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Lin X, Tang B, Li Z, Shi L, Zhu H. Genome-wide identification and expression analyses of CYP450 genes in sweet potato (Ipomoea batatas L.). BMC Genomics 2024; 25:58. [PMID: 38218763 PMCID: PMC10787477 DOI: 10.1186/s12864-024-09965-x] [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: 09/28/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Cytochrome P450 monooxygenases (CYP450s) play a crucial role in various biochemical reactions involved in the synthesis of antioxidants, pigments, structural polymers, and defense-related compounds in plants. As sweet potato (Ipomoea batatas L.) holds significant economic importance, a comprehensive analysis of CYP450 genes in this plant species can offer valuable insights into the evolutionary relationships and functional characteristics of these genes. RESULTS In this study, we successfully identified and categorized 95 CYP450 genes from the sweet potato genome into 5 families and 31 subfamilies. The predicted subcellular localization results indicate that CYP450s are distributed in the cell membrane system. The promoter region of the IbCYP450 genes contains various cis-acting elements related to plant hormones and stress responses. In addition, ten conserved motifs (Motif1-Motif10) have been identified in the IbCYP450 family proteins, with 5 genes lacking introns and only one exon. We observed extensive duplication events within the CYP450 gene family, which may account for its expansion. The gene duplication analysis results showed the presence of 15 pairs of genes with tandem repeats. Interaction network analysis reveals that IbCYP450 families can interact with multiple target genes and there are protein-protein interactions within the family. Transcription factor interaction analysis suggests that IbCYP450 families interact with multiple transcription factors. Furthermore, gene expression analysis revealed tissue-specific expression patterns of CYP450 genes in sweet potatoes, as well as their response to abiotic stress and plant hormones. Notably, quantitative real-time polymerase chain reaction (qRT‒PCR) analysis indicated the involvement of CYP450 genes in the defense response against nonbiological stresses in sweet potatoes. CONCLUSIONS These findings provide a foundation for further investigations aiming to elucidate the biological functions of CYP450 genes in sweet potatoes.
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Affiliation(s)
- Xiongjian Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Binquan Tang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zhenqin Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Lei Shi
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.
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2
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Shen C, Li X. Genome-wide analysis of the P450 gene family in tea plant (Camellia sinensis) reveals functional diversity in abiotic stress. BMC Genomics 2023; 24:535. [PMID: 37697232 PMCID: PMC10494425 DOI: 10.1186/s12864-023-09619-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Cytochrome P450 (Cytochrome P450s) genes are involved in the catalysis of various reactions, including growth, development, and secondary metabolite biosynthetic pathways. However, little is known about the characteristics and functions of the P450 gene family in Camellia sinensis (C. sinensis). RESULTS To reveal the mechanisms of tea plant P450s coping with abiotic stresses, analyses of the tea plant P450 gene family were conducted using bioinformatics-based methods. In total, 273 putative P450 genes were identified from the genome database of C. sinensis. The results showed that P450s were well-balanced across the chromosomes I to XV of entire genome, with amino acid lengths of 268-612 aa, molecular weights of 30.95-68.5 kDa, and isoelectric points of 4.93-10.17. Phylogenetic analysis divided CsP450s into 34 subfamilies, of which CYP71 was the most abundant. The predicted subcellular localization results showed that P450 was distributed in a variety of organelles, with chloroplasts, plasma membrane,,and cytoplasm localized more frequently. The promoter region of CsP450s contained various cis-acting elements related to phytohormones and stress responses. In addition, ten conserved motifs (Motif1-Motif10) were identified in the CsP450 family proteins, with 27 genes lacking introns and only one exon. The results of genome large segment duplication showed that there were 37 pairs of genes with tandem duplication. Interaction network analysis showed that CsP450 could interact with multiple types of target genes, and there are protein interactions within the family. Tissue expression analysis showed that P450 was highly expressed in roots and stems. Moreover, qPCR analysis of the relative expression level of the gene under drought and cold stress correlated with the sequencing results. CONCLUSIONS This study lays the foundation for resolving the classification and functional study of P450 family genes and provides a reference for the molecular breeding of C. sinensis.
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Affiliation(s)
- Chuan Shen
- Shaannan Eco-Economy Research Center, Ankang University, Ankang, 725000, China.
| | - Xia Li
- Department of Electronic and Information Engineering, Ankang University, Ankang, 725000, China
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3
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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: 0] [Impact Index Per Article: 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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4
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Zhou M, Jiang Y, Liu X, Kong W, Zhang C, Yang J, Ke S, Li Y. Genome-Wide Identification and Evolution Analysis of the CYP76 Subfamily in Rice ( Oryza sativa). Int J Mol Sci 2023; 24:ijms24108522. [PMID: 37239869 DOI: 10.3390/ijms24108522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
The CYP76 subfamily, a member of the CYP superfamily, plays crucial roles in the biosynthesis of phytohormones in plants, involving biosynthesis of secondary metabolites, hormone signaling, and response to environmental stresses. Here, we conducted a genome-wide analysis of the CYP76 subfamily in seven AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, and Oryza glumaepatula. These were identified and classified into three groups, and it was found that Group 1 contained the largest number of members. Analysis of cis-acting elements revealed a large number of elements related to jasmonic acid and light response. The gene duplication analysis revealed that the CYP76 subfamily expanded mainly in SD/WGD and tandem forms and underwent strong purifying selection during evolution. Expression pattern analysis of OsCYP76s in various developmental stages revealed that the majority of OsCYP76s exhibit relatively restricted expression patterns in leaves and roots. We further analyzed the expression of CYP76s in O. sativa, japonica, and O. sativa, indica under cold, flooding, drought, and salt abiotic stresses by qRT-PCR. We found that OsCYP76-11 showed a huge increase in relative expression after drought and salt stresses. After flooding stress, OsiCYP76-4 showed a greater increase in expression compared to other genes. CYP76 in japonica and indica showed different response patterns to the same abiotic stresses, revealing functional divergence in the gene family during evolution; these may be the key genes responsible for the differences in tolerance to indica japonica. Our results provide valuable insights into the functional diversity and evolutionary history of the CYP76 subfamily and pave the way for the development of new strategies for improving stress tolerance and agronomic traits in rice.
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Affiliation(s)
- Mingao Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yifei Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xuhui Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Shenzhen Branch, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China
| | - Jian Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Simin Ke
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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5
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Gupta R. Melatonin: A promising candidate for maintaining food security under the threat of phytopathogens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107691. [PMID: 37031544 DOI: 10.1016/j.plaphy.2023.107691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/17/2023] [Accepted: 04/03/2023] [Indexed: 05/07/2023]
Abstract
Plant immune response is tightly controlled by an interplay of various phytohormones and plant growth regulators. Among them, the role of salicylic acid, jasmonic acid, and ethylene is well established while some others such as nitric oxide, polyamines, and hydrogen sulfide have appeared to be key regulators of plant immunity. In addition, some other chemicals, such as melatonin (N-acetyl-5-methoxytryptamine), are apparently turning out to be the novel regulators of plant defense responses. Melatonin has shown promising results in enhancing resistance of plants to a variety of pathogens including fungi, bacteria, and viruses, however, the molecular mechanism of melatonin-mediated plant immune regulation is currently elusive. Evidence gathered so far indicates that melatonin regulates plant immunity by (1) facilitating the maintenance of ROS homeostasis, (2) interacting with other phytohormones and growth regulators, and (3) inducing the accumulation of defense molecules. Therefore, engineering crops with improved melatonin production could enhance crop productivity under stress conditions. This review extends our understanding of the multifaceted role of melatonin in the regulation of plant defense response and presents a putative pathway of melatonin functioning and its interaction with phytohormones during biotic stress.
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Affiliation(s)
- Ravi Gupta
- College of General Education, Kookmin University, Seoul, 02707, South Korea.
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Jiu S, Chen B, Dong X, Lv Z, Wang Y, Yin C, Xu Y, Zhang S, Zhu J, Wang J, Liu X, Sun W, Yang G, Li M, Li S, Zhang Z, Liu R, Wang L, Manzoor MA, José QG, Wang S, Lei Y, Yang L, Dirlewanger E, Dong Y, Zhang C. Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L. HORTICULTURE RESEARCH 2023; 10:uhad062. [PMID: 37220556 PMCID: PMC10200261 DOI: 10.1093/hr/uhad062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/02/2023] [Indexed: 05/25/2023]
Abstract
Prunus pusilliflora is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled P. pusilliflora genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we de novo assembled a chromosome-scale P. pusilliflora genome using Oxford Nanopore, Illumina, and chromosome conformation capture sequencing. The assembled genome size was 309.62 Mb, with 76 scaffolds anchored to eight pseudochromosomes. We predicted 33 035 protein-coding genes, functionally annotated 98.27% of them, and identified repetitive sequences covering 49.08% of the genome. We found that P. pusilliflora is closely related to Prunus serrulata and Prunus yedoensis, having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that P. pusilliflora has 643 expanded and 1128 contracted gene families. Furthermore, we found that P. pusilliflora is more resistant to Colletotrichum viniferum, Phytophthora capsici, and Pseudomonas syringae pv. tomato (Pst) DC3000 infections than cultivated Prunus avium. P. pusilliflora also has considerably more nucleotide-binding site-type resistance gene analogs than P. avium, which explains its stronger disease resistance. The cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in P. pusilliflora. Furthermore, 81 MADS-box genes were identified in P. pusilliflora, accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality P. pusilliflora genome will be valuable for further research on cherries and molecular breeding.
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Affiliation(s)
| | | | - Xiao Dong
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Zhengxin Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yuxuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Chunjin Yin
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Sen Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Jijun Zhu
- Shanghai Botanical Garden, Shanghai, 200231, P. R. China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Wanxia Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Guoqian Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Meng Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu Province, 200037, P. R. China
| | - Shufeng Li
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Zhuo Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ruie Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Quero-García José
- INRAe, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d'Ornon, France
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yahui Lei
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Ling Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
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7
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Role of Cytochrome P450 Enzyme in Plant Microorganisms' Communication: A Focus on Grapevine. Int J Mol Sci 2023; 24:ijms24054695. [PMID: 36902126 PMCID: PMC10003686 DOI: 10.3390/ijms24054695] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023] Open
Abstract
Cytochromes P450 are ancient enzymes diffused in organisms belonging to all kingdoms of life, including viruses, with the largest number of P450 genes found in plants. The functional characterization of cytochromes P450 has been extensively investigated in mammals, where these enzymes are involved in the metabolism of drugs and in the detoxification of pollutants and toxic chemicals. The aim of this work is to present an overview of the often disregarded role of the cytochrome P450 enzymes in mediating the interaction between plants and microorganisms. Quite recently, several research groups have started to investigate the role of P450 enzymes in the interactions between plants and (micro)organisms, focusing on the holobiont Vitis vinifera. Grapevines live in close association with large numbers of microorganisms and interact with each other, regulating several vine physiological functions, from biotic and abiotic stress tolerance to fruit quality at harvest.
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Zhang Z, Liu Z, Li S, Xiong T, Ye F, Han Y, Sun M, Cao J, Luo T, Zhang C, Chen J, Zhang W, Lian S, Yuan H. Effect of prior drought and heat stress on Camellia sinensis transcriptome changes to Ectropis oblique (Lepidoptera: Geometridae) resistance. Genomics 2022; 114:110506. [PMID: 36265745 DOI: 10.1016/j.ygeno.2022.110506] [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: 07/05/2022] [Revised: 10/14/2022] [Accepted: 10/16/2022] [Indexed: 01/15/2023]
Abstract
Tea plants are continuously confronted with a wide range of biotic and abiotic stressors in the field, which can occur concurrently or sequentially. To elucidate the molecular mechanisms in responses to such individual and combined stresses, we used RNAseq to compare the temporal changes in the transcriptome of Camellia sinensis to Ectropis oblique Prout alone or in combination with exposure to drought and heat. Compared with the individual stress, tea plants exhibit significant differences in transcriptome profiles under the combined stresses. Additionally, many unique genes exhibited significant differences in expression in individual and combined stress conditions. Our research showed novel insights into the molecular mechanisms of E. oblique Prout resistance in tea plants and provided a valuable resource for developing tea varieties with broad spectrum stress tolerance.
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Affiliation(s)
- Zaibao Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
| | - Zixiao Liu
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, Henan, China
| | - Shuangru Li
- Shandong Academy of Sciences Yida Technology Consulting Co., Ltd., Shangdong, China
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Fan Ye
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Yanting Han
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Mengke Sun
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Jiajia Cao
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Tian Luo
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Chi Zhang
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Jiahui Chen
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Wei Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Shuaibin Lian
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, Henan, China.
| | - Hongyu Yuan
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
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Molecular characterization of three CYP450 genes reveals their role in withanolides formation and defense in Withania somnifera, the Indian Ginseng. Sci Rep 2022; 12:1602. [PMID: 35102209 PMCID: PMC8803918 DOI: 10.1038/s41598-022-05634-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/17/2022] [Indexed: 12/24/2022] Open
Abstract
The medicinal properties of Ashwagandha (Withania somnifera) are attributed to triterpenoid steroidal lactones, withanolides, which are proposed to be derived from phytosterol pathway, through the action of cytochrome P450 (CYP450) enzymes. Here, we report the characterization of three transcriptome-mined CYP450 genes (WsCYP749B1, WsCYP76 and WsCYP71B10), which exhibited induced expression in response to methyl jasmonate treatment indicating their role in secondary metabolism. All three WsCYP450s had the highest expression in leaf compared to other tissues. In planta characterization of WsCYP450s through virus induced gene silencing (VIGS) and transient overexpression approaches and subsequent metabolite analysis indicated differential modulation in the accumulation of certain withanolides in W. somnifera leaves. While WsCYP749B1-vigs significantly enhanced withaferin A (~ 450%) and reduced withanolide A (~ 50%), its overexpression drastically led to enhanced withanolide A (> 250%) and withanolide B (> 200%) levels and reduced 12-deoxywithastramonolide (~ 60%). Whereas WsCYP76-vigs led to reduced withanolide A (~ 60%) and its overexpression increased withanolide A (~ 150%) and reduced 12-deoxywithastramonolide (~ 60%). Silencing and overexpression of WsCYP71B10 resulted in significant reduction of withanolide B (~ 50%) and withanolide A (~ 60%), respectively. Further, while VIGS of WsCYP450s negatively affected the expression of pathogenesis-related (PR) genes and compromised tolerance to bacteria P. syringae DC3000, their overexpression in W. somnifera and transgenic tobacco led to improved tolerance to the bacteria. Overall, these results showed that the identified WsCYP450s have a role in one or several steps of withanolides biosynthetic pathway and are involved in conferring tolerance to biotic stress.
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Luo M, Sun X, Qi Y, Zhou J, Wu X, Tian Z. Phytophthora infestans RXLR effector Pi04089 perturbs diverse defense-related genes to suppress host immunity. BMC PLANT BIOLOGY 2021; 21:582. [PMID: 34886813 PMCID: PMC8656059 DOI: 10.1186/s12870-021-03364-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The oomycete pathogen secretes many effectors into host cells to manipulate host defenses. For the majority of effectors, the mechanisms related to how they alter the expression of host genes and reprogram defenses are not well understood. In order to investigate the molecular mechanisms governing the influence that the Phytophthora infestans RXLR effector Pi04089 has on host immunity, a comparative transcriptome analysis was conducted on Pi04089 stable transgenic and wild-type potato plants. RESULTS Potato plants stably expressing Pi04089 were more susceptible to P. infestans. RNA-seq analysis revealed that 658 upregulated genes and 722 downregulated genes were characterized in Pi04089 transgenic lines. A large number of genes involved in the biological process, including many defense-related genes and certain genes that respond to salicylic acid, were suppressed. Moreover, the comparative transcriptome analysis revealed that Pi04089 significantly inhibited the expression of many flg22 (a microbe-associated molecular pattern, PAMP)-inducible genes, including various Avr9/Cf-9 rapidly elicited (ACRE) genes. Four selected differentially expressed genes (StWAT1, StCEVI57, StKTI1, and StP450) were confirmed to be involved in host resistance against P. infestans when they were transiently expressed in Nicotiana benthamiana. CONCLUSION The P. infestans effector Pi04089 was shown to suppress the expression of many resistance-related genes in potato plants. Moreover, Pi04089 was found to significantly suppress flg22-triggered defense signaling in potato plants. This research provides new insights into how an oomycete effector perturbs host immune responses at the transcriptome level.
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Affiliation(s)
- Ming Luo
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Xinyuan Sun
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Yetong Qi
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Jing Zhou
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Xintong Wu
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China
| | - Zhendong Tian
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Wuhan, 430070, Hubei, China.
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, Hubei, China.
- Potato Engineering and Technology Research Center (HZAU), Wuhan, 430070, Hubei, China.
- Hubei Hongshan laboratory. Huazhong Agricultural University (HZAU), No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China.
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11
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Zhang Y, Zhang Y, Sun Q, Lu S, Chai L, Ye J, Deng X. Citrus transcription factor CsHB5 regulates abscisic acid biosynthetic genes and promotes senescence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:151-168. [PMID: 34414618 DOI: 10.1111/tpj.15431] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Senescence is a gradual physiological process involving the integration of numerous internal and environmental signals. Abscisic acid (ABA) is a well-known inducer of senescence. However, the regulatory mechanisms underlying ABA-mediated senescence remain largely unknown. Here, we report that the citrus homeodomain leucine zipper I (HD-ZIP I) transcription factor CsHB5 functions as a regulator of ABA-triggered senescence. CsHB5 acts as a nucleus-localized transcriptional activator, the expression of which appeared to be closely associated with citrus senescence. Overexpression of CsHB5 in citrus calli upregulated the expression of ABA- and reactive oxygen species (ROS)-related genes, and significantly increased the content of ABA and hydrogen peroxide (H2 O2 ), whereas silencing CsHB5 in citrus calli downregulated the expression of ABA-related genes. Additionally, heterogenous overexpression of CsHB5 in Solanum lycopersicum (tomato) and Arabidopsis thaliana (Arabidopsis) leads to early leaf yellowing under dark-induced senescence conditions. Meanwhile, the levels of ABA and H2 O2 in transgenic tomatoes increased significantly and the lycopene content decreased. Transcriptome analysis of CsHB5-overexpressing citrus calli and tomato showed that CsHB5 was involved in multiple senescence-associated processes, including chlorophyll degradation, nutrient compound biosynthesis and transport, as well as ABA and ROS signal transduction. The results of yeast one-hybrid assays, electrophoretic mobility shift assays and dual luciferase assays indicated that CsHB5 directly binds to the promoters of ABA biosynthetic genes, including β-carotene hydroxylase 1 (BCH1) and 9-cis-epoxycarotenoid dioxygenase 2 (NCED2), thereby activating their transcription. Our findings revealed that CsHB5 participates in senescence, at least partly, by directly controlling ABA accumulation. Our work provides insight into the regulatory mechanisms underlying ABA-mediated senescence.
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Affiliation(s)
- Yin Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingzi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Quan Sun
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Suwen Lu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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12
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Singh A, Panwar R, Mittal P, Hassan MI, Singh IK. Plant cytochrome P450s: Role in stress tolerance and potential applications for human welfare. Int J Biol Macromol 2021; 184:874-886. [PMID: 34175340 DOI: 10.1016/j.ijbiomac.2021.06.125] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 01/06/2023]
Abstract
Cytochrome P450s (CYPs) are a versatile group of enzymes and one of the largest families of proteins, controlling various physiological processes via biosynthetic and detoxification pathways. CYPs perform multiple roles through a critical irreversible enzymatic reaction in which an oxygen atom is inserted within hydrophobic molecules, converting them into the reactive and hydro soluble components. During evolution, plants have acquired significantly more number of CYPs and represent about 1% of the encoded genes . CYPs are highly conserved proteins involved in growth, development and tolerance against biotic and abiotic stresses. Furthermore, CYPs reinforce plants' molecular and chemical defense mechanisms by regulating the biosynthesis of secondary metabolites, enhancing reactive oxygen species (ROS) scavenging and controlling biosynthesis and homeostasis of phytohormones, including abscisic acid (ABA) and jasmonates. Thus, they are the critical targets of metabolic engineering for enhancing plant defense against environmental stresses. Additionally, CYPs are also used as biocatalysts in the fields of pharmacology and phytoremediation. Herein, we highlight the role of CYPs in plant stress tolerance and their applications for human welfare.
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Affiliation(s)
- Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi 110007, India.
| | - Ruby Panwar
- Department of Botany, Hansraj College, University of Delhi, New Delhi 110007, India
| | - Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Indrakant Kumar Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India.
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13
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Yu XZ, Lu CJ, Tang S, Zhang Q. Transcriptomic analysis of cytochrome P450 genes and pathways involved in chromium toxicity in Oryza sativa. ECOTOXICOLOGY (LONDON, ENGLAND) 2020; 29:503-513. [PMID: 31119592 DOI: 10.1007/s10646-019-02046-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/19/2019] [Indexed: 06/09/2023]
Abstract
In plants, cytochrome P450 monooxygenase (CYP) plays an important role in detoxifying xenobiotic chemicals and coordinating abiotic stresses. Agilent 44 K rice microarray has been used to focus on the transcriptional profile of osCYP genes in rice seedling exposed to Cr solution containing K2CrO4 or Cr(NO3)3. Our study showed that expression profiles of 264 osCYP genes identified were tissue, dose and stimulus specific in rice seedlings. Comparative genomics analysis revealed that more differentially expressed osCYP genes were discovered in roots than in shoots under both Cr exposures. Results from Venn diagram analysis of differentially expressed osCYP genes demonstrated that there were common osCYP genes and unique osCYP genes present in different rice tissue as well as in different Cr treatments, which may control and/or regulate involvement of different CYP isoenzymes under Cr exposure individually or combinedly. KEGG analysis indicated that significant up- and down-regulated osCYP genes in rice tissues were chiefly related to "biosynthesis of secondary metabolites". However, involvements of osCYP genes mapped in the "biosynthesis of secondary metabolites" were tissue and dose specific, implying their distinctly responsive and adaptive mechanisms during Cr exposure. Overall, our findings are evident to describe and clarify their individual roles of specific osCYP genes in regulating involvement of CYP isoforms in Cr detoxification by rice seedlings.
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Affiliation(s)
- Xiao-Zhang Yu
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China.
| | - Chun-Jiao Lu
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China
| | - Shen Tang
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China
| | - Qing Zhang
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China
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14
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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: 162] [Impact Index Per Article: 40.5] [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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15
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Gu L, Dou L, Guo Y, Wang H, Li L, Wang C, Ma L, Wei H, Yu S. The WRKY transcription factor GhWRKY27 coordinates the senescence regulatory pathway in upland cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2019; 19:116. [PMID: 30922232 PMCID: PMC6440019 DOI: 10.1186/s12870-019-1688-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 02/19/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Premature senescence can reduce the yield and quality of crops. WRKY transcription factors (TFs) play important roles during leaf senescence, but little is known about their ageing mechanisms in cotton. RESULTS In this study, a group III WRKY TF, GhWRKY27, was isolated and characterized. The expression of GhWRKY27 was induced by leaf senescence and was higher in an early-ageing cotton variety than in a non-early-ageing cotton variety. Overexpression of GhWRKY27 in Arabidopsis promoted leaf senescence, as determined by reduced chlorophyll content and elevated expression of senescence-associated genes (SAGs). Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that GhWRKY27 interacted with an MYB TF, GhTT2. Putative target genes of GhWRKY27 were identified via chromatin immunoprecipitation followed by sequencing (ChIP-seq). Yeast one-hybrid (Y1H) assay and electrophoretic mobility shift assay (EMSA) revealed that GhWRKY27 binds directly to the promoters of cytochrome P450 94C1 (GhCYP94C1) and ripening-related protein 2 (GhRipen2-2). In addition, the expression patterns of GhTT2, GhCYP94C1 and GhRipen2-2 were identified during leaf senescence. Transient dual-luciferase reporter assay indicated that GhWRKY27 could activate the expression of GhCYP94C1 and GhRipen2-2. CONCLUSIONS Our work lays the foundation for further study of the functional roles of WRKY genes during leaf senescence in cotton. In addition, our data provide new insights into the senescence-associated mechanisms of WRKY genes in cotton.
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Affiliation(s)
- Lijiao Gu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Lingling Dou
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Yaning Guo
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Libei Li
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Congcong Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
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16
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Kong J, Jin J, Dong Q, Qiu J, Li Y, Yang Y, Shi Y, Si W, Gu L, Yang F, Cheng B, Peng Y. Maize factors ZmUBP15, ZmUBP16 and ZmUBP19 play important roles for plants to tolerance the cadmium stress and salt stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:77-89. [PMID: 30824031 DOI: 10.1016/j.plantsci.2018.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
Ubiquitin-Specific Protease16 (UBP16) has been described involved in cadmium stress and salt stress in Arabidopsis, however nothing is known about the functions of its homologs in maize. In this study, we investigate the functions of ZmUBP15, ZmUBP16 and ZmUBP19, three Arabidopsis UBP16 homologs in maize. Our results indicate that ZmUBP15, ZmUBP16 and ZmUBP19 are ubiquitously expressed throughout plant development, and ZmUBP15, ZmUBP16 and ZmUBP19 proteins are mainly localized in plasma membrane. Complementation analyses show that over-expression of ZmUBP15 or ZmUBP16 can rescue the defective phenotype of ubp16-1 in cadmium stress. In addition, over-expression of ZmUBP15, ZmUBP16 or ZmUBP19 can increase the plant tolerance to cadmium stress. These results indicate that ZmUBP15, ZmUBP16 and ZmUBP19 are required for plant to tolerance the cadmium stress. Consistent with this point, cadmium-related genes are markedly up-regulated in seedlings over-expressing ZmUBP15, ZmUBP16 or ZmUBP19. Furthermore, our data indicate that ZmUBP15, ZmUBP16 and ZmUBP19 partially rescue the salt-stress phenotype of ubp16-1. Thus, our research uncover the functions of three novel maize proteins, ZmUBP15, ZmUBP16 and ZmUBP19, which are required for plants in response to cadmium stress and salt stress.
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Affiliation(s)
- Jingjing Kong
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Jing Jin
- School of horticulture and landscape, Yangzhou Polytechnic College, Yangzhou 225009, China
| | - Qing Dong
- Maize Research Center, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jianle Qiu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yangyang Li
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yuehan Yang
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yutian Shi
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Weina Si
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Longjiang Gu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Feiyang Yang
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Yuancheng Peng
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
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17
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Reza SH, Delhomme N, Street NR, Ramachandran P, Dalman K, Nilsson O, Minina EA, Bozhkov PV. Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death. PLoS One 2018; 13:e0192945. [PMID: 29499063 PMCID: PMC5834160 DOI: 10.1371/journal.pone.0192945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/09/2018] [Indexed: 01/04/2023] Open
Abstract
The terminal differentiation and elimination of the embryo-suspensor is the earliest manifestation of programmed cell death (PCD) during plant ontogenesis. Molecular regulation of suspensor PCD remains poorly understood. Norway spruce (Picea abies) embryos provide a powerful model for studying embryo development because of their large size, sequenced genome, and the possibility to obtain a large number of embryos at a specific developmental stage through somatic embryogenesis. Here, we have carried out global gene expression analysis of the Norway spruce embryo-suspensor versus embryonal mass (a gymnosperm analogue of embryo proper) using RNA sequencing. We have identified that suspensors have enhanced expression of the NAC domain-containing transcription factors, XND1 and ANAC075, previously shown to be involved in the initiation of developmental PCD in Arabidiopsis. The analysis has also revealed enhanced expression of Norway spruce homologues of the known executioners of both developmental and stress-induced cell deaths, such as metacaspase 9 (MC9), cysteine endopeptidase-1 (CEP1) and ribonuclease 3 (RNS3). Interestingly, a spruce homologue of bax inhibitor-1 (PaBI-1, for Picea abies BI-1), an evolutionarily conserved cell death suppressor, was likewise up-regulated in the embryo-suspensor. Since Arabidopsis BI-1 so far has been implicated only in the endoplasmic reticulum (ER)-stress induced cell death, we investigated its role in embryogenesis and suspensor PCD using RNA interference (RNAi). We have found that PaBI-1-deficient lines formed a large number of abnormal embryos with suppressed suspensor elongation and disturbed polarity. Cytochemical staining of suspensor cells has revealed that PaBI-1 deficiency suppresses vacuolar cell death and induces necrotic type of cell death previously shown to compromise embryo development. This study demonstrates that a large number of cell-death components are conserved between angiosperms and gymnosperms and establishes a new role for BI-1 in the progression of vacuolar cell death.
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Affiliation(s)
- Salim H. Reza
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
- * E-mail: (SHR); (EAM); (PVB)
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Nathaniel R. Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Prashanth Ramachandran
- Department of Organismal Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Uppsala University, Uppsala, SE, Sweden
| | - Kerstin Dalman
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
| | - Ove Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Elena A. Minina
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
- * E-mail: (SHR); (EAM); (PVB)
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, SE, Sweden
- * E-mail: (SHR); (EAM); (PVB)
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18
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Rasool S, Mohamed R. Plant cytochrome P450s: nomenclature and involvement in natural product biosynthesis. PROTOPLASMA 2016; 253:1197-209. [PMID: 26364028 DOI: 10.1007/s00709-015-0884-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/31/2015] [Indexed: 05/10/2023]
Abstract
Cytochrome P450s constitute the largest family of enzymatic proteins in plants acting on various endogenous and xenobiotic molecules. They are monooxygenases that insert one oxygen atom into inert hydrophobic molecules to make them more reactive and hydro-soluble. Besides for physiological functions, the extremely versatile cytochrome P450 biocatalysts are highly demanded in the fields of biotechnology, medicine, and phytoremediation. The nature of reactions catalyzed by P450s is irreversible, which makes these enzymes attractions in the evolution of plant metabolic pathways. P450s are prime targets in metabolic engineering approaches for improving plant defense against insects and pathogens and for production of secondary metabolites such as the anti-neoplastic drugs taxol or indole alkaloids. The emerging examples of P450 involvement in natural product synthesis in traditional medicinal plant species are becoming increasingly interesting, as they provide new alternatives to modern medicines. In view of the divergent roles of P450s, we review their classification and nomenclature, functions and evolution, role in biosynthesis of secondary metabolites, and use as tools in pharmacology.
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Affiliation(s)
- Saiema Rasool
- Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Rozi Mohamed
- Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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19
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Niu F, Wang C, Yan J, Guo X, Wu F, Yang B, Deyholos MK, Jiang YQ. Functional characterization of NAC55 transcription factor from oilseed rape (Brassica napus L.) as a novel transcriptional activator modulating reactive oxygen species accumulation and cell death. PLANT MOLECULAR BIOLOGY 2016; 92:89-104. [PMID: 27312204 DOI: 10.1007/s11103-016-0502-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 05/25/2016] [Indexed: 05/20/2023]
Abstract
NAC transcription factors (TFs) are plant-specific and play important roles in development, responses to biotic and abiotic cues and hormone signaling. So far, only a few NAC genes have been reported to regulate cell death. In this study, we identified and characterized a NAC55 gene isolated from oilseed rape (Brassica napus L.). BnaNAC55 responds to multiple stresses, including cold, heat, abscisic acid (ABA), jasmonic acid (JA) and a necrotrophic fungal pathogen Sclerotinia sclerotiorum. BnaNAC55 has transactivation activity and is located in the nucleus. BnaNAC55 is able to form homodimers in planta. Unlike ANAC055, full-length BnaNAC55, but not either the N-terminal NAC domain or C-terminal regulatory domain, induces ROS accumulation and hypersensitive response (HR)-like cell death when expressed both in oilseed rape protoplasts and Nicotiana benthamiana. Furthermore, BnaNAC55 expression causes obvious nuclear DNA fragmentation. Moreover, quantitative reverse transcription PCR (qRT-PCR) analysis identified that the expression levels of multiple genes regulating ROS production and scavenging, defense response as well as senescence are significantly induced. Using a dual luciferase reporter assay, we further confirm that BnaNAC55 could activate the expression of a few ROS and defense-related gene expression. Taken together, our work has identified a novel NAC TF from oilseed rape that modulates ROS accumulation and cell death.
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Affiliation(s)
- Fangfang Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jingli Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaohua Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Feifei Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bo Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Michael K Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - Yuan-Qing Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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20
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Awasthi P, Mahajan V, Rather IA, Gupta AP, Rasool S, Bedi YS, Vishwakarma RA, Gandhi SG. Plant Omics: Isolation, Identification, and Expression Analysis of Cytochrome P450 Gene Sequences fromColeus forskohlii. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:782-92. [DOI: 10.1089/omi.2015.0148] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Praveen Awasthi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Jammu, India
- Shri Mata Vaishno Devi University, Katra, India
| | - Vidushi Mahajan
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Jammu, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
| | - Irshad Ahmad Rather
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Jammu, India
| | - Ajai Prakash Gupta
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Jammu, India
| | | | - Yashbir S. Bedi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Jammu, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
| | - Ram A. Vishwakarma
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Jammu, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
| | - Sumit G. Gandhi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Jammu, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
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Mao G, Seebeck T, Schrenker D, Yu O. CYP709B3, a cytochrome P450 monooxygenase gene involved in salt tolerance in Arabidopsis thaliana. BMC PLANT BIOLOGY 2013; 13:169. [PMID: 24164720 PMCID: PMC3819737 DOI: 10.1186/1471-2229-13-169] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 08/28/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Within the Arabidopsis genome, there are 272 cytochrome P450 monooxygenase (P450) genes. However, the biological functions of the majority of these P450s remain unknown. The CYP709B family of P450s includes three gene members, CYP709B1, CYP709B2 and CYP709B3, which have high amino acid sequence similarity and lack reports elucidating biological functions. RESULTS We identified T-DNA insertion-based null mutants of the CYP709B subfamily of genes. No obvious morphological phenotypes were exhibited under normal growth conditions. When the responses to ABA and salt stress were studied in these mutants, only the cyp709b3 mutant showed sensitivity to ABA and salt during germination. Under moderate salt treatment (150 mM NaCl), cyp709b3 showed a higher percentage of damaged seedlings, indicating a lower tolerance to salt stress. CYP709B3 was highly expressed in all analyzed tissues and especially high in seedlings and leaves. In contrast, CYP709B1 and CYP709B2 were highly expressed in siliques, but were at very low levels in other tissues. Under salt stress condition, CYP709B3 gene expression was induced after 24 hr and remained at high expression level. Expression of the wild type CYP709B3 gene in the cyp709b3 mutant fully complemented the salt intolerant phenotype. Furthermore, metabolite profiling analysis revealed some differences between wild type and cyp709b3 mutant plants, supporting the salt intolerance phenotype of the cyp709b3 mutant. CONCLUSIONS These results suggest that CYP709B3 plays a role in ABA and salt stress response and provides evidence to support the functions of cytochrome P450 enzymes in plant stress response.
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Affiliation(s)
- Guohong Mao
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
- Present address: Conagen Inc., 1005 North Warson Road, St., Louis, MO 63132, USA
| | - Timothy Seebeck
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
- Present address: Conagen Inc., 1005 North Warson Road, St., Louis, MO 63132, USA
| | - Denyse Schrenker
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
- Present address: The Pennsylvania State University, 115 Agricultural Sciences and Industries Building, University Park, PA 16802, USA
| | - Oliver Yu
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
- Present address: Conagen Inc., 1005 North Warson Road, St., Louis, MO 63132, USA
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22
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Rowe JM, Dunigan DD, Blanc G, Gurnon JR, Xia Y, Van Etten JL. Evaluation of higher plant virus resistance genes in the green alga, Chlorella variabilis NC64A, during the early phase of infection with Paramecium bursaria chlorella virus-1. Virology 2013; 442:101-13. [PMID: 23701839 PMCID: PMC4107423 DOI: 10.1016/j.virol.2013.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/18/2013] [Accepted: 04/20/2013] [Indexed: 01/25/2023]
Abstract
With growing industrial interest in algae plus their critical roles in aquatic systems, the need to understand the effects of algal pathogens is increasing. We examined a model algal host-virus system, Chlorella variabilis NC64A and virus, PBCV-1. C. variabilis encodes 375 homologs to genes involved in RNA silencing and in response to virus infection in higher plants. Illumina RNA-Seq data showed that 325 of these homologs were expressed in healthy and early PBCV-1 infected (≤60min) cells. For each of the RNA silencing genes to which homologs were found, mRNA transcripts were detected in healthy and infected cells. C. variabilis, like higher plants, may employ certain RNA silencing pathways to defend itself against virus infection. To our knowledge this is the first examination of RNA silencing genes in algae beyond core proteins, and the first analysis of their transcription during virus infection.
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Affiliation(s)
- Janet M. Rowe
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0900, United States
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, United States
| | - David D. Dunigan
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0900, United States
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, United States
| | - Guillaume Blanc
- Structural and Génomique Information Laboratoire, UMR7256 CNRS, Aix-Marseille Université, Marseille, FR-13385, France
| | - James R. Gurnon
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0900, United States
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, United States
| | - Yuannan Xia
- Center for Biotechnology, University of Nebraska, Lincoln, NE 68588-0665, United States
| | - James L. Van Etten
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0900, United States
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, United States
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Characterization of the defense transcriptome responsive to Fusarium oxysporum-infection in Arabidopsis using RNA-seq. Gene 2013; 512:259-66. [DOI: 10.1016/j.gene.2012.10.036] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/15/2012] [Accepted: 10/19/2012] [Indexed: 12/17/2022]
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Bak S, Beisson F, Bishop G, Hamberger B, Höfer R, Paquette S, Werck-Reichhart D. Cytochromes p450. THE ARABIDOPSIS BOOK 2011; 9:e0144. [PMID: 22303269 PMCID: PMC3268508 DOI: 10.1199/tab.0144] [Citation(s) in RCA: 238] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
There are 244 cytochrome P450 genes (and 28 pseudogenes) in the Arabidopsis genome. P450s thus form one of the largest gene families in plants. Contrary to what was initially thought, this family diversification results in very limited functional redundancy and seems to mirror the complexity of plant metabolism. P450s sometimes share less than 20% identity and catalyze extremely diverse reactions leading to the precursors of structural macromolecules such as lignin, cutin, suberin and sporopollenin, or are involved in biosynthesis or catabolism of all hormone and signaling molecules, of pigments, odorants, flavors, antioxidants, allelochemicals and defense compounds, and in the metabolism of xenobiotics. The mechanisms of gene duplication and diversification are getting better understood and together with co-expression data provide leads to functional characterization.
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Affiliation(s)
- Søren Bak
- Plant Biochemistry Laboratory, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Fred Beisson
- Department of Plant Biology and Environmental Microbiology, CEA/CNRS/Aix-Marseille Université, UMR 6191 Cadarache, F-13108 Saint-Paul-lez-Durance, France
| | - Gerard Bishop
- Division of Biology, Faculty of Natural Sciences, Imperial College London, SW7 2AZ
| | - Björn Hamberger
- Plant Biochemistry Laboratory, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - René Höfer
- Institute of Plant Molecular Biology, CNRS UPR 2357, University of Strasbourg, 28 rue Goethe, F-67083 Strasbourg Cedex, France
| | - Suzanne Paquette
- Plant Biochemistry Laboratory, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Department of Biological Structure, HSB G-514, Box 357420, University of Washington, Seattle, WA, 98195-9420
| | - Danièle Werck-Reichhart
- Institute of Plant Molecular Biology, CNRS UPR 2357, University of Strasbourg, 28 rue Goethe, F-67083 Strasbourg Cedex, France
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Degenkolbe T, Do PT, Zuther E, Repsilber D, Walther D, Hincha DK, Köhl KI. Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. PLANT MOLECULAR BIOLOGY 2009; 69:133-53. [PMID: 18931976 PMCID: PMC2709230 DOI: 10.1007/s11103-008-9412-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 09/27/2008] [Indexed: 05/19/2023]
Abstract
Understanding the molecular basis of plant performance under water-limiting conditions will help to breed crop plants with a lower water demand. We investigated the physiological and gene expression response of drought-tolerant (IR57311 and LC-93-4) and drought-sensitive (Nipponbare and Taipei 309) rice (Oryza sativa L.) cultivars to 18 days of drought stress in climate chamber experiments. Drought stressed plants grew significantly slower than the controls. Gene expression profiles were measured in leaf samples with the 20 K NSF oligonucleotide microarray. A linear model was fitted to the data to identify genes that were significantly regulated under drought stress. In all drought stressed cultivars, 245 genes were significantly repressed and 413 genes induced. Genes differing in their expression pattern under drought stress between tolerant and sensitive cultivars were identified by the genotype x environment (G x E) interaction term. More genes were significantly drought regulated in the sensitive than in the tolerant cultivars. Localizing all expressed genes on the rice genome map, we checked which genes with a significant G x E interaction co-localized with published quantitative trait loci regions for drought tolerance. These genes are more likely to be important for drought tolerance in an agricultural environment. To identify the metabolic processes with a significant G x E effect, we adapted the analysis software MapMan for rice. We found a drought stress induced shift toward senescence related degradation processes that was more pronounced in the sensitive than in the tolerant cultivars. In spite of higher growth rates and water use, more photosynthesis related genes were down-regulated in the tolerant than in the sensitive cultivars.
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Affiliation(s)
- Thomas Degenkolbe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Phuc Thi Do
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ellen Zuther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Dirk Repsilber
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
- Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Dirk Walther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Dirk K. Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Karin I. Köhl
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
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26
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Ehlting J, Sauveplane V, Olry A, Ginglinger JF, Provart NJ, Werck-Reichhart D. An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana. BMC PLANT BIOLOGY 2008; 8:47. [PMID: 18433503 PMCID: PMC2383897 DOI: 10.1186/1471-2229-8-47] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Accepted: 04/23/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become the largest family of enzymes in secondary metabolism. The proportion of P450 enzymes with characterized biochemical function(s) is however very small. If P450 diversification mirrors evolution of chemical diversity, this points to an unexpectedly poor understanding of plant metabolism. We assumed that extensive analysis of gene expression might guide towards the function of P450 enzymes, and highlight overlooked aspects of plant metabolism. RESULTS We have created a comprehensive database, 'CYPedia', describing P450 gene expression in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana, based on public Affymetrix ATH1 microarray expression data. P450 expression was then combined with the expression of 4,130 re-annotated genes, predicted to act in plant metabolism, for co-expression analyses. Based on the annotation of co-expressed genes from diverse pathway annotation databases, co-expressed pathways were identified. Predictions were validated for most P450s with known functions. As examples, co-expression results for P450s related to plastidial functions/photosynthesis, and to phenylpropanoid, triterpenoid and jasmonate metabolism are highlighted here. CONCLUSION The large scale hypothesis generation tools presented here provide leads to new pathways, unexpected functions, and regulatory networks for many P450s in plant metabolism. These can now be exploited by the community to validate the proposed functions experimentally using reverse genetics, biochemistry, and metabolic profiling.
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Affiliation(s)
- Jürgen Ehlting
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique UPR 2357, Université Louis Pasteur, 28 rue Goethe, 67000 Strasbourg, France
| | - Vincent Sauveplane
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique UPR 2357, Université Louis Pasteur, 28 rue Goethe, 67000 Strasbourg, France
| | - Alexandre Olry
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique UPR 2357, Université Louis Pasteur, 28 rue Goethe, 67000 Strasbourg, France
| | - Jean-François Ginglinger
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique UPR 2357, Université Louis Pasteur, 28 rue Goethe, 67000 Strasbourg, France
| | - Nicholas J Provart
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Danièle Werck-Reichhart
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique UPR 2357, Université Louis Pasteur, 28 rue Goethe, 67000 Strasbourg, France
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27
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Sperotto RA, Boff T, Duarte GL, Fett JP. Increased senescence-associated gene expression and lipid peroxidation induced by iron deficiency in rice roots. PLANT CELL REPORTS 2008; 27:183-95. [PMID: 17717672 DOI: 10.1007/s00299-007-0432-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 07/06/2007] [Accepted: 08/02/2007] [Indexed: 05/08/2023]
Abstract
Iron deficiency is among the most common nutritional disorders in plants. Low iron supply causes decreased root growth and even plant death. However, there are no reports about the specific pathways that lead Fe-deficient roots to senescence and death. To investigate the molecular mechanisms that regulate rice roots response to Fe-deficiency, rice seedlings were grown for 3, 6 and 9 days in the presence or absence of Fe. Sequences of 28 induced genes in rice roots under Fe-deficiency were identified by representational difference analysis (RDA). About 40% of these sequences have been previously reported as senescence-related. Differential expression of selected genes was confirmed by semi-quantitative RT-PCR analysis. Classical senescence-related sequences, such as MYB and WRKY transcription factors, cysteine protease, ubiquitin-conjugating enzyme, lipid transfer protein, fatty acid hydroxylase, beta-glucosidase and cytochrome P450 oxydoreductase were identified. Fe-deficiency also resulted in decreased dry weight, increased lipid peroxidation (detected by TBA and histochemical methods) as well as evident membrane damage in Fe-deficient roots. Taken together, the results indicate that Fe-deficiency in roots is linked to typical senescence pathways, associated with lipid peroxidation.
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Affiliation(s)
- Raul Antonio Sperotto
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, P.O. Box 15005, 91501-970, Porto Alegre, RS, Brazil
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28
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Yamada T, Ichimura K, Kanekatsu M, van Doorn WG. Gene expression in opening and senescing petals of morning glory (Ipomoea nil) flowers. PLANT CELL REPORTS 2007; 26:823-35. [PMID: 17221229 DOI: 10.1007/s00299-006-0285-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Revised: 12/10/2006] [Accepted: 12/14/2006] [Indexed: 05/13/2023]
Abstract
We isolated several senescence-associated genes (SAGs) from the petals of morning glory (Ipomoea nil) flowers, with the aim of furthering our understanding of programmed cell death. Samples were taken from the closed bud stage to advanced visible senescence. Actinomycin D, an inhibitor of transcription, if given prior to 4 h after opening, suppressed the onset of visible senescence, which occurred at about 9 h after flower opening. The isolated genes all showed upregulation. Two cell-wall related genes were upregulated early, one encoding an extensin and one a caffeoyl-CoA-3-O-methyltransferase, involved in lignin production. A pectinacetylesterase was upregulated after flower opening and might be involved in cell-wall degradation. Some identified genes showed high homology with published SAGs possibly involved in remobilisation processes: an alcohol dehydrogenase and three cysteine proteases. One transcript encoded a leucine-rich repeat receptor protein kinase, putatively involved in signal transduction. Another transcript encoded a 14-3-3 protein, also a protein kinase. Two genes have apparently not been associated previously with senescence: the first encoded a putative SEC14, which is required for Golgi vesicle transport, the second was a putative ataxin-2, which has been related to RNA metabolism. Induction of the latter has been shown to result in cell death in yeast, due to defects in actin filament formation. The possible roles of these genes in programmed cell death are discussed.
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Affiliation(s)
- Tetsuya Yamada
- National Institute of Floricultural Science, Ibaraki, Japan.
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29
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Pagnussat GC, Yu HJ, Ngo QA, Rajani S, Mayalagu S, Johnson CS, Capron A, Xie LF, Ye D, Sundaresan V. Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis. Development 2005; 132:603-14. [PMID: 15634699 DOI: 10.1242/dev.01595] [Citation(s) in RCA: 393] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The plant life cycle involves an alternation of generations between sporophyte and gametophyte. Currently, the genes and pathways involved in gametophytic development and function in flowering plants remain largely unknown. A large-scale mutant screen of Ds transposon insertion lines was employed to identify 130 mutants of Arabidopsis thaliana with defects in female gametophyte development and function. A wide variety of mutant phenotypes were observed, ranging from defects in different stages of early embryo sac development to mutants with apparently normal embryo sacs, but exhibiting defects in processes such as pollen tube guidance, fertilization or early embryo development. Unexpectedly, nearly half of the mutants isolated in this study were found to be primarily defective in post-fertilization processes dependent on the maternal allele, suggesting that genes expressed from the female gametophyte or the maternal genome play a major role in the early development of plant embryos. Sequence identification of the genes disrupted in the mutants revealed genes involved in protein degradation, cell death, signal transduction and transcriptional regulation required for embryo sac development, fertilization and early embryogenesis. These results provide a first comprehensive overview of the genes and gene products involved in female gametophyte development and function within a flowering plant.
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Affiliation(s)
- Gabriela C Pagnussat
- Section of Plant Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
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Guan Y, Nothnagel EA. Binding of arabinogalactan proteins by Yariv phenylglycoside triggers wound-like responses in Arabidopsis cell cultures. PLANT PHYSIOLOGY 2004; 135:1346-66. [PMID: 15235117 PMCID: PMC519053 DOI: 10.1104/pp.104.039370] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2004] [Revised: 03/29/2004] [Accepted: 04/03/2004] [Indexed: 05/18/2023]
Abstract
Arabinogalactan-proteins (AGPs) are cell wall proteoglycans and are widely distributed in the plant kingdom. Classical AGPs and some nonclassical AGPs are predicted to have a glycosylphosphatidylinositol lipid anchor and have been suggested to be involved in cell-cell signaling. Yariv phenylglycoside is a synthetic probe that specifically binds to plant AGPs and has been used to study AGP functions. We treated Arabidopsis suspension cell cultures with Yariv phenylglycoside and observed decreased cell viability, increased cell wall apposition and cytoplasmic vesiculation, and induction of callose deposition. The induction of cell wall apposition and callose synthesis led us to hypothesize that Yariv binding of plant surface AGPs triggers wound-like responses. To study the effect of Yariv binding to plant surface AGPs and to further understand AGP functions, an Arabidopsis whole genome array was used to monitor the transcriptional modifications after Yariv treatment. By comparing the genes that are induced by Yariv treatment with genes whose expressions have been previously shown to be induced by other conditions, we conclude that the gene expression profile induced by Yariv phenylglycoside treatment is most similar to that of wound induction. It remains uncertain whether the Yariv phenylglycoside cross-linking of cell surface AGPs induces these genes through a specific AGP-based signaling mechanism or through a general mechanical perturbation of the cell surface.
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Affiliation(s)
- Yu Guan
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
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31
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Narusaka Y, Narusaka M, Seki M, Umezawa T, Ishida J, Nakajima M, Enju A, Shinozaki K. Crosstalk in the responses to abiotic and biotic stresses in Arabidopsis: analysis of gene expression in cytochrome P450 gene superfamily by cDNA microarray. PLANT MOLECULAR BIOLOGY 2004; 55:327-42. [PMID: 15604685 DOI: 10.1007/s11103-004-0685-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
From Arabidopsis full-length cDNA libraries, we collected ca. 7000 (7K) independent full-length cDNAs to prepare a cDNA microarray. The 7K cDNA collection contains 49 cytochrome P450 genes. In this study, expression patterns of these cytochrome P450 genes were analyzed by a full-length cDNA microarray under various treatments, such as hormones (salicylic acid, jasmonic acid, ethylene, abscisic acid), pathogen-inoculation ( Alternaria brassicicola , Alternaria alternata ), paraquat, rose bengal, UV stress (UV-C), heavy metal stress (CuSO4), mechanical wounding, drought, high salinity and low temperature. Expression of 29 cytochrome P450 genes among them was induced by various treatments. Inoculation with A. brassicicola and A. alternata as biotic stresses increased transcript levels of 12 and 5 genes in Arabidopsis plants, respectively. In addition, some of the genes were also expressed by abiotic stresses. This suggests crosstalk between abiotic and biotic stresses. The promoter sequences and cis -acting elements of each gene were studied on the basis of full-length cDNA sequences. Most cytochrome P450 genes induced by both abiotic and biotic stresses contained the recognition sites of MYB and MYC, ACGT-core sequence, TGA-box and W-box for WRKY transcription factors in their promoters. These cis -acting elements are known to participate in the regulation of plant defense. The response of each gene to multiple stresses is strictly regulated.
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Affiliation(s)
- Yoshihiro Narusaka
- Department of Biology, Tokyo Gakugei University, 4-1-1 Nukuikita-machi, Koganei-shi, Japan
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32
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Glombitza S, Dubuis PH, Thulke O, Welzl G, Bovet L, Götz M, Affenzeller M, Geist B, Hehn A, Asnaghi C, Ernst D, Seidlitz HK, Gundlach H, Mayer KF, Martinoia E, Werck-Reichhart D, Mauch F, Schäffner AR. Crosstalk and differential response to abiotic and biotic stressors reflected at the transcriptional level of effector genes from secondary metabolism. PLANT MOLECULAR BIOLOGY 2004; 54:817-35. [PMID: 15604654 DOI: 10.1007/s11103-004-0274-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant secondary metabolism significantly contributes to defensive measures against adverse abiotic and biotic cues. To investigate stress-induced, transcriptional alterations of underlying effector gene families, which encode enzymes acting consecutively in secondary metabolism and defense reactions, a DNA array (MetArray) harboring gene-specific probes was established. It comprised complete sets of genes encoding 109 secondary product glycosyltransferases and 63 glutathione-utilizing enzymes along with 62 cytochrome P450 monooxygenases and 26 ABC transporters. Their transcriptome was monitored in different organs of unstressed plants and in shoots in response to herbicides, UV-B radiation, endogenous stress hormones, and pathogen infection. A principal component analysis based on the transcription of these effector gene families defined distinct responses and crosstalk. Methyl jasmonate and ethylene treatments were separated from a group combining reactions towards two sulfonylurea herbicides, salicylate and an avirulent strain of Pseudomonas syringae pv. tomato . The responses to the herbicide bromoxynil and UV-B radiation were distinct from both groups. In addition, these analyses pinpointed individual effector genes indicating their role in these stress responses. A small group of genes was diagnostic in differentiating the response to two herbicide classes used. Interestingly, a subset of genes induced by P. syringae was not responsive to the applied stress hormones. Small groups of comprehensively induced effector genes indicate common defense strategies. Furthermore, homologous members within branches of these effector gene families displayed differential expression patterns either in both organs or during stress responses arguing for their non-redundant functions.
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Affiliation(s)
- Sabine Glombitza
- Department of Environmental Engineering, Institute of Biochemical Plant Pathology, Institute of Developmental Genetics, National Research Center for Environment and Health, Neuherberg, Germany
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Buchanan-Wollaston V, Earl S, Harrison E, Mathas E, Navabpour S, Page T, Pink D. The molecular analysis of leaf senescence--a genomics approach. PLANT BIOTECHNOLOGY JOURNAL 2003; 1:3-22. [PMID: 17147676 DOI: 10.1046/j.1467-7652.2003.00004.x] [Citation(s) in RCA: 371] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Senescence in green plants is a complex and highly regulated process that occurs as part of plant development or can be prematurely induced by stress. In the last decade, the main focus of research has been on the identification of senescence mutants, as well as on genes that show enhanced expression during senescence. Analysis of these is beginning to expand our understanding of the processes by which senescence functions. Recent rapid advances in genomics resources, especially for the model plant species Arabidopsis, are providing scientists with a dazzling array of tools for the identification and functional analysis of the genes and pathways involved in senescence. In this review, we present the current understanding of the mechanisms by which plants control senescence and the processes that are involved.
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Abstract
There are 272 cytochrome P450 genes (including 26 pseudogenes) in the Arabidopsis genome. P450s thus form one of the largest families of proteins in higher plants. This explosion of the P450 family is thought to have occurred via gene duplication and conversion, and to result from the need of sessile plants to adapt to a harsh environment and to protect themselves from pathogens and predators. P450s sometimes share less than 20% identity and catalyze extremely diverse reactions. Their biological functions range from the synthesis of structural macromolecules such as lignin, cutin or suberin, to the synthesis or catabolism of all types of hormone or signaling molecules, the synthesis of pigments and defense compounds, and to the metabolism of xenobiotics. In despite of a huge acceleration in our understanding of plant P450 functions in the recent years, the vast majority of these functions remain completely unknown.
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Affiliation(s)
- Danièle Werck-Reichhart
- Department Plant Stress Response, Institute of Plant Molecular Biology, CNRS UPR 2357, 28 rue Goethe, F-67083 Strasbourg Cedex, France
- Corresponding author:
; phone: (33) 3 90 24 18 54; fax: (33) 3 90 24 18 84
| | - Søren Bak
- Plant Biochemistry Laboratory, Department of Plant Biology, and Center of Molecular Plant Physiology (PlaCe), Royal Veterinary and Agricultural University, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Suzanne Paquette
- Plant Biochemistry Laboratory, Department of Plant Biology, and Center of Molecular Plant Physiology (PlaCe), Royal Veterinary and Agricultural University, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Dept. of Biological Structure, HSB G-514, Box 357420, University of Washington, Seattle, WA, 98195-942
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35
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Yoshida S, Ito M, Nishida I, Watanabe A. Isolation and RNA gel blot analysis of genes that could serve as potential molecular markers for leaf senescence in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2001; 42:170-8. [PMID: 11230571 DOI: 10.1093/pcp/pce021] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nine cDNAs, representing genes in which the transcripts accumulated in senescent leaves of Arabidopsis thaliana, were isolated by differential display reverse transcription polymerase chain reaction (DDRT-PCR) and the genes were designated yellow-leaf-specific gene 1 to 9 (YLS1-YLS9). Sequence analysis revealed that none of the YLS genes, except YLS6, had been reported as senescence-up-regulated genes. RNA gel blot analysis revealed that the transcripts of YLS3 accumulated at the highest level at an early senescence stage, whereas the transcripts from the other YLS genes reached their maximum levels in late senescence stages. Transcripts of YLS genes showed various accumulation patterns under natural senescence, and under artificial senescence induced by darkness, ethylene or ABA. These expression characteristics of YLS genes will be useful as potential molecular markers, which will enhance our understanding of natural and artificial senescence processes.
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Affiliation(s)
- S Yoshida
- Department of Biological Sciences, Graduated School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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36
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Czernic P, Visser B, Sun W, Savouré A, Deslandes L, Marco Y, Van Montagu M, Verbruggen N. Characterization of an Arabidopsis thaliana receptor-like protein kinase gene activated by oxidative stress and pathogen attack. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 18:321-327. [PMID: 10377997 DOI: 10.1046/j.1365-313x.1999.00447.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An Arabidopsis thaliana cDNA clone that encodes a putative receptor-like protein kinase gene (At-RLK3) was characterized. The deduced 667-amino acid protein consists of an amino-terminal signal sequence, an extracellular domain, a single transmembrane domain, and a cytoplasmic domain with characteristics of serine/threonine protein kinase. Because of the original features of its extracellular domain, the At-RLK3 protein is a member of a new class of receptor-like protein kinases. The At-RLK3 gene is present as a single copy within the Arabidopsis genome and its transcripts are detected in root, stem, leaf and flower. In cultured cells, the At-RLK3 gene is activated upon oxidative stress and salicylic acid treatment. In plants, the gene appears to be differentially regulated during various plant-pathogen interactions: upon inoculation with strains of Pseudomonas syringae pv. tomato harboring or not, different avr genes, At-RLK3 transcripts accumulate transiently at similar levels during both compatible and incompatible interactions. This gene is, however, preferentially expressed during the incompatible interaction induced by the soil-borne vascular bacteria, Ralstonia solanacearum. The involvement of At-RLK3 in signal transduction pathways during pathogen attack is discussed.
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Affiliation(s)
- P Czernic
- Departement Planten genetica, Universiteit Gent, Belgium
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