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Li X, Zhang Y, Zhu C, Zheng P, Chen C, Zhang N, Ji H, Dong C, Yu J, Ren J, Zhu Y, Wang Y. Enzymatic Characterization of SpPAL Genes in S. polyrhiza and Overexpression of the SpPAL3. PLANTS (BASEL, SWITZERLAND) 2024; 13:2607. [PMID: 39339582 PMCID: PMC11435183 DOI: 10.3390/plants13182607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Revised: 09/16/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024]
Abstract
Phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) catalyzes the deamination of phenylalanine, which is the initial step in the biosynthesis of phenylpropanoids. It serves as a crucial enzyme that facilitates the transfer of carbon from primary to secondary metabolism in plants. Duckweed is regarded as a promising chassis plant in synthetic biology research and application, due to its being rich in secondary metabolites and other advantages. The genes encoding PAL in Spirodela polyrhiza (L.) Schleid, the giant duckweed, were investigated in this study. Three SpPAL genes (SpPAL1-SpPAL3) were identified and cloned. All of them were successfully expressed in E. coli, and their recombinant proteins all showed PAL activity. In addition, SpPAL1 and SpPAL2 proteins could also utilize tyrosine as substrate, although the activity was low. A qRT-PCR analysis demonstrated that the expression of SpPAL3 was most pronounced in young fronds. It was found that the expression of SpPAL1 and SpPAL3 was significantly induced by MeJA treatment. Overexpression of SpPAL3 in Lemna turionifera inhibited the growth of fronds and adventitious roots in the transgenic plants, indicating the importance of SpPAL3 in duckweed besides its involvement in the secondary metabolism.
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Affiliation(s)
- Xiaoxue Li
- Institute of Agricultural Products Preservation and Processing Technology, National Engineering Technology Research Center for Preservation of Agriculture Product, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Yinxing Zhang
- School of Life Science, Tianjin University, Tianjin 300072, China
| | - Chunfeng Zhu
- School of Life Science, Tianjin University, Tianjin 300072, China
| | - Pufan Zheng
- Institute of Agricultural Products Preservation and Processing Technology, National Engineering Technology Research Center for Preservation of Agriculture Product, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Cunkun Chen
- Institute of Agricultural Products Preservation and Processing Technology, National Engineering Technology Research Center for Preservation of Agriculture Product, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Na Zhang
- Institute of Agricultural Products Preservation and Processing Technology, National Engineering Technology Research Center for Preservation of Agriculture Product, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Haipeng Ji
- Institute of Agricultural Products Preservation and Processing Technology, National Engineering Technology Research Center for Preservation of Agriculture Product, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Chenghu Dong
- Institute of Agricultural Products Preservation and Processing Technology, National Engineering Technology Research Center for Preservation of Agriculture Product, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Jinze Yu
- Institute of Agricultural Products Preservation and Processing Technology, National Engineering Technology Research Center for Preservation of Agriculture Product, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Jie Ren
- College of Food Science and Biological Engineering, Tianjin Agricultural University, Tianjin 300392, China
| | - Yerong Zhu
- College of Life Science, Nankai University, Tianjin 300071, China
| | - Yong Wang
- College of Life Science, Nankai University, Tianjin 300071, China
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Xu C, Fan X, Shen G, Guo B. Genome-wide identification of the phenylalanine ammonia-lyase gene from Epimedium Pubescens Maxim. (Berberidaceae): novel insight into the evolution of the PAL gene family. BMC PLANT BIOLOGY 2024; 24:831. [PMID: 39232677 PMCID: PMC11373271 DOI: 10.1186/s12870-024-05480-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 08/01/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Phenylalanine ammonia-lyase (PAL) serves as a key gateway enzyme, bridging primary metabolism and the phenylpropanoid pathway, and thus playing an indispensable role in flavonoid, anthocyanin and lignin biosynthesis. PAL gene families have been extensively studied across species using public genomes. However, a comprehensive exploration of PAL genes in Epimedium species, especially those involved in prenylated flavonol glycoside, anthocyanin, or lignin biosynthesis, is still lacking. Moreover, an in-depth investigation into PAL gene family evolution is warranted. RESULTS Seven PAL genes (EpPAL1-EpPAL7) were identified. EpPAL2 and EpPAL3 exhibit low sequence identity to other EpPALs (ranging from 61.09 to 64.38%) and contain two unique introns, indicating distinct evolutionary origins. They evolve at a rate ~ 10 to ~ 54 times slower compared to EpPAL1 and EpPAL4-7, suggesting strong purifying selection. EpPAL1 evolved independently and is another ancestral gene. EpPAL1 formed EpPAL4 through segmental duplication, which lead to EpPAL5 and EpPAL6 through tandem duplications, and EpPAL7 through transposed duplication, shaping modern EpPALs. Correlation analysis suggests EpPAL1, EpPAL2 and EpPAL3 play important roles in prenylated flavonol glycosides biosynthesis, with EpPAL2 and EpPAL3 strongly correlated with both Epimedin C and total prenylated flavonol glycosides. EpPAL1, EpPAL2 and EpPAL3 may play a role in anthocyanin biosynthesis in leaves. EpPAL2, EpPAL3, EpPAL6, and EpPAL7 might be engaged in anthocyanin production in petals, and EpPAL2 and EpPAL3 might also contribute to anthocyanin synthesis in sepals. Further experiments are needed to confirm these hypotheses. Novel insights into the evolution of PAL gene family suggest that it might have evolved from a monophyletic group in bryophytes to large-scale sequence differentiation in gymnosperms, basal angiosperms, and Magnoliidae. Ancestral gene duplications and vertical inheritance from gymnosperms to angiosperms likely occurred during PAL evolution. Most early-diverging eudicotyledons and monocotyledons have distinct histories, while modern angiosperm PAL gene families share similar patterns and lack distant gene types. CONCLUSIONS EpPAL2 and EpPAL3 may play crucial roles in biosynthesis of prenylated flavonol glycosides and anthocyanins in leaves and flowers. This study provides novel insights into PAL gene family evolution. The findings on PAL genes in E. pubescens will aid in synthetic biology research on prenylated flavonol glycosides production.
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Affiliation(s)
- Chaoqun Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, No.151 MaLianWa North Road, Haidian District, Beijing, 100193, China
| | - Xuelan Fan
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, No.151 MaLianWa North Road, Haidian District, Beijing, 100193, China
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Guoan Shen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, No.151 MaLianWa North Road, Haidian District, Beijing, 100193, China
| | - Baolin Guo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, No.151 MaLianWa North Road, Haidian District, Beijing, 100193, China.
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Qin S, Wei G, Lin Q, Tang D, Li C, Tan Z, Yao L, Huang L, Wei F, Liang Y. Analysis of the Spatholobus suberectus full-length transcriptome identified an R2R3-MYB transcription factor-encoding gene SsMYB158 that regulates flavonoid biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108929. [PMID: 39002304 DOI: 10.1016/j.plaphy.2024.108929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/14/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
Spatholobus suberectus Dunn (Leguminosae) has been used for medicinal purposes for a long period. Flavonoids are the major bioactive components of S. suberectus. However, there is still limited knowledge of the exact method via which transcription factors (TFs) regulate flavonoid biosynthesis. The full-length transcriptome of S. suberectus was analyzed using SMRT sequencing; 61,548 transcripts were identified, including 12,311 new gene loci, 53,336 novel transcripts, 44,636 simple sequence repeats, 36,414 complete coding sequences, 871 long non-coding RNAs and 6781 TFs. The SsMYB158 TF, which is associated with flavonoid biosynthesis, belongs to the R2R3-MYB class and is localized subcellularly to the nucleus. The overexpression of SsMYB158 in Nicotiana benthamiana and the transient overexpression of SsMYB158 in S. suberectus resulted in a substantial enhancement in both flavonoids and catechin levels. In addition, there was a remarkable upregulation in the expression of essential enzyme-coding genes associated with the flavonoid biosynthesis pathways. Our study revealed SsMYB158 as a critical regulator of flavonoid biosynthesis in S. suberectus and laying the foundation for its molecular breeding.
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Affiliation(s)
- Shuangshuang Qin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Guili Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Quan Lin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Danfeng Tang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Cui Li
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhien Tan
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lixiang Yao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lirong Huang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Ying Liang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
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Shahidi P, Bahramnejad B, Vafaee Y, Dastan D, Heidari P. Isolation and Characterization of Phenylalanine Ammonia Lyase ( PAL) Genes in Ferula pseudalliacea: Insights into the Phenylpropanoid Pathway. Genes (Basel) 2024; 15:771. [PMID: 38927707 PMCID: PMC11203166 DOI: 10.3390/genes15060771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Phenylalanine ammonia lyase (PAL) is a key enzyme regulating the biosynthesis of the compounds of the phenylpropanoid pathway. This study aimed to isolate and characterize PAL genes from Ferula pseudalliacea Rech.f. (Apiales: Apiaceae) to better understand the regulation of metabolite production. Three PAL gene isoforms (FpPAL1-3) were identified and cloned using the 3'-RACE technique and confirmed by sequencing. Bioinformatics analysis revealed important structural features, such as phosphorylation sites, physicochemical properties, and evolutionary relationships. Expression analysis by qPCR demonstrated the differential transcription profiles of each FpPAL isoform across roots, stems, leaves, flowers, and seeds. FpPAL1 showed the highest expression in stems, FpPAL2 in roots and flowers, and FpPAL3 in flowers. The presence of three isoforms of PAL in F. pseudalliacea, along with the diversity of PAL genes and their tissue-specific expression profiles, suggests that complex modes of regulation exist for phenylpropanoid biosynthesis in this important medicinal plant. The predicted interaction network revealed associations with key metabolic pathways, emphasizing the multifaceted roles of these PAL genes. In silico biochemical analyses revealed the hydrophilicity of the FpPAL isozyme; however, further analysis of substrate specificity and enzyme kinetics can clarify the specific role of each FpPAL isozyme. These comprehensive results increase the understanding of PAL genes in F. pseudalliacea, helping to characterize their contributions to secondary metabolite biosynthesis.
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Affiliation(s)
- Pegah Shahidi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Bahman Bahramnejad
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Yavar Vafaee
- Department of Horticultural Sciences, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Dara Dastan
- Department of Pharmacognosy, School of Pharmacy, Medicinal Plants and Natural Products Research Center, Hamadan University of Medical Sciences, Hamadan 6517838736, Iran;
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood 3619995161, Iran
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Chai P, Cui M, Zhao Q, Chen L, Guo T, Guo J, Wu C, Du P, Liu H, Xu J, Zheng Z, Huang B, Dong W, Han S, Zhang X. Genome-Wide Characterization of the Phenylalanine Ammonia-Lyase Gene Family and Their Potential Roles in Response to Aspergillus flavus L. Infection in Cultivated Peanut ( Arachis hypogaea L.). Genes (Basel) 2024; 15:265. [PMID: 38540324 PMCID: PMC10970321 DOI: 10.3390/genes15030265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 06/15/2024] Open
Abstract
Phenylalanine ammonia-lyase (PAL) is an essential enzyme in the phenylpropanoid pathway, in which numerous aromatic intermediate metabolites play significant roles in plant growth, adaptation, and disease resistance. Cultivated peanuts are highly susceptible to Aspergillus flavus L. infection. Although PAL genes have been characterized in various major crops, no systematic studies have been conducted in cultivated peanuts, especially in response to A. flavus infection. In the present study, a systematic genome-wide analysis was conducted to identify PAL genes in the Arachis hypogaea L. genome. Ten AhPAL genes were distributed unevenly on nine A. hypogaea chromosomes. Based on phylogenetic analysis, the AhPAL proteins were classified into three groups. Structural and conserved motif analysis of PAL genes in A. hypogaea revealed that all peanut PAL genes contained one intron and ten motifs in the conserved domains. Furthermore, synteny analysis indicated that the ten AhPAL genes could be categorized into five pairs and that each AhPAL gene had a homologous gene in the wild-type peanut. Cis-element analysis revealed that the promoter region of the AhPAL gene family was rich in stress- and hormone-related elements. Expression analysis indicated that genes from Group I (AhPAL1 and AhPAL2), which had large number of ABRE, WUN, and ARE elements in the promoter, played a strong role in response to A. flavus stress.
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Affiliation(s)
- Pengpei Chai
- The Shennong Laboratory/Postgraduate T&R Base of Zhengzhou University, Xinxiang 453500, China; (P.C.); (M.C.); (Q.Z.); (T.G.); (J.G.); (C.W.); (P.D.)
| | - Mengjie Cui
- The Shennong Laboratory/Postgraduate T&R Base of Zhengzhou University, Xinxiang 453500, China; (P.C.); (M.C.); (Q.Z.); (T.G.); (J.G.); (C.W.); (P.D.)
| | - Qi Zhao
- The Shennong Laboratory/Postgraduate T&R Base of Zhengzhou University, Xinxiang 453500, China; (P.C.); (M.C.); (Q.Z.); (T.G.); (J.G.); (C.W.); (P.D.)
| | - Linjie Chen
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou 450002, China; (L.C.); (H.L.); (J.X.); (Z.Z.); (B.H.); (W.D.)
| | - Tengda Guo
- The Shennong Laboratory/Postgraduate T&R Base of Zhengzhou University, Xinxiang 453500, China; (P.C.); (M.C.); (Q.Z.); (T.G.); (J.G.); (C.W.); (P.D.)
| | - Jingkun Guo
- The Shennong Laboratory/Postgraduate T&R Base of Zhengzhou University, Xinxiang 453500, China; (P.C.); (M.C.); (Q.Z.); (T.G.); (J.G.); (C.W.); (P.D.)
| | - Chendi Wu
- The Shennong Laboratory/Postgraduate T&R Base of Zhengzhou University, Xinxiang 453500, China; (P.C.); (M.C.); (Q.Z.); (T.G.); (J.G.); (C.W.); (P.D.)
| | - Pei Du
- The Shennong Laboratory/Postgraduate T&R Base of Zhengzhou University, Xinxiang 453500, China; (P.C.); (M.C.); (Q.Z.); (T.G.); (J.G.); (C.W.); (P.D.)
| | - Hua Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou 450002, China; (L.C.); (H.L.); (J.X.); (Z.Z.); (B.H.); (W.D.)
| | - Jing Xu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou 450002, China; (L.C.); (H.L.); (J.X.); (Z.Z.); (B.H.); (W.D.)
| | - Zheng Zheng
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou 450002, China; (L.C.); (H.L.); (J.X.); (Z.Z.); (B.H.); (W.D.)
| | - Bingyan Huang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou 450002, China; (L.C.); (H.L.); (J.X.); (Z.Z.); (B.H.); (W.D.)
| | - Wenzhao Dong
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou 450002, China; (L.C.); (H.L.); (J.X.); (Z.Z.); (B.H.); (W.D.)
| | - Suoyi Han
- The Shennong Laboratory/Postgraduate T&R Base of Zhengzhou University, Xinxiang 453500, China; (P.C.); (M.C.); (Q.Z.); (T.G.); (J.G.); (C.W.); (P.D.)
| | - Xinyou Zhang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou 450002, China; (L.C.); (H.L.); (J.X.); (Z.Z.); (B.H.); (W.D.)
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Kaur A, Yadav VG, Pawar SV, Sembi JK. Insights to Phenylalanine Ammonia Lyase (PAL) and Secondary Metabolism in Orchids: An in silico Approach. Biochem Genet 2024; 62:413-435. [PMID: 37358673 DOI: 10.1007/s10528-023-10428-3] [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: 11/23/2022] [Accepted: 06/07/2023] [Indexed: 06/27/2023]
Abstract
The phenylalanine ammonia lyase (PAL) catalyses the first step of phenylpropanoid metabolic pathway which leads to the biosynthesis of a diverse group of secondary metabolites. Orchids serve as a rich source of metabolites and the availability of genome or transcriptome for selected orchid species provides an opportunity to analyse the PAL genes in orchids. In the present study, 21 PAL genes were characterized using bioinformatics tools in nine orchid species (Apostasia shenzhenica, Cypripedium formosanum, Dendrobium catenatum, Phalaenopsis aphrodite, Phalaenopsis bellina, Phalaenopsis equestris, Phalaenopsis lueddemanniana, Phalaenopsis modesta and Phalaenopsis schilleriana). Multiple sequence alignment confirmed the presence of PAL-specific conserved domains (N-terminal, MIO, core, shielding and C-terminal domain). All these proteins were predicted to be hydrophobic in nature and to have cytoplasmic localisation. Structural modelling depicted the presence of alpha helices, extended strands, beta turns and random coils in their structure. Ala-Ser-Gly triad known for substrate binding and catalysis of MIO-domain was found to be completely conserved in all the proteins. Phylogenetic study showed that the PALs of pteridophytes, gymnosperms and angiosperms clustered together in separate clades. Expression profiling showed tissue-specific expression for all the 21 PAL genes in the various reproductive and vegetative tissues which suggested their diverse role in growth and development. This study provides insights to the molecular characterization of PAL genes which may help in developing biotechnological strategies to enhance the synthesis of phenylpropanoids in orchids and other heterologous systems for pharmaceutical applications.
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Affiliation(s)
- Arshpreet Kaur
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Vikramaditya G Yadav
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
| | - Sandip V Pawar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Jaspreet K Sembi
- Department of Botany, Panjab University, Chandigarh, 160014, India.
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Gao X, Hu Y, Xu Z, Peng D, Guo Q. Expression profiling of the phenylalanine ammonia-lyase ( PAL) gene family in ginkgo biloba L. PLANT SIGNALING & BEHAVIOR 2023; 18:2271807. [PMID: 37903458 PMCID: PMC10761125 DOI: 10.1080/15592324.2023.2271807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/12/2023] [Indexed: 11/01/2023]
Abstract
The PAL gene family plays an important role in plant growth, development, and response to abiotic stresses and has been identified in a variety of plants. However, a systematic characterization is still lacking in Ginkgo biloba. Using a bioinformatics approach, 11 GbPAL members of the PAL gene family identified in ginkgo were identified in this study. The protein structure and physicochemical properties indicated that the GbPAL genes were highly similar. Based on their exon-intron structures, they can be classified into three groups. A total of 62 cis-elements for hormone, light, and abiotic stress responses were identified in the promoters of GbPAL genes, indicating that PAL is a multifunctional gene family. GbPAL genes were specifically expressed in different tissues and ploidy of ginkgo. These results provide a theoretical basis for further studies on the functional expression of the GbPAL genes.
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Affiliation(s)
- Xiaoge Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaping Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - ZhiBiao Xu
- Yancheng forest farm, Yancheng, Jiangsu, China
| | - Daqing Peng
- Yancheng forest farm, Yancheng, Jiangsu, China
| | - Qirong Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Zhang H, Zhang X, Zhao H, Hu J, Wang Z, Yang G, Zhou X, Wan H. Genome-wide identification and expression analysis of phenylalanine ammonia-lyase (PAL) family in rapeseed (Brassica napus L.). BMC PLANT BIOLOGY 2023; 23:481. [PMID: 37814209 PMCID: PMC10563225 DOI: 10.1186/s12870-023-04472-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/17/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Phenylalanine ammonia-lyase (PAL), as a key enzyme in the phenylalanine metabolism pathway in plants, plays an important role in the response to environmental stress. However, the PAL family responding to abiotic stress has not been fully characterized in rapeseed. RESULTS In this study, we conducted a genome-wide study of PAL family, and analyzed their gene structure, gene duplication, conserved motifs, cis-acting elements and response to stress treatment. A total of 17 PALs were identified in the rapeseed genome. Based on phylogenetic analysis, the BnPALs were divided into four clades (I, II, IV, and V). The prediction of protein structure domain presented that all BnPAL members contained a conservative PAL domain. Promoter sequence analysis showed that the BnPALs contain many cis-acting elements related to hormone and stress responses, indicating that BnPALs are widely involved in various biological regulatory processes. The expression profile showed that the BnPALs were significantly induced under different stress treatments (NaCl, Na2CO3, AlCl3, and PEG), suggesting that BnPAL family played an important role in response to abiotic stress. CONCLUSIONS Taken together, our research results comprehensively characterized the BnPAL family, and provided a valuable reference for revealing the role of BnPALs in the regulation of abiotic stress responses in rapeseed.
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Affiliation(s)
- Haiyan Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Xiaohui Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Huixia Zhao
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Wuhan, 430056, China
| | - Jin Hu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Zhaoyang Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 570288, China
| | - Guangsheng Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 570288, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianming Zhou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
- College of Tropical Crops, Hainan University, Haikou, 570288, China.
| | - Heping Wan
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Wuhan, 430056, China.
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9
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Xin J, Li Y, Zhao C, Ge W, Tian R. An integrated transcriptome, metabolomic, and physiological investigation uncovered the underlying tolerance mechanisms of Monochoria korsakowii in response to acute/chronic cadmium exposure. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107888. [PMID: 37442048 DOI: 10.1016/j.plaphy.2023.107888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 07/08/2023] [Indexed: 07/15/2023]
Abstract
Identifying the physiological response and tolerance mechanism of wetland plants to heavy metal exposure can provide theoretical guidance for an early warning for acute metal pollution and metal-contaminated water phytoremediation. A hydroponic experiment was employed to investigate variations in the antioxidant enzyme activity, chlorophyll content, and photosynthesis in leaves of Monochoria korsakowii under 0.12 mM cadmium ion (Cd2+) acute (4 d) and chronic (21 d) exposure. Transcriptome and metabolome were analyzed to elucidate the underlying defensive strategies. The acute/chronic Cd2+ exposure decreased chlorophyll a and b contents, and disturbed photosynthesis in the leaves. The acute Cd2+ exposure increased catalase activity by 36.42%, while the chronic Cd2+ exposure markedly increased ascorbate peroxidase, superoxide dismutase, and glutathione peroxidase activities in the leaves. A total of 2 685 differentially expressed genes (DEGs) in the leaves were identified with the plants exposed to the acute/chronic Cd2+ contamination. In the acute Cd2+ exposure treatment, DEGs were preferentially enriched in the plant hormone transduction pathway, followed by phenylrpopanoid biosynthesis. However, the chronic Cd2+ exposure induced DEGs enriched in the biosynthesis of secondary metabolites pathway as priority. With acute/chronic Cd2+ exposure, a total of 157 and 227 differentially expressed metabolites were identified in the leaves. Conjoint transcriptome and metabolome analysis indicated the plant hormone signal transduction pathway and biosynthesis of secondary metabolites was preferentially activated by the acute and chronic Cd2+ exposure, respectively. The phenylpropanoid pathway functioned as a chemical defense, and the positive role of deoxyxylulose phosphate pathway in leaves against acute/chronic Cd2+ exposure was impaired.
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Affiliation(s)
- Jianpan Xin
- College of Architecture Landscape, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Yan Li
- College of Architecture Landscape, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Chu Zhao
- College of Architecture Landscape, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Wenjia Ge
- College of Architecture Landscape, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Runan Tian
- College of Architecture Landscape, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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10
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Darnet E, Teixeira B, Schaller H, Rogez H, Darnet S. Elucidating the Mesocarp Drupe Transcriptome of Açai ( Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds. Int J Mol Sci 2023; 24:ijms24119315. [PMID: 37298279 DOI: 10.3390/ijms24119315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
Euterpe oleracea palm, endemic to the Amazon region, is well known for açai, a fruit violet beverage with nutritional and medicinal properties. During E. oleracea fruit ripening, anthocyanin accumulation is not related to sugar production, contrarily to grape and blueberry. Ripened fruits have a high content of anthocyanins, isoprenoids, fibers, and proteins, and are poor in sugars. E. oleracea is proposed as a new genetic model for metabolism partitioning in the fruit. Approximately 255 million single-end-oriented reads were generated on an Ion Proton NGS platform combining fruit cDNA libraries at four ripening stages. The de novo transcriptome assembly was tested using six assemblers and 46 different combinations of parameters, a pre-processing and a post-processing step. The multiple k-mer approach with TransABySS as an assembler and Evidential Gene as a post-processer have shown the best results, with an N50 of 959 bp, a read coverage mean of 70x, a BUSCO complete sequence recovery of 36% and an RBMT of 61%. The fruit transcriptome dataset included 22,486 transcripts representing 18 Mbp, of which a proportion of 87% had significant homology with other plant sequences. Approximately 904 new EST-SSRs were described, and were common and transferable to Phoenix dactylifera and Elaeis guineensis, two other palm trees. The global GO classification of transcripts showed similar categories to that in P. dactylifera and E. guineensis fruit transcriptomes. For an accurate annotation and functional description of metabolism genes, a bioinformatic pipeline was developed to precisely identify orthologs, such as one-to-one orthologs between species, and to infer multigenic family evolution. The phylogenetic inference confirmed an occurrence of duplication events in the Arecaceae lineage and the presence of orphan genes in E. oleracea. Anthocyanin and tocopherol pathways were annotated entirely. Interestingly, the anthocyanin pathway showed a high number of paralogs, similar to in grape, whereas the tocopherol pathway exhibited a low and conserved gene number and the prediction of several splicing forms. The release of this exhaustively annotated molecular dataset of E. oleracea constitutes a valuable tool for further studies in metabolism partitioning and opens new great perspectives to study fruit physiology with açai as a model.
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Affiliation(s)
- Elaine Darnet
- Centre for Valorization of Amazonian Bioactive Compounds (CVACBA) & Institute of Biological Sciences, Federal University of Pará (UFPA), Belém 66075-750, PA, Brazil
- International Associated Laboratory PALMHEAT, Frech Scientific Research National Center (CNRS)/UFPA, 75016 Paris, France
| | - Bruno Teixeira
- Centre for Valorization of Amazonian Bioactive Compounds (CVACBA) & Institute of Biological Sciences, Federal University of Pará (UFPA), Belém 66075-750, PA, Brazil
| | - Hubert Schaller
- International Associated Laboratory PALMHEAT, Frech Scientific Research National Center (CNRS)/UFPA, 75016 Paris, France
- Plant Isoprenoid Biology, Institute of Molecular Biology of Plants of the Scientific Research National Center, Strasbourg University, 67081 Strasbourg, France
| | - Hervé Rogez
- Centre for Valorization of Amazonian Bioactive Compounds (CVACBA) & Institute of Biological Sciences, Federal University of Pará (UFPA), Belém 66075-750, PA, Brazil
| | - Sylvain Darnet
- Centre for Valorization of Amazonian Bioactive Compounds (CVACBA) & Institute of Biological Sciences, Federal University of Pará (UFPA), Belém 66075-750, PA, Brazil
- International Associated Laboratory PALMHEAT, Frech Scientific Research National Center (CNRS)/UFPA, 75016 Paris, France
- Plant Isoprenoid Biology, Institute of Molecular Biology of Plants of the Scientific Research National Center, Strasbourg University, 67081 Strasbourg, France
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11
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Heidari Z, Noruzi P, Rezapour-Fard J, Jabbarzadeh Z. Different LED light spectra's and nano-chelated potassium affect the quality traits of Dolce Vita cut roses in soilless culture condition. Sci Rep 2023; 13:6769. [PMID: 37185995 PMCID: PMC10130164 DOI: 10.1038/s41598-023-34056-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
Roses are classified as neutral day plants, but high light and cool temperatures produce high quality flowers in roses. As light quantity, the light quality and its special spectra can affect the flower yield and quality. This research aimed to study of the effect of LED light (control (sunlight), blue and red spectra's) and nano-chelated potassium at three levels (0, 1.5 and 3 g/l) on some morphophysiological and biochemical traits of Rosa hybrida cv. Dolce Vita. Light and nano-chelated potassium treatments have a significant effect on most traits measured in the present study. According to the results, the use of red light and nano-chelated potassium in rose cultivation improved the quality characteristics and increased vase life. The highest fresh and dry weight of flowering branch and plant height was observed in red light treatment and the concentration of 3 g/l nano-chelated potassium. Biochemical parameters such as phenolic compounds, leaf and petal flavonoids, petal anthocyanin content, antioxidant capacity and vase life were also significantly increased under red light and with the concentration of 3 g/l nano-chelated potassium compared to the control. In general, it can be said that the use of red light and a concentration of 3 g/l nano-chelated potassium, can be effective in improving the quality of rose flowers, especially in low light condition.
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Affiliation(s)
- Zahra Heidari
- Department of Horticultural Sciences, Faculty of Agriculture, Urmia University, P.O. Box: 165-5715944931, Urmia, Iran
| | - Parviz Noruzi
- Department of Horticultural Sciences, Faculty of Agriculture, Urmia University, P.O. Box: 165-5715944931, Urmia, Iran.
| | - Javad Rezapour-Fard
- Department of Horticultural Sciences, Faculty of Agriculture, Urmia University, P.O. Box: 165-5715944931, Urmia, Iran
| | - Zohreh Jabbarzadeh
- Department of Horticultural Sciences, Faculty of Agriculture, Urmia University, P.O. Box: 165-5715944931, Urmia, Iran
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12
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Liu A, Zhu Y, Wang Y, Wang T, Zhao S, Feng K, Li L, Wu P. Molecular identification of phenylalanine ammonia lyase-encoding genes EfPALs and EfPAL2-interacting transcription factors in Euryale ferox. FRONTIERS IN PLANT SCIENCE 2023; 14:1114345. [PMID: 37008508 PMCID: PMC10064797 DOI: 10.3389/fpls.2023.1114345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Flavonoids are one of the most important secondary metabolites in plants, and phenylalanine ammonia-lyase (PAL) is the first rate-limiting enzyme for their biosynthesis. However, detailed information on the regulation of PAL in plants is still little. In this study, PAL in E. ferox was identified and functionally analyzed, and its upstream regulatory network was investigated. Through genome-wide identification, we obtained 12 putative PAL genes from E. ferox. Phylogenetic tree and synteny analysis revealed that PAL in E. ferox was expanded and mostly preserved. Subsequently, enzyme activity assays demonstrated that EfPAL1 and EfPAL2 both catalyzed the production of cinnamic acid from phenylalanine only, with EfPAL2 exhibiting a superior enzyme activity. Overexpression of EfPAL1 and EfPAL2 in Arabidopsis thaliana, respectively, both enhanced the biosynthesis of flavonoids. Furthermore, two transcription factors, EfZAT11 and EfHY5, were identified by yeast one-hybrid library assays as binding to the promoter of EfPAL2, and further luciferase (LUC) activity analysis indicated that EfZAT11 promoted the expression of EfPAL2, while EfHY5 repressed the expression of EfPAL2. These results suggested that EfZAT11 and EfHY5 positively and negatively regulate flavonoid biosynthesis, respectively. Subcellular localization revealed that EfZAT11 and EfHY5 were localized in the nucleus. Our findings clarified the key EfPAL1 and EfPAL2 of flavonoid biosynthesis in E. ferox and established the upstream regulatory network of EfPAL2, which would provide novel information for the study of flavonoid biosynthesis mechanism.
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Affiliation(s)
- AiLian Liu
- College of Horticulture and Landscape Architecture, Yangzhou, Jiangsu, China
| | - Yue Zhu
- College of Horticulture and Landscape Architecture, Yangzhou, Jiangsu, China
| | - YuHao Wang
- College of Horticulture and Landscape Architecture, Yangzhou, Jiangsu, China
| | - TianYu Wang
- College of Horticulture and Landscape Architecture, Yangzhou, Jiangsu, China
| | - ShuPing Zhao
- College of Horticulture and Landscape Architecture, Yangzhou, Jiangsu, China
| | - Kai Feng
- College of Horticulture and Landscape Architecture, Yangzhou, Jiangsu, China
| | - LiangJun Li
- College of Horticulture and Landscape Architecture, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Peng Wu
- College of Horticulture and Landscape Architecture, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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13
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Choi SJ, Lee Z, Kim S, Jeong E, Shim JS. Modulation of lignin biosynthesis for drought tolerance in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1116426. [PMID: 37152118 PMCID: PMC10157170 DOI: 10.3389/fpls.2023.1116426] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/06/2023] [Indexed: 05/09/2023]
Abstract
Lignin is a complex polymer that is embedded in plant cell walls to provide physical support and water protection. For these reasons, the production of lignin is closely linked with plant adaptation to terrestrial regions. In response to developmental cues and external environmental conditions, plants use an elaborate regulatory network to determine the timing and location of lignin biosynthesis. In this review, we summarize the canonical lignin biosynthetic pathway and transcriptional regulatory network of lignin biosynthesis, consisting of NAC and MYB transcription factors, to explain how plants regulate lignin deposition under drought stress. Moreover, we discuss how the transcriptional network can be applied to the development of drought tolerant plants.
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14
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Pezeshki S, Warmbier I, Busch T, Bauerbach E, Szövenyi P, Petersen M. The first step into phenolic metabolism in the hornwort Anthoceros agrestis: molecular and biochemical characterization of two phenylalanine ammonia-lyase isoforms. PLANTA 2022; 256:33. [PMID: 35796843 PMCID: PMC9262799 DOI: 10.1007/s00425-022-03944-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Two isoforms of phenylalanine ammonia-lyase (PAL) have been isolated as cDNA sequences from the hornwort Anthoceros agrestis. The encoded enzymes convert L-phenylalanine and to lower extents L-tyrosine and L-histidine. Thus, the functional presence of the general phenylpropanoid pathway in one of the earliest land plant groups is established. The hornwort Anthoceros agrestis has an elaborated phenolic metabolism resulting in phenolic compounds, such as rosmarinic acid or megacerotonic acid. The general phenylpropanoid pathway is involved in the biosynthesis of these compounds. Two phenylalanine ammonia-lyase (PAL) genes, AaPAL1 and AaPAL2, have been identified in Anthoceros agrestis and the protein with an N-terminal 6xHis-tag heterologously synthesized in Escherichia coli for a full biochemical characterization. Both PAL proteins accept L-phenylalanine, L-tyrosine as well as L-histidine as substrates, although the activity is explicitly the highest with L-phenylalanine. Km values as well as catalytic efficiencies were determined for phenylalanine (Km AaPAL1 39 µM, AaPAL2 18 µM) and tyrosine (Km AaPAL1 3.3 mM, AaPAL2 3.5 mM). In suspension cultures of Anthoceros agrestis, PAL genes were transcribed in parallel to rosmarinic acid (RA) accumulation and both showed highest abundance in the early growth phase. In a phylogenetic tree, both AaPAL amino acid sequences grouped within a clade with PAL amino acid sequences of diverse origin ranging from non-vascular to vascular plants, while most PALs from eudicots and monocots were mainly found in two other clades. The similarity of the hornwort PAL amino acid sequences to PAL sequences from vascular plants is more than 80% showing a strong conservation within the land plants. With this characterization of PALs from Anthoceros agrestis together with former investigations concerning cinnamic acid 4-hydroxylase and 4-coumaric acid CoA-ligase, the functional presence of the general phenylpropanoid pathway in this hornwort is proven.
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Affiliation(s)
- Soheil Pezeshki
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Ina Warmbier
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Tobias Busch
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Elke Bauerbach
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Peter Szövenyi
- Institut für Systematische und Evolutionäre Botanik, Universität Zürich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Maike Petersen
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany.
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15
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Mo F, Li L, Zhang C, Yang C, Chen G, Niu Y, Si J, Liu T, Sun X, Wang S, Wang D, Chen Q, Chen Y. Genome-Wide Analysis and Expression Profiling of the Phenylalanine Ammonia-Lyase Gene Family in Solanum tuberosum. Int J Mol Sci 2022; 23:ijms23126833. [PMID: 35743276 PMCID: PMC9224352 DOI: 10.3390/ijms23126833] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Phenylalanine ammonia-lyase is one of the most widely studied enzymes in the plant kingdom. It is a crucial pathway from primary metabolism to significant secondary phenylpropanoid metabolism in plants, and plays an essential role in plant growth, development, and stress defense. Although PAL has been studied in many actual plants, only one report has been reported on potato, one of the five primary staple foods in the world. In this study, 14 StPAL genes were identified in potato for the first time using a genome-wide bioinformatics analysis, and the expression patterns of these genes were further investigated using qRT-PCR. The results showed that the expressions of StPAL1, StPAL6, StPAL8, StPAL12, and StPAL13 were significantly up-regulated under drought and high temperature stress, indicating that they may be involved in the stress defense of potato against high temperature and drought. The expressions of StPAL1, StPAL2, and StPAL6 were significantly up-regulated after MeJa hormone treatment, indicating that these genes are involved in potato chemical defense mechanisms. These three stresses significantly inhibited the expression of StPAL7, StPAL10, and StPAL11, again proving that PAL is a multifunctional gene family, which may give plants resistance to multiple and different stresses. In the future, people may improve critical agronomic traits of crops by introducing other PAL genes. This study aims to deepen the understanding of the versatility of the PAL gene family and provide a valuable reference for further genetic improvement of the potato.
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Affiliation(s)
- Fangyu Mo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Long Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Chao Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Chenghui Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Gong Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Yang Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Jiaxin Si
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Tong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Xinxin Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Shenglan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Dongdong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
| | - Qin Chen
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
- Correspondence: (Q.C.); (Y.C.)
| | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; (F.M.); (L.L.); (C.Z.); (C.Y.); (G.C.); (Y.N.); (J.S.); (T.L.); (X.S.); (S.W.); (D.W.)
- Correspondence: (Q.C.); (Y.C.)
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Shi R, Tao L, Tu X, Zhang C, Xiong Z, Rami Horowitz A, Asher JB, He J, Hu F. Metabolite Profiling and Transcriptome Analyses Provide Insight Into Phenolic and Flavonoid Biosynthesis in the Nutshell of Macadamia Ternifolia. Front Genet 2022; 12:809986. [PMID: 35265099 PMCID: PMC8899216 DOI: 10.3389/fgene.2021.809986] [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: 11/05/2021] [Accepted: 12/29/2021] [Indexed: 12/30/2022] Open
Abstract
Macadamia ternifolia is a dynamic oil-producing nut crop in the world. However, the nutshell is frequently considered as a low-quality material. Further, its metabolic profile is still uncharacterized. In order to explore the industrial significance of the nutshell, this study performed metabolic and transcriptomic analyses at various developmental stages of the nutshell. The qualitative and quantitative metabolic data analysis identified 596 metabolic substances including several species of phenolic acids, flavonoids, lipids, organic acids, amino acids and derivatives, nucleotides and derivatives, alkaloids, lignans, coumarins, terpenoids, tannins, and others. However, phenolic acids and flavonoids were predominant, and their abundance levels were significantly altered across various developmental stages of the nutshell. Comparative transcriptome analysis revealed that the expression patterns of phenolic acid and flavonoid pathway related genes were significantly changed during the nutshell growth. In particular, the expression of phenylalanine ammonia-lyase, C4H, 4CL, CHS, CHI, F3H, and FLS had dynamic differences at the various developmental stages of the nutshell. Our integrative metabolomic and transcriptomic analyses identified the key metabolic substances and their abundance levels. We further discussed the regulatory mechanism of phenolic and flavonoid biosynthesis in the nutshell of M. ternifolia. Our results provide new insights into the biological profiles of the nutshell of M. ternifolia and help to elucidate the molecular mechanisms of phenolic and flavonoid biosynthesis in the nutshell of M. ternifolia.
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Affiliation(s)
- Rui Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, International Ecological Foresty Research Center of Kunming, Horticulture and Landscape Architecture, Southwest Forestry University, Kunming, Yunnan, China
| | - Liang Tao
- Yunnan Institute of Tropical Crops, Xishuangbanna, Yunnan, China
| | - Xinghao Tu
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Chunsheng Zhang
- Office of Academic Affairs, Yunnan University of Finance and Economics, Kunming, China
- *Correspondence: Chunsheng Zhang, ; Jun He, ; Faguang Hu,
| | - Zhi Xiong
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, International Ecological Foresty Research Center of Kunming, Horticulture and Landscape Architecture, Southwest Forestry University, Kunming, Yunnan, China
| | - Abraham Rami Horowitz
- French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Jiftah Ben Asher
- French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Jun He
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Chunsheng Zhang, ; Jun He, ; Faguang Hu,
| | - Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China
- *Correspondence: Chunsheng Zhang, ; Jun He, ; Faguang Hu,
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Li X, Jiang J, Chen Z, Jackson A. Transcriptomic, Proteomic and Metabolomic Analysis of Flavonoid Biosynthesis During Fruit Maturation in Rubus chingii Hu. FRONTIERS IN PLANT SCIENCE 2021; 12:706667. [PMID: 34447402 PMCID: PMC8384110 DOI: 10.3389/fpls.2021.706667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/30/2021] [Indexed: 05/09/2023]
Abstract
Rubus chingii HU, is a medicinal and nutritious fruit, which is very rich in flavonoids. However, the biosynthesis of its flavonoids is poorly understood. This study examined flavonoids and the genes/proteins at four fruit ripening phases using LC-MS/MS and qPCR. Six major kinds of anthocyanins, primarily consisted of flavanol-anthocyanins, which differed in form or concentration from other Rubus species. In contrast to other known raspberries species, R. chingii had a decline in flavonoids during fruit ripening, which was due to down-regulation of genes and proteins involved in phenylpropanoid and flavonoid biosynthesis. Unexpectedly, anthocyanin also continuously decreased during fruit maturation. This suggests that anthocyanins are not responsible for the fruit's reddish coloration. Flavanol-anthocyanins were derived from the proanthocyanidin pathway, which consumed two flavonoid units both produced through the same upstream pathway. Their presence indicates a reduction in the potential biosynthesis of anthocyanin production. Also, the constantly low expression of RchANS gene resulted in low levels of anthocyanin biosynthesis. The lack of RchF3'5'H gene/protein hindered the production of delphinidin glycosides. Flavonoids primarily comprising of quercetin/kaempferol-glycosides were predominately located at fruit epidermal-hair and placentae. The proportion of receptacle/drupelets changes with the maturity of the fruit and may be related to a decrease in the content of flavonoids per unit mass as the fruit matures. The profile and biosynthesis of R. chingii flavonoids are unique to Rubus. The unique flavonol pathways of R. chingii could be used to broaden the genetic diversity of raspberry cultivars and to improve their fruit quality.
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Affiliation(s)
- Xiaobai Li
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | | | - Zhen Chen
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Aaron Jackson
- Independent Researcher, Stuttgart, AR, United States
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18
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Hoffmann J, Berni R, Sutera FM, Gutsch A, Hausman JF, Saffie-Siebert S, Guerriero G. The Effects of Salinity on the Anatomy and Gene Expression Patterns in Leaflets of Tomato cv. Micro-Tom. Genes (Basel) 2021; 12:genes12081165. [PMID: 34440339 PMCID: PMC8392013 DOI: 10.3390/genes12081165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 10/26/2022] Open
Abstract
Salinity is a form of abiotic stress that impacts growth and development in several economically relevant crops and is a top-ranking threat to agriculture, considering the average rise in the sea level caused by global warming. Tomato is moderately sensitive to salinity and shows adaptive mechanisms to this abiotic stressor. A case study on the dwarf tomato model Micro-Tom is here presented in which the response to salt stress (NaCl 200 mM) was investigated to shed light on the changes occurring at the expression level in genes involved in cell wall-related processes, phenylpropanoid pathway, stress response, volatiles' emission and secondary metabolites' production. In particular, the response was analyzed by sampling older/younger leaflets positioned at different stem heights (top and bottom of the stem) and locations along the rachis (terminal and lateral) with the goal of identifying the most responsive one(s). Tomato plants cv. Micro-Tom responded to increasing concentrations of NaCl (0-100-200-400 mM) by reducing the leaf biomass, stem diameter and height. Microscopy revealed stronger effects on leaves sampled at the bottom and the expression analysis identified clusters of genes expressed preferentially in older or younger leaflets. Stress-related genes displayed a stronger induction in lateral leaflets sampled at the bottom. In conclusion, in tomato cv. Micro-Tom subjected to salt stress, the bottom leaflets showed stronger stress signs and response, while top leaflets were less impacted by the abiotic stressor and had an increased expression of cell wall-related genes involved in expansion.
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Affiliation(s)
- Jonas Hoffmann
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940 Hautcharage, Luxembourg; (J.H.); (A.G.); (J.-F.H.)
| | - Roberto Berni
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium;
| | - Flavia Maria Sutera
- SiSaf Ltd., Surrey Research Park, Guildford GU2 7RE, UK; (F.M.S.); (S.S.-S.)
| | - Annelie Gutsch
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940 Hautcharage, Luxembourg; (J.H.); (A.G.); (J.-F.H.)
| | - Jean-Francois Hausman
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940 Hautcharage, Luxembourg; (J.H.); (A.G.); (J.-F.H.)
| | | | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, L-4940 Hautcharage, Luxembourg; (J.H.); (A.G.); (J.-F.H.)
- Correspondence: ; Tel.: +352-27-5888-5096
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19
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Tolba SRT, Rosso LC, Pentimone I, Colagiero M, Moustafa MMA, Elshawaf IIS, Bubici G, Prigigallo MI, Ciancio A. Root Endophytism by Pochonia chlamydosporia Affects Defense-Gene Expression in Leaves of Monocot and Dicot Hosts under Multiple Biotic Interactions. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10040718. [PMID: 33917204 PMCID: PMC8068004 DOI: 10.3390/plants10040718] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 05/10/2023]
Abstract
A study was carried out on the effect of the root endophytic fungus Pochonia chlamydosporia on plant systemic signal of defense related genes during fungal or nematode parasitism. Different biotic stress factors were examined, inoculating roots of dicot and monocot hosts with the endophyte, and measuring the expression of defense genes in leaves. A first greenhouse assay was carried out on expression of PAL, PIN II, PR1 and LOX D in leaves of tomato cv Tondino inoculated with Phytophthora infestans (CBS 120920), inoculating or not the roots of infected plants with P. chlamydosporia DSM 26985. In a second assay, plants of banana (Musa acuminata cv Grand Naine) were artificially infected with Fusarium oxysporum f. sp. cubense Tropical race 4 (TR4) and inoculated or not with DSM 26985. In a further experiment, banana plants were inoculated or not with P. chlamydosporia plus juveniles of the root knot nematode (RKN) Meloidogyne incognita. A similar assay was also carried out in vitro with adults and juveniles of the lesion nematode Pratylenchus goodeyi. Differential expression of the defense genes examined was observed for all plant-stress associations, indicative of early, upward systemic signals induced by the endophyte. Changes in expression profiles included a 5-fold down-regulation of PIN II at 2 dai in leaves of tomato plants treated with P. infestans and/or P. chlamydosporia, and the up-regulation of PAL by the endophyte alone, at 2 and 7 dai. In the TR4 assay, PR1 was significantly up-regulated at 7 dai in banana leaves, but only in the P. chlamydosporia treated plants. At 10 dai, PIN II expression was significantly higher in leaves of plants inoculated only with TR4. The banana-RKN assay showed a PR1 expression significantly higher than controls at 4 and 7 dai in plants inoculated with P. chlamydosporia alone, and a down-regulation at 4 dai in leaves of plants also inoculated with RKN, with a PR1 differential up-regulation at 10 dai. Pratylenchus goodeyi down-regulated PIN at 21 dai, with or without the endophyte, as well as PAL but only in presence of P. chlamydosporia. When inoculated alone, the endophyte up-regulated PR1 and LOX. The gene expression patterns observed in leaves suggest specific and time-dependent relationships linking host plants and P. chlamydosporia in presence of biotic stress factors, functional to a systemic, although complex, activation of defense genes.
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Affiliation(s)
- Shimaa R T Tolba
- Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Moshtohor 13736, Egypt
| | - Laura C Rosso
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via G. Amendola 122/D, 70126 Bari, Italy
| | - Isabella Pentimone
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via G. Amendola 122/D, 70126 Bari, Italy
| | - Mariantonietta Colagiero
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via G. Amendola 122/D, 70126 Bari, Italy
| | - Mahmoud M A Moustafa
- Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Moshtohor 13736, Egypt
| | - Ibrahim I S Elshawaf
- Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Moshtohor 13736, Egypt
| | - Giovanni Bubici
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via G. Amendola 122/D, 70126 Bari, Italy
| | - Maria Isabella Prigigallo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via G. Amendola 122/D, 70126 Bari, Italy
| | - Aurelio Ciancio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via G. Amendola 122/D, 70126 Bari, Italy
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20
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Host-pathogen interaction in sugarcane and red rot pathogen: exploring expression of phytoalexin biosynthesis pathway genes. INDIAN PHYTOPATHOLOGY 2021. [DOI: 10.1007/s42360-020-00306-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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21
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Changwal C, Shukla T, Hussain Z, Singh N, Kar A, Singh VP, Abdin MZ, Arora A. Regulation of Postharvest Tomato Fruit Ripening by Endogenous Salicylic Acid. FRONTIERS IN PLANT SCIENCE 2021; 12:663943. [PMID: 34163503 PMCID: PMC8216237 DOI: 10.3389/fpls.2021.663943] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/06/2021] [Indexed: 05/22/2023]
Abstract
Exogenous application of salicylic acid (SA) has been known for delaying ripening in many fruit and vegetables. But the function of endogenous SA in relation to postharvest fruit performance is still unexplored. To understand the role of endogenous SA in postharvest fruit ripening of tomato, 33 tomato lines were examined for their endogenous SA content, membrane stability index (MSI), and shelf life (SL) at turning and red stages of tomato fruit ripening. Six tomato lines having contrasting shelf lives from these categories were subjected further for ethylene (ET) evolution, 1-aminocyclopropane-1-carboxylic acid synthase (ACS), 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), polygalacturonase (PG), pectin methyl esterase (PME), antioxidant assays and lipid peroxidation. It was found that high endogenous SA has a direct association with low ET evolution, which leads to the high SL of fruit. High lycopene content was also found to be correlated with high SA. Total antioxidants, PG, and PME decreased and lipid peroxidation increased from turning to red stage of tomato fruit development. Furthermore, these lines were subjected to expression analysis for SA biosynthesis enzymes viz. Solanum lycopersicum Isochorismate Synthase (SlICS) and SlPAL. Real-time PCR data revealed that high SL lines have high SlPAL4 expression and low SL lines have high SlPAL6 expression. Based on the results obtained in this study, it was concluded that endogenous SA regulates ET evolution and SL with the aid of the antioxidative defense system, and SlPAL4 and SlPAL6 genes play significant but opposite roles during fruit ripening.
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Affiliation(s)
- Chunoti Changwal
- Division of Plant Physiology, ICAR - Indian Agricultural Research Institute, New Delhi, India
- Department of Biotechnology, Faculty of Science, Center for Transgenic Plant Development, Jamia Hamdard, New Delhi, India
| | - Tushita Shukla
- Division of Plant Physiology, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Zakir Hussain
- Division of Vegetable Sciences, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Neera Singh
- Division of Agricultural Chemicals, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Abhijit Kar
- Division of Post-harvest Technology, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Virendra P. Singh
- Division of Plant Physiology, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - M. Z. Abdin
- Department of Biotechnology, Faculty of Science, Center for Transgenic Plant Development, Jamia Hamdard, New Delhi, India
| | - Ajay Arora
- Division of Plant Physiology, ICAR - Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Ajay Arora
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22
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Ghareeb RY, Alfy H, Fahmy AA, Ali HM, Abdelsalam NR. Utilization of Cladophora glomerata extract nanoparticles as eco-nematicide and enhancing the defense responses of tomato plants infected by Meloidogyne javanica. Sci Rep 2020; 10:19968. [PMID: 33203960 PMCID: PMC7672092 DOI: 10.1038/s41598-020-77005-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Tomato (Solanum Lycopersicum L.) is an important vegetable crop that belongs to the family Solanaceae. Root-knot nematodes reflect the highly critical economically damaging genera of phytoparasitic nematodes on tomato plants. In this study, the eco-nematicide activity of freshwater green macroalga Cladophora glomerata aqueous extract and their synthesized silver nanoparticles (Ag-NPs) against root-knot nematodes Meloidogyne javanica was investigated on tomato plants. The formation and chemical structure of Ag-NPs was examined. The aqueous extract from C. glomerata was applied against the root-knot nematodes besides the biosynthesized green silver nanoparticles with 100, 75, 50, and 25% (S, S/2, S/3, S/4) concentrations. To investigate the plant response toward the Green Synthesized Silver Nanoparticles (GSNPs) treatment, expression profiling of Phenylalanine Ammonia-Lyase (PAL), Poly Phenol Oxidase (PPO), and Peroxidase (POX) in tomato were examined using Quantitative Real-Time PCR (Q-PCR). The results indicated that GSNPs from C. glomerata exhibited the highest eco-nematicide activity in the laboratory bioassay on egg hatchability and juveniles (J2S) mortality of M. javanica compared with the chemical commercial nematicide Rugby 60%. Also, results showed a significant reduction in galls number, egg masses, females per root system/plant, and mortality of juveniles. The results of PAL and PPO enzyme expression for the control plants remained relatively stable, while the plant inoculated with nematode M. javanica as well as the activity of genes in scope was increased from 14 to 28 Days after Nematode Inoculation (DANI). These activities were improved in inoculated plants and treated with C. glomerata extract and their green syntheses of Ag-NPs and the other plants treated with Rugby 60% (4 mL/L). The greatest activities of the three enzymes were evident after 14 days after the nematode inoculation. It can be concluded that the green synthesized nanoparticles using C. glomerata could be used as potent nematicides against M. javanica which induces the immune system to defend against nematode infection.
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Affiliation(s)
- Rehab Y Ghareeb
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, The City of Scientific Research and Technological Applications, New Borg El Arab, Alexandria, 21934, Egypt.
| | - Hanan Alfy
- Plant Protection Research Institute, Field Crop Pests Department, Agricultural Research Center, Giza, 12627, Egypt
| | - Antwan A Fahmy
- Biotechnology Dep, Faculty of Agriculture, Ain Shams University, Ain Shams, 13766, Egypt
| | - Hayssam M Ali
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.,Timber Trees Research Department, Agriculture Research Center, Sabahia Horticulture Research Station, Horticulture Research Institute, Alexandria, 21526, Egypt
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt.
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23
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Lefevere H, Bauters L, Gheysen G. Salicylic Acid Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:338. [PMID: 32362901 PMCID: PMC7182001 DOI: 10.3389/fpls.2020.00338] [Citation(s) in RCA: 215] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/06/2020] [Indexed: 05/19/2023]
Abstract
Salicylic acid (SA) is an important plant hormone that is best known for mediating host responses upon pathogen infection. Its role in plant defense activation is well established, but its biosynthesis in plants is not fully understood. SA is considered to be derived from two possible pathways; the ICS and PAL pathway, both starting from chorismate. The importance of both pathways for biosynthesis differs between plant species, rendering it hard to make generalizations about SA production that cover the entire plant kingdom. Yet, understanding SA biosynthesis is important to gain insight into how plant pathogen responses function and how pathogens can interfere with them. In this review, we have taken a closer look at how SA is synthesized and the importance of both biosynthesis pathways in different plant species.
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Affiliation(s)
| | | | - Godelieve Gheysen
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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24
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Casarrubias-Castillo K, Montero-Vargas JM, Dabdoub-González N, Winkler R, Martinez-Gallardo NA, Zañudo-Hernández J, Avilés-Arnaut H, Délano-Frier JP. Distinct gene expression and secondary metabolite profiles in suppressor of prosystemin-mediated responses2 (spr2) tomato mutants having impaired mycorrhizal colonization. PeerJ 2020; 8:e8888. [PMID: 32337100 PMCID: PMC7167247 DOI: 10.7717/peerj.8888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/11/2020] [Indexed: 11/20/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) colonization, sampled at 32-50 days post-inoculation (dpi), was significantly reduced in suppressor of prosystemin-mediated responses2 (spr2) mutant tomato plants impaired in the ω-3 FATTY ACID DESATURASE7 (FAD7) gene that limits the generation of linolenic acid and, consequently, the wound-responsive jasmonic acid (JA) burst. Contrary to wild-type (WT) plants, JA levels in root and leaves of spr2 mutants remained unchanged in response to AMF colonization, further supporting its regulatory role in the AM symbiosis. Decreased AMF colonization in spr2 plants was also linked to alterations associated with a disrupted FAD7 function, such as enhanced salicylic acid (SA) levels and SA-related defense gene expression and a reduction in fatty acid content in both mycorrhizal spr2 roots and leaves. Transcriptomic data revealed that lower mycorrhizal colonization efficiency in spr2 mutants coincided with the modified expression of key genes controlling gibberellin and ethylene signaling, brassinosteroid, ethylene, apocarotenoid and phenylpropanoid synthesis, and the wound response. Targeted metabolomic analysis, performed at 45 dpi, revealed augmented contents of L-threonic acid and DL-malic acid in colonized spr2 roots which suggested unfavorable conditions for AMF colonization. Additionally, time- and genotype-dependent changes in root steroid glycoalkaloid levels, including tomatine, suggested that these metabolites might positively regulate the AM symbiosis in tomato. Untargeted metabolomic analysis demonstrated that the tomato root metabolomes were distinctly affected by genotype, mycorrhizal colonization and colonization time. In conclusion, reduced AMF colonization efficiency in spr2 mutants is probably caused by multiple and interconnected JA-dependent and independent gene expression and metabolomic alterations.
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Affiliation(s)
- Kena Casarrubias-Castillo
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Jalisco, Mexico
| | - Josaphat M. Montero-Vargas
- Departamento de Investigación en Inmunogenética y Alergia, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Mexico City, Mexico
| | - Nicole Dabdoub-González
- Instituto de Biotecnología de la Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Nicolas de los Garza, Nuevo Leon, Mexico
| | - Robert Winkler
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Irapuato, Irapuato, Guanajuato, México
| | - Norma A. Martinez-Gallardo
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Irapuato, Irapuato, Guanajuato, México
| | - Julia Zañudo-Hernández
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Jalisco, Mexico
| | - Hamlet Avilés-Arnaut
- Instituto de Biotecnología de la Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Nicolas de los Garza, Nuevo Leon, Mexico
| | - John P. Délano-Frier
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Irapuato, Irapuato, Guanajuato, México
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25
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Azarafshan M, Peyvandi M, Abbaspour H, Noormohammadi Z, Majd A. The effects of UV-B radiation on genetic and biochemical changes of Pelargonium graveolens L'Her. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:605-616. [PMID: 32205934 PMCID: PMC7078430 DOI: 10.1007/s12298-020-00758-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/08/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
Ultraviolet radiation induces biochemical and genetic changes in plants. The aim of this study was to investigate the effects of UV-B radiation on genetic stability, phenolic compounds and antioxidant activity of Pelargonium graveolens L'Her. Plant cuttings were exposed to 0, 0.12. 0.26 and 0.38 W/m2 of UV-B radiation. Results indicated that by increasing the UV-B radiation intensity, total phenols, flavonoids and anthocyanin contents, Phenylalanine ammonia lyase activity and antioxidant capacity were increased. Analysis of four flavonols (quercetin, myricetin, kaempferol and rutin) contents of leaves extract by HPLC indicated that these four flavonols were enhanced in all treated plants and also the ratio of quercetin to kaempferol (Q/K) showed a significant increase (P ≤ 0.05) in UV-B treated plants in compare to control. To evaluate the genetic variation in treated plants, 10 ISSR primers were used. The highest level of percentage of polymorphism (P%), Shannon index (I), number of effective allele (Ne) and Nei' genetic diversity (He), were observed at the highest UV-B radiation (0.38 W/m2). The AMOVA analysis also showed a significant genetic differentiation (P ≥ 0.001) among the studied groups, and confirmed the differentiation of groups obtained by the cluster analysis of molecular data. Overall, these results showed that biochemical changes in different intensities of UV-B were in line with genetic variations, so that the highest biochemical and genetic variations were observed in 0.38 W/m2 treatment.
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Affiliation(s)
- Marjan Azarafshan
- Department of Biology, Faculty of Biological Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Peyvandi
- Department of Biology, Faculty of Biological Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Hossein Abbaspour
- Department of Biology, Faculty of Biological Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Zahra Noormohammadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ahmad Majd
- Department of Biology, Faculty of Biological Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
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26
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Zhu J, Xu Q, Zhao S, Xia X, Yan X, An Y, Mi X, Guo L, Samarina L, Wei C. Comprehensive co-expression analysis provides novel insights into temporal variation of flavonoids in fresh leaves of the tea plant (Camellia sinensis). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110306. [PMID: 31779914 DOI: 10.1016/j.plantsci.2019.110306] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 05/18/2023]
Abstract
Flavonoids are the major class of characteristic secondary compounds in Camellia sinensis that affect quality of tea. However, the temporal variation and the underlying regulatory mechanism of flavonoid biosynthesis during different growth months require a further investigation. Here, we combined analyses of the metabolomics and transcriptomics to tea leaves freshly collected during five different months for a comprehensive understanding of flavonoid metabolism regulation in tea plants. Through loading plot analysis, significant changes in the contents of metabolites during growing months were discovered, and further co-expression and association analysis indicated that one flavone glycoside (naringenin-7-O-glucoside) and two flavonol glycosides (quercetin-3-O-galactoside and kaemferol-3-O-(6″-O-p-courmaroyl)-glucoside) were evaluated as growth markers, which may explain the high bitterness and astringency of August teas; additionally, the high levels of two flavan-3-ols (gallocatechin and catechin gallate) may contribute to the flavor formation of April tea. Meanwhile, multiple flavonoid-related structural genes, MYB and bHLH transcription factors exhibit specific expression patterns to modulate the biosynthesis of these key flavonoids. A co-expression regulatory sub-network was constructed based on profiles of differentially expressed genes; one CsbHLH and six transcription factors (three CsbHLHs and three CsMYBs) exhibited negative and positive roles in the regulation of flavonoid biosynthetic genes, respectively. Taken together, our results provide new insights into the regulation of principle flavonoids for unique flavor of tea regulated by many flavonoid-related structural genes and transcription factors during different growth months.
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Affiliation(s)
- Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Qingshan Xu
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shiqi Zhao
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Xiaomei Yan
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Lingxiao Guo
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China
| | - Lidiia Samarina
- Russian Research Institute of Floriculture and Subtropical Crops, 354002 Yana Fabritsiusa st. 2/28, Sochi, Russian Federation
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization/Key Laboratory of Tea Biology and Processing, Ministry of Agriculture, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036 Anhui, China.
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Zhang X, Li C, Wang L, Fei Y, Qin W. Analysis of Centranthera grandiflora Benth Transcriptome Explores Genes of Catalpol, Acteoside and Azafrin Biosynthesis. Int J Mol Sci 2019; 20:ijms20236034. [PMID: 31795510 PMCID: PMC6928798 DOI: 10.3390/ijms20236034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/21/2019] [Accepted: 11/27/2019] [Indexed: 12/13/2022] Open
Abstract
Cardiovascular diseases (CVDs) are a major cause of health loss in the world. Prevention and treatment of this disease by traditional Chinese medicine is a promising method. Centranthera grandiflora Benth is a high-value medicinal herb in the prevention and treatment of CVDs; its main medicinal components include iridoid glycosides, phenylethanoid glycosides, and azafrin in roots. However, biosynthetic pathways of these components and their regulatory mechanisms are unknown. Furthermore, there are no genomic resources of this herb. In this article, we provide sequence and transcript abundance data for the root, stem, and leaf transcriptome of C. grandiflora Benth obtained by the Illumina Hiseq2000. More than 438 million clean reads were obtained from root, stem, and leaf libraries, which produced 153,198 unigenes. Based on databases annotation, a total of 557, 213, and 161 unigenes were annotated to catalpol, acteoside, and azafrin biosynthetic pathways, respectively. Differentially expressed gene analysis identified 14,875 unigenes differentially enriched between leaf and root with 8,054 upregulated genes and 6,821 downregulated genes. Candidate MYB transcription factors involved in catalpol, acteoside, and azafrin biosynthesis were also predicated. This work is the first transcriptome analysis in C. grandiflora Benth which will aid the deciphering of biosynthesis pathways and regulatory mechanisms of active components.
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Affiliation(s)
- Xiaodong Zhang
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi 653100, China; (X.Z.); (C.L.); (L.W.)
- Food and Bioengineering College, Xuchang University, Xuchang 461000, China
| | - Caixia Li
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi 653100, China; (X.Z.); (C.L.); (L.W.)
- Food and Bioengineering College, Xuchang University, Xuchang 461000, China
| | - Lianchun Wang
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi 653100, China; (X.Z.); (C.L.); (L.W.)
| | - Yahong Fei
- Yuxi Flyingbear Agricultural Development Company Limited, Yuxi 653100, China;
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
- Correspondence: ; Tel.: +1-807-343-8467
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Plant Fibers and Phenolics: A Review on Their Synthesis, Analysis and Combined Use for Biomaterials with New Properties. FIBERS 2019. [DOI: 10.3390/fib7090080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Devising environmental-friendly processes in biotechnology is a priority in the current economic scenario. We are witnessing a constant and steady push towards finding sustainable solutions to societal challenges by promoting innovation-driven activities minimizing the environmental impact and valorizing natural resources. In bioeconomy, plants are among the most important renewable sources of both fibers (woody and cellulosic) and phytochemicals, which find applications in many industrial sectors, spanning from the textile, to the biocomposite, medical, nutraceutical, and pharma sectors. Given the key role of plants as natural sources of (macro)molecules, we here provide a compendium on the use of plant fibers functionalized/impregnated with phytochemicals (in particular phenolic extracts). The goal is to review the various applications of natural fibers functionalized with plant phenolics and to valorize those plants that are source of both fibers and phytochemicals.
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Developmental Regulation of the Expression of Amaryllidaceae Alkaloid Biosynthetic Genes in Narcissus papyraceus. Genes (Basel) 2019; 10:genes10080594. [PMID: 31394782 PMCID: PMC6723416 DOI: 10.3390/genes10080594] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023] Open
Abstract
Amaryllidaceae alkaloids (AAs) have multiple biological effects, which are of interest to the pharmaceutical industry. To unleash the potential of Amaryllidaceae plants as pharmaceutical crops and as sources of AAs, a thorough understanding of the AA biosynthetic pathway is needed. However, only few enzymes in the pathway are known. Here, we report the transcriptome of AA-producing paperwhites (Narcissus papyraceus Ker Gawl). We present a list of 21 genes putatively encoding enzymes involved in AA biosynthesis. Next, a cDNA library was created from 24 different samples of different parts at various developmental stages of N. papyraceus. The expression of AA biosynthetic genes was analyzed in each sample using RT-qPCR. In addition, the alkaloid content of each sample was analyzed by HPLC. Leaves and flowers were found to have the highest abundance of heterocyclic compounds, whereas the bulb, the lowest. Lycorine was also the predominant AA. The gene expression results were compared with the heterocyclic compound profiles for each sample. In some samples, a positive correlation was observed between the gene expression levels and the amount of compounds accumulated. However, due to a probable transport of enzymes and alkaloids in the plant, a negative correlation was also observed, particularly at stage 2.
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Li X, Jin L, Pan X, Yang L, Guo W. Proteins expression and metabolite profile insight into phenolic biosynthesis during highbush blueberry fruit maturation. Food Chem 2019; 290:216-228. [PMID: 31000040 DOI: 10.1016/j.foodchem.2019.03.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/14/2019] [Accepted: 03/22/2019] [Indexed: 10/27/2022]
Abstract
Blueberry is one of the richest phenolic sources, providing health benefits. To study blueberry phenolic biosynthesis, we investigated phenolics and proteomics at three typical fruit maturation phases. Multiple isoforms of enzymes and multiple members of transcription factors involved in phenolic biosynthesis were divergent and differently regulated. Regulation of some proteins resulted in change of phenolic content. During fruit maturation, down-regulation of VcOMT (CUFF.177.1) and VcLAR2 (CUFF.16780.1) was associated with decreases of ferulic acid and catechin, respectively; Up-regulation of VcFLS (CUFF.41155.1), and VcF3'5'H (CUFF.51711.1) and VcF3'5'H (gene.g10884.t1.1) likely drove increases of their products (quercetin and myricetin); Up-regulation of VcUFGALT (CUFF.20951.1) and VcUFGT73 (4333_g.1) and down-regulation of VcU5GT (CUFF.51258.1) were correlated to accumulation of anthocyanins with 3-glucoside/galactoside. Additionally, four TFs, VcAPRR2 (CUFF.24826.1), VcbHLH3 (CUFF.37765.1), VcWD (CUFF.28282.2) and VcWD (CUFF.28273.1) were probably related to regulation of anthocyanin biosynthesis. These proteins were potential targets for genetic improvement in a breeding program.
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Affiliation(s)
- Xiaobai Li
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Liang Jin
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xuhao Pan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Li Yang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Weidong Guo
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
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Ghasemi S, Kumleh HH, Kordrostami M. Changes in the expression of some genes involved in the biosynthesis of secondary metabolites in Cuminum cyminum L. under UV stress. PROTOPLASMA 2019; 256:279-290. [PMID: 30083789 DOI: 10.1007/s00709-018-1297-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 07/29/2018] [Indexed: 05/08/2023]
Abstract
Biotic and abiotic stresses cause special defense reactions in plant organs, which after a series of reactions, these stresses produce secondary metabolites. The effect of ultraviolet radiation on the expression of key genes involved in the biosynthesis of secondary metabolites (Phenylalanine ammonia lyase (PAL), Hydroxymethylglutaryl-CoA reductase (HMG-CoA reductase), GPP synthases, Deoxyribonino heptulosinate 7-phosphate synthase (DAHP), and Deoxy Xylose Phosphate Synthase (DXS)), and the association of these genes with different amounts of secondary metabolites (phenol, terpene, flavonoids, anthocyanins, alkaloids, lycopene, and beta-carotene) was investigated in this study. The results of this study showed that the application of UV-B stress significantly increased the expression of GPPs, HMG-CoA reductase, DXS, DAHPs, and PAL genes compared to the control plants. The expression of two key genes involved in the biosynthesis of phenylpropanoids, including DAHPs and PAL, increased with UV-B stress, and the highest expression was related to the PAL gene. The results revealed that UV-B stress caused a significant increase in total levels of terpenoids, phenols, flavonoids, anthocyanins, alkaloids, beta-carotene, and lycopene. The highest relative expression of all genes was obtained in treatment A (UV-B radiation for 1 h), while in treatment B (UV-B radiation for 2 h), no significant changes were observed in the expression of the genes.
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Affiliation(s)
- Sepideh Ghasemi
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, P.O. Box 41635-1314, Rasht, Iran
| | - Hassan Hassani Kumleh
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, P.O. Box 41635-1314, Rasht, Iran.
| | - Mojtaba Kordrostami
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, P.O. Box 41635-1314, Rasht, Iran
- Rice Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran
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Yu SI, Kim H, Yun DJ, Suh MC, Lee BH. Post-translational and transcriptional regulation of phenylpropanoid biosynthesis pathway by Kelch repeat F-box protein SAGL1. PLANT MOLECULAR BIOLOGY 2019; 99:135-148. [PMID: 30542810 DOI: 10.1007/s11103-018-0808-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/05/2018] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE A Kelch repeat F-box containing protein, SMALL AND GLOSSY LEAVES1 (SAGL1) regulates phenylpropanoid biosynthesis as a post-translational regulator for PAL1 (phenylalanine ammonia-lyase) and an indirect transcriptional regulator for ANTHOCYANIDIN SYNTHASE. Phenylpropanoid biosynthesis in plants produces diverse aromatic metabolites with important biological functions. Phenylalanine ammonia-lyase (PAL) catalyzes the first step in phenylpropanoid biosynthesis by converting L-phenylalanine to trans-cinnamic acid. Here, we report that SMALL AND GLOSSY LEAVES1 (SAGL1), a Kelch repeat F-box protein, interacts with PAL1 protein for proteasome-mediated degradation to regulate phenylpropanoid biosynthesis in Arabidopsis. Mutations in SAGL1 caused high accumulation of anthocyanins and lignin derived from the phenylpropanoid biosynthesis pathway. We found that PAL enzyme activity increased in SAGL1-defective mutants, sagl1, but decreased in SAGL1-overexpressing Arabidopsis (SAGL1OE) without changes in the transcript levels of PAL genes, suggesting protein-level regulation by SAGL1. Indeed, the levels of PAL1-GFP fusion protein were reduced when both SAGL1 and PAL1-GFP were transiently co-expressed in leaves of Nicotiana benthamiana. In addition, bimolecular fluorescence complementation analysis suggested an interaction between SAGL1 and PAL1. We also found that the transcript levels of ANTHOCYANIDIN SYNTHASE (ANS) increased in the sagl1 mutants but decreased in SAGL1OE. Our results suggest that SAGL1 regulates phenylpropanoid biosynthesis post-translationally at PAL1 and transcriptionally at ANS.
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Affiliation(s)
- Si-In Yu
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Hyojin Kim
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Mi Chung Suh
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea.
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Fay JV, Watkins CJ, Shrestha RK, Litwiñiuk SL, Talavera Stefani LN, Rojas CA, Argüelles CF, Ferreras JA, Caccamo M, Miretti MM. Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles. BMC Genomics 2018; 19:891. [PMID: 30526481 PMCID: PMC6286616 DOI: 10.1186/s12864-018-5240-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 11/12/2018] [Indexed: 12/27/2022] Open
Abstract
Background The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration currently consumed in > 90% of homes in Argentina, in Paraguay and Uruguay. The economy of entire provinces heavily relies on the production, collection and manufacture of Ilex paraguariensis, the fifth plant species with highest antioxidant activity. Polyphenols are associated to relevant health benefits including strong antioxidant properties. Despite its regional relevance and potential biotechnological applications, little is known about functional genomics and genetics underlying phenotypic variation of relevant traits. By generating tissue specific transcriptomic profiles, we aimed to comprehensively annotate genes in the Ilex paraguariensis phenylpropanoid pathway and to evaluate differential expression profiles. Results In this study we generated a reliable transcriptome assembly based on a collection of 15 RNA-Seq libraries from different tissues of Ilex paraguariensis. A total of 554 million RNA-Seq reads were assembled into 193,897 transcripts, where 24,612 annotated full-length transcripts had complete ORF. We assessed the transcriptome assembly quality, completeness and accuracy using BUSCO and TransRate; consistency was also evaluated by experimentally validating 11 predicted genes by PCR and sequencing. Functional annotation against KEGG Pathway database identified 1395 unigenes involved in biosynthesis of secondary metabolites, 531 annotated transcripts corresponded to the phenylpropanoid pathway. The top 30 differentially expressed genes among tissue revealed genes involved in photosynthesis and stress response. These significant differences were then validated by qRT-PCR. Conclusions Our study is the first to provide data from whole genome gene expression profiles in different Ilex paraguariensis tissues, experimentally validating in-silico predicted genes key to the phenylpropanoid (antioxidant) pathway. Our results provide essential genomic data of potential use in breeding programs for polyphenol content. Further studies are necessary to assess if the observed expression variation in the phenylpropanoid pathway annotated genes is related to variations in leaves’ polyphenol content at the population scale. These results set the current reference for Ilex paraguariensis genomic studies and provide a substantial contribution to research and biotechnological applications of phenylpropanoid secondary metabolites. Electronic supplementary material The online version of this article (10.1186/s12864-018-5240-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica V Fay
- Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biología Subtropical (IBS UNaM-CONICET), Universidad Nacional de Misiones, Jujuy 1745, CP3300, Posadas, Misiones, Argentina
| | - Christopher J Watkins
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Ram K Shrestha
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Sergio L Litwiñiuk
- Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biología Subtropical (IBS UNaM-CONICET), Universidad Nacional de Misiones, Jujuy 1745, CP3300, Posadas, Misiones, Argentina
| | - Liliana N Talavera Stefani
- Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biología Subtropical (IBS UNaM-CONICET), Universidad Nacional de Misiones, Jujuy 1745, CP3300, Posadas, Misiones, Argentina
| | - Cristian A Rojas
- Universidad Federal de la Integración Latinoamericana, Foz de Iguazú, PR, Brazil
| | - Carina F Argüelles
- Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biología Subtropical (IBS UNaM-CONICET), Universidad Nacional de Misiones, Jujuy 1745, CP3300, Posadas, Misiones, Argentina
| | - Julian A Ferreras
- Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biología Subtropical (IBS UNaM-CONICET), Universidad Nacional de Misiones, Jujuy 1745, CP3300, Posadas, Misiones, Argentina
| | - Mario Caccamo
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Marcos M Miretti
- Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biología Subtropical (IBS UNaM-CONICET), Universidad Nacional de Misiones, Jujuy 1745, CP3300, Posadas, Misiones, Argentina.
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Liu X, He Z, Yin Y, Xu X, Wu W, Li L. Transcriptome sequencing and analysis during seed growth and development in Euryale ferox Salisb. BMC Genomics 2018; 19:343. [PMID: 29743016 PMCID: PMC5944168 DOI: 10.1186/s12864-018-4707-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 04/22/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Euryale ferox Salisb., an annual aquatic plant, is the only species in the genus Euryale in the Nymphaeaceae. Seeds of E. ferox are a nutritious food and also used in traditional Chinese medicine (Qian Shi in Mandarin). The molecular events that occurred during seed development in E. ferox have not yet been characterized. In this study, we performed transcriptomic analysis of four developmental stages (T1, T2, T3, and T4) in E. ferox seeds with three biological replicates per developmental stage to understand the physiological and biochemical processes during E. ferox seeds development. RESULTS 313,844,425 clean reads were assembled into 160,107 transcripts and 85,006 unigenes with N50 lengths of 2052 bp and 1399 bp, respectively. The unigenes were annotated using five public databases (NR, COG, Swiss-Prot, KEGG, and GO). In the KEGG database, all of the unigenes were assigned to 127 pathways, of which phenylpropanoid biosynthesis was associated with the synthesis of secondary metabolites during E. ferox seed growth and development. Phenylalanine ammonia-lyase (PAL) as the first key enzyme catalyzed the conversion of phenylalanine to trans-cinnamic acid, then was related to the synthesis of flavonoids, lignins and alkaloid. The expression of PAL1 reached its peak at T3 stage, followed by a slight decrease at T4 stage. Cytochrome P450 (P450), encoded by CYP84A1 (which also called ferulate-5-hydroxylase (F5H) in Arabidopsis), was mainly involved in the biosynthesis of lignins. CONCLUSIONS Our study provides a transcriptomic analysis to better understand the morphological changes and the accumulation of medicinal components during E. ferox seed development. The increasing expression of PAL and P450 encoded genes in phenylpropanoid biosynthesis may promote the maturation of E. ferox seed including size, color, hardness and accumulation of medicinal components.
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Affiliation(s)
- Xian Liu
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Yulai Yin
- Suzhou Vegetable Research Institute, 188 Xitang Road, Suzhou, Jiangsu Province 215008 People’s Republic of China
| | - Xu Xu
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Weiwen Wu
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Liangjun Li
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
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Nanda S, Mohanty JN, Mishra R, Joshi RK. Metabolic Engineering of Phenylpropanoids in Plants. REFERENCE SERIES IN PHYTOCHEMISTRY 2017. [DOI: 10.1007/978-3-319-28669-3_30] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Clifford M, Jaganath IB, Ludwig IA, Crozier A. Chlorogenic acids and the acyl-quinic acids: discovery, biosynthesis, bioavailability and bioactivity. Nat Prod Rep 2017; 34:1391-1421. [DOI: 10.1039/c7np00030h] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review is focussed upon the acyl-quinic acids, the most studied group within theca.400 chlorogenic acids so far reported.
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Affiliation(s)
- Michael N. Clifford
- School of Biosciences and Medicine
- Faculty of Health and Medical Sciences
- University of Surrey
- Guildford
- UK
| | - Indu B. Jaganath
- Malaysian Agricultural Research and Development Institute
- Kuala Lumpur
- Malaysia
| | - Iziar A. Ludwig
- Department of Food Technology
- University of Lleida
- Lleida
- Spain
| | - Alan Crozier
- Department of Nutrition
- University of California
- Davis
- USA
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Chaudhary PR, Bang H, Jayaprakasha GK, Patil BS. Variation in Key Flavonoid Biosynthetic Enzymes and Phytochemicals in 'Rio Red' Grapefruit (Citrus paradisi Macf.) during Fruit Development. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:9022-9032. [PMID: 27808514 DOI: 10.1021/acs.jafc.6b02975] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In the current study, the phytochemical contents and expression of genes involved in flavonoid biosynthesis in Rio Red grapefruit were studied at different developmental and maturity stages for the first time. Grapefruit were harvested in June, August, November, January, and April and analyzed for the levels of carotenoids, vitamin C, limonoids, flavonoids, and furocoumarins by HPLC. In addition, genes encoding for phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), and 1,2-rhamnosyltransferase (2RT) were isolated, and their expression in grapefruit juice vesicles was studied. Fruit maturity had significant influence on the expression of the genes, with PAL, CHS, and CHI having higher expression in immature fruits (June), whereas 2RT expression was higher in mature fruits (November and January). The levels of flavonoids (except naringin and poncirin), vitamin C, and furocoumarins gradually decreased from June to April. Furthermore, limonin levels sharply decreased in January. Lycopene decreased whereas β-carotene gradually increased with fruit maturity. Naringin did not exactly follow the pattern of 2RT or of PAL, CHS, and CHI expression, indicating that the four genes may have complementary effects on the level of naringin. Nevertheless, of the marketable fruit stages, early-season grapefruits harvested in November contained more beneficial phytochemicals as compared to mid- and late-season fruits harvested in January and April, respectively.
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Affiliation(s)
- Priyanka R Chaudhary
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University , College Station, Texas 77845, United States
| | - Haejeen Bang
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University , College Station, Texas 77845, United States
| | | | - Bhimanagouda S Patil
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University , College Station, Texas 77845, United States
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Kong JQ. Phenylalanine ammonia-lyase, a key component used for phenylpropanoids production by metabolic engineering. RSC Adv 2015. [DOI: 10.1039/c5ra08196c] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Phenylalanine ammonia-lyase, a versatile enzyme with industrial and medical applications.
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Affiliation(s)
- Jian-Qiang Kong
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products
- Beijing
- China
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39
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Zhang X, Liu CJ. Multifaceted regulations of gateway enzyme phenylalanine ammonia-lyase in the biosynthesis of phenylpropanoids. MOLECULAR PLANT 2015; 8:17-27. [PMID: 25578269 DOI: 10.1016/j.molp.2014.11.001] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 10/25/2014] [Indexed: 05/03/2023]
Abstract
Phenylpropanoid biosynthesis in plants engenders a vast variety of aromatic metabolites critically important for their growth, development, and environmental adaptation. Some of these aromatic compounds have high economic value. Phenylalanine ammonia-lyase (PAL) is the first committed enzyme in the pathway; it diverts the central flux of carbon from the primary metabolism to the synthesis of myriad phenolics. Over the decades, many studies have shown that exquisite regulatory mechanisms at multiple levels control the transcription and the enzymatic activity of PALs. In this review, a current overview of our understanding of the complicated regulatory mechanisms governing the activity of PAL is presented; recent progress in unraveling its post-translational modifications, its metabolite feedback regulation, and its enzyme organization is highlighted.
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Affiliation(s)
- Xuebin Zhang
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Chang-Jun Liu
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
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Duan L, Liu H, Li X, Xiao J, Wang S. Multiple phytohormones and phytoalexins are involved in disease resistance to Magnaporthe oryzae invaded from roots in rice. PHYSIOLOGIA PLANTARUM 2014; 152:486-500. [PMID: 24684436 DOI: 10.1111/ppl.12192] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 02/13/2014] [Accepted: 02/16/2014] [Indexed: 05/04/2023]
Abstract
Blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating diseases of rice worldwide. Phenylalanine ammonia lyase (PAL) is a key enzyme in the phenylpropanoid pathway, which leads to the biosynthesis of defense-related phytohormone salicylic acid (SA) and flavonoid-type phytoalexins sakuranetin and naringenin. However, the roles and biochemical features of individual rice PALs in defense responses to pathogens remain unclear. Here, we report that rice OsPAL06, which can catalyze the formation of trans-cinnamate using l-phenylalanine, is involved in rice root-M. oryzae interaction. OsPAL06-knockout mutant showed increased susceptibility to M. oryzae invaded from roots and developed typical leaf blast symptoms, accompanied by nearly complete disappearance of sakuranetin and naringenin and a two-third reduction of the SA level in roots. This mutant also showed compensatively induced expression of chalcone synthase, which is involved in flavonoid biosynthesis, isochorismate synthase 1, which is putatively involved in SA synthesis via another pathway, reduced jasmonate content and increased ethylene content. These results suggest that OsPAL06 is a positive regulator in preventing M. oryzae infection from roots. It may regulate defense by promoting both phytoalexin accumulation and SA signaling that synergistically and antagonistically interacts with jasmonate- and ethylene-dependent signaling, respectively.
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Affiliation(s)
- Liu Duan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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Wu Z, Gui S, Wang S, Ding Y. Molecular evolution and functional characterisation of an ancient phenylalanine ammonia-lyase gene (NnPAL1) from Nelumbo nucifera: novel insight into the evolution of the PAL family in angiosperms. BMC Evol Biol 2014; 14:100. [PMID: 24884360 PMCID: PMC4102242 DOI: 10.1186/1471-2148-14-100] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/28/2014] [Indexed: 11/16/2022] Open
Abstract
Background Phenylalanine ammonia-lyase (PAL; E.C.4.3.1.5) is a key enzyme of the phenylpropanoid pathway in plant development, and it catalyses the deamination of phenylalanine to trans-cinnamic acid, leading to the production of secondary metabolites. This enzyme has been identified in many organisms, ranging from prokaryotes to higher plants. Because Nelumbo nucifera is a basal dicot rich in many secondary metabolites, it is a suitable candidate for research on the phenylpropanoid pathway. Results Three PAL members, NnPAL1, NnPAL2 and NnPAL3, have been identified in N. nucifera using genome-wide analysis. NnPAL1 contains two introns; however, both NnPAL2 and NnPAL3 have only one intron. Molecular and evolutionary analysis of NnPAL1 confirms that it is an ancient PAL member of the angiosperms and may have a different origin. However, PAL clusters, except NnPAL1, are monophyletic after the split between dicots and monocots. These observations suggest that duplication events remain an important occurrence in the evolution of the PAL gene family. Molecular assays demonstrate that the mRNA of the NnPAL1 gene is 2343 bp in size and encodes a 717 amino acid polypeptide. The optimal pH and temperature of the recombinant NnPAL1 protein are 9.0 and 55°C, respectively. The NnPAL1 protein retains both PAL and weak TAL catalytic activities with Km values of 1.07 mM for L-phenylalanine and 3.43 mM for L-tyrosine, respectively. Cis-elements response to environmental stress are identified and confirmed using real-time PCR for treatments with abscisic acid (ABA), indoleacetic acid (IAA), ultraviolet light, Neurospora crassa (fungi) and drought. Conclusions We conclude that the angiosperm PAL genes are not derived from a single gene in an ancestral angiosperm genome; therefore, there may be another ancestral duplication and vertical inheritance from the gymnosperms. The different evolutionary histories for PAL genes in angiosperms suggest different mechanisms of functional regulation. The expression patterns of NnPAL1 in response to stress may be necessary for the survival of N. nucifera since the Cretaceous Period. The discovery and characterisation of the ancient NnPAL1 help to elucidate PAL evolution in angiosperms.
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Affiliation(s)
| | | | | | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, Hubei Province 430072, People's Republic of China.
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Dong CJ, Shang QM. Genome-wide characterization of phenylalanine ammonia-lyase gene family in watermelon (Citrullus lanatus). PLANTA 2013; 238:35-49. [PMID: 23546528 DOI: 10.1007/s00425-013-1869-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/05/2013] [Indexed: 05/09/2023]
Abstract
Phenylalanine ammonia-lyase (PAL), the first enzyme in the phenylpropanoid pathway, plays a critical role in plant growth, development, and adaptation. PAL enzymes are encoded by a gene family in plants. Here, we report a genome-wide search for PAL genes in watermelon. A total of 12 PAL genes, designated ClPAL1-12, are identified . Nine are arranged in tandem in two duplication blocks located on chromosomes 4 and 7, and the other three ClPAL genes are distributed as single copies on chromosomes 2, 3, and 8. Both the cDNA and protein sequences of ClPALs share an overall high identity with each other. A phylogenetic analysis places 11 of the ClPALs into a separate cucurbit subclade, whereas ClPAL2, which belongs to neither monocots nor dicots, may serve as an ancestral PAL in plants. In the cucurbit subclade, seven ClPALs form homologous pairs with their counterparts from cucumber. Expression profiling reveals that 11 of the ClPAL genes are expressed and show preferential expression in the stems and male and female flowers. Six of the 12 ClPALs are moderately or strongly expressed in the fruits, particularly in the pulp, suggesting the potential roles of PAL in the development of fruit color and flavor. A promoter motif analysis of the ClPAL genes implies redundant but distinctive cis-regulatory structures for stress responsiveness. Finally, duplication events during the evolution and expansion of the ClPAL gene family are discussed, and the relationships between the ClPAL genes and their cucumber orthologs are estimated.
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Affiliation(s)
- Chun-Juan Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
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Seifi HS, Curvers K, De Vleesschauwer D, Delaere I, Aziz A, Höfte M. Concurrent overactivation of the cytosolic glutamine synthetase and the GABA shunt in the ABA-deficient sitiens mutant of tomato leads to resistance against Botrytis cinerea. THE NEW PHYTOLOGIST 2013; 199:490-504. [PMID: 23627463 DOI: 10.1111/nph.12283] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/14/2013] [Indexed: 05/22/2023]
Abstract
Deficiency of abscisic acid (ABA) in the sitiens mutant of tomato (Solanum lycopersicum) culminates in increased resistance to Botrytis cinerea through a rapid epidermal hypersensitive response (HR) and associated phenylpropanoid pathway-derived cell wall fortifications. This study focused on understanding the role of primary carbon : nitrogen (C : N) metabolism in the resistance response of sitiens to B. cinerea. How alterations in C : N metabolism are linked with the HR-mediated epidermal arrest of the pathogen has been also investigated. Temporal alterations in the γ-aminobutyric acid (GABA) shunt, glutamine synthetase/glutamate synthase (GS/GOGAT) cycle and phenylpropanoid pathway were transcriptionally, enzymatically and metabolically monitored in both wild-type and sitiens plants. Virus-induced gene silencing, microscopic analyses and pharmacological assays were used to further confirm the data. Our results on the sitiens-B. cinerea interaction favor a model in which cell viability in the cells surrounding the invaded tissue is maintained by a constant replenishment of the tricarboxylic acid (TCA) cycle through overactivation of the GS/GOGAT cycle and the GABA shunt, resulting in resistance through both tightly controlling the defense-associated HR and slowing down the pathogen-induced senescence. Collectively, this study shows that maintaining cell viability via alterations in host C : N metabolism plays a vital role in the resistance response against necrotrophic pathogens.
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Affiliation(s)
- Hamed Soren Seifi
- Laboratory of Phytopathology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Katrien Curvers
- Laboratory of Applied Molecular Genetics, Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - David De Vleesschauwer
- Laboratory of Phytopathology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Ilse Delaere
- Laboratory of Phytopathology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Aziz Aziz
- Laboratory of SDRP - URVVC EA 4707, University of Reims, Campus Moulin de la Housse, 51687, Reims Cedex 2, France
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
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Docimo T, Consonni R, Coraggio I, Mattana M. Early phenylpropanoid biosynthetic steps in Cannabis sativa: link between genes and metabolites. Int J Mol Sci 2013; 14:13626-44. [PMID: 23812081 PMCID: PMC3742207 DOI: 10.3390/ijms140713626] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/13/2013] [Accepted: 06/14/2013] [Indexed: 02/04/2023] Open
Abstract
Phenylalanine ammonia-lyase (PAL), Cinnamic acid 4-hydroxylase (C4H) and 4-Coumarate: CoA ligase (4CL) catalyze the first three steps of the general phenylpropanoid pathway whereas chalcone synthase (CHS) catalyzes the first specific step towards flavonoids production. This class of specialized metabolites has a wide range of biological functions in plant development and defence and a broad spectrum of therapeutic activities for human health. In this study, we report the isolation of hemp PAL and 4CL cDNA and genomic clones. Through in silico analysis of their deduced amino acid sequences, more than an 80% identity with homologues genes of other plants was shown and phylogenetic relationships were highlighted. Quantitative expression analysis of the four above mentioned genes, PAL and 4CL enzymatic activities, lignin content and NMR metabolite fingerprinting in different Cannabis sativa tissues were evaluated. Furthermore, the use of different substrates to assay PAL and 4CL enzymatic activities indicated that different isoforms were active in different tissues. The diversity in secondary metabolites content observed in leaves (mainly flavonoids) and roots (mainly lignin) was discussed in relation to gene expression and enzymatic activities data.
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Affiliation(s)
- Teresa Docimo
- Institute of Agricultural Biology and Biotechnology, CNR, Via Bassini 15, Milan 20133, Italy; E-Mails: (T.D.); (I.C.)
| | - Roberto Consonni
- Institute for Macromolecular Studies, NMR Department, CNR, Via Bassini 15, Milan 20133, Italy; E-Mail:
| | - Immacolata Coraggio
- Institute of Agricultural Biology and Biotechnology, CNR, Via Bassini 15, Milan 20133, Italy; E-Mails: (T.D.); (I.C.)
| | - Monica Mattana
- Institute of Agricultural Biology and Biotechnology, CNR, Via Bassini 15, Milan 20133, Italy; E-Mails: (T.D.); (I.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-02-2369-9677; Fax: +39-02-2369-9411
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The impact of organic farming on quality of tomatoes is associated to increased oxidative stress during fruit development. PLoS One 2013; 8:e56354. [PMID: 23437115 PMCID: PMC3577808 DOI: 10.1371/journal.pone.0056354] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 01/14/2013] [Indexed: 12/31/2022] Open
Abstract
This study was conducted with the objective of testing the hypothesis that tomato fruits from organic farming accumulate more nutritional compounds, such as phenolics and vitamin C as a consequence of the stressing conditions associated with farming system. Growth was reduced in fruits from organic farming while titratable acidity, the soluble solids content and the concentrations in vitamin C were respectively +29%, +57% and +55% higher at the stage of commercial maturity. At that time, the total phenolic content was +139% higher than in the fruits from conventional farming which seems consistent with the more than two times higher activity of phenylalanine ammonia lyase (PAL) we observed throughout fruit development in fruits from organic farming. Cell membrane lipid peroxidation (LPO) degree was 60% higher in organic tomatoes. SOD activity was also dramatically higher in the fruits from organic farming. Taken together, our observations suggest that tomato fruits from organic farming experienced stressing conditions that resulted in oxidative stress and the accumulation of higher concentrations of soluble solids as sugars and other compounds contributing to fruit nutritional quality such as vitamin C and phenolic compounds.
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Tohge T, Watanabe M, Hoefgen R, Fernie AR. The evolution of phenylpropanoid metabolism in the green lineage. Crit Rev Biochem Mol Biol 2013; 48:123-52. [PMID: 23350798 DOI: 10.3109/10409238.2012.758083] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Phenolic secondary metabolites are only produced by plants wherein they play important roles in both biotic and abiotic defense in seed plants as well as being potentially important bioactive compounds with both nutritional and medicinal benefits reported for animals and humans as a consequence of their potent antioxidant activity. During the long evolutionary period in which plants have adapted to the environmental niches in which they exist (and especially during the evolution of land plants from their aquatic algal ancestors), several strategies such as gene duplication and convergent evolution have contributed to the evolution of this pathway. In this respect, diversity and redundancy of several key genes of phenolic secondary metabolism such as polyketide synthases, cytochrome P450s, Fe(2+)/2-oxoglutarate-dependent dioxygenases and UDP-glycosyltransferases have played an essential role. Recent technical developments allowing affordable whole genome sequencing as well as a better inventory of species-by-species chemical diversity have resulted in a dramatic increase in the number of tools we have to assess how these pathways evolved. In parallel, reverse genetics combined with detailed molecular phenotyping is allowing us to elucidate the functional importance of individual genes and metabolites and by this means to provide further mechanistic insight into their biological roles. In this review, phenolic metabolite-related gene sequences (for a total of 65 gene families including shikimate biosynthetic genes) are compared across 23 independent species, and the phenolic metabolic complement of various plant species are compared with one another, in attempt to better understand the evolution of diversity in this crucial pathway.
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Affiliation(s)
- Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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Capanoglu E, Beekwilder J, Matros A, Boyacioglu D, Hall RD, Mock HP. Correlation of rutin accumulation with 3-O-glucosyl transferase and phenylalanine ammonia-lyase activities during the ripening of tomato fruit. PLANT FOODS FOR HUMAN NUTRITION (DORDRECHT, NETHERLANDS) 2012; 67:371-376. [PMID: 23117480 DOI: 10.1007/s11130-012-0321-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In tomato, the predominant flavonoid is quercetin-3-rutinoside (rutin). In this study, we aim to investigate the phenylalanine ammonia-lyase (PAL) and the quercetin-3-O-glucosyl transferase (3-GT) reactions in the formation of rutin during tomato fruit ripening. Tomatoes of the Moneymaker variety at different development stages (green, breaker, turning, pink, red, and deep red) were divided into flesh and peel fractions. In each sample, both the content of rutin and the enzymatic activities for PAL and 3-GT were recorded. The highest activities of PAL were recorded in the peel of turning fruit (3,000 μkat/mg fresh weight). In fruit flesh, maximal activity was observed in red fruit (917.3 μkat/mg). For both tissues, PAL activity strongly decreased at the final (deep red) fruit stage. The activity of 3-GT in peel peaked in the turning fruit stage (50.7 pkat/mg), while in flesh maximal activity (33.4 pkat/mg) was observed in green fruit, which rapidly declined at the turning stage. Higher levels of rutin were detected in the tomato peel compared to the flesh part with the highest level being found at the green stage. The relation of PAL and 3-GT activities to rutin content is also evaluated.
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Affiliation(s)
- Esra Capanoglu
- Faculty of Chemical and Metallurgical Engineering, Food Engineering Department, Istanbul Technical University, Maslak, 34469 Istanbul, Turkey.
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Cloning, bioinformatics and the enzyme activity analyses of a phenylalanine ammonia-lyase gene involved in dragon’s blood biosynthesis in Dracaena cambodiana. Mol Biol Rep 2012; 40:97-107. [DOI: 10.1007/s11033-012-2032-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
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49
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Shang QM, Li L, Dong CJ. Multiple tandem duplication of the phenylalanine ammonia-lyase genes in Cucumis sativus L. PLANTA 2012; 236:1093-105. [PMID: 22572777 DOI: 10.1007/s00425-012-1659-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 04/23/2012] [Indexed: 05/25/2023]
Abstract
Phenylalanine ammonia-lyase (PAL) is the first entry enzyme of the phenylpropanoid pathway, and therefore plays a key role in both plant development and stress defense. In many plants, PAL is encoded by a multi-gene family, and each member is differentially regulated in response to environmental stimuli. In the present study, we report that PAL in cucumber (Cucumis sativus L.) is encoded for by a family of seven genes (designated as CsPAL1-7). All seven CsPALs are arranged in tandem in two duplication blocks, which are located on chromosomes 4 and 6, respectively. The cDNA and protein sequences of the CsPALs share an overall high identity to each other. Homology modeling reveals similarities in their protein structures, besides several slight differences, implying the different activities in conversion of phenylalanine. Phylogenic analysis places CsPAL1-7 in a separate cluster rather than clustering with other plant PALs. Analyses of expression profiles in different cucumber tissues or in response to various stress or plant hormone treatments indicate that CsPAL1-7 play redundant, but divergent roles in cucumber development and stress response. This is consistent with our finding that CsPALs possess overlapping but different cis-elements in their promoter regions. Finally, several duplication events are discussed to explain the evolution of the cucumber PAL genes.
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MESH Headings
- Abscisic Acid/pharmacology
- Amino Acid Sequence
- Cucumis sativus/drug effects
- Cucumis sativus/enzymology
- Cucumis sativus/genetics
- Cucumis sativus/physiology
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Gene Duplication
- Gene Expression Regulation, Enzymologic/genetics
- Gene Expression Regulation, Plant/genetics
- Models, Molecular
- Molecular Sequence Data
- Multigene Family
- Organ Specificity
- Phenylalanine Ammonia-Lyase/genetics
- Phylogeny
- Plant Components, Aerial/drug effects
- Plant Components, Aerial/enzymology
- Plant Components, Aerial/genetics
- Plant Components, Aerial/physiology
- Plant Growth Regulators/physiology
- Plant Proteins/genetics
- Plant Roots/drug effects
- Plant Roots/enzymology
- Plant Roots/genetics
- Plant Roots/physiology
- Promoter Regions, Genetic/genetics
- Seedlings/drug effects
- Seedlings/enzymology
- Seedlings/genetics
- Seedlings/physiology
- Sequence Alignment
- Sequence Analysis, DNA
- Stress, Physiological
- Tandem Repeat Sequences
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Affiliation(s)
- Qing-Mao Shang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No12 Zhongguancun South Street, Beijing 100081, People's Republic of China
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Kaur H, Shaker K, Heinzel N, Ralph J, Gális I, Baldwin IT. Environmental stresses of field growth allow cinnamyl alcohol dehydrogenase-deficient Nicotiana attenuata plants to compensate for their structural deficiencies. PLANT PHYSIOLOGY 2012; 159:1545-70. [PMID: 22645069 PMCID: PMC3425196 DOI: 10.1104/pp.112.196717] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 05/03/2012] [Indexed: 05/02/2023]
Abstract
The organized lignocellulosic assemblies of cell walls provide the structural integrity required for the large statures of terrestrial plants. Silencing two CINNAMYL ALCOHOL DEHYDROGENASE (CAD) genes in Nicotiana attenuata produced plants (ir-CAD) with thin, red-pigmented stems, low CAD and sinapyl alcohol dehydrogenase activity, low lignin contents, and rubbery, structurally unstable stems when grown in the glasshouse (GH). However, when planted into their native desert habitat, ir-CAD plants produced robust stems that survived wind storms as well as the wild-type plants. Despite efficient silencing of NaCAD transcripts and enzymatic activity, field-grown ir-CAD plants had delayed and restricted spread of red stem pigmentation, a color change reflecting blocked lignification by CAD silencing, and attained wild-type-comparable total lignin contents. The rubbery GH phenotype was largely restored when field-grown ir-CAD plants were protected from wind, herbivore attack, and ultraviolet B exposure and grown in restricted rooting volumes; conversely, it was lost when ir-CAD plants were experimentally exposed to wind, ultraviolet B, and grown in large pots in growth chambers. Transcript and liquid chromatography-electrospray ionization-time-of-flight analysis revealed that these environmental stresses enhanced the accumulation of various phenylpropanoids in stems of field-grown plants; gas chromatography-mass spectrometry and nuclear magnetic resonance analysis revealed that the lignin of field-grown ir-CAD plants had GH-grown comparable levels of sinapaldehyde and syringaldehyde cross-linked into their lignins. Additionally, field-grown ir-CAD plants had short, thick stems with normal xylem element traits, which collectively enabled field-grown ir-CAD plants to compensate for the structural deficiencies associated with CAD silencing. Environmental stresses play an essential role in regulating lignin biosynthesis in lignin-deficient plants.
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Affiliation(s)
| | | | | | - John Ralph
- Department of Molecular Ecology (H.K., N.H., I.G., I.T.B.) and Department of Biosynthesis/Nuclear Magnetic Resonance (K.S.), Max-Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biochemistry and Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 (J.R.); and Institute of Plant Science and Resources, Okayama University, Okayama 710–0046, Japan (I.G.)
| | - Ivan Gális
- Department of Molecular Ecology (H.K., N.H., I.G., I.T.B.) and Department of Biosynthesis/Nuclear Magnetic Resonance (K.S.), Max-Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biochemistry and Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 (J.R.); and Institute of Plant Science and Resources, Okayama University, Okayama 710–0046, Japan (I.G.)
| | - Ian T. Baldwin
- Department of Molecular Ecology (H.K., N.H., I.G., I.T.B.) and Department of Biosynthesis/Nuclear Magnetic Resonance (K.S.), Max-Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biochemistry and Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 (J.R.); and Institute of Plant Science and Resources, Okayama University, Okayama 710–0046, Japan (I.G.)
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