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Rolli E, Ghitti E, Mapelli F, Borin S. Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity. FRONTIERS IN PLANT SCIENCE 2024; 15:1429096. [PMID: 39036359 PMCID: PMC11258928 DOI: 10.3389/fpls.2024.1429096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/13/2024] [Indexed: 07/23/2024]
Abstract
Introduction The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized. Methods Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms. Results Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation. Discussion These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.
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Affiliation(s)
| | | | | | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Gao Q, Li X, Xiang C, Li R, Xie H, Liu J, Li X, Zhang G, Yang S, Liang Y, Zhai C, Zhao Y. EbbHLH80 Enhances Salt Responses by Up-Regulating Flavonoid Accumulation and Modulating ROS Levels. Int J Mol Sci 2023; 24:11080. [PMID: 37446256 DOI: 10.3390/ijms241311080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
bHLH transcription factors are involved in multiple aspects of plant biology, such as the response to abiotic stress. Erigeron breviscapus is a composite plant, and its rich flavonoids have strong preventive and therapeutic effects on cardio cerebral vascular disease. EbbHLH80, a gene from E. breviscapus that positively regulates flavonoid synthesis, was previously characterized. However, it is unclear whether EbbHLH80 increases flavonoid accumulation, which affects salt tolerance. The function of EbbHLH80 in transgenic tobacco seeds was identified by phylogenetic analysis and metabolome-transcriptome analysis. We investigated the role of EbbHLH80 in salt stress response. Our results showed that the expression of EbbHLH80 increased following salt treatment. Integrating the metabolome and transcriptome analysis of EbbHLH80-OE and Yunyan 87 (WT) seeds, we identified several genes and metabolites related to flavonoid biosynthesis and salt stress. Moreover, EbbHLH80-OE plants displayed higher salt tolerance than wild-type plants during seed germination and seedling growth. After salt treatment, transgenic tobacco had significantly lower levels of reactive oxygen species (ROS) than WT, with enhanced levels of antioxidant enzyme expression. Altogether, our results demonstrated that EbbHLH80 might be a positive regulator, promoting salt tolerance by modulating ROS scavenging and increasing stress-responsive genes.
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Affiliation(s)
- Qingqing Gao
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Xia Li
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Chunfan Xiang
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Ruolan Li
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Hongchun Xie
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Jia Liu
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Xiaoning Li
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Guanghui Zhang
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Shengchao Yang
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yanli Liang
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Chenxi Zhai
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Yan Zhao
- National-Local Joint Engineering Research Center on Gemplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming 650201, China
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Xie J, Ma Y, Li X, Wu J, Martin F, Zhang D. Multifeature analysis of age-related microbiome structures reveals defense mechanisms of Populus tomentosa trees. THE NEW PHYTOLOGIST 2023; 238:1636-1650. [PMID: 36856329 DOI: 10.1111/nph.18847] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Root microbiota composition shifts during the development of most annual plants. Although some perennial plants can live for centuries, the host-microbiome partnerships and interaction mechanisms underlying their longevity remain unclear. To address this gap, we investigated age-related changes in the root metabolites, transcriptomes, and microbiome compositions of 1- to 35-yr-old Populus tomentosa trees. Ten co-response clusters were obtained according to their accumulation patterns, and members of each cluster displayed a uniform and clear pattern of abundance. Multi-omics network analysis demonstrated that the increased abundance of Actinobacteria with tree age was strongly associated with the flavonoid biosynthesis. Using genetic approaches, we demonstrate that the flavonoid biosynthesis regulator gene Transparent Testa 8 is associated with the recruitment of flavonoid-associated Actinobacteria. Further inoculation experiments of Actinobacteria isolates indicated that their colonization could significantly improve the host's phenotype. Site-directed mutagenesis revealed that the hyBl gene cluster, involved in biosynthesis of an aminocyclitol hygromycin B analog in Streptomyces isolate bj1, is associated with disease suppression. We hypothesize that interactions between perennial plants and soil microorganisms lead to gradual enrichment of a subset of microorganisms that may harbor a wealth of currently unknown functional traits.
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Affiliation(s)
- Jianbo Xie
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
| | - Yuchao Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
| | - Xian Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
| | - Jiadong Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
| | - Francis Martin
- INRA-Université de Lorraine, INRAe, UMR 1136, Interactions Arbres/Microorganismes, INRAe-Grand Est-Nancy, 54280, Champenoux, France
| | - Deqiang Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
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Jan R, Asaf S, Lubna, Asif S, Kim EG, Jang YH, Kim N, Al-Harrasi A, Lee GS, Kim KM. Enhancing the Expression of the OsF3H Gene in Oryza sativa Leads to the Regulation of Multiple Biosynthetic Pathways and Transcriptomic Changes That Influence Insect Resistance. Int J Mol Sci 2022; 23:15308. [PMID: 36499636 PMCID: PMC9737463 DOI: 10.3390/ijms232315308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The white-backed planthopper (WBPH) is a major pest of rice crops and causes severe loss of yield. We previously developed the WBPH-resistant rice cultivar "OxF3H" by overexpressing the OsF3H gene. Although there was a higher accumulation of the flavonoids kaempferol (Kr) and quercetin (Qu) as well as salicylic acid (SA) in OxF3H transgenic (OsF3H or Trans) plants compared to the wild type (WT), it is still unclear how OsF3H overexpression affects these WBPH resistant-related changes in gene expression in OxF3H plants. In this study, we analyze RNA-seq data from OxF3H and WT at several points (0 h, 3 h, 12 h, and 24 h) after WBPH infection to explain how overall changes in gene expression happen in these two cultivars. RT-qPCR further validated a number of the genes. Results revealed that the highest number of DEGs (4735) between the two genotypes was detected after 24 h of infection. Interestingly, it was found that several of the DEGs between the WT and OsF3H under control conditions were also differentially expressed in OsF3H in response to WBPH infestation. These results indicate that significant differences in gene expression between the "OxF3H" and "WT" exist as the infection time increases. Many of these DEGs were related to oxidoreductase activity, response to stress, salicylic acid biosynthesis, metabolic process, defense response to pathogen, cellular response to toxic substance, and regulation of hormone levels. Moreover, genes involved in salicylic acid (SA) and ethylene (Et) biosynthesis were upregulated in OxF3H plants, while jasmonic acid (JA), brassinosteroid (Br), and abscisic acid (ABA) signaling pathways were found downregulated in OxF3H plants during WBPH infestation. Interestingly, many DEGs related to pathogenesis, such as OsPR1, OsPR1b, OsNPR1, OsNPR3, and OsNPR5, were found to be significantly upregulated in OxF3H plants. Additionally, genes related to the MAPKs pathway and about 30 WRKY genes involved in different pathways were upregulated in OxF3H plants after WBPH infestation. This suggests that overexpression of the OxF3H gene leads to multiple transcriptomic changes and impacts plant hormones and pathogenic-related and secondary-metabolites-related genes, enhancing the plant's resistance to WBPH infestation.
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Affiliation(s)
- Rahmatullah Jan
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, Nizwa 611, Oman
| | - Lubna
- Department of Botany, Garden Campus, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Saleem Asif
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eun-Gyeong Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yoon-Hee Jang
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Nari Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Science Research Center, University of Nizwa, Nizwa 611, Oman
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Kyung-Min Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
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Singh G, Sharma S, Rawat S, Sharma RK. Plant Specialised Glycosides (PSGs): their biosynthetic enzymatic machinery, physiological functions and commercial potential. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1009-1028. [PMID: 36038144 DOI: 10.1071/fp21294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Plants, the primary producers of our planet, have evolved from simple aquatic life to very complex terrestrial habitat. This habitat transition coincides with evolution of enormous chemical diversity, collectively termed as 'Plant Specialised Metabolisms (PSMs)', to cope the environmental challenges. Plant glycosylation is an important process of metabolic diversification of PSMs to govern their in planta stability, solubility and inter/intra-cellular transport. Although, individual category of PSMs (terpenoids, phenylpropanoids, flavonoids, saponins, alkaloids, phytohormones, glucosinolates and cyanogenic glycosides) have been well studied; nevertheless, deeper insights of physiological functioning and genomic aspects of plant glycosylation/deglycosylation processes including enzymatic machinery (CYPs, GTs, and GHs) and regulatory elements are still elusive. Therefore, this review discussed the paradigm shift on genomic background of enzymatic machinery, transporters and regulatory mechanism of 'Plant Specialised Glycosides (PSGs)'. Current efforts also update the fundamental understanding about physiological, evolutionary and adaptive role of glycosylation/deglycosylation processes during the metabolic diversification of PSGs. Additionally, futuristic considerations and recommendations for employing integrated next-generation multi-omics (genomics, transcriptomics, proteomics and metabolomics), including gene/genome editing (CRISPR-Cas) approaches are also proposed to explore commercial potential of PSGs.
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Affiliation(s)
- Gopal Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India; and Present address: Department of Plant Functional Metabolomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Shikha Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
| | - Sandeep Rawat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Present address: G. B. Pant National Institute of Himalayan Environment and Sustainable Development, Sikkim Regional Centre, Pangthang, Gangtok 737101, Sikkim, India
| | - Ram Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
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Sipari N, Lihavainen J, Keinänen M. Metabolite Profiling of Paraquat Tolerant Arabidopsis thaliana Radical-induced Cell Death1 ( rcd1)-A Mediator of Antioxidant Defence Mechanisms. Antioxidants (Basel) 2022; 11:antiox11102034. [PMID: 36290757 PMCID: PMC9598866 DOI: 10.3390/antiox11102034] [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: 09/09/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
RADICAL-INDUCED CELL DEATH1 (RCD1) is an Arabidopsis thaliana nuclear protein that is disrupted during oxidative stress. RCD1 is considered an important integrative node in development and stress responses, and the rcd1 plants have several phenotypes and altered resistance to a variety of abiotic and biotic stresses. One of the phenotypes of rcd1 is resistance to the herbicide paraquat, but the mechanisms behind it are unknown. Paraquat causes a rapid burst of reactive oxygen species (ROS) initially in the chloroplast. We performed multi-platform metabolomic analyses in wild type Col-0 and paraquat resistant rcd1 plants to identify pathways conveying resistance and the function of RCD1 in this respect. Wild type and rcd1 plants were clearly distinguished by their abundance of antioxidants and specialized metabolites and their responses to paraquat. The lack of response in rcd1 suggested constitutively active defense against ROS via elevated flavonoid, glutathione, β-carotene, and tocopherol levels, whereas its ascorbic acid levels were compromised under non-stressed control conditions when compared to Col-0. We propose that RCD1 acts as a hub that maintains basal antioxidant system, and its inactivation induces defense responses by enhancing the biosynthesis and redox cycling of low molecular weight antioxidants and specialized metabolites with profound antioxidant activities alleviating oxidative stress.
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Affiliation(s)
- Nina Sipari
- Viikki Metabolomics Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, FI-00014 Helsinki, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Correspondence: (N.S.); (M.K.)
| | - Jenna Lihavainen
- Umeå Plant Science Center, Department of Plant Physiology, Umeå Universitet, 90 187 Umeå, Sweden
| | - Markku Keinänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Institute of Photonics, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Correspondence: (N.S.); (M.K.)
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Gao Q, Song W, Li X, Xiang C, Chen G, Xiang G, Liu X, Zhang G, Li X, Yang S, Zhai C, Zhao Y. Genome-wide identification of bHLH transcription factors: Discovery of a candidate regulator related to flavonoid biosynthesis in Erigeron breviscapus. FRONTIERS IN PLANT SCIENCE 2022; 13:977649. [PMID: 36186051 PMCID: PMC9515989 DOI: 10.3389/fpls.2022.977649] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Erigeron breviscapus is a Compositae plant, and its rich flavonoids have shown strong preventative and curative effects in the treatment of cardio- and cerebrovascular diseases. bHLH genes play a crucial role in plant growth and development. There are 116 EbbHLH genes in E. breviscapus, and each gene has been named based on its chromosome location. Our phylogenetic analysis divided these genes into 18 subfamilies. To further investigate its function, EbbHLH80 was isolated from E. breviscapus leaves. Next, transcriptomic and metabolomic analyses of tobacco leaves were performed. Among 421 differentially accumulated compounds, 98 flavonoids were identified. In addition, differentially expressed genes were identified using RNA-seq, and further analysis suggested that EbbHLH80-OE could not only regulate the expression of some structural genes in the flavonoid biosynthesis pathway to achieve flavonoid accumulation but also be involved in the regulation of a series of downstream pathways, such as stress response, ABA and ethylene signal transduction, to affect plant growth and development. The results of our analysis provide new insights into the function of EbbHLH80 and lay the foundation for future functional studies on E. breviscapus.
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Affiliation(s)
- Qingqing Gao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Wanling Song
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Xia Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Chunfan Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Geng Chen
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Guisheng Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiangyu Liu
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Guanghui Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiaoning Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Shengchao Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Chenxi Zhai
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, United States
| | - Yan Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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Ferrari RC, Kawabata AB, Ferreira SS, Hartwell J, Freschi L. A matter of time: regulatory events behind the synchronization of C4 and crassulacean acid metabolism in Portulaca oleracea. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4867-4885. [PMID: 35439821 DOI: 10.1093/jxb/erac163] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Portulaca species can switch between C4 and crassulacean acid metabolism (CAM) depending on environmental conditions. However, the regulatory mechanisms behind this rare photosynthetic adaptation remain elusive. Using Portulaca oleracea as a model system, here we investigated the involvement of the circadian clock, plant hormones, and transcription factors in coordinating C4 and CAM gene expression. Free-running experiments in constant conditions suggested that C4 and CAM gene expression are intrinsically connected to the circadian clock. Detailed time-course, drought, and rewatering experiments revealed distinct time frames for CAM induction and reversion (days versus hours, respectively), which were accompanied by changes in abscisic acid (ABA) and cytokinin metabolism and signaling. Exogenous ABA and cytokinins were shown to promote and repress CAM expression in P. oleracea, respectively. Moreover, the drought-induced decline in C4 transcript levels was completely recovered upon cytokinin treatment. The ABA-regulated transcription factor genes HB7, NFYA7, NFYC9, TT8, and ARR12 were identified as likely candidate regulators of CAM induction following this approach, whereas NFYC4 and ARR9 were connected to C4 expression patterns. Therefore, we provide insights into the signaling events controlling C4-CAM transitions in response to water availability and over the day/night cycle, highlighting candidate genes for future functional studies in the context of facultative C4-CAM photosynthesis.
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Affiliation(s)
- Renata Callegari Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Aline Bastos Kawabata
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
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9
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Yan L, Yang H, Ye Q, Huang Z, Zhou H, Cui D. Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L. PeerJ 2022; 10:e13659. [PMID: 35811818 PMCID: PMC9261937 DOI: 10.7717/peerj.13659] [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: 09/22/2021] [Accepted: 06/09/2022] [Indexed: 01/17/2023] Open
Abstract
Dioscorea cirrhosa is a plant that is used as a dye as well as in medicine. Many metabolites with pharmacological activity exist in the tubers of D. cirrhosa. However, little is known about the mechanism regulating biosynthesis in these metabolites. In this study, transcriptome and metabolome profiling were performed in four color tubers. A total of 531 metabolites, including 62 flavonoids, were identified. Epicatechin and proanthocyanin B2 were the key metabolites that exhibited high content levels in the four tubers. These metabolites were divided into nine classes with distinct change patterns. A total of 22,865 differentially expressed genes (DEGs) were identified by transcriptome analysis. Among these DEGs, we identified 67 candidate genes related to the flavonoid biosynthesis pathway and three genes that played pivotal roles in proanthocyanin (PA) synthesis. A weighted gene co-expression network analysis (WGCNA) revealed that the two modules, "MEblue" and "MEblack," were two key gene sets strongly associated with phenylpropanoid and flavonoid biosynthesis. We also found that the plant hormone signal transduction biological process exhibited activity in the late stage of tuber color formation. Additionally, we identified 37 hub transcript factors related to flavonoid biosynthesis, of which 24 were found to be highly associated with flavonoid pathway genes. In addition to the MYB-bHLH-WD40 (MBW) genes, we found that the plant hormone gene families exhibited high expression levels. This study provides a reference for understanding the synthesis of D. cirrhosa tuber metabolites at the molecular level and provides a foundation for the further development of D. cirrhosa related plant pigments as well as its further use in the pharmaceutical industry.
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Affiliation(s)
- Lin Yan
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Haijun Yang
- Center of Experimental Teaching for Common Basic Courses, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qiang Ye
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhihua Huang
- Shenzhen Liangzi Fashion Industeial Co. Ltd., Shenzhen, Guangdong, China
| | - Hongying Zhou
- Shenzhen Tianyi Xunyuan Ecological Culture Investment Co.Ltd., Shenzhen, Guangdong, China
| | - Dafang Cui
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
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10
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Aguilar-Benitez D, Casimiro-Soriguer I, Ferrandiz C, Torres AM. Study and QTL mapping of reproductive and morphological traits implicated in the autofertility of faba bean. BMC PLANT BIOLOGY 2022; 22:175. [PMID: 35387612 PMCID: PMC8985305 DOI: 10.1186/s12870-022-03499-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Autofertility describes the ability of faba bean flowers to self-fertilize thereby ensuring the productivity of this crop in the absence of pollinators or mechanical disturbance. In the legume crop faba bean (Vicia faba L.), lack of autofertility in a context of insufficient pollination can lead to a severe decrease in grain yield. Here we performed the first QTL analysis aimed at identifying the genomic regions controlling autofertility in this crop. We combined pod and seed setting scores from a recombinant inbred population (RIL) segregating for autofertility in different environments and years with measurements of morphological floral traits and pollen production and viability. This approach revealed 19 QTLs co-localizing in six genomic regions. Extensive co-localization was evident for various floral features whose QTLs clustered in chrs. I, II and V, while other QTLs in chrs. III, IV and VI revealed co-localization of flower characteristics and pod and seed set data. The percentage of phenotypic variation explained by the QTLs ranged from 8.9 for style length to 25.7 for stigma angle. In the three QTLs explaining the highest phenotypic variation (R 2 > 20), the marker alleles derived from the autofertile line Vf27. We further inspected positional candidates identified by these QTLs which represent a valuable resource for further validation. Our results advance the understanding of autofertility in faba bean and will aid the identification of responsible genes for genomic-assisted breeding in this crop.
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Affiliation(s)
- David Aguilar-Benitez
- Área de Mejora y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo. 3092, 14080, Córdoba, Spain
| | - Inés Casimiro-Soriguer
- Área de Mejora y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo. 3092, 14080, Córdoba, Spain.
| | - Cristina Ferrandiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politécnica de Valencia, 46022, Valencia, Spain
| | - Ana M Torres
- Área de Mejora y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo. 3092, 14080, Córdoba, Spain
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11
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Wurms K, Ah Chee A, Stannard K, Anderson R, Jensen D, Cooney J, Hedderley D. Defence Responses Associated with Elicitor-Induced, Cultivar-Associated Resistance to Latania Scale in Kiwifruit. PLANTS (BASEL, SWITZERLAND) 2021; 11:10. [PMID: 35009014 PMCID: PMC8747134 DOI: 10.3390/plants11010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Latania scale insect is a pest of global significance affecting kiwifruit. The sessile insect (life stage: settled crawler-mature adult) is covered with a waxy cap that protects it from topical pesticides, so increasingly, a selection of resistant cultivars and application of elicitors are being used in pest control. Thus far, the application of a salicylic acid (SA) phytohormone pathway elicitor, acibenzolar-S-methyl (ASM), has been shown to reduce insect development (as indicated by cap size) on one kiwifruit cultivar ('Hayward'). To investigate how cultivar-associated resistance is affected by the ability to respond to different elicitors, we measured phytohormones (by LCMS) and gene expression (by qPCR and NanoString) on latania scale-tolerant 'Hort16A' and susceptible 'Hayward' kiwifruit over two seasons. Potted plants in the presence/absence of settled latania scales were treated with ASM (0.2 g/L) or methyl jasmonate (MeJA, 0.05% v/v), representing elicitors of the SA and JA signalling pathways, respectively. 'Hort16A' cultivar resistance to latania scale was associated with elevated expression of SA and SA-related defence genes (PR1 and two PR2 family genes) in the ASM treatment. MeJA treatments did not significantly affect insect development in 'Hayward' (latania scale did not survive on 'Hort16A') and did not correlate with phytohormone and gene expression measurements in either cultivar. 'Hayward' had greater concentrations than 'Hort16A' of inert storage forms of both SA and JA across all treatments. This information contributes to the selection of tolerant cultivars and the effective use of elicitors for control of latania scale in kiwifruit.
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Affiliation(s)
- Kirstin Wurms
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Private Bag 3230, Waikato Mail Centre, Hamilton 3240, New Zealand; (A.A.C.); (D.J.); (J.C.)
| | - Annette Ah Chee
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Private Bag 3230, Waikato Mail Centre, Hamilton 3240, New Zealand; (A.A.C.); (D.J.); (J.C.)
| | - Kate Stannard
- Plant & Food Research, 412 No. 1 Road, RD2, Te Puke 3182, New Zealand; (K.S.); (R.A.)
| | - Rachelle Anderson
- Plant & Food Research, 412 No. 1 Road, RD2, Te Puke 3182, New Zealand; (K.S.); (R.A.)
| | - Dwayne Jensen
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Private Bag 3230, Waikato Mail Centre, Hamilton 3240, New Zealand; (A.A.C.); (D.J.); (J.C.)
| | - Janine Cooney
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Private Bag 3230, Waikato Mail Centre, Hamilton 3240, New Zealand; (A.A.C.); (D.J.); (J.C.)
| | - Duncan Hedderley
- Plant & Food Research, Private Bag 11600, Palmerston North 4442, New Zealand;
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12
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Gao R, Han T, Xun H, Zeng X, Li P, Li Y, Wang Y, Shao Y, Cheng X, Feng X, Zhao J, Wang L, Gao X. MYB transcription factors GmMYBA2 and GmMYBR function in a feedback loop to control pigmentation of seed coat in soybean. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4401-4418. [PMID: 33825878 DOI: 10.1093/jxb/erab152] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Soybean has undergone extensive selection pressures for seed nutrient composition and seed color during domestication, but the major genetic loci controlling seed coat color have not been completely understood, and the transcriptional regulation relationship among the loci remains elusive. Here, two major regulators, GmMYBA2 and GmMYBR, were functionally characterized as an anthocyanin activator and repressor, respectively. Ectopic expression of GmMYBA2 in soybean hairy roots conferred the enhanced accumulation of delphinidin and cyanidin types of anthocyanins in W1t and w1T backgrounds, respectively, through activating anthocyanin biosynthetic genes in the reported loci. The seed coat pigmentation of GmMYBA2-overexpressing transgenic plants in the W1 background mimicked the imperfect black phenotype (W1/w1, i, R, t), suggesting that GmMYBA2 was responsible for the R locus. Molecular and biochemical analysis showed that GmMYBA2 interacted with GmTT8a to directly activate anthocyanin biosynthetic genes. GmMYBA2 and GmMYBR might form a feedback loop to fine-tune seed coat coloration, which was confirmed in transgenic soybeans. Both GmTT8a and GmMYBR that were activated by GmMYBA2 in turn enhanced and obstructed the formation of the GmMYBA2-GmTT8a module, respectively. The results revealed the sophisticated regulatory network underlying the soybean seed coat pigmentation loci and shed light on the understanding of the seed coat coloration and other seed inclusions.
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Affiliation(s)
- Ruifang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Taotao Han
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Hongwei Xun
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Agro-Biotechnology Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiangsheng Zeng
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Yanan Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Yan Shao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xin Cheng
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
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13
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Abbasi S, Sadeghi A, Omidvari M, Tahan V. The stimulators and responsive genes to induce systemic resistance against pathogens: An exclusive focus on tomato as a model plant. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.101993] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Zhan X, Qi J, Zhou B, Mao B. Metabolomic and transcriptomic analyses reveal the regulation of pigmentation in the purple variety of Dendrobium officinale. Sci Rep 2020; 10:17700. [PMID: 33077850 PMCID: PMC7573623 DOI: 10.1038/s41598-020-74789-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/06/2020] [Indexed: 01/02/2023] Open
Abstract
We performed an integrated analysis of the transcriptome and metabolome from purple (Pr) and normal cultivated varieties (CK) of Dendrobium officinale to gain insights into the regulatory networks associated with phenylpropanoid metabolism and to identify the key regulatory genes of pigmentation. Metabolite and transcript profiling were conducted by ultra-performance liquid chromatography electrospray tandem mass spectrometry (UPLC-ESI-MS/MS) and RNA sequencing. Pr had more flavonoids in the stem than did CK. Metabolome analyses showed that 148 differential metabolites are involved in the biosynthesis of phenylpropanoids, amino acids, purines, and organic acids. Among them, the delphinidin and quercetin derivatives were significantly higher in Pr. A total of 4927 differentially expressed genes (DEGs) were significantly enriched (p ≤ 0.01) in 50 Gene Ontology (GO) terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed significantly enriched phenylpropanoid biosynthesis and phytohormone signal transduction in Pr versus CK. The expression levels of flavanone 3-hydroxylase (F3H) and leucoanthocyanidin dioxygenase (LDOX) affected the flux of dihydroflavonol, which led to a color change in Pr. Moreover, DEG enrichment and metabolite analyses reflected flavonoid accumulation in Pr related to brassinosteroid (BR) and auxin metabolism. The results of this study elucidate phenylpropanoid biosynthesis in D. officinale.
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Affiliation(s)
- Xinqiao Zhan
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China.
| | - Jufeng Qi
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Bin Zhou
- Zhejiang Baihua Landscape Group Co., Ltd., Taizhou, 318000, China
| | - Bizeng Mao
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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15
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Dong X, Guo Y, Xiong C, Sun L. Evaluation of Two Major Rhodiola Species and the Systemic Changing Characteristics of Metabolites of Rhodiola crenulata in Different Altitudes by Chemical Methods Combined with UPLC-QqQ-MS-Based Metabolomics. Molecules 2020; 25:E4062. [PMID: 32899531 PMCID: PMC7570721 DOI: 10.3390/molecules25184062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 01/15/2023] Open
Abstract
Rhodiola species have a long history of use in traditional medicine in Asian and European countries and have been considered to possess resistance to the challenges presented by extreme altitudes. However, the influence of different Rhodiola species on quality is unclear, as well as the influence of altitude on phytochemicals. In this study, the phenolic components and antioxidant abilities of two major Rhodiola species are compared, namely Rhodiolacrenulata and Rhodiola rosea, and the metabolomes of Rhodiolacrenulata from two representative elevations of 2907 and 5116 m are analyzed using a UPLC-QqQ-MS-based metabolomics approach. The results show that the phenolic components and antioxidant activities of Rhodiolacrenulata are higher than those of Rhodiola rosea, and that these effects in the two species are positively correlated with elevation. Here, 408 metabolites are identified, of which 178 differential metabolites (128 upregulated versus 50 downregulated) and 19 biomarkers are determined in Rhodiola crenulata. Further analysis of these differential metabolites showed a significant upregulation of flavonoids, featuring glucosides, the enhancement of the phenylpropanoid pathway, and the downregulation of hydrolyzed tannins in Rhodiola crenulata as elevation increased. Besides, the amino acids of differential metabolites were all upregulated as the altitude increased. Our results contribute to further exploring the Rhodiola species and providing new insights into the Rhodiola crenulata phytochemical response to elevation.
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Affiliation(s)
| | | | | | - Liwei Sun
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.D.); (Y.G.); (C.X.)
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16
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Alternative splicing and duplication of PI-like genes in maize. Gene 2020; 769:145064. [PMID: 32891770 DOI: 10.1016/j.gene.2020.145064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/30/2020] [Accepted: 08/17/2020] [Indexed: 11/20/2022]
Abstract
Alternative splicing and duplication provide the possibility of functional divergence of MADS-box genes. Compared with its Arabidopsis counterpart PI gene, Zmm16 in maize recruits a new role in carpel abortion and floral asymmetry, whereas the other two duplicated genes, Zmm18/29, have not yet been attributed to any function in flower development as a typical B class gene does. Here, alternatively spliced transcripts of three PIL genes were analyzed, among which we described the candidate functional isoforms and analyzed the potential effects of alternative splicing (AS) on protein-protein interactions as well, then their phylogenetic relationships with orthologs in typical grasses were further analyzed. Furthermore, we compared the cis-acting elements specific for three maize PIL genes, especially the elements related to methyl jasmonate (MeJA) and gibberellic acid (GA), both hormones involved in the sex-determination process in maize. Together with the results from the co-expression networks during reproductive organ development, we speculated that, due to duplication and alternative splicing, Zmm18/29 may play a role in GA- and MeJA-related developmental process. These results provide novel clues for experimental validation of the evolutional meaning of maize PIL genes.
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17
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Yu Y, Qian Y, Jiang M, Xu J, Yang J, Zhang T, Gou L, Pi E. Regulation Mechanisms of Plant Basic Leucine Zippers to Various Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2020; 11:1258. [PMID: 32973828 PMCID: PMC7468500 DOI: 10.3389/fpls.2020.01258] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/30/2020] [Indexed: 05/05/2023]
Affiliation(s)
| | | | | | | | | | | | | | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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18
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Li SF, Allen PJ, Napoli RS, Browne RG, Pham H, Parish RW. MYB-bHLH-TTG1 Regulates Arabidopsis Seed Coat Biosynthesis Pathways Directly and Indirectly via Multiple Tiers of Transcription Factors. PLANT & CELL PHYSIOLOGY 2020; 61:1005-1018. [PMID: 32154880 DOI: 10.1093/pcp/pcaa027] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
MYB-bHLH-WDR (MBW) transcription factor (TF) complexes regulate Arabidopsis seed coat development including mucilage and tannin biosynthesis. The R2R3 MYBs MYB5, MYB23 and TRANSPARENT TESTA2 (TT2) participate in the MBW complexes with the WD-repeat protein TRANSPARENT TESTA GLABRA1 (TTG1). These complexes regulate GLABRA2 (GL2) and TTG2 expression in developing seeds. Microarray transcriptome analysis of ttg1-1- and wild-type (Ler) developing seeds identified 246 TTG1-regulated genes, which include all known metabolic genes of the tannin biosynthetic pathway. The first detailed TTG1-dependent metabolic pathways could be proposed for the biosynthesis of mucilage, jasmonic acid (JA) and cuticle including wax ester in developing seeds. We also assigned many known and previously uncharacterized genes to the activation/inactivation of hormones, plant immunity and nutrient transport. The promoters of six cuticle pathway genes were active in developing seeds. Expression of 11 genes was determined in the developing seeds of the combinatorial mutants of MYB5, MYB23 and TT2, and in the combinatorial mutants of GL2, HOMEODOMAIN GLABROUS2 (HDG2) and TTG2. These six TFs positively co-regulated the expression of four repressor genes while three of the six TFs repressed the wax biosynthesis genes examined, suggesting that the three TFs upregulate the expression of these repressor genes, which, in turn, repress the wax biosynthesis genes. Chromatin immunoprecipitation analysis identified 21 genes directly regulated by MYB5 including GL2, HDG2, TTG2, four repressor genes and various metabolic genes. We propose a multi-tiered regulatory mechanism by which MBWs regulate tannin, mucilage, JA and cuticle biosynthetic pathways.
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Affiliation(s)
- Song Feng Li
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Patrick J Allen
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Ross S Napoli
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Richard G Browne
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Hanh Pham
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
| | - Roger W Parish
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, Melbourne, VIC 3086, Australia
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19
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Wan L, Lei Y, Yan L, Liu Y, Pandey MK, Wan X, Varshney RK, Fang J, Liao B. Transcriptome and metabolome reveal redirection of flavonoids in a white testa peanut mutant. BMC PLANT BIOLOGY 2020; 20:161. [PMID: 32293272 PMCID: PMC7161308 DOI: 10.1186/s12870-020-02383-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/02/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Coat color determines both appearance and nutrient quality of peanut. White seed coat in peanut can enhance the processing efficiency and quality of peanut oil. An integrative analysis of transcriptomes, metabolomes and histocytology was performed on wsc mutant and its wild type to investigate the regulatory mechanisms underlying color pigmentation. RESULT Metabolomes revealed flavonoids were redirected in wsc, while multi-omics analyses of wsc mutant seeds and testae uncovered WSC influenced the flavonoids biosynthesis in testa as well as suberin formation, glycolysis, the TCA cycle and amino acid metabolism. The mutation also enhanced plant hormones synthesis and signaling. Further, co-expression analysis showed that FLS genes co-expressed with MBW complex member genes. Combining tissue expression patterns, genetic analyses, and the annotation of common DEGs for these three stages revealed that three testa specific expressed candidate genes, Araip.M7RY3, Aradu.R8PMF and Araip.MHR6K were likely responsible for the white testa phenotype. WSC might be regulated expression competition between FLS and DFR by controlling hormone synthesis and signaling as well as the MBW complex. CONCLUSIONS The results of this study therefore provide both candidate genes and novel approaches that can be applied to improve peanut with desirable seed coat color and flavonoid quality.
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Affiliation(s)
- Liyun Wan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yue Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Manish K Pandey
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
| | - Xia Wan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western, Australia, Crawley, WA, Australia
| | - Jiahai Fang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China.
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20
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Gupta A, Sinha R, Fernandes JL, Abdelrahman M, Burritt DJ, Tran LSP. Phytohormones regulate convergent and divergent responses between individual and combined drought and pathogen infection. Crit Rev Biotechnol 2020; 40:320-340. [DOI: 10.1080/07388551.2019.1710459] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Aarti Gupta
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Joel Lars Fernandes
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Mostafa Abdelrahman
- Arid Land Research Center, Tottori University, Tottori, Japan
- Botany Department, Faculty of Science, Aswan University, Aswan, Egypt
| | | | - Lam-Son Phan Tran
- Plant Stress Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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21
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Shimizu Y, Rai A, Okawa Y, Tomatsu H, Sato M, Kera K, Suzuki H, Saito K, Yamazaki M. Metabolic diversification of nitrogen-containing metabolites by the expression of a heterologous lysine decarboxylase gene in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:505-521. [PMID: 31364191 PMCID: PMC6899585 DOI: 10.1111/tpj.14454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 05/03/2019] [Accepted: 06/25/2019] [Indexed: 05/04/2023]
Abstract
Lysine decarboxylase converts l-lysine to cadaverine as a branching point for the biosynthesis of plant Lys-derived alkaloids. Although cadaverine contributes towards the biosynthesis of Lys-derived alkaloids, its catabolism, including metabolic intermediates and the enzymes involved, is not known. Here, we generated transgenic Arabidopsis lines by expressing an exogenous lysine/ornithine decarboxylase gene from Lupinus angustifolius (La-L/ODC) and identified cadaverine-derived metabolites as the products of the emerged biosynthetic pathway. Through untargeted metabolic profiling, we observed the upregulation of polyamine metabolism, phenylpropanoid biosynthesis and the biosynthesis of several Lys-derived alkaloids in the transgenic lines. Moreover, we found several cadaverine-derived metabolites specifically detected in the transgenic lines compared with the non-transformed control. Among these, three specific metabolites were identified and confirmed as 5-aminopentanal, 5-aminopentanoate and δ-valerolactam. Cadaverine catabolism in a representative transgenic line (DC29) was traced by feeding stable isotope-labeled [α-15 N]- or [ε-15 N]-l-lysine. Our results show similar 15 N incorporation ratios from both isotopomers for the specific metabolite features identified, indicating that these metabolites were synthesized via the symmetric structure of cadaverine. We propose biosynthetic pathways for the metabolites on the basis of metabolite chemistry and enzymes known or identified through catalyzing specific biochemical reactions in this study. Our study shows that this pool of enzymes with promiscuous activities is the driving force for metabolite diversification in plants. Thus, this study not only provides valuable information for understanding the catabolic mechanism of cadaverine but also demonstrates that cadaverine accumulation is one of the factors to expand plant chemodiversity, which may lead to the emergence of Lys-derived alkaloid biosynthesis.
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Affiliation(s)
- Yohei Shimizu
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
- RIKEN Center for Sustainable Resource Science1‐7‐22 Suehiro‐cho, Tsurumi‐kuYokohama230‐0045Japan
| | - Amit Rai
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
| | - Yuko Okawa
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
| | - Hajime Tomatsu
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
- Present address:
Human Metabolome Technologies, Inc.246‐2 Mizukami, KakuganjiTsuruokaYamagata997‐0052Japan
| | - Masaru Sato
- Kazusa DNA Research Institute2‐6‐7 Kazusa‐KamatariKisarazuChiba292‐0818Japan
| | - Kota Kera
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
- Present address:
Department of Biomolecular EngineeringGraduate School of EngineeringTohoku UniversityAobayama 6‐6‐07Sendai980‐8579Japan
| | - Hideyuki Suzuki
- Kazusa DNA Research Institute2‐6‐7 Kazusa‐KamatariKisarazuChiba292‐0818Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
- RIKEN Center for Sustainable Resource Science1‐7‐22 Suehiro‐cho, Tsurumi‐kuYokohama230‐0045Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical SciencesChiba University1‐8‐1 Inohana, Chuo‐kuChiba260‐8675Japan
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22
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Pan D, Pavagadhi S, Umashankar S, Rai A, Benke PI, Rai M, Saxena G, Gangu V, Swarup S. Resource partitioning strategies during toxin production in Microcystis aeruginosa revealed by integrative omics analysis. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Mao TY, Liu YY, Zhu HH, Zhang J, Yang JX, Fu Q, Wang N, Wang Z. Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plant Nelumbo nucifera. PeerJ 2019; 7:e7153. [PMID: 31231599 PMCID: PMC6573809 DOI: 10.7717/peerj.7153] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/17/2019] [Indexed: 12/20/2022] Open
Abstract
Lotus (Nelumbo nucifera Gaertn.) is an economically important aquatic plant with multiple applications, but water salinity and cold stress seriously affect lotus yield and distribution. The basic helix-loop-helix (bHLH) transcription factors (TFs) play a vital role in plant growth and development, metabolic regulation processes and responses to environmental changes. However, systematic analyses of the bHLH TF family in lotus has not yet been reported. Here, we report the identification and description of bHLH genes in lotus (NnbHLHs) with a focus on functional prediction, particularly for those involved in stress resistance. In all, 115 NnbHLHs were identified in the lotus genome and classified into 19 subfamilies. The chromosomal distribution, physicochemical properties, bHLH domain, conserved motif compositions and evolution of these 115 NnbHLHs were further analyzed. To better understand the functions of the lotus bHLH family, gene ontology, cis-element, and phylogenetic analyses were conducted. NnbHLHs were predicted to be involved in plant development, metabolic regulation and responses to stress, in accordance with previous findings. Overall, 15 NnbHLHs were further investigated with functional prediction via quantitative real-time PCR analyses. Meanwhile, expression profiles of NnbHLHs in four tissues indicated that many NnbHLHs showed tissue preference in their expression. This study is supposed to provide a good foundation for further research into the functions and evolution of NnbHLHs, and identifies candidate genes for stress resistance in lotus.
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Affiliation(s)
- Tian-Yu Mao
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Yao-Yao Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Huan-Huan Zhu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jie Zhang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ju-Xiang Yang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiang Fu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Nian Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ze Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
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24
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25
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Wang W, Hao Q, Wang W, Li Q, Chen F, Ni F, Wang Y, Fu D, Wu J, Wang W. The involvement of cytokinin and nitrogen metabolism in delayed flag leaf senescence in a wheat stay-green mutant, tasg1. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 278:70-79. [PMID: 30471731 DOI: 10.1016/j.plantsci.2018.10.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/18/2018] [Accepted: 10/31/2018] [Indexed: 05/10/2023]
Abstract
In the present study on a wheat stay-green mutant, tasg1, we found that its delayed senescence at the late filling stage was related to the high cytokinin (CK) and N contents. RNA sequencing suggested that several genes may be responsible for the different senescence processes between wild-type (WT) and tasg1 plants. WT and tasg1 seedlings were treated with NH4NO3, lovastatin, and 6-benzylaminopurine (BAP), and the results suggested that the feedback of CK with N content regulated the leaf senescence in the tasg1 plants. Furthermore, a knock-out of the candidate gene cisZOGT1 (catalytic O-glucosylation in cis-zeatin) in the wheat mutant pool 'Kronos' exhibited delayed senescence at the late grain filling stage. Overall, our results suggested the cisZOGT1 gene has an important role in regulating wheat leaf senescence by regulating CK and N metabolism. At the same time, CK and N metabolism involved in delayed flag leaf senescence of tasg1 may be by a feedback pattern.
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Affiliation(s)
- Wenqiang Wang
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, China; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Qunqun Hao
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA; State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Wenlong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Qinxue Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Fengjuan Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Fei Ni
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Daolin Fu
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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26
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Pang Q, Zhang T, Wang Y, Kong W, Guan Q, Yan X, Chen S. Metabolomics of Early Stage Plant Cell-Microbe Interaction Using Stable Isotope Labeling. FRONTIERS IN PLANT SCIENCE 2018; 9:760. [PMID: 29922325 PMCID: PMC5996122 DOI: 10.3389/fpls.2018.00760] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/17/2018] [Indexed: 05/02/2023]
Abstract
Metabolomics has been used in unraveling metabolites that play essential roles in plant-microbe (including pathogen) interactions. However, the problem of profiling a plant metabolome with potential contaminating metabolites from the coexisting microbes has been largely ignored. To address this problem, we implemented an effective stable isotope labeling approach, where the metabolome of a plant bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 was labeled with heavy isotopes. The labeled bacterial cells were incubated with Arabidopsis thaliana epidermal peels (EPs) with guard cells, and excessive bacterial cells were subsequently removed from the plant tissues by washing. The plant metabolites were characterized by liquid chromatography mass spectrometry using multiple reactions monitoring, which can differentiate plant and bacterial metabolites. Targeted metabolomic analysis suggested that Pst DC3000 infection may modulate stomatal movement by reprograming plant signaling and primary metabolic pathways. This proof-of-concept study demonstrates the utility of this strategy in differentiation of the plant and microbe metabolomes, and it has broad applications in studying metabolic interactions between microbes and other organisms.
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Affiliation(s)
- Qiuying Pang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Tong Zhang
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Yang Wang
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Wenwen Kong
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Qijie Guan
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Xiufeng Yan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- *Correspondence: Xiufeng Yan, Sixue Chen,
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, United States
- *Correspondence: Xiufeng Yan, Sixue Chen,
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27
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Singh G, Tiwari M, Singh SP, Singh R, Singh S, Shirke PA, Trivedi PK, Misra P. Sterol glycosyltransferases required for adaptation of Withania somnifera at high temperature. PHYSIOLOGIA PLANTARUM 2017; 160:297-311. [PMID: 28299798 DOI: 10.1111/ppl.12563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/31/2017] [Accepted: 02/14/2017] [Indexed: 05/06/2023]
Abstract
Heat is a major environmental stress factor that confines growth, productivity, and metabolism of plants. Plants respond to such unfavorable conditions through changes in their physiological, biochemical and developmental processes. Withania somnifera, an important medicinal plant, grows in hot and dry conditions, however, molecular mechanisms related to such adaptive properties are not known. Here, we elucidated that members of the sterol glycosyltransferases (SGT) gene family play important roles in the survival of W. somnifera under adverse conditions through maintaining the integrity of the membrane. SGTs are enzymes involved in sterol modifications and participate in metabolic flexibility during stress. Silencing of WsSGT members, for instance WsSGTL1, WsSGTL2 and WsSGTL4, was inimical for important physiological parameters, such as electron transport rate, photochemical quantum yield, acceptor side limitation, non-photochemical quenching (NPQ), Fv/Fm and net photosynthetic rate, whereas stomatal conductance, transpiration rate and dark respiration rates (Rds) were increased. Decreased NPQ and increased Rds helped to generate significant amount of ROS in the Wsamisgt lines. After heat stress, H2 O2 , lipid peroxidation and nitric oxide production increased in the Wsamisgt lines due to high ROS generation. The expression of HSPs in Wsamisgt lines might be involved in regulation of physiological processes during stress. We have also observed increased proline accumulation which might be involved in restricting water loss in the Wsamisgt lines. Taken together, our observations revealed that SGTL enzyme activity is required to maintain the internal damages of the cell against high temperature by maintaining the sterol vs sterol glycosides ratio in the membranes of W. somnifera.
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Affiliation(s)
- Gaurav Singh
- CSIR, National Botanical Research Institute, Lucknow, India
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Manish Tiwari
- Department of Plant Systems Biology, VIB, Ghent University, Ghent, Belgium
| | | | - Ruchi Singh
- CSIR, National Botanical Research Institute, Lucknow, India
| | - Surendra Singh
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | | | | | - Pratibha Misra
- CSIR, National Botanical Research Institute, Lucknow, India
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28
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Rai A, Saito K, Yamazaki M. Integrated omics analysis of specialized metabolism in medicinal plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:764-787. [PMID: 28109168 DOI: 10.1111/tpj.13485] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/19/2023]
Abstract
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high-throughput large-scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant-based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
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Affiliation(s)
- Amit Rai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
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Metabolomics, a Powerful Tool for Agricultural Research. Int J Mol Sci 2016; 17:ijms17111871. [PMID: 27869667 PMCID: PMC5133871 DOI: 10.3390/ijms17111871] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 11/17/2022] Open
Abstract
Metabolomics, which is based mainly on nuclear magnetic resonance (NMR), gas-chromatography (GC) or liquid-chromatography (LC) coupled to mass spectrometry (MS) analytical technologies to systematically acquire the qualitative and quantitative information of low-molecular-mass endogenous metabolites, provides a direct snapshot of the physiological condition in biological samples. As complements to transcriptomics and proteomics, it has played pivotal roles in agricultural and food science research. In this review, we discuss the capacities of NMR, GC/LC-MS in the acquisition of plant metabolome, and address the potential promise and diverse applications of metabolomics, particularly lipidomics, to investigate the responses of Arabidopsis thaliana, a primary plant model for agricultural research, to environmental stressors including heat, freezing, drought, and salinity.
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