang Q, Wang P, Li J. Transcriptomic analysis of saffron at different flowering stages using RNA sequencing uncovers cytochrome P450 genes involved in crocin biosynthesis. Mol Biol Rep 2021; 48:3451-3461. [PMID: 33934248 DOI: 10.1007/s11033-021-06374-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/24/2021] [Indexed: 01/02/2023]
Abstract
Saffron is a well-known Chinese traditional herb, and crocin biosynthesis is related to the yield and quality of saffron. This study aimed to screen differentially expressed genes (DEGs) in saffron at different flowering stages and identify cytochrome P450 (CYP) genes involved in crocin biosynthesis. Saffron samples at different flowering stages were used for RNA sequencing, and DEGs between the samples at three days before the flowering stage (- 3da) and two days after the flowering stage (+ 2da) were screened. Thereafter, significantly differentially expressed CYP genes were identified, and CYP gene expression at different flowering stages and in various tissues of saffron was determined using real-time quantitative polymerase chain reaction (RT-qPCR). After sequencing and analysis, 1508 DEGs between the samples at - 3da and + 2da were identified, including 487 upregulated and 1021 downregulated genes, which were enriched in 16 biological processes, 5 cellular components, 3 molecular functions, and 11 KEGG pathways, including protein processing in endoplasmic reticulum, pentose and glucuronate interconversions, starch and sucrose metabolism, estrogen signaling pathway, and mitogen-activated protein kinase signaling pathway. In addition, 12 significantly differentially expressed CYP genes were identified. The RT-qPCR results showed that CYP76C4, CYP72A15, CYP72A219, CYP97B2, CYP714C2, CYP71A1, CYP94C1, and CYP86A8 were all expressed in the pistils, and CYP72A219, CYP72A15, CYP97B2, CYP71A1, and CYP86A8 were highly expressed in the pistils. Our study established a transcriptome library of saffron and found that CYP72A219, CYP72A15, CYP97B2, CYP71A1, and CYP86A8 may be candidates involved crocin biosynthesis in saffron.
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Affiliation(s)
- Guangchun Gao
- College of Medicine, Jiaxing University, Jiaxing, 314001, Zhengjiang, People's Republic of China
| | - Jiming Wu
- College of Medicine, Jiaxing University, Jiaxing, 314001, Zhengjiang, People's Republic of China
| | - Bai Li
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 314016, Zhejiang, People's Republic of China
| | - Qi Jiang
- College of Medicine, Jiaxing University, Jiaxing, 314001, Zhengjiang, People's Republic of China
| | - Ping Wang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.
| | - Jun Li
- Jiaxing Vocational and Technical College, Jiaxing, 314036, Zhejiang, People's Republic of China.
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23
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Khlaimongkhon S, Chakhonkaen S, Tongmark K, Sangarwut N, Panyawut N, Wasinanon T, Sikaewtung K, Wanchana S, Mongkolsiriwatana C, Chunwonges J, Muangprom A. RNA Sequencing Reveals Rice Genes Involved in Male Reproductive Development under Temperature Alteration. PLANTS 2021; 10:plants10040663. [PMID: 33808467 PMCID: PMC8066911 DOI: 10.3390/plants10040663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 11/25/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important food crops, providing food for nearly half of the world population. Rice grain yields are affected by temperature changes. Temperature stresses, both low and high, affect male reproductive development, resulting in yield reduction. Thermosensitive genic male sterility (TGMS) rice is sterile at high temperature and fertile at low temperature conditions, facilitating hybrid production, and is a good model to study effects of temperatures on male development. Semithin sections of the anthers of a TGMS rice line under low (fertile) and high (sterile) temperature conditions showed differences starting from the dyad stage, suggesting that genes involved in male development play a role during postmeiotic microspore development. Using RNA sequencing (RNA-Seq), transcriptional profiling of TGMS rice panicles at the dyad stage revealed 232 genes showing differential expression (DEGs) in a sterile, compared to a fertile, condition. Using qRT-PCR to study expression of 20 selected DEGs using panicles of TGMS and wild type rice plants grown under low and high temperature conditions, revealed that six out of the 20 selected genes may be unique to TGMS, while the other 14 genes showed common responses to temperatures in both TGMS and wild-type rice plants. The results presented here would be useful for further investigation into molecular mechanisms controlling TGMS and rice responses to temperature alteration.
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Affiliation(s)
- Sudthana Khlaimongkhon
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen 73140, Thailand; (S.K.); (J.C.)
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
| | - Sriprapai Chakhonkaen
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Keasinee Tongmark
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Numphet Sangarwut
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Natjaree Panyawut
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Thiwawan Wasinanon
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Kannika Sikaewtung
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Chareerat Mongkolsiriwatana
- Division of Genetics, Faculty of Liberal Arts and Science, Kasetsart University, Nakhon Pathom 73140, Thailand;
| | - Julapark Chunwonges
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen 73140, Thailand; (S.K.); (J.C.)
- Department of Horticulture, Faculty of Agriculture, Kasetsart University, Nakhon Pathom 73140, Thailand
| | - Amorntip Muangprom
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen 73140, Thailand; (S.K.); (J.C.)
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
- Correspondence: ; Tel.: +66-25646700 (ext. 3348)
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24
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Cohen C, Liltved WR, Colville JF, Shuttleworth A, Weissflog J, Svatoš A, Bytebier B, Johnson SD. Sexual deception of a beetle pollinator through floral mimicry. Curr Biol 2021; 31:1962-1969.e6. [PMID: 33770493 DOI: 10.1016/j.cub.2021.03.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/13/2021] [Accepted: 03/10/2021] [Indexed: 12/28/2022]
Abstract
Sexual mimicry is a complex multimodal strategy used by some plants to lure insects to flowers for pollination.1-4 It is notable for being highly species-specific and is typically mediated by volatiles belonging to a restricted set of chemical compound classes.3,4 Well-documented cases involve exploitation of bees and wasps (Hymenoptera)5,6 and flies (Diptera).7-9 Although beetles (Coleoptera) are the largest insect order and are well known as pollinators of both early and modern plants,10,11 it has been unclear whether they are sexually deceived by plants during flower visits.12,13 Here we report the discovery of an unambiguous case of sexual deception of a beetle: male longhorn beetles (Chorothyse hessei, Cerambycidae) pollinate the elaborate insectiform flowers of a rare southern African orchid (Disa forficaria), while exhibiting copulatory behavior including biting the antennae-like petals, curving the abdomen into the hairy lip cleft, and ejaculating sperm. The beetles are strongly attracted by (16S,9Z)-16-ethyl hexadec-9-enolide, a novel macrolide that we isolated from the floral scent. Structure-activity studies14,15 confirmed that chirality and other aspects of the structural geometry of the macrolide are critical for the attraction of the male beetles. These results demonstrate a new biological function for plant macrolides and confirm that beetles can be exploited through sexual deception to serve as pollinators.
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Affiliation(s)
- Callan Cohen
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa
| | - William R Liltved
- Compton Herbarium, South African National Biodiversity Institute, Newlands, Cape Town 7735, South Africa
| | - Jonathan F Colville
- Kirstenbosch Research Centre, South African National Biodiversity Institute, Newlands, Cape Town 7735, South Africa; Statistics in Ecology, Environment and Conservation, Department of Statistical Sciences, University of Cape Town, Rondebosch 7701, South Africa
| | - Adam Shuttleworth
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg 3209, South Africa
| | - Jerrit Weissflog
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, D-07745 Jena, Germany
| | - Aleš Svatoš
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, D-07745 Jena, Germany
| | - Benny Bytebier
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg 3209, South Africa
| | - Steven D Johnson
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg 3209, South Africa.
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25
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Silva AT, Gao B, Fisher KM, Mishler BD, Ekwealor JTB, Stark LR, Li X, Zhang D, Bowker MA, Brinda JC, Coe KK, Oliver MJ. To dry perchance to live: Insights from the genome of the desiccation-tolerant biocrust moss Syntrichia caninervis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1339-1356. [PMID: 33277766 DOI: 10.1111/tpj.15116] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/30/2020] [Indexed: 05/24/2023]
Abstract
With global climate change, water scarcity threatens whole agro/ecosystems. The desert moss Syntrichia caninervis, an extremophile, offers novel insights into surviving desiccation and heat. The sequenced S. caninervis genome consists of 13 chromosomes containing 16 545 protein-coding genes and 2666 unplaced scaffolds. Syntenic relationships within the S. caninervis and Physcomitrella patens genomes indicate the S. caninervis genome has undergone a single whole genome duplication event (compared to two for P. patens) and evidence suggests chromosomal or segmental losses in the evolutionary history of S. caninervis. The genome contains a large sex chromosome composed primarily of repetitive sequences with a large number of Copia and Gypsy elements. Orthogroup analyses revealed an expansion of ELIP genes encoding proteins important in photoprotection. The transcriptomic response to desiccation identified four structural clusters of novel genes. The genomic resources established for this extremophile offer new perspectives for understanding the evolution of desiccation tolerance in plants.
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Affiliation(s)
- Anderson T Silva
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
| | - Bei Gao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, 830011, China
| | - Kirsten M Fisher
- Department of Biological Sciences, California State University, Los Angeles, California, 90032, USA
| | - Brent D Mishler
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, California, 94720-2465, USA
| | - Jenna T B Ekwealor
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, California, 94720-2465, USA
| | - Lloyd R Stark
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, 89154-4004, USA
| | - Xiaoshuang Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, 830011, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, 830011, China
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - John C Brinda
- Missouri Botanical Garden, St. Louis, Missouri, 63110-0299, USA
| | - Kirsten K Coe
- Department of Biology, Middlebury College, Middlebury, Vermont, 40506-0225, USA
| | - Melvin J Oliver
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, 65211, USA
- USDA-ARS-MWA, Plant Genetics Research Unit, Columbia, Missouri, 65211, USA
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26
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Li Q, Chakrabarti M, Taitano NK, Okazaki Y, Saito K, Al-Abdallat AM, van der Knaap E. Differential expression of SlKLUH controlling fruit and seed weight is associated with changes in lipid metabolism and photosynthesis-related genes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1225-1244. [PMID: 33159787 PMCID: PMC7904157 DOI: 10.1093/jxb/eraa518] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/02/2020] [Indexed: 05/21/2023]
Abstract
The sizes of plant organs such as fruit and seed are crucial yield components. Tomato KLUH underlies the locus fw3.2, an important regulator of fruit and seed weight. However, the mechanism by which the expression levels of KLUH affect organ size is poorly understood. We found that higher expression of SlKLUH increased cell proliferation in the pericarp within 5 d post-anthesis in tomato near-isogenic lines. Differential gene expression analyses showed that lower expression of SlKLUH was associated with increased expression of genes involved in lipid metabolism. Lipidomic analysis revealed that repression of SlKLUH mainly increased the contents of certain non-phosphorus glycerolipids and phospholipids and decreased the contents of four unknown lipids. Co-expression network analyses revealed that lipid metabolism was possibly associated with but not directly controlled by SlKLUH, and that this gene instead controls photosynthesis-related processes. In addition, many transcription factors putatively involved in the KLUH pathway were identified. Collectively, we show that SlKLUH regulates fruit and seed weight which is associated with altered lipid metabolism. The results expand our understanding of fruit and seed weight regulation and offer a valuable resource for functional studies of candidate genes putatively involved in regulation of organ size in tomato and other crops.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Manohar Chakrabarti
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Nathan K Taitano
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | | | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Department of Horticulture, University of Georgia, Athens, GA, USA
- Correspondence:
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Schink C, Spielvogel S, Imhof W. Synthesis of 13 C-labelled cutin and suberin monomeric dicarboxylic acids of the general formula HO 213 C-(CH 2 ) n - 13 CO 2 H (n = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28). J Labelled Comp Radiopharm 2021; 64:14-29. [PMID: 33063895 DOI: 10.1002/jlcr.3885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022]
Abstract
13 C-labeled dicarboxylic acids HO213 C-(CH2 )n -13 CO2 H (n = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28) have been synthesized as internal standards for LC-MS and GC-MS analysis of cutin and suberin monomer degradation by soil-based microorganisms. Different synthetic strategies had to be applied depending on the chain length of the respective synthetic target and because of economic considerations. 13 C-labels were introduced by nucleophilic substitution of a suitable leaving group with labelled potassium cyanide and subsequent hydrolysis of the nitriles to produce the corresponding dicarboxylic acids. All new compounds are characterized by GC/MS, IR, and NMR methods as well as by elemental analysis.
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Affiliation(s)
- Carina Schink
- Institute of Integrated Natural Sciences, University Koblenz-Landau, Koblenz, Germany
| | - Sandra Spielvogel
- Institute of Plant Nutrition and Soil Science, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Wolfgang Imhof
- Institute of Integrated Natural Sciences, University Koblenz-Landau, Koblenz, Germany
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Simon SJ, Tschaplinski TJ, M. LeBoldus J, Keefover‐Ring K, Azeem M, Chen J, Macaya‐Sanz D, MacDonald WL, Muchero W, DiFazio SP. Host plant genetic control of associated fungal and insect species in a Populus hybrid cross. Ecol Evol 2020; 10:5119-5134. [PMID: 32551087 PMCID: PMC7297788 DOI: 10.1002/ece3.6266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/05/2020] [Accepted: 03/23/2020] [Indexed: 11/10/2022] Open
Abstract
Plants employ a diverse set of defense mechanisms to mediate interactions with insects and fungi. These relationships can leave lasting impacts on host plant genome structure such as rapid expansion of gene families through tandem duplication. These genomic signatures provide important clues about the complexities of plant/biotic stress interactions and evolution. We used a pseudo-backcross hybrid family to identify quantitative trait loci (QTL) controlling associations between Populus trees and several common Populus diseases and insects. Using whole-genome sequences from each parent, we identified candidate genes that may mediate these interactions. Candidates were partially validated using mass spectrometry to identify corresponding QTL for defensive compounds. We detected significant QTL for two interacting fungal pathogens and three insects. The QTL intervals contained candidate genes potentially involved in physical and chemical mechanisms of host-plant resistance and susceptibility. In particular, we identified adjoining QTLs for a phenolic glycoside and Phyllocolpa sawfly abundance. There was also significant enrichment of recent tandem duplications in the genomic intervals of the native parent, but not the exotic parent. Tandem gene duplication may be an important mechanism for rapid response to biotic stressors, enabling trees with long juvenile periods to reach maturity despite many coevolving biotic stressors.
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Affiliation(s)
- Sandra J. Simon
- Department of BiologyWest Virginia UniversityMorgantownWest Virginia
| | - Timothy J. Tschaplinski
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - Jared M. LeBoldus
- Forest Engineering, Resources & ManagementOregon State UniversityCorvallisOregon
- Botany and Plant PathologyOregon State UniversityCorvallisOregon
| | - Ken Keefover‐Ring
- Department of BotanyUniversity of Wisconsin-MadisonMadisonWisconsin
- Department of GeographyUniversity of WisconsinMadisonWisconsin
| | - Muhammad Azeem
- Department of BotanyUniversity of Wisconsin-MadisonMadisonWisconsin
- Department of GeographyUniversity of WisconsinMadisonWisconsin
- Department of ChemistryCOMSATS University IslamabadAbbottabadPakistan
| | - Jin‐Gui Chen
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - David Macaya‐Sanz
- Department of BiologyWest Virginia UniversityMorgantownWest Virginia
| | - William L. MacDonald
- Division of Plant and Soil SciencesWest Virginia UniversityMorgantownWest Virginia
| | - Wellington Muchero
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
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Pandian BA, Sathishraj R, Djanaguiraman M, Prasad PV, Jugulam M. Role of Cytochrome P450 Enzymes in Plant Stress Response. Antioxidants (Basel) 2020; 9:antiox9050454. [PMID: 32466087 PMCID: PMC7278705 DOI: 10.3390/antiox9050454] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/20/2022] Open
Abstract
Cytochrome P450s (CYPs) are the largest enzyme family involved in NADPH- and/or O2-dependent hydroxylation reactions across all the domains of life. In plants and animals, CYPs play a central role in the detoxification of xenobiotics. In addition to this function, CYPs act as versatile catalysts and play a crucial role in the biosynthesis of secondary metabolites, antioxidants, and phytohormones in higher plants. The molecular and biochemical processes catalyzed by CYPs have been well characterized, however, the relationship between the biochemical process catalyzed by CYPs and its effect on several plant functions was not well established. The advent of next-generation sequencing opened new avenues to unravel the involvement of CYPs in several plant functions such as plant stress response. The expression of several CYP genes are regulated in response to environmental stresses, and they also play a prominent role in the crosstalk between abiotic and biotic stress responses. CYPs have an enormous potential to be used as a candidate for engineering crop species resilient to biotic and abiotic stresses. The objective of this review is to summarize the latest research on the role of CYPs in plant stress response.
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Affiliation(s)
- Balaji Aravindhan Pandian
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
| | - Rajendran Sathishraj
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
| | - Maduraimuthu Djanaguiraman
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003, India
| | - P.V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
- Correspondence: ; Tel.: +1-785-532-2755
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Mele MA, Kang HM, Lee YT, Islam MZ. Grape terpenoids: flavor importance, genetic regulation, and future potential. Crit Rev Food Sci Nutr 2020; 61:1429-1447. [PMID: 32401037 DOI: 10.1080/10408398.2020.1760203] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Terpenes significantly affect the flavor and quality of grapes and wine. This review summarizes recent research on terpenoids with regard to grape wine. Although, the grapevine terpene synthase gene family is the largest identified, genetic modifications involving terpenes to improve wine flavor have received little attention. Key enzyme modulation alters metabolite production. Over the last decade, the heterologous manipulation of grape glycosidase has been used to alter terpenoids, and cytochrome P450s may affect terpene synthesis. Metabolic and genetic engineering can further modify terpenoid metabolism, while using transgenic grapevines (trait transfer to the plant) could yield more flavorful wine. We also discuss traits involved in wine aroma quality, and the strategies that can be used to improve grapevine breeding technology.
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Affiliation(s)
- Mahmuda Akter Mele
- Department of Horticulture, Kangwon National University, Chuncheon, Republic of Korea
| | - Ho-Min Kang
- Department of Horticulture, Kangwon National University, Chuncheon, Republic of Korea
| | - Young-Tack Lee
- Department of Food Science and Biotechnology, Gachon University, Seongnam, Republic of Korea
| | - Mohammad Zahirul Islam
- Department of Food Science and Biotechnology, Gachon University, Seongnam, Republic of Korea
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Zhang D, Yang H, Wang X, Qiu Y, Tian L, Qi X, Qu LQ. Cytochrome P450 family member CYP96B5 hydroxylates alkanes to primary alcohols and is involved in rice leaf cuticular wax synthesis. THE NEW PHYTOLOGIST 2020; 225:2094-2107. [PMID: 31618451 DOI: 10.1111/nph.16267] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/09/2019] [Indexed: 05/24/2023]
Abstract
Odd-numbered primary alcohols are components of plant cuticular wax, but their biosynthesis remains unknown. We isolated a rice wax crystal-sparse leaf 5 (WSL5) gene using a map-based cloning strategy. The function of WSL5 was illustrated by overexpression and knockout in rice, heterologous expression in Arabidopsis and transient expression in tobacco leaves. WSL5 is predicted to encode a cytochrome P450 family member CYP96B5. The wsl5 mutant lacked crystalloid platelets on the surface of cuticle membrane, and its cuticle membrane was thicker than that of the wild-type. The wsl5 mutant is more tolerant to drought stress. The load of C23 -C33 alkanes increased, whereas the C29 primary alcohol reduced significantly in wsl5 mutant and WSL5 knockout transgenic plants. Overexpression of WSL5 increased the C29 primary alcohol and decreased alkanes in rice leaves. Heterologous expression of WSL5 increased the C29 primary alcohol and decreased alkanes, secondary alcohol, and ketone in Arabidopsis stem wax. Transient expression of WSL5 in tobacco leaves also increased the production C29 primary alcohol. WSL5 catalyzes the terminal hydroxylation of alkanes, yielding odd-numbered primary alcohols, and is involved in the formation of epidermal wax crystals on rice leaf, affecting drought sensitivity.
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Affiliation(s)
- Du Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Huifang Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaochen Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yijian Qiu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lihong Tian
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Le Qing Qu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
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Lopes ST, Sobral D, Costa B, Perdiguero P, Chaves I, Costa A, Miguel CM. Phellem versus xylem: genome-wide transcriptomic analysis reveals novel regulators of cork formation in cork oak. TREE PHYSIOLOGY 2020; 40:129-141. [PMID: 31860724 DOI: 10.1093/treephys/tpz118] [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: 08/21/2019] [Accepted: 11/15/2019] [Indexed: 05/23/2023]
Abstract
Cork cambium (or phellogen) is a secondary meristem responsible for the formation of phelloderm and phellem/cork, which together compose the periderm. In Quercus suber L., the phellogen is active throughout the entire life of the tree, producing a continuous and renewable outer bark of cork. To identify specific candidate genes associated with cork cambium activity and phellem differentiation, we performed a comparative transcriptomic study of Q. suber secondary growth tissues (xylem and phellogen/phellem) using RNA-seq. The present work provides a high-resolution map of all the transcripts identified in the phellogen/phellem tissues. A total of 6013 differentially expressed genes were identified, with 2875 of the transcripts being specifically enriched during the cork formation process versus secondary xylem formation. Furthermore, cork samples originating from the original phellogen (`virgin' cork) and from a traumatic phellogen (`amadia' cork) were also compared. Our results point to a shortlist of potentially relevant candidate genes regulating phellogen activity and phellem differentiation, including novel genes involved in the suberization process, as well as genes associated to ethylene and jasmonate signaling and to meristem function. The future functional characterization of some of the identified candidate genes will help to elucidate the molecular mechanisms underlying cork cambium activity and phellem differentiation.
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Affiliation(s)
- Susana T Lopes
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Daniel Sobral
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 2780-156 Oeiras, Portugal
| | - Bruno Costa
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Pedro Perdiguero
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Inês Chaves
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Augusta Costa
- Instituto Nacional de Investigação Agrária e Veterinária, Avenida da República, Quinta do Marquês 2780-157 Oeiras, Portugal
| | - Célia M Miguel
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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Thesseling FA, Hutter MC, Wiek C, Kowalski JP, Rettie AE, Girhard M. Novel insights into oxidation of fatty acids and fatty alcohols by cytochrome P450 monooxygenase CYP4B1. Arch Biochem Biophys 2020; 679:108216. [PMID: 31801692 DOI: 10.1016/j.abb.2019.108216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 10/25/2022]
Abstract
CYP4B1 is an enigmatic mammalian cytochrome P450 monooxygenase acting at the interface between xenobiotic and endobiotic metabolism. A prominent CYP4B1 substrate is the furan pro-toxin 4-ipomeanol (IPO). Our recent investigation on metabolism of IPO related compounds that maintain the furan functionality of IPO while replacing its alcohol group with alkyl chains of varying structure and length revealed that, in addition to cytotoxic reactive metabolite formation (resulting from furan activation) non-cytotoxic ω-hydroxylation at the alkyl chain can also occur. We hypothesized that substrate reorientations may happen in the active site of CYP4B1. These findings prompted us to re-investigate oxidation of unsaturated fatty acids and fatty alcohols with C9-C16 carbon chain length by CYP4B1. Strikingly, we found that besides the previously reported ω- and ω-1-hydroxylations, CYP4B1 is also capable of α-, β-, γ-, and δ-fatty acid hydroxylation. In contrast, fatty alcohols of the same chain length are exclusively hydroxylated at ω, ω-1, and ω-2 positions. Docking results for the corresponding CYP4B1-substrate complexes revealed that fatty acids can adopt U-shaped bonding conformations, such that carbon atoms in both arms may approach the heme-iron. Quantum chemical estimates of activation energies of the hydrogen radical abstraction by the reactive compound 1 as well as electron densities of the substrate orbitals led to the conclusion that fatty acid and fatty alcohol oxidations by CYP4B1 are kinetically controlled reactions.
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Affiliation(s)
- Florian A Thesseling
- Institute of Biochemistry, Heinrich-Heine University, 40225, Düsseldorf, Germany.
| | - Michael C Hutter
- Center for Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225, Düsseldorf, Germany.
| | - John P Kowalski
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, 98195, USA.
| | - Allan E Rettie
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, 98195, USA.
| | - Marco Girhard
- Institute of Biochemistry, Heinrich-Heine University, 40225, Düsseldorf, Germany.
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Identification of Differentially Expressed Proteins in Sugarcane in Response to Infection by Xanthomonas albilineans Using iTRAQ Quantitative Proteomics. Microorganisms 2020; 8:microorganisms8010076. [PMID: 31947808 PMCID: PMC7023244 DOI: 10.3390/microorganisms8010076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/16/2019] [Accepted: 12/28/2019] [Indexed: 01/02/2023] Open
Abstract
Sugarcane can suffer severe yield losses when affected by leaf scald, a disease caused by Xanthomonas albilineans. This bacterial pathogen colonizes the vascular system of sugarcane, which can result in reduced plant growth and plant death. In order to better understand the molecular mechanisms involved in the resistance of sugarcane to leaf scald, a comparative proteomic study was performed with two sugarcane cultivars inoculated with X. albilineans: one resistant (LCP 85-384) and one susceptible (ROC20) to leaf scald. The iTRAQ (isobaric tags for relative and absolute quantification) approach at 0 and 48 h post-inoculation (hpi) was used to identify and annotate differentially expressed proteins (DEPs). A total of 4295 proteins were associated with 1099 gene ontology (GO) terms by GO analysis. Among those, 285 were DEPs during X. albilineans infection in cultivars LCP 85-384 and ROC20. One hundred seventy-two DEPs were identified in resistant cultivar LCP 85-384, and 113 of these proteins were upregulated and 59 were downregulated. One hundred ninety-two DEPs were found in susceptible cultivar ROC20 and half of these (92) were upregulated, whereas the other half corresponded to downregulated proteins. The significantly upregulated DEPs in LCP 85-384 were involved in metabolic pathways, the biosynthesis of secondary metabolites, and the phenylpropanoid biosynthesis pathway. Additionally, the expression of seven candidate genes related to photosynthesis and glycolytic pathways, plant innate immune system, glycosylation process, plant cytochrome P450, and non-specific lipid transfer protein was verified based on transcription levels in sugarcane during infection by X. albilineans. Our findings shed new light on the differential expression of proteins in sugarcane cultivars in response to infection by X. albilineans. The identification of these genes provides important information for sugarcane variety improvement programs using molecular breeding strategies.
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Poehlman WL, Schnabel EL, Chavan SA, Frugoli JA, Feltus FA. Identifying Temporally Regulated Root Nodulation Biomarkers Using Time Series Gene Co-Expression Network Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1409. [PMID: 31737022 PMCID: PMC6836625 DOI: 10.3389/fpls.2019.01409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
Root nodulation results from a symbiotic relationship between a plant host and Rhizobium bacteria. Synchronized gene expression patterns over the course of rhizobial infection result in activation of pathways that are unique but overlapping with the highly conserved pathways that enable mycorrhizal symbiosis. We performed RNA sequencing of 30 Medicago truncatula root maturation zone samples at five distinct time points. These samples included plants inoculated with Sinorhizobium medicae and control plants that did not receive any Rhizobium. Following gene expression quantification, we identified 1,758 differentially expressed genes at various time points. We constructed a gene co-expression network (GCN) from the same data and identified link community modules (LCMs) that were comprised entirely of differentially expressed genes at specific time points post-inoculation. One LCM included genes that were up-regulated at 24 h following inoculation, suggesting an activation of allergen family genes and carbohydrate-binding gene products in response to Rhizobium. We also identified two LCMs that were comprised entirely of genes that were down regulated at 24 and 48 h post-inoculation. The identity of the genes in these modules suggest that down-regulating specific genes at 24 h may result in decreased jasmonic acid production with an increase in cytokinin production. At 48 h, coordinated down-regulation of a specific set of genes involved in lipid biosynthesis may play a role in nodulation. We show that GCN-LCM analysis is an effective method to preliminarily identify polygenic candidate biomarkers of root nodulation and develop hypotheses for future discovery.
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Zheng X, Li P, Lu X. Research advances in cytochrome P450-catalysed pharmaceutical terpenoid biosynthesis in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4619-4630. [PMID: 31037306 DOI: 10.1093/jxb/erz203] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Terpenoids, the biggest class of plant secondary metabolites, have a wide range of significant physiological roles, while many of them are important natural drugs. Biosynthesis of pharmaceutical terpenoids in plants is a fairly complex process, most of which involves cytochrome P450 (CYP450) monooxygenases. CYP450 enzymes are versatile biocatalysts that play critical roles in terpenoid skeleton modification and structural diversity. Therefore, the discovery and identification of CYP450 genes is significant for elucidating the terpenoid biosynthetic pathway. This review summarizes the progress and cloning strategies relating to CYP450s in pharmaceutical terpenoid biosynthesis of the past decade.
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Affiliation(s)
- Xiaoyan Zheng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xu Lu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
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Ansari WA, Atri N, Ahmad J, Qureshi MI, Singh B, Kumar R, Rai V, Pandey S. Drought mediated physiological and molecular changes in muskmelon (Cucumis melo L.). PLoS One 2019; 14:e0222647. [PMID: 31550269 PMCID: PMC6759176 DOI: 10.1371/journal.pone.0222647] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/03/2019] [Indexed: 01/08/2023] Open
Abstract
Water deficiency up to a certain level and duration leads to a stress condition called drought. It is a multi-dimensional stress causing alteration in the physiological, morphological, biochemical, and molecular traits in plants resulting in improper plant growth and development. Drought is one of the major abiotic stresses responsible for loss of crops including muskmelon (Cucumis melo. L). Muskmelon genotype SC-15, which exhibits high drought resistance as reported in our earlier reports, was exposed to deficient water condition and studied for alteration in physiological, molecular and proteomic profile changes in the leaves. Drought stress results in reduced net photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration (E) rate. With expanded severity of drought, declination recorded in content of total chlorophyll and carotenoid while enhancement observed in phenol content indicating generation of oxidative stress. In contrary, activities of catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX), and guaiacol (POD) were increased under drought stress. Peptide mass fingerprinting (PMF) showed that drought increased the relative abundance of 38 spots while decreases10 spots of protein. The identified proteins belong to protein synthesis, photosynthesis, nucleotide biosynthesis, stress response, transcription regulation, metabolism, energy and DNA binding. A drought-induced MADS-box transcription factor was identified. The present findings indicate that under drought muskmelon elevates the abundance of defense proteins and suppresses catabolic proteins. The data obtained exhibits possible mechanisms adopted by muskmelon to counter the impacts of drought induced stress.
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Affiliation(s)
- Waquar Akhter Ansari
- ICAR–Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Neelam Atri
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Javed Ahmad
- Proteomics & Bioinformatics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Irfan Qureshi
- Proteomics & Bioinformatics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Bijendra Singh
- ICAR–Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Ram Kumar
- ICAR–National Research Centre on Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi, India
| | - Vandna Rai
- ICAR–National Research Centre on Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi, India
| | - Sudhakar Pandey
- ICAR–Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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Mi-Ichi F, Yoshida H. Unique Features of Entamoeba Sulfur Metabolism; Compartmentalization, Physiological Roles of Terminal Products, Evolution and Pharmaceutical Exploitation. Int J Mol Sci 2019; 20:ijms20194679. [PMID: 31546588 PMCID: PMC6801973 DOI: 10.3390/ijms20194679] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 11/16/2022] Open
Abstract
Sulfur metabolism is essential for all living organisms. Recently, unique features of the Entamoeba metabolic pathway for sulfated biomolecules have been described. Entamoeba is a genus in the phylum Amoebozoa and includes the causative agent for amoebiasis, a global public health problem. This review gives an overview of the general features of the synthesis and degradation of sulfated biomolecules, and then highlights the characteristics that are unique to Entamoeba. Future biological and pharmaceutical perspectives are also discussed.
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Affiliation(s)
- Fumika Mi-Ichi
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan.
| | - Hiroki Yoshida
- Division of Molecular and Cellular Immunoscience, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan.
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Wang W, Singh SK, Li X, Sun H, Yang Y, Jiang M, Zi H, Liu R, Zhang H, Chu Z. Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots. PeerJ 2019; 7:e7102. [PMID: 31223535 PMCID: PMC6571136 DOI: 10.7717/peerj.7102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/07/2019] [Indexed: 02/05/2023] Open
Abstract
Background There have been few studies on the partial defoliation response of grass. It has been unclear how partial defoliation may affect roots at the levels of nutrient accumulation and transcriptional regulation. Hereby we report a comprehensive investigation on molecular impacts of partial defoliation by using a model grass species, Brachypodium distachyon. Results Our Inductively Coupled Plasma Mass Spectrometry analyses of B. distachyon revealed shoot- and root-specific accumulation patterns of a group of macronutrients including potassium (K), Phosphorus (P), Calcium (Ca), Magnesium (Mg), and micronutrients including Sodium (Na), iron (Fe), and Manganese (Mn). Meanwhile, our genome-wide profiling of gene expression patterns depicts transcriptional impacts on B. distachyon roots by cutting the aerial portion. The RNAseq analyses identified a total of 1,268 differentially expressed genes in B. distachyon with partial defoliation treatment. Our comprehensive analyses by means of multiple approaches, including Gene Ontology, InterPro and Pfam protein classification, KEGG pathways, and Plant TFDB, jointly highlight the involvement of hormone-mediated wounding response, primary and secondary metabolites, and ion homeostasis, in B. distachyon after the partial defoliation treatment. In addition, evidence is provided that roots respond to partial defoliation by modifying nutrient uptake and rhizosphere acidification rate, indicating that an alteration of the root/soil interaction occurs in response to this practice. Conclusions This study reveals how partial defoliation alters ion accumulation levels in shoots and roots, as well as partial defoliation-induced transcriptional reprogramming on a whole-genome scale, thereby providing insight into the molecular mechanisms underlying the recovery process of grass after partial defoliation.
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Affiliation(s)
- Wei Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Sunil Kumar Singh
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiwen Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China.,College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hui Sun
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Yang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Min Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Hailing Zi
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Renyi Liu
- Center for Agroforestry Mega Data Science and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhaoqing Chu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
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Pawełkowicz M, Pryszcz L, Skarzyńska A, Wóycicki RK, Posyniak K, Rymuszka J, Przybecki Z, Pląder W. Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination. PLANT REPRODUCTION 2019; 32:193-216. [PMID: 30719568 PMCID: PMC6500512 DOI: 10.1007/s00497-019-00362-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/18/2019] [Indexed: 05/26/2023]
Abstract
Transcriptome data and qPCR analysis revealed new insight into genes regulatory mechanism related to cucumber sex determination. Cucumber (Cucumis sativus L.) is an economically important crop cultivated worldwide. Enhancing the genomic resources for cucumber may enable the regulation of traits relevant to crop productivity and quality. Sequencing technologies and bioinformatics tools provide opportunities for the development of such resources. The aims of this study were to identify and characterize the genes involved in sex determination and flower morphogenesis in cucumber isogenic lines that differed regarding flower sex type. We obtained transcripts for 933 genes related to shoot apex development, among which 310 were differentially expressed genes (DEGs) among the male, female, and hermaphroditic lines. We performed gene ontology and molecular network analyses and explored the DEGs related to already known processes like: hormone synthesis and signaling, lipid and sugar metabolism; and also newly discovered processes related to cell wall, membrane, and cytoskeleton modifications; ion homeostasis which appears to be important for ethylene perception and signaling, and genes expression mediated by transcription factors related to floral organ identities. We proposed a new model of regulatory mechanism network of sex development in cucumber. Our results may be useful for clarifying the molecular genetics and the functional mechanisms underlying the sex determination processes.
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Affiliation(s)
- Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland.
| | - Leszek Pryszcz
- Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Rafał K Wóycicki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
- Philip Morris International R&D, Philip Morris Products S.A., 2000, Neuchâtel, Switzerland
| | - Kacper Posyniak
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Jacek Rymuszka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
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Yang M, Lu H, Xue F, Ma L. Identifying High Confidence microRNAs in the Developing Seeds of Jatropha curcas. Sci Rep 2019; 9:4510. [PMID: 30872797 PMCID: PMC6418140 DOI: 10.1038/s41598-019-41189-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/01/2019] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenously short noncoding regulatory RNAs implicated in plant development and physiology. Nine small RNA (sRNA) libraries from three typical seed developmental stages (young, intermediate, and mature) were generated by deep sequencing to identify the miRNAs of J. curcas, a potential oilseed crop for the production of renewable oil. Strict criteria were adopted to identify 93 high confidence miRNAs including 48 conserved miRNAs and 45 novel miRNAs. Target genes of these miRNAs were involved in a broad range of physiological functions, including gene expression regulation, primary & secondary metabolism, growth & development, signal transduction, and stress response. About one third (29 out of 93) miRNAs showed significant changes in expression levels during the seed developmental process, indicating that the miRNAs might regulate its targets by their changes of transcription levels in seed development. However, most miRNAs were found differentially expressed in the late stage of seed development, suggesting that miRNAs play more important roles in the stage when seed accumulating organic matters and suffering dehydration stress. This study presents the first large scale identification of high confidence miRNAs in the developing seeds of J. curcas.
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Affiliation(s)
- Mingfeng Yang
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China
| | - Heshu Lu
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China
| | - Feiyan Xue
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China
| | - Lanqing Ma
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China.
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Eminoğlu A, Aktürk Dizman Y, Güzel Ş, Beldüz AO. Molecular and in silico cloning, identification, and preharvest period expression analysis of a putative cytochrome P450 monooxygenase gene from Camellia sinensis (L.) Kuntze (tea). Turk J Biol 2019; 42:1-11. [PMID: 30814865 DOI: 10.3906/biy-1606-54] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Cytochrome P450 monooxygenases are one of the largest heme-containing protein groups, and the majority of them catalyze hydroxylation reactions dependent on nicotinamide adenine dinucleotide phosphate and oxygen. Cytochrome P450 (CYP) enzymes function in a wide range of monooxygenation reactions essential in primary and secondary metabolism in plants. Camellia sinensis (L.) Kuntze is a commercially and economically valuable plant due to its medicinally important secondary metabolites and as a beloved beverage. Cytochrome P450 monooxygenases play a significant role in the biosynthesis of a variety of secondary metabolites in tea. Although the biosynthesis of secondary metabolites has been investigated in detail, there have been limited studies conducted on identifying the genetic mechanisms of CYP-catalyzed secondary metabolic pathways in the C. sinensis (tea) plant. In our study, we characterized a putative C. sinensis (L.) Kuntze cytochrome P450 monooxygenase gene (Csp450), which has 1759 bp full-length cDNA with 49 bp of 5' and 183 bp of 3' untranslated regions. eTh CDS of the gene is 1527 bp and 508 amino acids in length. BLAST results of the deduced amino acid sequence revealed a high similarity with the CYP704C1-like superfamily. Preharvest period gene expression analysis from May, July, and September did not show any difference.
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Affiliation(s)
- Ayşenur Eminoğlu
- Molecular Biology Research Laboratories, Department of Biology, Recep Tayyip Erdoğan University , Rize , Turkey
| | - Yeşim Aktürk Dizman
- Molecular Biology Research Laboratories, Department of Biology, Recep Tayyip Erdoğan University , Rize , Turkey
| | - Şule Güzel
- Plant Ecology Research Laboratories, Department of Biology, Recep Tayyip Erdoğan University , Rize , Turkey
| | - Ali Osman Beldüz
- Department of Biology, Faculty of Science, Karadeniz Technical University , Trabzon , Turkey
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Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 146:112-122. [PMID: 30802474 DOI: 10.1016/j.pbiomolbio.2019.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 01/09/2023]
Abstract
Abiotic environmental stresses are important factors that limit the growth, fiber yield, and quality of cotton. In this study, an integrative meta-analysis and a system-biology analysis were performed to explore the underlying transcriptomic mechanisms that are critical for response to stresses. From the meta-analysis, it was observed that a total of 1465 differentially expressed genes (DEGs) between normal and stress conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were significantly enriched in the ubiquitin-dependent process, biosynthesis of secondary metabolites, plant hormone, and signaled transduction. The results also indicated that some of DEGs were assigned to transcription factors (TFs). A total of 148 TFs belonged to 25 conserved families were identified that among them S1Fa-like, ERF, NAC, bZIP families, were the most abundant groups. Moreover, we searched in upstream regions of DEGs for over-represented DNA motifs and were able to identify 11 conserved sequence motifs. The functional analysis of these motifs revealed that they were involved in regulation of transcription, DNA replication, cytoskeleton organization, and translation. Weighted gene co-expression network analysis (WGCNA) uncovered 12 distinct co-expression modules. Four modules were significantly associated with genes involved in response to stress and cell wall organization. The network analysis also identified hub genes such as RTNLB5 and PRA1, which may be involved in regulating stress response. The findings could help to understand the mechanisms of response to abiotic stress and introduce candidate genes that may be beneficial to cotton plant breeding programs.
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Transcriptome analysis identifies strong candidate genes for ginsenoside biosynthesis and reveals its underlying molecular mechanism in Panax ginseng C.A. Meyer. Sci Rep 2019; 9:615. [PMID: 30679448 PMCID: PMC6346045 DOI: 10.1038/s41598-018-36349-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/11/2018] [Indexed: 11/09/2022] Open
Abstract
Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal herbs for human health and medicine in which ginsenosides are known to play critical roles. The genes from the cytochrome P450 (CYP) gene superfamily have been shown to play important roles in ginsenoside biosynthesis. Here we report genome-wide identification of the candidate PgCYP genes for ginsenoside biosynthesis, development of functional SNP markers for its manipulation and systems analysis of its underlying molecular mechanism. Correlation analysis identified 100 PgCYP genes, including all three published ginsenoside biosynthesis PgCYP genes, whose expressions were significantly correlated with the ginsenoside contents. Mutation association analysis identified that six of these 100 PgCYP genes contained SNPs/InDels that were significantly associated with ginsenosides biosynthesis (P ≤ 1.0e-04). These six PgCYP genes, along with all ten published ginsenoside biosynthesis genes from the PgCYP and other gene families, formed a strong co-expression network, even though they varied greatly in spatio-temporal expressions. Therefore, this study has identified six new ginsenoside biosynthesis candidate genes, provided a genome-wide insight into how they are involved in ginsenoside biosynthesis and developed a set of functional SNP markers useful for enhanced ginsenoside biosynthesis research and breeding in ginseng and related species.
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45
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Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four Papaver Species. DATA 2018. [DOI: 10.3390/data3040055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Poppies are well-known plants in the family Papaveraceae that are rich in alkaloids. This family contains 61 species, and in this study we sequenced the transcriptomes of four species’ (Papaver rhoeas, Papaver nudicaule, Papaver fauriei, and Papaver somniferum) leaves. These transcripts were systematically assessed for the expression of secondary metabolite biosynthesis (SMB) genes and cytochromes, and their expression profiles were assessed for use in bioinformatics analyses. This study contributed 265 Gb (13 libraries with three biological replicates) of leaf transcriptome data from three Papaver plant developmental stages. Sequenced transcripts were assembled into 815 Mb of contigs, including 226 Mb of full-length transcripts. The transcripts for 53 KEGG pathways, 55 cytochrome superfamilies, and benzylisoquinoline alkaloid biosynthesis (BIA) were identified and compared to four other alkaloid-rich genomes. Additionally, 22 different alkaloids and their relative expression profiles in three developmental stages of Papaver species were assessed by targeted metabolomics using LC-QTOF-MS/MS. Collectively, the results are given in co-occurrence heat-maps to help researchers obtain an overview of the transcripts and their differential expression in the Papaver development life cycle, particularly in leaves. Moreover, this dataset will be a valuable resource to derive hypotheses to mitigate an array of Papaver developmental and secondary metabolite biosynthesis issues in the future.
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Wang Y, Li X, Lin Y, Wang Y, Wang K, Sun C, Lu T, Zhang M. Structural Variation, Functional Differentiation, and Activity Correlation of the Cytochrome P450 Gene Superfamily Revealed in Ginseng. THE PLANT GENOME 2018; 11:170106. [PMID: 30512034 DOI: 10.3835/plantgenome2017.11.0106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ginseng ( C.A. Mey.) is one of the most important medicinal herbs for human health and medicine, for which ginsenosides are the major bioactive components. The cytochrome P450 genes, , form a large gene superfamily; however, only three genes have been identified from ginseng and shown to be involved in ginsenoside biosynthesis, indicating the importance of the gene superfamily in the process. Here we report genome-wide identification and systems analysis of the genes in ginseng, defined as genes. We identified 414 genes, including the three published genes. These genes formed a superfamily consisting of 41 gene families, with a substantial diversity in phylogeny and dramatic variation in spatiotemporal expression. Gene ontology (GO) analysis categorized the gene superfamily into 12 functional subcategories distributing among all three primary functional categories, suggesting its functional differentiation. Nevertheless, the majority of its gene members expressed correlatively and tended to form a coexpression network and some of them were commonly regulated in expression across tissues and developmental stages. These results have led to genome-wide identification of genes useful for genome-wide identification of the genes involved in ginsenoside biosynthesis in ginseng and provided the first insight into how a gene superfamily functionally differentiates and acts correlatively in plants.
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CYP3C gene regulation by the aryl hydrocarbon and estrogen receptors in zebrafish. Toxicol Appl Pharmacol 2018; 362:77-85. [PMID: 30393146 DOI: 10.1016/j.taap.2018.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/14/2018] [Accepted: 10/24/2018] [Indexed: 11/23/2022]
Abstract
Cytochrome P450 (CYPs) enzymes are critical for the metabolism of exogenous and endogenous compounds. In mammals, the CYP3s are arguably the most important xenobiotic metabolizing enzymes and are all contained within the CYP3A subfamily. In fish, CYP3s include CYP3A and multiple subfamilies unique to the teleost lineage. The goal of this study was to provide insight on the regulation of genes in the CYP3C subfamily. Zebrafish, which have 4 CYP3C genes, were exposed to 17β-estradiol (E2; 0.001-10 μM) or β-naphthoflavone (βNF; 0.005-1 μM), prototypical ligands of the estrogen receptor (ER) and the aryl hydrocarbon receptor (AhR), respectively. Gene expression was measured in the liver, intestine and gonads using quantitative PCR. CYP1A and vitellogenin (VTG) gene expression were used as positive controls for AhR and ER regulation, respectively. Exposure to βNF resulted in the dose-dependant induction of CYP1A and CYP3C genes in the female intestine but not in the liver. E2 exposure resulted in the induction of all CYP3Cs in the male intestine and in the female liver. VTG was induced in both female and male livers. CYP3C3 and CYP3C4 were induced in the testis; CYP3C1 and CYP3C4 were slightly induced in the ovary. The time-course of gene induction was investigated in the liver and intestine after exposure to βNF (0.5 μM) and E2 (0.1 μM). Inducible genes were up-regulated within 12 h after exposure. These data support a role for the AhR and ER in the regulation of CYP3Cs. Overall, the induction of CYP3Cs by AhR and ER ligands is different from mammalian CYP3A and may suggest a functional role for CYP3Cs that involves planar aromatic hydrocarbons and steroids.
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Kawade K, Li Y, Koga H, Sawada Y, Okamoto M, Kuwahara A, Tsukaya H, Hirai MY. The cytochrome P450 CYP77A4 is involved in auxin-mediated patterning of the Arabidopsis thaliana embryo. Development 2018; 145:145/17/dev168369. [PMID: 30213790 DOI: 10.1242/dev.168369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/30/2018] [Indexed: 12/30/2022]
Abstract
Metabolism often plays an important role in developmental control, in addition to supporting basal physiological requirements. However, our understanding of this interaction remains limited. Here, we performed quantitative phenome analysis of Arabidopsis thaliana cytochrome P450 mutants to identify a novel interaction between development and metabolism. We found that cyp77a4 mutants exhibit specific defects in cotyledon development, including asymmetric positioning and cup-shaped morphology, which could be rescued by introducing the CYP77A4 gene. Microscopy revealed that the abnormal patterning was detected at least from the 8-cell stage of the cyp77a4 embryos. We next analysed auxin distribution in mutant embryos, as the phenotypes resembled those of auxin-related mutants. We found that the auxin response pattern was severely perturbed in the cyp77a4 embryos owing to an aberrant distribution of the auxin efflux carrier PIN1. CYP77A4 intracellularly localised to the endoplasmic reticulum, which is consistent with the notion that this enzyme acts as an epoxidase of unsaturated fatty acids in the microsomal fraction. We propose that the CYP77A4-dependent metabolic pathway is an essential element for the establishment of polarity in plant embryos.
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Affiliation(s)
- Kensuke Kawade
- Okazaki Institute for Integrative Bioscience, 5-1, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan .,National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yimeng Li
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Koga
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mami Okamoto
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ayuko Kuwahara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hirokazu Tsukaya
- Okazaki Institute for Integrative Bioscience, 5-1, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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Tobias PA, Guest DI, Külheim C, Park RF. De Novo Transcriptome Study Identifies Candidate Genes Involved in Resistance to Austropuccinia psidii (Myrtle Rust) in Syzygium luehmannii (Riberry). PHYTOPATHOLOGY 2018; 108:627-640. [PMID: 29231777 DOI: 10.1094/phyto-09-17-0298-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Austropuccinia psidii, causal agent of myrtle rust, was discovered in Australia in 2010 and has since become established on a wide range of species within the family Myrtaceae. Syzygium luehmannii, endemic to Australia, is an increasingly valuable berry crop. Plants were screened for responses to A. psidii inoculation, and specific resistance, in the form of localized necrosis, was determined in 29% of individuals. To understand the molecular basis underlying this response, mRNA was sequenced from leaf samples taken preinoculation, and at 24 and 48 h postinoculation, from four resistant and four susceptible plants. Analyses, based on de novo transcriptome assemblies for all plants, identified significant expression changes in resistant plants (438 transcripts) 48 h after pathogen exposure compared with susceptible plants (three transcripts). Most significantly up-regulated in resistant plants were gene homologs for transcription factors, receptor-like kinases, and enzymes involved in secondary metabolite pathways. A putative G-type lectin receptor-like kinase was exclusively expressed in resistant individuals and two transcripts incorporating toll/interleukin-1, nucleotide binding site, and leucine-rich repeat domains were up-regulated in resistant plants. The results of this study provide the first early gene expression profiles for a plant of the family Myrtaceae in response to the myrtle rust pathogen.
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Affiliation(s)
- Peri A Tobias
- First and second authors: Sydney Institute of Agriculture, School of Life and Environmental Sciences, University of Sydney, Biomedical Building C81, 1 Central Ave., Australian Technology Park, Eveleigh, NSW 2015, Australia; third author: Research School of Biology, College of Sciences, Australian National University, Canberra, ACT 2601, Australia; and fourth author: Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
| | - David I Guest
- First and second authors: Sydney Institute of Agriculture, School of Life and Environmental Sciences, University of Sydney, Biomedical Building C81, 1 Central Ave., Australian Technology Park, Eveleigh, NSW 2015, Australia; third author: Research School of Biology, College of Sciences, Australian National University, Canberra, ACT 2601, Australia; and fourth author: Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
| | - Carsten Külheim
- First and second authors: Sydney Institute of Agriculture, School of Life and Environmental Sciences, University of Sydney, Biomedical Building C81, 1 Central Ave., Australian Technology Park, Eveleigh, NSW 2015, Australia; third author: Research School of Biology, College of Sciences, Australian National University, Canberra, ACT 2601, Australia; and fourth author: Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
| | - Robert F Park
- First and second authors: Sydney Institute of Agriculture, School of Life and Environmental Sciences, University of Sydney, Biomedical Building C81, 1 Central Ave., Australian Technology Park, Eveleigh, NSW 2015, Australia; third author: Research School of Biology, College of Sciences, Australian National University, Canberra, ACT 2601, Australia; and fourth author: Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia
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50
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Rains MK, Gardiyehewa de Silva ND, Molina I. Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues. TREE PHYSIOLOGY 2018; 38:340-361. [PMID: 28575526 DOI: 10.1093/treephys/tpx060] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/18/2017] [Indexed: 05/09/2023]
Abstract
The tree bark periderm confers the first line of protection against pathogen invasion and abiotic stresses. The phellogen (cork cambium) externally produces cork (phellem) cells that are dead at maturity; while metabolically active, these tissues synthesize cell walls, as well as cell wall modifications, namely suberin and waxes. Suberin is a heteropolymer with aliphatic and aromatic domains, composed of acylglycerols, cross-linked polyphenolics and solvent-extractable waxes. Although suberin is essentially ubiquitous in vascular plants, the biochemical functions of many enzymes and the genetic regulation of its synthesis are poorly understood. We have studied suberin and wax composition in four developmental stages of hybrid poplar (Populus tremula x Populus alba) stem periderm. The amounts of extracellular ester-linked acyl lipids per unit area increased with tissue age, a trend not observed with waxes. We used RNA-Seq deep-sequencing technology to investigate the cork transcriptome at two developmental stages. The transcript analysis yielded 455 candidates for the biosynthesis and regulation of poplar suberin, including genes with proven functions in suberin metabolism, genes highlighted as candidates in other plant species and novel candidates. Among these, a gene encoding a putative lipase/acyltransferase of the GDSL-motif family emerged as a suberin polyester synthase candidate, and specific isoforms of peroxidase and laccase genes were preferentially expressed in cork, suggesting that their corresponding proteins may be involved in cross-linking aromatics to form lignin-like polyphenolics. Many transcriptional regulators with possible roles in meristem identity, cork differentiation and acyl-lipid metabolism were also identified. Our work provides the first large-scale transcriptomic dataset on the suberin-synthesizing tissue of poplar bark, contributing to our understanding of tree bark development at the molecular level. Based on these data, we have proposed a number of hypotheses that can be used in future research leading to novel biological insights into suberin biosynthesis and its physiological function.
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Affiliation(s)
- Meghan K Rains
- Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6
- Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4
| | - Nayana Dilini Gardiyehewa de Silva
- Department of Biology and Institute of Biochemistry, Nesbitt Biology Building, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
| | - Isabel Molina
- Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6
- Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4
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