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Adhikary D, Mehta D, Kisiala A, Basu U, Uhrig RG, Emery RN, Rahman H, Kav NNV. Proteome- and metabolome-level changes during early stages of clubroot infection in Brassica napus canola. Mol Omics 2024; 20:265-282. [PMID: 38334713 DOI: 10.1039/d3mo00210a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Clubroot is a destructive root disease of canola (Brassica napus L.) caused by Plasmodiophora brassicae Woronin. Despite extensive research into the molecular responses of B. napus to P. brassicae, there is limited information on proteome- and metabolome-level changes in response to the pathogen, especially during the initial stages of infection. In this study, we have investigated the proteome- and metabolome- level changes in the roots of clubroot-resistant (CR) and -susceptible (CS) doubled-haploid (DH) B. napus lines, in response to P. brassicae pathotype 3H at 1-, 4-, and 7-days post-inoculation (DPI). Root proteomes were analyzed using nanoflow liquid chromatography coupled with tandem mass spectrometry (nano LC-MS/MS). Comparisons of pathogen-inoculated and uninoculated root proteomes revealed 2515 and 1556 differentially abundant proteins at one or more time points (1-, 4-, and 7-DPI) in the CR and CS genotypes, respectively. Several proteins related to primary metabolites (e.g., amino acids, fatty acids, and lipids), secondary metabolites (e.g., glucosinolates), and cell wall reinforcement-related proteins [e.g., laccase, peroxidases, and plant invertase/pectin methylesterase inhibitors (PInv/PMEI)] were identified. Eleven nucleotides and nucleoside-related metabolites, and eight fatty acids and sphingolipid-related metabolites were identified in the metabolomics study. To our knowledge, this is the first report of root proteome-level changes and associated alterations in metabolites during the early stages of P. brassicae infection in B. napus.
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Affiliation(s)
- Dinesh Adhikary
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Anna Kisiala
- Biology Department, Trent University, Peterborough, ON, Canada
| | - Urmila Basu
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Rj Neil Emery
- Biology Department, Trent University, Peterborough, ON, Canada
| | - Habibur Rahman
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Nat N V Kav
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
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Peracchi LM, Panahabadi R, Barros-Rios J, Bartley LE, Sanguinet KA. Grass lignin: biosynthesis, biological roles, and industrial applications. FRONTIERS IN PLANT SCIENCE 2024; 15:1343097. [PMID: 38463570 PMCID: PMC10921064 DOI: 10.3389/fpls.2024.1343097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/06/2024] [Indexed: 03/12/2024]
Abstract
Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.
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Affiliation(s)
- Luigi M. Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Rahele Panahabadi
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Jaime Barros-Rios
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Laura E. Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Karen A. Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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Gong L, Li B, Zhu T, Xue B. Genome-wide identification and expression profiling analysis of DIR gene family in Setaria italica. FRONTIERS IN PLANT SCIENCE 2023; 14:1243806. [PMID: 37799547 PMCID: PMC10548141 DOI: 10.3389/fpls.2023.1243806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/28/2023] [Indexed: 10/07/2023]
Abstract
Dirigent (DIR) proteins play essential roles in regulating plant growth and development, as well as enhancing resistance to abiotic and biotic stresses. However, the whole-genome identification and expression profiling analysis of DIR gene family in millet (Setaria italica (Si)) have not been systematically understood. In this study, we conducted genome-wide identification and expression analysis of the S. italica DIR gene family, including gene structures, conserved domains, evolutionary relationship, chromosomal locations, cis-elements, duplication events, gene collinearity and expression patterns. A total of 38 SiDIR members distributed on nine chromosomes were screened and identified. SiDIR family members in the same group showed higher sequence similarity. The phylogenetic tree divided the SiDIR proteins into six subfamilies: DIR-a, DIR-b/d, DIR-c, DIR-e, DIR-f, and DIR-g. According to the tertiary structure prediction, DIR proteins (like SiDIR7/8/9) themselves may form a trimer to exert function. The result of the syntenic analysis showed that tandem duplication may play the major driving force during the evolution of SiDIRs. RNA-seq data displayed higher expression of 16 SiDIR genes in root tissues, and this implied their potential functions during root development. The results of quantitative real-time PCR (RT-qPCR) assays revealed that SiDIR genes could respond to the stress of CaCl2, CdCl, NaCl, and PEG6000. This research shed light on the functions of SiDIRs in responding to abiotic stress and demonstrated their modulational potential during root development. In addition, the membrane localization of SiDIR7/19/22 was confirmed to be consistent with the forecast. The results above will provide a foundation for further and deeper investigation of DIRs.
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Affiliation(s)
- Luping Gong
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Bingbing Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Tao Zhu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Baoping Xue
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, China
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Jia W, Xiong Y, Li M, Zhang S, Han Z, Li K. Genome-wide identification, characterization, evolution and expression analysis of the DIR gene family in potato ( Solanum tuberosum). Front Genet 2023; 14:1224015. [PMID: 37680198 PMCID: PMC10481866 DOI: 10.3389/fgene.2023.1224015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
The dirigent (DIR) gene is a key player in environmental stress response and has been identified in many multidimensional tube plant species. However, there are few studies on the StDIR gene in potato. In this study, we used genome-wide identification to identify 31 StDIR genes in potato. Among the 12 potato chromosomes, the StDIR gene was distributed on 11 chromosomes, among which the third chromosome did not have a family member, while the tenth chromosome had the most members with 11 members. 22 of the 31 StDIRs had a classical DIR gene structure, with one exon and no intron. The conserved DIR domain accounts for most of the proteins in the 27 StDIRs. The structure of the StDIR gene was analyzed and ten different motifs were detected. The StDIR gene was divided into three groups according to its phylogenetic relationship, and 22 duplicate genes were identified. In addition, four kinds of cis-acting elements were detected in all 31 StDIR promoter regions, most of which were associated with biotic and abiotic stress. The findings demonstrated that the StDIR gene exhibited specific responses to cold stress, salt stress, ABA, and drought stress. This study provides new candidate genes for improving potato's resistance to stress.
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Affiliation(s)
- Wenqi Jia
- Agricultural College, Yanbian University, Yanji, Jilin, China
| | - Yuting Xiong
- Agricultural College, Yanbian University, Yanji, Jilin, China
| | - Man Li
- Agricultural College, Yanbian University, Yanji, Jilin, China
| | - Shengli Zhang
- Jilin Academy of Vegetable and Flower Science, Changchun, Jilin, China
| | - Zhongcai Han
- Jilin Academy of Vegetable and Flower Science, Changchun, Jilin, China
| | - Kuihua Li
- Agricultural College, Yanbian University, Yanji, Jilin, China
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Pei Y, Cao W, Yu W, Peng C, Xu W, Zuo Y, Wu W, Hu Z. Identification and functional characterization of the dirigent gene family in Phryma leptostachya and the contribution of PlDIR1 in lignan biosynthesis. BMC PLANT BIOLOGY 2023; 23:291. [PMID: 37259047 DOI: 10.1186/s12870-023-04297-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Furofuran lignans, the main insecticidal ingredient in Phryma leptostachya, exhibit excellent controlling efficacy against a variety of pests. During the biosynthesis of furofuran lignans, Dirigent proteins (DIRs) are thought to be dominant in the stereoselective coupling of coniferyl alcohol to form ( ±)-pinoresinol. There are DIR family members in almost every vascular plant, but members of DIRs in P. leptostachya are unknown. To identify the PlDIR genes and elucidate their functions in lignan biosynthesis, this study performed transcriptome-wide analysis and characterized the catalytic activity of the PlDIR1 protein. RESULTS Fifteen full-length unique PlDIR genes were identified in P. leptostachya. A phylogenetic analysis of the PlDIRs classified them into four subfamilies (DIR-a, DIR-b/d, DIR-e, and DIR-g), and 12 conserved motifs were found among them. In tissue-specific expression analysis, except for PlDIR7, which displayed the highest transcript abundance in seeds, the other PlDIRs showed preferential expression in roots, leaves, and stems. Furthermore, the treatments with signaling molecules demonstrated that PlDIRs could be significantly induced by methyl jasmonate (MeJA), salicylic acid (SA), and ethylene (ETH), both in the roots and leaves of P. leptostachya. In examining the tertiary structure of the protein and the critical amino acids, it was found that PlDIR1, one of the DIR-a subfamily members, might be involved in the region- and stereo-selectivity of the phenoxy radical. Accordingly, LC-MS/MS analysis demonstrated the catalytic activity of recombinant PlDIR1 protein from Escherichia coli to direct coniferyl alcohol coupling into ( +)-pinoresinol. The active sites and hydrogen bonds of the interaction between PlDIR1 and bis-quinone methide (bisQM), the intermediate in ( +)-pinoresinol formation, were analyzed by molecular docking. As a result, 18 active sites and 4 hydrogen bonds (Asp-42, Ala-113, Leu-138, Arg-143) were discovered in the PlDIR1-bisQM complex. Moreover, correlation analysis indicated that the expression profile of PlDIR1 was closely connected with lignan accumulations after SA treatment. CONCLUSIONS The results of this study will provide useful clues for uncovering P. leptostachya's lignan biosynthesis pathway as well as facilitate further studies on the DIR family.
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Affiliation(s)
- Yakun Pei
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, China
- Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Wenhan Cao
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, China
- Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Wenwen Yu
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, China
- Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Chaoyang Peng
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Wenhao Xu
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yayun Zuo
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, China
- Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Wenjun Wu
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, China
- Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Zhaonong Hu
- Institute of Pesticide Science, College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, China.
- Key Laboratory for Botanical Pesticide R & D of Shaanxi Province, Yangling, 712100, Shaanxi, China.
- Key Laboratory of Integrated Pest Management On Crops in Northwestern Loess Plateau, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
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Yin Y, Ren Z, Zhang L, Qin L, Chen L, Liu L, Jia R, Xue K, Liu B, Wang X. In Situ Proteomic Analysis of Herbicide-Resistant Soybean and Hybrid Seeds via Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7140-7151. [PMID: 37098110 DOI: 10.1021/acs.jafc.3c00301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Transgenic soybean is the commercial crop with the largest cultivation area worldwide. During transgenic soybean cultivation, exogenous genes may be transferred to wild relatives through gene flow, posing unpredictable ecological risks. Accordingly, an environmental risk assessment should focus on fitness changes and underlying mechanisms in hybrids between transgenic and wild soybeans (Glycine soja). Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) was used for in situ detection and imaging of protein changes in the seeds of transgenic herbicide-resistant soybean harboring epsps and pat genes, non-transgenic soybean, wild soybean, and their F2 hybrid. Protein data clearly distinguished wild soybeans, while the F2 seeds had protein characteristics of both parents and were distinguished from wild soybean seeds. Using UPLC-Q-TOF-MS, 22 differentially expressed proteins (DEPs) were identified, including 13 specific to wild soybean. Sucrose synthase and stress response-related DEPs were differentially expressed in parental and offspring. Differences in these may underpin the greater adaptability of the latter. MSI revealed DEP distribution in transgenic, wild, and F2 seeds. Identifying DEPs related to fitness may elucidate mechanisms underlying fitness differences among the studied varieties. Our study shows that MALDI-MSI has the potential to become a visual method for transgenic soybean analysis.
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Affiliation(s)
- Yue Yin
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
- Nanjing Agro-Tech Extension and Service Center, Agricultural and Rural Bureau of Nanjing, Nanjing, Jiangsu 210029, China
| | - Zhentao Ren
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Li Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Liang Qin
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (State Ethnic Affairs Commission), Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
| | - Lulu Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (State Ethnic Affairs Commission), Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
| | - Laipan Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Ruizong Jia
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya 572025, China
| | - Kun Xue
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Biao Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Xiaodong Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (State Ethnic Affairs Commission), Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
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Luo R, Pan W, Liu W, Tian Y, Zeng Y, Li Y, Li Z, Cui L. The barley DIR gene family: An expanded gene family that is involved in stress responses. Front Genet 2022; 13:1042772. [PMID: 36406120 PMCID: PMC9667096 DOI: 10.3389/fgene.2022.1042772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/24/2022] [Indexed: 09/09/2023] Open
Abstract
Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.
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Affiliation(s)
- Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenqiang Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yuan Tian
- Xintai Urban and Rural Development Group Co., Ltd., Taian, Shandong, China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zhimin Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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Czajka KM, Nkongolo K. Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress. PLoS One 2022; 17:e0274740. [PMID: 36227867 PMCID: PMC9560071 DOI: 10.1371/journal.pone.0274740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/02/2022] [Indexed: 11/07/2022] Open
Abstract
Plants have evolved heavy metal tolerance mechanisms to adapt and cope with nickel (Ni) toxicity. Decrypting whole gene expression of Trembling Aspen (Pinus tremuloides) under nickel stress could elucidate the nickel resistance/tolerance mechanisms. The main objectives of the present research were to 1) characterize the P. tremuloides transcriptome, and 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing. Illumina Sequencing generated 27–45 million 2X150 paired-end reads of raw data per sample. The alignment performed with StringTie Software added two groups of transcripts to the draft genome annotation. One group contained 32,677 new isoforms that match to 17,254 genes. The second group contained 17,349 novel transcripts that represent 16,157 novel genes. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. With the high stringency (two-fold change, FDR value ≤ 0.05 and logFC value ≥1 (upregulated) or ≤ -1 (downregulated), after GSEA analysis and filtering for gene set size, 575 gene sets were upregulated and 146 were downregulated in nickel resistant phenotypes compared to susceptible genotypes. For biological process, genes associated with translation were significantly upregulated while signal transduction and cellular protein process genes were downregulated in resistant compared to susceptible genotypes. For molecular function, there was a significant downregulation of genes associated with DNA binding in resistant compared to susceptible lines. Significant upregulation was observed in genes located in ribosome while downregulation of genes in chloroplast and mitochondrion were preponderant in resistant genotypes compared to susceptible. Hence, from a whole transcriptome level, an upregulation in ribosomal and translation activities was identified as the main response to Ni toxicity in the resistant plants. More importantly, this study revealed that a metal transport protein (Potrs038704g29436 –ATOX1-related copper transport) was among the top upregulated genes in resistant genotypes when compared to susceptible plants. Other identified upregulated genes associated with abiotic stress include genes coding for Dirigent Protein 10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar transporter, and thiamine thiazole synthase.
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Affiliation(s)
- Karolina M. Czajka
- Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, Canada
| | - Kabwe Nkongolo
- Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, Canada
- Department of Biology, School of Natural Sciences, Laurentian University, Sudbury, Ontario, Canada
- * E-mail:
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Characterization, expression, and functional analysis of the pathogenesis-related gene PtDIR11 in transgenic poplar. Int J Biol Macromol 2022; 210:182-195. [PMID: 35545137 DOI: 10.1016/j.ijbiomac.2022.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/02/2022] [Indexed: 11/23/2022]
Abstract
Lignins and lignans are important for plant resistance to pathogens. Dirigent (DIR) proteins control the regio- and stereo-selectivity of coniferyl alcohol in lignan and lignin biosynthesis. DIR genes have been implicated in defense-related responses in several plant species, but their role in poplar immunity is unclear. We cloned PtDIR11 from Populus trichocarpa; we found that overexpression of PtDIR11 in poplar improved the lignan biosynthesis and enhanced the resistance of poplar to Septotis populiperda. PtDIR11 has a typical DIR domain; it belongs to the DIR-b/d family and is expressed in the cell membrane. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis showed that PtDIR11 expression was highest in stems, followed by leaves and roots. Furthermore, PtDIR11 expression was induced by S. populiperda, salicylic acid (SA), jasmonate (JA), and ethylene (ET) stresses. The recombinant PtDIR11 protein inhibited the growth of S. populiperda in vitro. Overexpressing (OE) PtDIR11 in "Nanlin 895" poplar enhanced growth. The OE lines exhibited minimal changes in lignin content, but their total lignan and flavonoid contents were significantly greater than in the wild-type (WT) lines. Overexpression of PtDIR11 affected multiple biological pathways of poplar, such as phenylpropanoid biosynthesis. The methanol extracts of OE-PtDIR11 lines showed greater anti-S. populiperda activity than did lignin extracts from the WT lines. Furthermore, OE-PtDIR11 lines upregulated genes that were related to phenylpropanoid biosynthesis and genes associated with the JA and ET signal transduction pathways; it downregulated genes that were related to SA signal transduction compared with the WT line under S. populiperda stress. Therefore, the OE transgenic plants analysis revealed that PtDIR11 is a good candidate gene for breeding of disease resistant poplar.
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10
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Zhang Z, Huang B, Chen J, Jiao Y, Guo H, Liu S, Ramakrishnan M, Qi G. Genome-Wide Identification of JRL Genes in Moso Bamboo and Their Expression Profiles in Response to Multiple Hormones and Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2022; 12:809666. [PMID: 35095981 PMCID: PMC8795371 DOI: 10.3389/fpls.2021.809666] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/27/2021] [Indexed: 05/13/2023]
Abstract
Jacalin-related lectins (JRLs) are a new subfamily of plant lectins that has recently been recognized and plays an important role in plant growth, development, and abiotic stress response. Although moso bamboo (Phyllostachys edulis) is an economically and industrially important bamboo worldwide, there has been no systematic identification of JRLs in this species. Here, we identified 25 JRL genes in moso bamboo, and these genes are unequally distributed among 10 genome scaffolds. Phylogenetic analysis showed that the moso bamboo JRLs were clustered into four JRL subgroups: I, II, V, and VII. Numerous stress-responsive and hormone-regulated cis-elements were detected in the upstream promoter regions of the JRLs. Genome collinearity analyses showed that the JRL genes of moso bamboo are more closely related to those of Brachypodium distachyon than to those of Oryza sativa and Zea mays. Sixty-four percent of the PeJRL genes are present as segmental and tandem duplicates. qRT-PCR expression analysis showed that JRL genes in the same subgroup were significantly downregulated in response to salicylic acid (SA), abscisic acid (ABA), and methyl jasmonate (MeJA) treatments and significantly upregulated under low temperature, drought, and salt stress; they also exhibited tissue-specific expression patterns. Subcellular localization experiments revealed that PeJRL04 and PeJRL13 were localized to the cell membrane, nucleus, and cytoplasm. Three dimensional structure prediction and yeast two-hybrid assays were used to verify that PeJRL13 exists as a self-interacting homodimer in vivo. These findings provide an important reference for understanding the functions of specific moso bamboo JRL genes and for the effective selection of stress-related genes.
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Affiliation(s)
- Zhijun Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, China
| | - Bin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, China
| | - Jialu Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, China
| | - Yang Jiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, China
| | - Hui Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Guoning Qi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, China
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11
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Vignesh P, Mahadevaiah C, Parimalan R, Valarmathi R, Dharshini S, Nisha S, Suresha GS, Swathi S, Mahadeva Swamy HK, Sreenivasa V, Mohanraj K, Hemaprabha G, Bakshi R, Appunu C. Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet. Sci Rep 2021; 11:24514. [PMID: 34972826 PMCID: PMC8720094 DOI: 10.1038/s41598-021-03735-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 12/08/2021] [Indexed: 11/09/2022] Open
Abstract
Erianthus arundinaceus [Retzius] Jeswiet, a wild relative of sugarcane has a high biomass production potential and a reservoir of many genes for superior agronomic traits and tolerance to biotic and abiotic stresses. A comparative physiological, anatomical and root transcriptome analysis were carried out to identify the salt-responsive genes and metabolic pathways associated with salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010. IND99-907 recorded growth of young leaves, higher proline content, higher relative water content, intact root anatomical structures and lower Na+/K+, Ca2+/K+ and Mg2+/K+ ratio as compared to the sugarcane genotype Co 97010. We have generated four de novo transcriptome assemblies between stressed and control root samples of IND99-907 and Co 97010. A total of 649 and 501 differentially expressed genes (FDR<0.01) were identified from the stressed and control libraries of IND99-907 and Co 97010 respectively. Genes and pathways related to early stress-responsive signal transduction, hormone signalling, cytoskeleton organization, cellular membrane stabilization, plasma membrane-bound calcium and proton transport, sodium extrusion, secondary metabolite biosynthesis, cellular transporters related to plasma membrane-bound trafficking, nucleobase transporter, clathrin-mediated endocytosis were highly enriched in IND99-907. Whereas in Co 97010, genes related to late stress-responsive signal transduction, electron transport system, senescence, protein degradation and programmed cell death, transport-related genes associated with cellular respiration and mitochondrial respiratory chain, vesicular trafficking, nitrate transporter and fewer secondary metabolite biosynthetic genes were highly enriched. A total of 27 pathways, 24 biological processes, three molecular functions and one cellular component were significantly enriched (FDR≤ 0.05) in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010, indicates the unique and distinct expression pattern of genes and metabolic pathways in both genotypes. The genomic resources developed from this study is useful for sugarcane crop improvement through development of genic SSR markers and genetic engineering approaches.
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Affiliation(s)
- P Vignesh
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - C Mahadevaiah
- ICAR-Sugarcane Breeding Institute, Coimbatore, India.
| | - R Parimalan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - R Valarmathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - S Dharshini
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Singh Nisha
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - G S Suresha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - S Swathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | | | - V Sreenivasa
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - K Mohanraj
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - G Hemaprabha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Ram Bakshi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - C Appunu
- ICAR-Sugarcane Breeding Institute, Coimbatore, India.
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12
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Lemcke R, Sjökvist E, Visentin S, Kamble M, James EK, Hjørtshøj R, Wright KM, Avrova A, Newton AC, Havis ND, Radutoiu S, Lyngkjær MF. Deciphering Molecular Host-Pathogen Interactions During Ramularia Collo-Cygni Infection on Barley. FRONTIERS IN PLANT SCIENCE 2021; 12:747661. [PMID: 34745181 PMCID: PMC8570322 DOI: 10.3389/fpls.2021.747661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/29/2021] [Indexed: 05/30/2023]
Abstract
Ramularia collo-cygni is the causal agent of Ramularia leaf spot disease (RLS) on barley and became, during the recent decades, an increasing threat for farmers across the world. Here, we analyze morphological, transcriptional, and metabolic responses of two barley cultivars having contrasting tolerance to RLS, when infected by an aggressive or mild R. collo-cygni isolate. We found that fungal biomass in leaves of the two cultivars does not correlate with their tolerance to RLS, and both cultivars displayed cell wall reinforcement at the point of contact with the fungal hyphae. Comparative transcriptome analysis identified that the largest transcriptional differences between cultivars are at the early stages of fungal colonization with differential expression of kinases, calmodulins, and defense proteins. Weighted gene co-expression network analysis identified modules of co-expressed genes, and hub genes important for cultivar responses to the two R. collo-cygni isolates. Metabolite analyses of the same leaves identified defense compounds such as p-CHDA and serotonin, correlating with responses observed at transcriptome and morphological level. Together these all-round responses of barley to R. collo-cygni provide molecular tools for further development of genetic and physiological markers that may be tested for improving tolerance of barley to this fungal pathogen.
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Affiliation(s)
- René Lemcke
- Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark
| | - Elisabet Sjökvist
- Crop and Soils Systems, Scotland’s Rural College, Edinburgh, United Kingdom
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stefano Visentin
- Ecological Sciences, The James Hutton Institute, Invergowrie, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, United Kingdom
| | - Manoj Kamble
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Euan K. James
- Ecological Sciences, The James Hutton Institute, Invergowrie, United Kingdom
| | | | - Kathryn M. Wright
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, United Kingdom
| | - Anna Avrova
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, United Kingdom
| | - Adrian C. Newton
- Ecological Sciences, The James Hutton Institute, Invergowrie, United Kingdom
| | - Neil D. Havis
- Crop and Soils Systems, Scotland’s Rural College, Edinburgh, United Kingdom
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Michael F. Lyngkjær
- Department of Plant and Environmental Sciences, Copenhagen University, Frederiksberg, Denmark
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13
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Genome-Wide Characterization of Dirigent Proteins in Populus: Gene Expression Variation and Expression Pattern in Response to Marssonina brunnea and Phytohormones. FORESTS 2021. [DOI: 10.3390/f12040507] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Marssonina brunnea causes a major disease that limits poplar growth. Lignin and lignan play essential roles in protecting plants from various biological stresses. Dirigent (DIR) proteins are thought to control the stereoselective coupling of coniferyl alcohol in the formation of lignan and lignin. DIR family members have been well studied in several plant species, but no previous detailed genome-wide analysis has been carried out in forest trees, such as poplar. We identified 40 PtDIR genes in Populus trichocarpa and classified them into three subgroups (DIR-a, DIR-b/d, and DIR-e) based on phylogenetic analyses. These genes are distributed on 11 poplar chromosomes, and 80% of PtDIRs (32/40) are intronless. The cis-element analysis inferred that PtDIRs possess many types of biological and abiotic stress-response cis-elements. We also analyzed intra- and inter-specific collinearity, which provided deep insights into the evolutionary characteristics of the poplar DIR genes. Analyses of the protein tertiary structure and critical amino acid residues showed that PtDIR7–10 and PtDIR13–16, which belong to the DIR-a subfamily, might be involved in the regio- and stereo-selectivity of bimolecular phenoxy radical coupling in poplars. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis revealed different expression patterns for the PtDIR genes of P. trichocarpa and the PeDIR genes of ‘Nanlin 895’ in various tissues. Additionally, we analyzed responses of PeDIRs to M. brunnea and different phytohormone treatments (abscisic acid, salicylic acid, methyl jasmonate, and ethylene) in ‘Nanlin 895’. The results showed that at least 18 genes responded strongly to M. brunnea, and these PeDIRs also showed significant responses to phytohormones. These results suggest that DIR genes are involved in the poplar defense response against M. brunnea, and this study will provide fundamental insights for future research on poplar DIR genes.
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14
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Yonekura-Sakakibara K, Yamamura M, Matsuda F, Ono E, Nakabayashi R, Sugawara S, Mori T, Tobimatsu Y, Umezawa T, Saito K. Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis. THE PLANT CELL 2021; 33:129-152. [PMID: 33751095 PMCID: PMC8136895 DOI: 10.1093/plcell/koaa014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/20/2020] [Indexed: 05/03/2023]
Abstract
Lignans/neolignans are generally synthesized from coniferyl alcohol (CA) in the cinnamate/monolignol pathway by oxidation to generate the corresponding radicals with subsequent stereoselective dimerization aided by dirigent proteins (DIRs). Genes encoding oxidases and DIRs for neolignan biosynthesis have not been identified previously. In Arabidopsis thaliana, the DIR AtDP1/AtDIR12 plays an essential role in the 8-O-4' coupling in neolignan biosynthesis by unequivocal structural determination of the compound missing in the atdp1 mutant as a sinapoylcholine (SC)-conjugated neolignan, erythro-3-{4-[2-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-1-hydroxymethylethoxy]-3,5-dimethoxyphenyl}acryloylcholine. Phylogenetic analyses showed that AtDP1/AtDIR12 belongs to the DIR-a subfamily composed of DIRs for 8-8' coupling of monolignol radicals. AtDP1/AtDIR12 is specifically expressed in outer integument 1 cells in developing seeds. As a putative oxidase for neolignan biosynthesis, we focused on AtLAC5, a laccase gene coexpressed with AtDP1/AtDIR12. In lac5 mutants, the abundance of feruloylcholine (FC)-conjugated neolignans decreased to a level comparable to those in the atdp1 mutant. In addition, SC/FC-conjugated neolignans were missing in the seeds of mutants defective in SCT/SCPL19, an enzyme that synthesizes SC. These results strongly suggest that AtDP1/AtDIR12 and AtLAC5 are involved in neolignan biosynthesis via SC/FC. A tetrazolium penetration assay showed that seed coat permeability increased in atdp1 mutants, suggesting a protective role of neolignans in A. thaliana seeds.
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Affiliation(s)
- Keiko Yonekura-Sakakibara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masaomi Yamamura
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Fumio Matsuda
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Eiichiro Ono
- Research Institute, Suntory Global Innovation Center Ltd., 8-1-1 Seikadai, Seika, Soraku-gun, Kyoto 619-0284, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Satoko Sugawara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
- Research Unit for Development of Global Sustainability, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Plant Molecular Science Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
- Author for correspondence: ,
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15
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Yadav V, Wang Z, Yang X, Wei C, Changqing X, Zhang X. Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress. Genes (Basel) 2021; 12:genes12030326. [PMID: 33668231 PMCID: PMC7996225 DOI: 10.3390/genes12030326] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/16/2022] Open
Abstract
Dirigent (DIR) proteins are induced under various stress conditions and involved in sterio- and regio-selective coupling of monolignol. A striking lack of information about dirigent genes in cucurbitaceae plants underscores the importance of functional characterization. In this study, 112 DIR genes were identified in six species, and 61 genes from major cultivated species were analyzed. DIRs were analyzed using various bioinformatics tools and complemented by expression profiling. Phylogenetic analysis segregated the putative DIRs into six distinctively known subgroups. Chromosomal mapping revealed uneven distribution of genes, whereas synteny analysis exhibited that duplication events occurred during gene evolution. Gene structure analysis suggested the gain of introns during gene diversification. Gene ontology (GO) enrichment analysis indicates the participation of proteins in lignification and pathogen resistance activities. We also determined their organ-specific expression levels in three species revealing preferential expression in root and leaves. Furthermore, the number of CmDIR (CmDIR1, 6, 7 and 12) and ClDIR (ClDIR2, 5, 8, 9 and 17) genes exhibited higher expression in resistant cultivars after powdery mildew (PM) inoculation. In summary, based on the expression and in-silico analysis, we propose a role of DIRs in disease resistance mechanisms.
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Affiliation(s)
- Vivek Yadav
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
| | - Zhongyuan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
| | - Xiaozhen Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
- Xi’an Agriculture Technology, Extension Center, Xi’an 710000, China
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
| | - Xuan Changqing
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
- Correspondence: ; Tel.: +86-186-2909-2147
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16
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Liu Z, Wang X, Sun Z, Zhang Y, Meng C, Chen B, Wang G, Ke H, Wu J, Yan Y, Wu L, Li Z, Yang J, Zhang G, Ma Z. Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes. BMC PLANT BIOLOGY 2021; 21:89. [PMID: 33568051 PMCID: PMC7876823 DOI: 10.1186/s12870-021-02859-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/27/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in enhancing stress resistance and in secondary cell-wall development, but systematical understanding is lacking in cotton. RESULTS In this study, 107 GbDIRs and 107 GhDIRs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. Most of these genes have a classical gene structure without intron and encode proteins containing a signal peptide. Phylogenetic analysis showed that cotton DIR genes were classified into four distinct subfamilies (a, b/d, e, and f). Of these groups, DIR-a and DIR-e were evolutionarily conserved, and segmental and tandem duplications contributed equally to their formation. In contrast, DIR-b/d mainly expanded by recent tandem duplications, accompanying with a number of gene clusters. With the rapid evolution, DIR-b/d-III was a Gossypium-specific clade involved in atropselective synthesis of gossypol. RNA-seq data highlighted GhDIRs in response to Verticillium dahliae infection and suggested that DIR gene family could confer Verticillium wilt resistance. We also identified candidate DIR genes related to fiber development in G. barbadense and G. hirsutum and revealed their differential expression. To further determine the involvement of DIR genes in fiber development, we overexpressed a fiber length-related gene GbDIR78 in Arabidopsis and validated its function in trichomes and hypocotyls. CONCLUSIONS These findings contribute novel insights towards the evolution of DIR gene family and provide valuable information for further understanding the roles of DIR genes in cotton fiber development as well as in stress responses.
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Affiliation(s)
- Zhengwen Liu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Jinhua Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Yuanyuan Yan
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Zhikun Li
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Jun Yang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China.
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071001, China.
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17
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Ma X, Xu W, Liu T, Chen R, Zhu H, Zhang H, Cai C, Li S. Functional characterization of soybean (Glycine max) DIRIGENT genes reveals an important role of GmDIR27 in the regulation of pod dehiscence. Genomics 2021; 113:979-990. [PMID: 33144217 DOI: 10.1016/j.ygeno.2020.10.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/02/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022]
Abstract
DIRIGENT (DIR) genes play important roles in regulating plant growth and development and have been studied in many plant species. However, information on DIR genes in soybean is limited. Here, we identified and characterized 54 GmDIRs and studied the characteristics of GmDIRs. Most of the GmDIRs contained a classical gene structure, one exon; 26 conserved motifs were found among these GmDIRs. The GmDIRs were grouped into four subfamilies, DIR-a, DIR-b, DIR-e and DIR-f, based on a phylogenetic analysis, and 24 duplicated gene pairs were identified. Differences in the cis-acting elements in the GmDIR promoter regions might result in distinct expression patterns of GmDIRs in different tissues. In addition, GmDIR27 had a close relationship with the pod dehiscence gene GmPdh1, and overexpression of GmDIR27 increased pod dehiscence by affecting several pod dehiscence-related gene expressions. Generally, our results provide essential information that aids future efforts to functionally characterize soybean GmDIR genes.
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Affiliation(s)
- Xiaofei Ma
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenying Xu
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Tong Liu
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Ruying Chen
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Huiying Zhang
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Chunmei Cai
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuai Li
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China.
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18
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Laoué J, Depardieu C, Gérardi S, Lamothe M, Bomal C, Azaiez A, Gros-Louis MC, Laroche J, Boyle B, Hammerbacher A, Isabel N, Bousquet J. Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce. FRONTIERS IN PLANT SCIENCE 2021; 12:675108. [PMID: 34079574 PMCID: PMC8166253 DOI: 10.3389/fpls.2021.675108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/08/2021] [Indexed: 05/05/2023]
Abstract
Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.
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Affiliation(s)
- Justine Laoué
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- *Correspondence: Justine Laoué
| | - Claire Depardieu
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Claude Bomal
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Aïda Azaiez
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Marie-Claude Gros-Louis
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Almuth Hammerbacher
- Department of Zoology, Entomology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Jean Bousquet
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Tiwari P, Srivastava D, Chauhan AS, Indoliya Y, Singh PK, Tiwari S, Fatima T, Mishra SK, Dwivedi S, Agarwal L, Singh PC, Asif MH, Tripathi RD, Shirke PA, Chakrabarty D, Chauhan PS, Nautiyal CS. Root system architecture, physiological analysis and dynamic transcriptomics unravel the drought-responsive traits in rice genotypes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111252. [PMID: 32916530 DOI: 10.1016/j.ecoenv.2020.111252] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/12/2020] [Accepted: 08/24/2020] [Indexed: 05/26/2023]
Abstract
Drought is the major abiotic factors that limit crop productivity worldwide. To withstand stress conditions, plants alter numerous mechanisms for adaption and tolerance. Therefore, in the present study, 106 rice varieties were screened for drought tolerance phenotype via exposing different concentrations of polyethylene glycol 6000 (PEG) in the hydroponic nutrient medium at the time interval of 1, 3, and 7 days to evaluate the changes in their root system architecture. Further, based on root phenotype obtained after PEG-induced drought, two contrasting varieties drought-tolerant Heena and -sensitive Kiran were selected to study transcriptional and physiological alterations at the same stress durations. Physiological parameters (photosynthesis rate, stomatal conductance, transpiration), and non-enzymatic antioxidants (carotenoids, anthocyanins, total phenol content) production indicated better performance of Heena than Kiran. Comparatively higher accumulation of carotenoid and anthocyanin content and the increased photosynthetic rate was also observed in Heena. Root morphology (length, numbers of root hairs, seminal roots and adventitious roots) and anatomical data (lignin deposition, xylem area) enable tolerant variety Heena to better maintain membrane integrity and relative water content, which also contribute to comparatively higher biomass accumulation in Heena under drought. In transcriptome profiling, significant drought stress-associated differentially expressed genes (DEGs) were identified in both the varieties. A total of 1033 and 936 uniquely upregulated DEGs were found in Heena and Kiran respectively. The significant modulation of DEGs that were mainly associated with phytohormone signaling, stress-responsive genes (LEA, DREB), transcription factors (TFs) (AP2/ERF, MYB, WRKY, bHLH), and genes involved in photosynthesis and antioxidative mechanisms indicate better adaptive nature of Heena in stress tolerance. Additionally, the QTL-mapping analysis showed a very high number of DEGs associated with drought stress at AQHP069 QTL in Heena in comparison to Kiran which further distinguishes the drought-responsive traits at the chromosomal level in both the contrasting varieties. Overall, results support the higher capability of Heena over Kiran variety to induce numerous genes along with the development of better root architecture to endure drought stress.
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Affiliation(s)
- Poonam Tiwari
- CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | | | - Abhishek Singh Chauhan
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Yuvraj Indoliya
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pradyumna Kumar Singh
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shalini Tiwari
- CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Touseef Fatima
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Integral University, Lucknow, 226026, India
| | - Shashank Kumar Mishra
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sanjay Dwivedi
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Lalit Agarwal
- CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Poonam C Singh
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mehar H Asif
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rudra D Tripathi
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pramod A Shirke
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debasis Chakrabarty
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Puneet Singh Chauhan
- CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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20
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Singh DK, Mehra S, Chatterjee S, Purty RS. In silico identification and validation of miRNA and their DIR specific targets in Oryza sativa Indica under abiotic stress. Noncoding RNA Res 2020; 5:167-177. [PMID: 33024905 PMCID: PMC7522899 DOI: 10.1016/j.ncrna.2020.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/13/2020] [Accepted: 09/15/2020] [Indexed: 11/08/2022] Open
Abstract
Several biotic (bacterial and viral pathogenesis) and abiotic stress factors like salt, drought, cold, and extreme temperatures significantly reduce crop productivity and grain quality throughout the world. MicroRNAs (miRNAs) are small (~22 nucleotides) non-coding endogenous RNA molecules which negatively regulate gene expression at the post-transcriptional level either by degrading the target protein-coding mRNA genes or suppressing translation in plants. Dirigent (DIR) gene protein plays a crucial role as they are involved to dictate the stereochemistry of a compound synthesized by other enzymes as well as in lignifications against biotic and abiotic stress. In plants, several miRNAs, as well as their targets, are known to regulate stress response but systematic identification of the same is limited. The present work has been designed for in silico identification of miRNAs against a total of sixty-one DIR genes in Oryza sativa Indica followed by target prediction of identified miRNAs through the computational approach and thereafter validation of potential miRNAs in rice genotypes. We systematically identified 3 miRNA and their respective DIR specific target gene in Oryza sativa Indica. The expression of these three miRNAs and their respective DIR specific targets were validated in rice seedlings subjected to five different abiotic stress conditions (heavy metal, high temperature, low temperature, salinity and drought) by quantitative Real-Time PCR (qRT-PCR). Expression analysis indicated that miRNA under stress conditions regulates the gene expression of the DIR gene in rice. To the best of our knowledge this is this is the first report in any organism showing the expression of ath-miRf10317-akr, and osamiRf10761-akr miRNAs in response to various abiotic stresses. Total 61 DIR proteins were identified & classified into 6 groups based on phylogeny analysis in Oryza sativa Indica. Three miRNAs ath-miRf10317-akr, cre-miR910 and osa-miRf10761-akr were identified via computational approach. These 3 miRNAs in response to abiotic stresses showed inverse expression pattern in the respective target genes. This is the first report on expression of ath-miRf10317-akr, and osa-miRf10761-akr miRNAs in response to abiotic stresses.
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Affiliation(s)
- Deepak Kumar Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Shourya Mehra
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Sayan Chatterjee
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Ram Singh Purty
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
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Plant Cell Wall Proteomes: Bioinformatics and Cell Biology Tools to Assess the Bona Fide Cell Wall Localization of Proteins. Methods Mol Biol 2020. [PMID: 32617950 DOI: 10.1007/978-1-0716-0621-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The purification of plant cell walls is challenging because they constitute an open compartment which is not limited by a membrane like the cell organelles. Different strategies have been established to limit the contamination by proteins of other compartments in cell wall proteomics studies. Non-destructive methods rely on washing intact cells with various types of solutions without disrupting the plasma membrane in order to elute cell wall proteins. In contrast, destructive protocols involve the purification of cell walls prior to the extraction of proteins with salt solutions. In both cases, proteins known to be intracellular have been identified by mass spectrometry in cell wall proteomes. The aim of this chapter is to provide tools to assess the subcellular localization of the proteins identified in cell wall proteomics studies, including: (1) bioinformatic predictions, (2) immunocytolocalization of proteins of interest on tissue sections and (3) in muro observation of proteins of interest fused to reporter fluorescent proteins by confocal microscopy. Finally, a qualitative assessment of the work can be performed and the strategy used to prepare the samples can be optimized if necessary.
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Mnich E, Bjarnholt N, Eudes A, Harholt J, Holland C, Jørgensen B, Larsen FH, Liu M, Manat R, Meyer AS, Mikkelsen JD, Motawia MS, Muschiol J, Møller BL, Møller SR, Perzon A, Petersen BL, Ravn JL, Ulvskov P. Phenolic cross-links: building and de-constructing the plant cell wall. Nat Prod Rep 2020; 37:919-961. [PMID: 31971193 DOI: 10.1039/c9np00028c] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Covering: Up to 2019Phenolic cross-links and phenolic inter-unit linkages result from the oxidative coupling of two hydroxycinnamates or two molecules of tyrosine. Free dimers of hydroxycinnamates, lignans, play important roles in plant defence. Cross-linking of bound phenolics in the plant cell wall affects cell expansion, wall strength, digestibility, degradability, and pathogen resistance. Cross-links mediated by phenolic substituents are particularly important as they confer strength to the wall via the formation of new covalent bonds, and by excluding water from it. Four biopolymer classes are known to be involved in the formation of phenolic cross-links: lignins, extensins, glucuronoarabinoxylans, and side-chains of rhamnogalacturonan-I. Lignins and extensins are ubiquitous in streptophytes whereas aromatic substituents on xylan and pectic side-chains are commonly assumed to be particular features of Poales sensu lato and core Caryophyllales, respectively. Cross-linking of phenolic moieties proceeds via radical formation, is catalyzed by peroxidases and laccases, and involves monolignols, tyrosine in extensins, and ferulate esters on xylan and pectin. Ferulate substituents, on xylan in particular, are thought to be nucleation points for lignin polymerization and are, therefore, of paramount importance to wall architecture in grasses and for the development of technology for wall disassembly, e.g. for the use of grass biomass for production of 2nd generation biofuels. This review summarizes current knowledge on the intra- and extracellular acylation of polysaccharides, and inter- and intra-molecular cross-linking of different constituents. Enzyme mediated lignan in vitro synthesis for pharmaceutical uses are covered as are industrial exploitation of mutant and transgenic approaches to control cell wall cross-linking.
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Affiliation(s)
- Ewelina Mnich
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark.
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Hano CF, Dinkova-Kostova AT, Davin LB, Cort JR, Lewis NG. Editorial: Lignans: Insights Into Their Biosynthesis, Metabolic Engineering, Analytical Methods and Health Benefits. FRONTIERS IN PLANT SCIENCE 2020; 11:630327. [PMID: 33510765 PMCID: PMC7835672 DOI: 10.3389/fpls.2020.630327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/08/2020] [Indexed: 05/03/2023]
Affiliation(s)
- Christophe F. Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, Université d'Orléans, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, Chartres, France
- *Correspondence: Christophe F. Hano
| | - Albena T. Dinkova-Kostova
- Division of Cellular Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Albena T. Dinkova-Kostova
| | - Laurence B. Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Laurence B. Davin
| | - John R. Cort
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- John R. Cort
| | - Norman G. Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- Norman G. Lewis
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24
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Dixon RA, Barros J. Lignin biosynthesis: old roads revisited and new roads explored. Open Biol 2019; 9:190215. [PMID: 31795915 PMCID: PMC6936255 DOI: 10.1098/rsob.190215] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/30/2019] [Indexed: 12/31/2022] Open
Abstract
Lignin is a major component of secondarily thickened plant cell walls and is considered to be the second most abundant biopolymer on the planet. At one point believed to be the product of a highly controlled polymerization procedure involving just three potential monomeric components (monolignols), it is becoming increasingly clear that the composition of lignin is quite flexible. Furthermore, the biosynthetic pathways to the major monolignols also appear to exhibit flexibility, particularly as regards the early reactions leading to the formation of caffeic acid from coumaric acid. The operation of parallel pathways to caffeic acid occurring at the level of shikimate esters or free acids may help provide robustness to the pathway under different physiological conditions. Several features of the pathway also appear to link monolignol biosynthesis to both generation and detoxification of hydrogen peroxide, one of the oxidants responsible for creating monolignol radicals for polymerization in the apoplast. Monolignol transport to the apoplast is not well understood. It may involve passive diffusion, although this may be targeted to sites of lignin initiation/polymerization by ordered complexes of both biosynthetic enzymes on the cytosolic side of the plasma membrane and structural anchoring of proteins for monolignol oxidation and polymerization on the apoplastic side. We present several hypothetical models to illustrate these ideas and stimulate further research. These are based primarily on studies in model systems, which may or may not reflect the major lignification process in forest trees.
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Affiliation(s)
- Richard A. Dixon
- Hagler Institute for Advanced Studies and Department of Biological Sciences, Texas A&M University, College Station, TX, USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203-5017, USA
| | - Jaime Barros
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203-5017, USA
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Nemacheck JA, Schemerhorn BJ, Scofield SR, Subramanyam S. Phenotypic and molecular characterization of Hessian fly resistance in diploid wheat, Aegilops tauschii. BMC PLANT BIOLOGY 2019; 19:439. [PMID: 31640550 PMCID: PMC6805508 DOI: 10.1186/s12870-019-2058-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND The Hessian fly (Mayetiola destructor), belonging to the gall midge family (Cecidomyiidae), is a devastating pest of wheat (Triticum aestivum) causing significant yield losses. Despite identification and characterization of numerous Hessian fly-responsive genes and associated biological pathways involved in wheat defense against this dipteran pest, their functional validation has been challenging. This is largely attributed to the large genome, polyploidy, repetitive DNA, and limited genetic resources in hexaploid wheat. The diploid progenitor Aegilops tauschii, D-genome donor of modern-day hexaploid wheat, offers an ideal surrogate eliminating the need to target all three homeologous chromosomes (A, B and D) individually, and thereby making the functional validation of candidate Hessian fly-responsive genes plausible. Furthermore, the well-annotated sequence of Ae. tauschii genome and availability of genetic resources amenable to manipulations makes the functional assays less tedious and time-consuming. However, prior to utilization of this diploid genome for downstream studies, it is imperative to characterize its physical and molecular responses to Hessian fly. RESULTS In this study we screened five Ae. tauschii accessions for their response to the Hessian fly biotypes L and vH13. Two lines were identified that exhibited a homozygous resistance response to feeding by both Hessian fly biotypes. Studies using physical measurements and neutral red staining showed that the resistant Ae. tauschii accessions resembled hexaploid wheat in their phenotypic responses to Hessian fly, that included similarities in larval developmental stages, leaf and plant growth, and cell wall permeability. Furthermore, molecular responses, characterized by gene expression profiling using quantitative real-time PCR, in select resistant Ae. tauschii lines also revealed similarities with resistant hexaploid wheat. CONCLUSIONS Phenotypic and molecular characterization of Ae. tauschii to Hessian fly infestation revealed resistant accessions that shared similarities to hexaploid wheat. Resembling the resistant hexaploid wheat, the Ae. tauschii accessions mount an early defense strategy involving defense proteins including lectins, secondary metabolites and reactive oxygen species (ROS) radicals. Our results reveal the suitability of the diploid progenitor for use as an ideal tool for functional genomics research in deciphering the wheat-Hessian fly molecular interactions.
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Affiliation(s)
- Jill A Nemacheck
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Brandon J Schemerhorn
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Steven R Scofield
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Subhashree Subramanyam
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA.
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
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26
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Markulin L, Corbin C, Renouard S, Drouet S, Gutierrez L, Mateljak I, Auguin D, Hano C, Fuss E, Lainé E. Pinoresinol-lariciresinol reductases, key to the lignan synthesis in plants. PLANTA 2019; 249:1695-1714. [PMID: 30895445 DOI: 10.1007/s00425-019-03137-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/12/2019] [Indexed: 05/20/2023]
Abstract
This paper provides an overview on activity, stereospecificity, expression and regulation of pinoresinol-lariciresinol reductases in plants. These enzymes are shared by the pathways to all 8-8' lignans derived from pinoresinol. Pinoresinol-lariciresinol reductases (PLR) are enzymes involved in the lignan biosynthesis after the initial dimerization of two monolignols. They catalyze two successive reduction steps leading to the production of lariciresinol or secoisolariciresinol from pinoresinol. Two secoisolariciresinol enantiomers can be synthetized with different fates. Depending on the plant species, these enantiomers are either final products (e.g., in the flaxseed where it is stored after glycosylation) or are the starting point for the synthesis of a wide range of lignans, among which the aryltetralin type lignans are used to semisynthesize anticancer drugs such as Etoposide®. Thus, the regulation of the gene expression of PLRs as well as the possible specificities of these reductases for one reduction step or one enantiomer are key factors to fine-tune the lignan synthesis. Results published in the last decade have shed light on the presence of more than one PLR in each plant and revealed various modes of action. Nevertheless, there are not many results published on the PLRs and most of them were obtained in a limited range of species. Indeed, a number of them deal with wild and cultivated flax belonging to the genus Linum. Despite the occurrence of lignans in bryophytes, pteridophytes and monocots, data on PLRs in these taxa are still missing and indeed the whole diversity of PLRs is still unknown. This review summarizes the data, published mainly in the last decade, on the PLR gene expression, enzymatic activity and biological function.
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Affiliation(s)
| | | | | | - Samantha Drouet
- Centre Régional de Ressources en Biologie Moléculaire (CRRBM), Université Picardie Jules Verne, 33 rue Saint-Leu, 80039, Amiens, France
| | - Laurent Gutierrez
- Centre Régional de Ressources en Biologie Moléculaire (CRRBM), Université Picardie Jules Verne, 33 rue Saint-Leu, 80039, Amiens, France
| | - Ivan Mateljak
- LBLGC, INRA USC 1328 Université d'Orléans, Orléans, France
| | - Daniel Auguin
- LBLGC, INRA USC 1328 Université d'Orléans, Orléans, France
| | | | - Elisabeth Fuss
- Interfaculty Institute of Biochemistry, Hoppe-Seyler-St. 4, 72076, Tübingen, Germany
| | - Eric Lainé
- LBLGC, INRA USC 1328 Université d'Orléans, Orléans, France.
- LBLGC, INRA USC 1328 Antenne Scientifique Universitaire de Chartres, 21 rue de Loigny, 28000, Chartres, France.
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27
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Chen LM, Fang YS, Zhang CJ, Hao QN, Cao D, Yuan SL, Chen HF, Yang ZL, Chen SL, Shan ZH, Liu BH, Jing-Wang, Zhan Y, Zhang XJ, Qiu DZ, Li WB, Zhou XA. GmSYP24, a putative syntaxin gene, confers osmotic/drought, salt stress tolerances and ABA signal pathway. Sci Rep 2019; 9:5990. [PMID: 30979945 PMCID: PMC6461667 DOI: 10.1038/s41598-019-42332-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/24/2019] [Indexed: 12/11/2022] Open
Abstract
As major environment factors, drought or high salinity affect crop growth, development and yield. Transgenic approach is an effective way to improve abiotic stress tolerance of crops. In this study, we comparatively analyzed gene structures, genome location, and the evolution of syntaxin proteins containing late embryogenesis abundant (LEA2) domain. GmSYP24 was identified as a dehydration-responsive gene. Our study showed that the GmSYP24 protein was located on the cell membrane. The overexpression of GmSYP24 (GmSYP24ox) in soybean and heteroexpression of GmSYP24 (GmSYP24hx) in Arabidopsis exhibited insensitivity to osmotic/drought and high salinity. However, wild type soybean, Arabidopsis, and the mutant of GmSYP24 homologous gene of Arabidopsis were sensitive to the stresses. Under the abiotic stresses, transgenic soybean plants had greater water content and higher activities of POD, SOD compared with non-transgenic controls. And the leaf stomatal density and opening were reduced in transgenic Arabidopsis. The sensitivity to ABA was decreased during seed germination of GmSYP24ox and GmSYP24hx. GmSYP24hx induced up-regulation of ABA-responsive genes. GmSYP24ox alters the expression of some aquaporins under osmotic/drought, salt, or ABA treatment. These results demonstrated that GmSYP24 played an important role in osmotic/drought or salt tolerance in ABA signal pathway.
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Affiliation(s)
- Li-Miao Chen
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Yi-Sheng Fang
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Chan-Juan Zhang
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Qing-Nan Hao
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Dong Cao
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Song-Li Yuan
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Hai-Feng Chen
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Zhong-Lu Yang
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Shui-Lian Chen
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Zhi-Hui Shan
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Bao-Hong Liu
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Jing-Wang
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Yong Zhan
- Crop Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Key Lab of Cereal Quality Research and Genetic Improvement, Xinjiang Production and Construction Crops, 832000, Shihezi, China
| | - Xiao-Juan Zhang
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - De-Zhen Qiu
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Wen-Bin Li
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
- Division of Soybean Breeding and Seed, Soybean Research & Development Center, CARS (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Harbin, 150030, China.
| | - Xin-An Zhou
- Key Laboratory of Oil Crop Biology, Ministry of Agriculture, Wuhan, 430062, China.
- Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, 430062, China.
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Song M, Peng X. Genome-Wide Identification and Characterization of DIR Genes in Medicago truncatula. Biochem Genet 2019; 57:487-506. [PMID: 30649641 DOI: 10.1007/s10528-019-09903-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/04/2019] [Indexed: 11/29/2022]
Abstract
Dirigent proteins (DIRs) are critically involved in the formation of lignans, a diverse and widely distributed class of secondary plant metabolites exhibiting interesting pharmacological activities and implicated in natural plant defense. However, no detailed information is available about DIR gene family in Medicago truncatula. In this study, a total of 45 DIR genes were identified in M. truncatula. DIR proteins have variability in sequence. Most MtDIR genes have no intron. All MtDIR proteins contain single dirigent domain. A large number of MtDIR genes were expanded via gene duplication, and 37 MtDIR genes were duplicated in tandem. Digital expression data showed that 40% MtDIR genes had a higher expression level in the root. Analysis of RNA-seq and microarray data indicated that more than 30% MtDIR genes were responsive to biotic and/or abiotic treatments. This study will facilitate further studies on DIR family and provide useful clues for functional validation of DIR genes in higher plants.
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Affiliation(s)
- Min Song
- College of Life Science, Qufu Normal University, Qufu, 273165, People's Republic of China.
| | - Xiangyong Peng
- College of Life Science, Qufu Normal University, Qufu, 273165, People's Republic of China
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Stein RJ, Duarte GL, Scheunemann L, Spohr MG, de Araújo Júnior AT, Ricachenevsky FK, Rosa LMG, Zanchin NIT, dos Santos RP, Fett JP. Genotype Variation in Rice ( Oryza sativa L.) Tolerance to Fe Toxicity Might Be Linked to Root Cell Wall Lignification. FRONTIERS IN PLANT SCIENCE 2019; 10:746. [PMID: 31244872 PMCID: PMC6581717 DOI: 10.3389/fpls.2019.00746] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/21/2019] [Indexed: 05/09/2023]
Abstract
Iron (Fe) is an essential element to plants, but can be harmful if accumulated to toxic concentrations. Fe toxicity can be a major nutritional disorder in rice (Oryza sativa) when cultivated under waterlogged conditions, as a result of excessive Fe solubilization of in the soil. However, little is known about the basis of Fe toxicity and tolerance at both physiological and molecular level. To identify mechanisms and potential candidate genes for Fe tolerance in rice, we comparatively analyzed the effects of excess Fe on two cultivars with distinct tolerance to Fe toxicity, EPAGRI 108 (tolerant) and BR-IRGA 409 (susceptible). After excess Fe treatment, BR-IRGA 409 plants showed reduced biomass and photosynthetic parameters, compared to EPAGRI 108. EPAGRI 108 plants accumulated lower amounts of Fe in both shoots and roots compared to BR-IRGA 409. We conducted transcriptomic analyses of roots from susceptible and tolerant plants under control and excess Fe conditions. We found 423 up-regulated and 92 down-regulated genes in the susceptible cultivar, and 42 up-regulated and 305 down-regulated genes in the tolerant one. We observed striking differences in root gene expression profiles following exposure to excess Fe: the two cultivars showed no genes regulated in the same way (up or down in both), and 264 genes were oppositely regulated in both cultivars. Plants from the susceptible cultivar showed down-regulation of known Fe uptake-related genes, indicating that plants are actively decreasing Fe acquisition. On the other hand, plants from the tolerant cultivar showed up-regulation of genes involved in root cell wall biosynthesis and lignification. We confirmed that the tolerant cultivar has increased lignification in the outer layers of the cortex and in the vascular bundle compared to the susceptible cultivar, suggesting that the capacity to avoid excessive Fe uptake could rely in root cell wall remodeling. Moreover, we showed that increased lignin concentrations in roots might be linked to Fe tolerance in other rice cultivars, suggesting that a similar mechanism might operate in multiple genotypes. Our results indicate that changes in root cell wall and Fe permeability might be related to Fe toxicity tolerance in rice natural variation.
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Affiliation(s)
| | | | - Lívia Scheunemann
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marta Gomes Spohr
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Luis Mauro Gonçalves Rosa
- Departamento de Plantas Forrageiras e Agrometeorologia, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Janette Palma Fett
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Janette Palma Fett,
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The Casparian strip-one ring to bring cell biology to lignification? Curr Opin Biotechnol 2018; 56:121-129. [PMID: 30502636 DOI: 10.1016/j.copbio.2018.10.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 11/20/2022]
Abstract
Lignin research has long been motivated by the outstanding importance of wood for human societies. The annual, non-woody Arabidopsis thaliana, has nevertheless contributed greatly to our understanding of lignification, due to its unrivalled genetic resources. Arabidopsis is also great for cell and developmental biology, allowing precise imaging and tracking of cell types. Root endodermis differentiation involves the precise lignification of the Casparian Strip, as an apoplastic barrier; while barrier damage triggers a less localized, compensatory lignification. Transcriptional reprogramming and peptide-induced signalling emerge as promising tools for the study of endodermal lignification. We argue that endodermis lignification is an attractive model complementary to equally powerful, cellular xylem differentiation systems, as it might better represent the restricted - often localized - lignification seen in non-vascular cells.
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Corbin C, Drouet S, Markulin L, Auguin D, Lainé É, Davin LB, Cort JR, Lewis NG, Hano C. A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation. PLANT MOLECULAR BIOLOGY 2018; 97:73-101. [PMID: 29713868 DOI: 10.1007/s11103-018-0725-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/02/2018] [Indexed: 05/21/2023]
Abstract
Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset of genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.
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Affiliation(s)
- Cyrielle Corbin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Lucija Markulin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Éric Lainé
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - John R Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA.
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France.
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France.
- Pôle Universitaire d'Eure et Loir, 21 Rue de Loigny la Bataille, 28000, Chartres, France.
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Cheng X, Su X, Muhammad A, Li M, Zhang J, Sun Y, Li G, Jin Q, Cai Y, Lin Y. Molecular Characterization, Evolution, and Expression Profiling of the Dirigent ( DIR) Family Genes in Chinese White Pear ( Pyrus bretschneideri). Front Genet 2018; 9:136. [PMID: 29713336 PMCID: PMC5911567 DOI: 10.3389/fgene.2018.00136] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/03/2018] [Indexed: 01/24/2023] Open
Abstract
Stone cells content and size are the key factors determining the internal quality of the pear fruit. Synthesis of lignin and thickening of secondary cell wall are the keys to the development of stone cells. The polymerization of monolignols and secondary cell wall formation requires the participation of dirigent proteins (DIRs). In recent years, DIR family have been studied in higher plants, but lack of comprehensive study in the pear DIR (PbDIR) family. This study focuses on the identification and analysis of PbDIR family for the first time. We identified 35 PbDIRs from the pear genome, 89% of which are intronless genes. Phylogenetic tree and chromosome localization analysis showed that 35 PbDIRs were divided into four subfamilies (DIR-a, -b/d, -e, and -g) and irregularly distributed among 10 chromosomes. In addition, we identified 29, 26, and 14 DIRs from the other three Rosids (peach, Mei, and grape), respectively. Interspecies microsynteny analysis revealed the collinear gene pairs between pear and peach are the most. Temporal expression analysis showed that the expression changes of seven PbDIRs (DIR-a subfamily: PbDIR4 and PbDIR5; DIR-b/d subfamily: PbDIR11; DIR-g subfamily: PbDIR19; DIR-e subfamily: PbDIR23, 25 and 26) in fruits were consistent with the changes of fruit lignin and stone cells contents. In addition, the subfamily of PbDIRs in fruits showed significant responses after treatment with ABA, SA, and MeJA. According to the protein tertiary structure, key amino acid residues and expression patterns analysis found that PbDIR4 might be involved in the metabolism of lignin and related to stone cells contents in pear fruits. In this study, we systematically analyzed the structure, evolution, function and expression of PbDIR family, which not only confirmed the characteristics of PbDIR family, but also laid the foundation for revealing the role of DIR in pear stone cell development and lignin polymerization.
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Affiliation(s)
- Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Manli Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Jinyun Zhang
- School of Life Science, Anhui Agricultural University, Hefei, China.,Institute of Horticultural, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yanming Sun
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
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Genome-wide analysis of dirigent gene family in pepper (Capsicum annuum L.) and characterization of CaDIR7 in biotic and abiotic stresses. Sci Rep 2018; 8:5500. [PMID: 29615685 PMCID: PMC5883049 DOI: 10.1038/s41598-018-23761-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 03/19/2018] [Indexed: 11/22/2022] Open
Abstract
The dirigent (DIR and DIR-like) proteins involved in lignification, play a pivotal role against biotic and abiotic stresses in plants. However, no information is available about DIR gene family in pepper (Capsicum annuum L.). In this study, 24 putative dirigent genes (CaDIRs) were identified, their gene structure, genome location, gene duplication and phylogenetic relationship were elucidated. Tissue-specific expression analysis displayed the highest transcription levels in flower, stem and leaf. Some CaDIRs were up-regulated by virulent (CaDIR2, 3, 6, 7, 11, 14, 16, 22 and 23) and avirulent (CaDIR3, 5, 7, 16, 20, 22, 23 and 24) Phytophthora capsici strains, as well as by Methyl jasmonate, salicylic acid, NaCl and mannitol stresses. Acid-soluble lignin content increased (103.21%) after P. capsici inoculation (48-hour). Silencing of CaDIR7 weakened plant defense by reducing (~50%) root activity and made plants more susceptible (35.7%) to P. capsici and NaCl (300 mM). Leaf discs of the CaDIR7:silenced plants exposed to NaCl and mannitol (300 mM each), exhibited a significant decrease (56.25% and 48% respectively) in the chlorophyll content. These results suggested that CaDIR7 is involved in pepper defense response against pathogen and abiotic stresses and the study will provide basic insights for future research regarding CaDIRs.
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He X, Zhu L, Wassan GM, Wang Y, Miao Y, Shaban M, Hu H, Sun H, Zhang X. GhJAZ2 attenuates cotton resistance to biotic stresses via the inhibition of the transcriptional activity of GhbHLH171. MOLECULAR PLANT PATHOLOGY 2018; 19:896-908. [PMID: 28665036 PMCID: PMC6638010 DOI: 10.1111/mpp.12575] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/29/2017] [Accepted: 06/26/2017] [Indexed: 05/19/2023]
Abstract
Plants have evolved effective mechanisms to protect themselves against multiple stresses, and employ jasmonates (JAs) as vital defence signals to defend against pathogen infection. The accumulation of JA, induced by signals from biotic and abiotic stresses, results in the degradation of Jasmonate-ZIM-domain (JAZ) proteins, followed by the de-repression of JAZ-repressed transcription factors (such as MYC2) to activate defence responses and developmental processes. Here, we characterized a JAZ family protein, GhJAZ2, from cotton (Gossypium hirsutum) which was induced by methyl jasmonate (MeJA) and inoculation of Verticillium dahliae. The overexpression of GhJAZ2 in cotton impairs the sensitivity to JA, decreases the expression level of JA-response genes (GhPDF1.2 and GhVSP) and enhances the susceptibility to V. dahliae and insect herbivory. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that GhJAZ2 may be involved in the regulation of cotton disease resistance by interaction with further disease-response proteins, such as pathogenesis-related protein GhPR10, dirigent-like protein GhD2, nucleotide-binding site leucine-rich repeat (NBS-LRR) disease-resistant protein GhR1 and a basic helix-loop-helix transcription factor GhbHLH171. Unlike MYC2, overexpression of GhbHLH171 in cotton activates the JA synthesis and signalling pathway, and improves plant tolerance to the fungus V. dahliae. Molecular and genetic evidence shows that GhJAZ2 can interact with GhbHLH171 and inhibit its transcriptional activity and, as a result, can restrain the JA-mediated defence response. This study provides new insights into the molecular mechanisms of GhJAZ2 in the regulation of the cotton defence response.
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Affiliation(s)
- Xin He
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Ghulam Mustafa Wassan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Yujing Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Yuhuan Miao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Haiyan Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Heng Sun
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
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Liu C, Qin Z, Zhou X, Xin M, Wang C, Liu D, Li S. Expression and functional analysis of the Propamocarb-related gene CsDIR16 in cucumbers. BMC PLANT BIOLOGY 2018; 18:16. [PMID: 29347906 PMCID: PMC5774166 DOI: 10.1186/s12870-018-1236-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 01/14/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Cucumber downy mildew is among the most important diseases that can disrupt cucumber production. Propamocarb, also known as propyl-[3-(dimethylamino)propyl]carbamate (PM), is a systemic carbamate fungicide pesticide that is widely applied in agricultural production because of its high efficiency of pathogens control, especially cucumber downy mildew. However, residual PM can remain in cucumbers after the disease has been controlled. To explore the molecular mechanisms of PM retention, cucumber cultivars 'D9320' (with the highest residual PM content) and 'D0351' (lowest residual PM content) were studied. High-throughput tag-sequencing (Tag-Seq) results showed that the CsDIR16 gene was related to PM residue, which was verified using transgenic technology. RESULTS We investigated the activity of a dirigent cucumber protein encoded by the CsDIR16 in gene response to stress induced by PM treatment. Gene-expression levels of CsDIR16 were up-regulated in the fruits, leaves, and stems of 'D0351' plants in response to PM treatment. However, in cultivar 'D9320', CsDIR16 levels were down-regulated in the leaves and stems after PM treatment, with no statistically significant differences observed in the fruits. Induction by jasmonic acid, abscisic acid, polyethylene glycol 4000, NaCl, and Corynespora cassiicola Wei (Cor) resulted in CsDIR16 up-regulation in 'D0351' and 'D9320'. Expression after salicylic acid treatment was up-regulated in 'D0351', but was down-regulated in 'D9320'. CsDIR16 overexpression lowered PM residues, and these were more rapidly reduced in CsDIR16(+) transgenic 'D9320' plants than in wild-type 'D9320' and CsDIR16(-) transgenic plants. CONCLUSIONS Analyses of the CsDIR16-expression patterns in the cucumber cultivars with the highest and lowest levels of PM residue, and transgenic validation indicated that CsDIR16 plays a positive role in reducing PM residues. The findings of this study help understand the regulatory mechanisms occurring in response to PM stress in cucumbers and in establishing the genetic basis for developing low-pesticide residue cucumber cultivars.
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Affiliation(s)
- Chunhong Liu
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030 China
- Department of Applied Chemistry, College of Science, Northeast Agricultural University, Harbin, 150030 China
| | - Zhiwei Qin
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030 China
| | - Xiuyan Zhou
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030 China
| | - Ming Xin
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030 China
| | - Chunhua Wang
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030 China
| | - Dong Liu
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030 China
| | - Shengnan Li
- College of Horticulture and Landscape Architecture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Harbin, 150030 China
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Nguyen TKO, Jamali A, Grand E, Morreel K, Marcelo P, Gontier E, Dauwe R. Phenylpropanoid profiling reveals a class of hydroxycinnamoyl glucaric acid conjugates in Isatis tinctoria leaves. PHYTOCHEMISTRY 2017; 144:127-140. [PMID: 28930667 DOI: 10.1016/j.phytochem.2017.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 05/10/2023]
Abstract
The brassicaceous herb, Isatis tinctoria, is an ancient medicinal plant whose rosette leaf extracts have anti-inflammatory and anti-allergic activity. Brassicaceae are known to accumulate a variety of phenylpropanoids in their rosette leaves acting as antioxidants and a UV-B shield, and these compounds often have pharmacological potential. Nevertheless, knowledge about the phenylpropanoid content of I. tinctoria leaves remains limited to the characterization of a number of flavonoids. In this research, we profiled the methanol extracts of I. tinctoria fresh leaf extracts by liquid chromatography - mass spectrometry (LC-MS) and focused on the phenylpropanoid derivatives. We report the structural characterization of 99 compounds including 18 flavonoids, 21 mono- or oligolignols, 2 benzenoids, and a wide spectrum of 58 hydroxycinnamic acid esters. Besides the sinapate esters of malate, glucose and gentiobiose, which are typical of brassicaceous plants, these conjugates comprised a large variety of glucaric acid esters that have not previously been reported in plants. Feeding with 13C6-glucaric acid showed that glucaric acid is an acyl acceptor of an as yet unknown acyltransferase activity in I. tinctoria rosette leaves. The large amount of hydroxycinnamic acid derivatives changes radically our view of the woad metabolite profile and potentially contributes to the pharmacological activity of I. tinctoria leaf extracts.
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Affiliation(s)
- Thi-Kieu-Oanh Nguyen
- Department of Pharmacological Medical and Agronomical Biotechnology, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam.
| | - Arash Jamali
- Plateforme de Microscopie Electronique, Université de Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens Cedex, France.
| | - Eric Grand
- LG2A, UFR Sciences, Université de Picardie Jules Verne, CNRS UMR 7378, Institut de Chimie de Picardie, CNRS FR 3085, 33 rue Saint Leu, 80039 Amiens Cedex, France.
| | - Kris Morreel
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.
| | - Paulo Marcelo
- Plateforme ICAP, Centre Universitaire de Recherche en Santé, Université de Picardie Jules Verne, 1-3, rue des Louvels, 80036 Amiens Cedex 1, Amiens, France.
| | - Eric Gontier
- EA3900 BioPI, UFR Sciences, Université de Picardie Jules Verne, 33 rue Saint Leu, 80039 Amiens Cedex, France.
| | - Rebecca Dauwe
- EA3900 BioPI, UFR Sciences, Université de Picardie Jules Verne, 33 rue Saint Leu, 80039 Amiens Cedex, France.
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Corbin C, Drouet S, Mateljak I, Markulin L, Decourtil C, Renouard S, Lopez T, Doussot J, Lamblin F, Auguin D, Lainé E, Fuss E, Hano C. Functional characterization of the pinoresinol-lariciresinol reductase-2 gene reveals its roles in yatein biosynthesis and flax defense response. PLANTA 2017; 246:405-420. [PMID: 28451749 DOI: 10.1007/s00425-017-2701-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/20/2017] [Indexed: 05/23/2023]
Abstract
MAIN CONCLUSION This study provides new insights into the biosynthesis regulation and in planta function of the lignan yatein in flax leaves. Pinoresinol-lariciresinol reductases (PLR) catalyze the conversion of pinoresinol into secoisolariciresinol (SECO) in lignan biosynthesis. Several lignans are accumulated in high concentrations, such as SECO accumulated as secoisolariciresinol diglucoside (SDG) in seeds and yatein in aerial parts, in the flax plant (Linum usitatissimum L.) from which two PLR enzymes of opposite enantioselectivity have been isolated. While LuPLR1 catalyzes the biosynthesis of (+)-SECO leading to (+)-SDG in seeds, the role(s) of the second PLR (LuPLR2) is not completely elucidated. This study provides new insights into the in planta regulation and function of the lignan yatein in flax leaves: its biosynthesis relies on a different PLR with opposite stereospecificity but also on a distinct expression regulation. RNAi technology provided evidence for the in vivo involvement of the LuPLR2 gene in the biosynthesis of (-)-yatein accumulated in flax leaves. LuPLR2 expression in different tissues and in response to stress was studied by RT-qPCR and promoter-reporter transgenesis showing that the spatio-temporal expression of the LuPLR2 gene in leaves perfectly matches the (-)-yatein accumulation and that LuPLR2 expression and yatein production are increased by methyl jasmonate and wounding. A promoter deletion approach yielded putative regulatory elements. This expression pattern in relation to a possible role for this lignan in flax defense is discussed.
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Affiliation(s)
- Cyrielle Corbin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Ivan Mateljak
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Lucija Markulin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Cédric Decourtil
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Sullivan Renouard
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Tatiana Lopez
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Joël Doussot
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
- Ecole SITI, Département CASER, Le CNAM, Paris, France
| | - Frédéric Lamblin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Eric Lainé
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Elisabeth Fuss
- Interfaculty Institute of Biochemistry, Hoppe-Seyler-St. 4, 72076, Tübingen, Germany
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France.
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Hoang NV, Furtado A, O’Keeffe AJ, Botha FC, Henry RJ. Association of gene expression with biomass content and composition in sugarcane. PLoS One 2017; 12:e0183417. [PMID: 28817735 PMCID: PMC5560616 DOI: 10.1371/journal.pone.0183417] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022] Open
Abstract
About 64% of the total aboveground biomass in sugarcane production is from the culm, of which ~90% is present in fiber and sugars. Understanding the transcriptome in the sugarcane culm, and the transcripts that are associated with the accumulation of the sugar and fiber components would facilitate the modification of biomass composition for enhanced biofuel and biomaterial production. The Sugarcane Iso-Seq Transcriptome (SUGIT) database was used as a reference for RNA-Seq analysis of variation in gene expression between young and mature tissues, and between 10 genotypes with varying fiber content. Global expression analysis suggests that each genotype displayed a unique expression pattern, possibly due to different chromosome combinations and maturation amongst these genotypes. Apart from direct sugar- and fiber-related transcripts, the differentially expressed (DE) transcripts in this study belonged to various supporting pathways that are not obviously involved in the accumulation of these major biomass components. The analysis revealed 1,649 DE transcripts between the young and mature tissues, while 555 DE transcripts were found between the low and high fiber genotypes. Of these, 151 and 23 transcripts respectively, were directly involved in sugar and fiber accumulation. Most of the transcripts identified were up-regulated in the young tissues (2 to 22-fold, FDR adjusted p-value <0.05), which could be explained by the more active metabolism in the young tissues compared to the mature tissues in the sugarcane culm. The results of analysis of the contrasting genotypes suggests that due to the large number of genes contributing to these traits, some of the critical DE transcripts could display less than 2-fold differences in expression and might not be easily identified. However, this transcript profiling analysis identified full-length candidate transcripts and pathways that were likely to determine the differences in sugar and fiber accumulation between tissue types and contrasting genotypes.
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Affiliation(s)
- Nam V. Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
| | - Angela J. O’Keeffe
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
- Sugar Research Australia, Indooroopilly, Queensland, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
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Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane. Mol Genet Genomics 2017; 292:1323-1340. [PMID: 28699001 DOI: 10.1007/s00438-017-1349-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/04/2017] [Indexed: 01/13/2023]
Abstract
Dirigent (DIR) proteins, encoded by DIR genes, are referred to as "dirigent" because they direct the outcome of the coupling of the monolignol coniferyl alcohol into (+) or (-) pinoresinol, the first intermediates in the enantiocomplementary pathways for lignan biosynthesis. DIR domain-containing or DIR-like proteins are, thus, termed for not having a clear characterization. A transcriptome- and genome-wide survey of DIR domain-containing proteins in sugarcane was carried out, in addition to phylogenetic, physicochemical and transcriptional analyses. A total of 120 non-redundant sequences containing the DIR domain were identified and classified into 64 groups according to phylogenetic and sequence alignment analyses. In silico analysis of transcript abundance showed that these sequences are expressed at low levels in leaves and genes in the same phylogenetic clade have similar expression patterns. Expression analysis of ShDIR1-like transcripts in the culm internodes of sugarcane demonstrates their abundance in mature internodes, their induction by nitrogen fertilization and their predominant expression in cells that have a lignified secondary cell wall, such as vascular bundles of young internodes and parenchymal cells of the pith of mature internodes. Due to the lack of information about the functional role of DIR in plants, a possible relationship is discussed between the ShDIR1-like transcriptional profile and cell wall development in parenchyma cells of sugarcane culm, which typically accumulates large amounts of sucrose. The number of genes encoding the DIR domain-containing proteins in sugarcane is intriguing and is an indication per se that these proteins may have an important metabolic role and thus deserve to be better studied.
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Li N, Zhao M, Liu T, Dong L, Cheng Q, Wu J, Wang L, Chen X, Zhang C, Lu W, Xu P, Zhang S. A Novel Soybean Dirigent Gene GmDIR22 Contributes to Promotion of Lignan Biosynthesis and Enhances Resistance to Phytophthora sojae. FRONTIERS IN PLANT SCIENCE 2017; 8:1185. [PMID: 28725237 PMCID: PMC5495835 DOI: 10.3389/fpls.2017.01185] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 06/21/2017] [Indexed: 05/20/2023]
Abstract
Phytophthora root and stem rot caused by the oomycete pathogen Phytophthora sojae is a destructive disease of soybean worldwide. Plant dirigent proteins (DIR) are proposed to have roles in biosynthesis of either lignan or lignin-like molecules, and are important for defense responses, secondary metabolism, and pathogen resistance. In the present work, a novel DIR gene expressed sequence tag is identified as up-regulated in the highly resistant soybean cultivar 'Suinong 10' inoculated with P. sojae. The full length cDNA is isolated using rapid amplification of cDNA ends, and designated GmDIR22 (GenBank accession no. HQ_993047). The full length GmDIR22 is 789 bp and contains a 567 bp open reading frame encoding a polypeptide of 188 amino acids. The sequence analysis indicated that GmDIR22 contains a conserved dirigent domain at amino acid residues 43-187. The quantitative real-time reverse transcription PCR demonstrated that soybean GmDIR22 mRNA is expressed most highly in stems, followed by roots and leaves. The treatments with stresses demonstrated that GmDIR22 is significantly induced by P. sojae and gibberellic acid (GA3), and also responds to salicylic acid, methyl jasmonic acid, and abscisic acid. The GmDIR22 is targeted to the cytomembrane when transiently expressed in Arabidopsis protoplasts. Moreover, The GmDIR22 recombinant protein purified from Escherichia coli could effectively direct E-coniferyl alcohol coupling into lignan (+)-pinoresinol. Accordingly, the overexpression of GmDIR22 in transgenic soybean increased total lignan accumulation. Moreover, the lignan extracts from GmDIR22 transgenic plants effectively inhibits P. sojae hyphal growth. Furthermore, the transgenic overexpression of GmDIR22 in the susceptible soybean cultivar 'Dongnong 50' enhances its resistance to P. sojae. Collectively, these data suggested that the primary role of GmDIR22 is probably involved in the regulation of lignan biosynthesis, and which contributes to resistance to P. sojae.
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Affiliation(s)
- Ninghui Li
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
- Jiamusi Branch of Heilongjiang Academy of Agricultural SciencesJiamusi, China
| | - Ming Zhao
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Tengfei Liu
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Lidong Dong
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Qun Cheng
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Junjiang Wu
- Key Laboratory of Soybean Cultivation of Ministry of Agriculture China, Soybean Research Institute, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Le Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Xi Chen
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Chuanzhong Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Wencheng Lu
- Heihe Branch of Heilongjiang Academy of Agricultural SciencesHeihe, China
| | - Pengfei Xu
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
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Paniagua C, Bilkova A, Jackson P, Dabravolski S, Riber W, Didi V, Houser J, Gigli-Bisceglia N, Wimmerova M, Budínská E, Hamann T, Hejatko J. Dirigent proteins in plants: modulating cell wall metabolism during abiotic and biotic stress exposure. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3287-3301. [PMID: 28472349 DOI: 10.1093/jxb/erx141] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Dirigent (DIR) proteins were found to mediate regio- and stereoselectivity of bimolecular phenoxy radical coupling during lignan biosynthesis. Here we summarize the current knowledge of the importance of DIR proteins in lignan and lignin biosynthesis and highlight their possible importance in plant development. We focus on the still rather enigmatic Arabidopsis DIR gene family, discussing the few members with known functional importance. We comment on recent discoveries describing the detailed structure of two DIR proteins with implications in the mechanism of DIR-mediated catalysis. Further, we summarize the ample evidence for stress-induced dirigent gene expression, suggesting the role of DIRs in adaptive responses. In the second part of our work, we present a preliminary bioinformatics-based characterization of the AtDIR family. The phylogenetic analysis of AtDIRs complemented by comparison with DIR proteins of mostly known function from other species allowed us to suggest possible roles for several members of this family and identify interesting AtDIR targets for further study. Finally, based on the available metadata and our in silico analysis of AtDIR promoters, we hypothesize about the existence of specific transcriptional controls for individual AtDIR genes and implicate them in various stress responses, hormonal regulations, and developmental processes.
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Affiliation(s)
- Candelas Paniagua
- Laboratory of Molecular Plant Physiology and Functional Genomics and Proteomics of Plants, CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Anna Bilkova
- Laboratory of Molecular Plant Physiology and Functional Genomics and Proteomics of Plants, CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
- Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Phil Jackson
- Laboratory of Molecular Plant Physiology and Functional Genomics and Proteomics of Plants, CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Siarhei Dabravolski
- Laboratory of Molecular Plant Physiology and Functional Genomics and Proteomics of Plants, CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Willi Riber
- Laboratory of Molecular Plant Physiology and Functional Genomics and Proteomics of Plants, CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Vojtech Didi
- Laboratory of Molecular Plant Physiology and Functional Genomics and Proteomics of Plants, CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Josef Houser
- Glycobiochemistry, CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Nora Gigli-Bisceglia
- Department of Biology, Norwegian University of Science and Technology 5, Hogskoleringen, N-7491 Trondheim, Norway
| | - Michaela Wimmerova
- Glycobiochemistry, CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Eva Budínská
- Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Thorsten Hamann
- Department of Biology, Norwegian University of Science and Technology 5, Hogskoleringen, N-7491 Trondheim, Norway
| | - Jan Hejatko
- Laboratory of Molecular Plant Physiology and Functional Genomics and Proteomics of Plants, CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Kamenice 5, CZ-625 00 Brno, Czech Republic
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de Vries J, de Vries S, Slamovits CH, Rose LE, Archibald JM. How Embryophytic is the Biosynthesis of Phenylpropanoids and their Derivatives in Streptophyte Algae? PLANT & CELL PHYSIOLOGY 2017; 58:934-945. [PMID: 28340089 DOI: 10.1093/pcp/pcx037] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/08/2017] [Indexed: 05/21/2023]
Abstract
The origin of land plants from algae is a long-standing question in evolutionary biology. It is becoming increasingly clear that many characters that were once assumed to be 'embryophyte specific' can in fact be found in their closest algal relatives, the streptophyte algae. One such case is the phenylpropanoid pathway. While biochemical data indicate that streptophyte algae harbor lignin-like components, the phenylpropanoid core pathway, which serves as the backbone of lignin biosynthesis, has been proposed to have arisen at the base of the land plants. Here we revisit this hypothesis using a wealth of new sequence data from streptophyte algae. Tracing the biochemical pathway towards lignin biogenesis, we show that most of the genes required for phenylpropanoid synthesis and the precursors for lignin production were already present in streptophyte algae. Nevertheless, phylogenetic analyses and protein structure predictions of one of the key enzyme classes in lignin production, cinnamyl alcohol dehydrogenase (CAD), suggest that CADs of streptophyte algae are more similar to sinapyl alcohol dehydrogenases (SADs). This suggests that the end-products of the pathway leading to lignin biosynthesis in streptophyte algae may facilitate the production of lignin-like compounds and defense molecules. We hypothesize that streptophyte algae already possessed the genetic toolkit from which the capacity to produce lignin later evolved in vascular plants.
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Affiliation(s)
- Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Population Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Toronto, ON, Canada
| | - Laura E Rose
- Population Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- CEPLAS - Cluster of Excellence in Plant Sciences, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Toronto, ON, Canada
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Abstract
In plant tissues, cells are glued to each other by a pectic polysaccharide rich material known as middle lamella (ML). Along with many biological functions, the ML plays a crucial role in maintaining the structural integrity of plant tissues and organs, as it prevents the cells from separating or sliding against each other. The macromolecular organization and the material properties of the ML are different from those of the adjacent primary cell walls that envelop all plant cells and provide them with a stiff casing. Due to its nanoscale dimensions and the extreme challenge to access the structure for material characterization, the ML is poorly characterized in terms of its distinct material properties. This review explores the ML beyond its functionality as a gluing agent. The putative molecular interactions of constituent macromolecules within the ML and at the interface between ML and primary cell wall are discussed. The correlation between the spatiotemporal distribution of pectic polysaccharides in the different portions of the ML and the subcellular distribution of mechanical stresses within the plant tissue are analyzed.
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Affiliation(s)
- M S Zamil
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore, Ste-Anne-de-Bellevue, QC H9X 3V9, Canada
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Koumba-Yoya G, Stevanovic T. Study of Organosolv Lignins as Adhesives in Wood Panel Production. Polymers (Basel) 2017; 9:polym9020046. [PMID: 30970725 PMCID: PMC6432122 DOI: 10.3390/polym9020046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 01/20/2017] [Accepted: 01/26/2017] [Indexed: 11/29/2022] Open
Abstract
Organosolv lignins obtained from sugar maple bark and wood were studied as adhesives for wood particleboard production. Organosolv pulping of sugar maple wood and bark was carried out in the presence of Lewis acid FeCl3 as a catalyst. The organosolv lignins recovered from this process were investigated by determination of Klason plus acid-soluble lignin content, of sugars by HPLC analysis, and of ash content. Structural characterizations of these lignins were performed by Fourier-transform infrared (FT-IR) and by 31P NMR. The results of the latter studies indicate that the content of free phenolic groups was more important in bark than in wood lignin. The gel permeation chromatography (GPC) analyses results suggested that the weight-average molecular mass of wood lignin was higher than that of bark lignin. The studied organosolv lignins were used for the preparation of particleboards as recovered and in combination with glyoxal or isocyanate. It was found that sugar maple bark lignin, as such or modified with isocyanate, was a more efficient adhesive than its wood counterpart. On the contrary, it was the organosolv wood lignin combined with glyoxal which was a more efficient adhesive than its bark counterpart. In combination with isocyanate, it was the sugar maple bark organosolv lignin which was determined to have the best adhesive performance of all studied lignins.
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Affiliation(s)
- Georges Koumba-Yoya
- Centre de recherche de sur les Matériaux renouvelables, Département des Sciences du bois et de la forêt, Université Laval, Québec, QC 7337, Canada.
| | - Tatjana Stevanovic
- Centre de recherche de sur les Matériaux renouvelables, Département des Sciences du bois et de la forêt, Université Laval, Québec, QC 7337, Canada.
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45
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Liao Y, Liu S, Jiang Y, Hu C, Zhang X, Cao X, Xu Z, Gao X, Li L, Zhu J, Chen R. Genome-wide analysis and environmental response profiling of dirigent family genes in rice (Oryza sativa). Genes Genomics 2016. [DOI: 10.1007/s13258-016-0474-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Kumar Y, Zhang L, Panigrahi P, Dholakia BB, Dewangan V, Chavan SG, Kunjir SM, Wu X, Li N, Rajmohanan PR, Kadoo NY, Giri AP, Tang H, Gupta VS. Fusarium oxysporum mediates systems metabolic reprogramming of chickpea roots as revealed by a combination of proteomics and metabolomics. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1589-603. [PMID: 26801007 PMCID: PMC5066658 DOI: 10.1111/pbi.12522] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 05/05/2023]
Abstract
Molecular changes elicited by plants in response to fungal attack and how this affects plant-pathogen interaction, including susceptibility or resistance, remain elusive. We studied the dynamics in root metabolism during compatible and incompatible interactions between chickpea and Fusarium oxysporum f. sp. ciceri (Foc), using quantitative label-free proteomics and NMR-based metabolomics. Results demonstrated differential expression of proteins and metabolites upon Foc inoculations in the resistant plants compared with the susceptible ones. Additionally, expression analysis of candidate genes supported the proteomic and metabolic variations in the chickpea roots upon Foc inoculation. In particular, we found that the resistant plants revealed significant increase in the carbon and nitrogen metabolism; generation of reactive oxygen species (ROS), lignification and phytoalexins. The levels of some of the pathogenesis-related proteins were significantly higher upon Foc inoculation in the resistant plant. Interestingly, results also exhibited the crucial role of altered Yang cycle, which contributed in different methylation reactions and unfolded protein response in the chickpea roots against Foc. Overall, the observed modulations in the metabolic flux as outcome of several orchestrated molecular events are determinant of plant's role in chickpea-Foc interactions.
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Affiliation(s)
- Yashwant Kumar
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Limin Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Priyabrata Panigrahi
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Bhushan B Dholakia
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Veena Dewangan
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Sachin G Chavan
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Shrikant M Kunjir
- Central NMR Facility, CSIR-National Chemical Laboratory, Pune, India
| | - Xiangyu Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Ning Li
- Key Laboratory of Magnetic Resonance in Biological Systems, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | | | - Narendra Y Kadoo
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Ashok P Giri
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Huiru Tang
- Key Laboratory of Magnetic Resonance in Biological Systems, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Genetic Engineering, Metabolomics and Systems Biology Laboratory, School of Life Sciences, Fudan University, Shanghai, China
| | - Vidya S Gupta
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
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Weidenbach D, Esch L, Möller C, Hensel G, Kumlehn J, Höfle C, Hückelhoven R, Schaffrath U. Polarized Defense Against Fungal Pathogens Is Mediated by the Jacalin-Related Lectin Domain of Modular Poaceae-Specific Proteins. MOLECULAR PLANT 2016; 9:514-27. [PMID: 26708413 DOI: 10.1016/j.molp.2015.12.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/04/2015] [Accepted: 12/09/2015] [Indexed: 05/19/2023]
Abstract
Modular proteins are an evolutionary answer to optimize performance of proteins that physically interact with each other for functionality. Using a combination of genetic and biochemical experiments, we characterized the rice protein OsJAC1, which consists of a jacalin-related lectin (JRL) domain predicted to bind mannose-containing oligosaccharides, and a dirigent domain which might function in stereoselective coupling of monolignols. Transgenic overexpression of OsJAC1 in rice resulted in quantitative broad-spectrum resistance against different pathogens including bacteria, oomycetes, and fungi. Overexpression of this gene or its wheat ortholog TAJA1 in barley enhanced resistance against the powdery mildew fungus. Both protein domains of OsJAC1 are required to establish resistance as indicated by single or combined transient expression of individual domains. Expression of artificially separated and fluorescence-tagged protein domains showed that the JRL domain is sufficient for targeting the powdery mildew penetration site. Nevertheless, co-localization of the lectin and the dirigent domain occurred. Phylogenetic analyses revealed orthologs of OsJAC1 exclusively within the Poaceae plant family. Dicots, by contrast, only contain proteins with either JRL or dirigent domain(s). Altogether, our results identify OsJAC1 as a representative of a novel type of resistance protein derived from a plant lineage-specific gene fusion event for better function in local pathogen defense.
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Affiliation(s)
- Denise Weidenbach
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - Lara Esch
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - Claudia Möller
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Caroline Höfle
- Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85350 Freising, Germany
| | - Ralph Hückelhoven
- Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85350 Freising, Germany
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany.
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48
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Identification ofMycosphaerella eumusaeresponsive unique genes/transcripts from a resistant banana cultivar. ACTA ACUST UNITED AC 2016. [DOI: 10.17660/actahortic.2016.1114.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Perello C, Llamas E, Burlat V, Ortiz-Alcaide M, Phillips MA, Pulido P, Rodriguez-Concepcion M. Differential Subplastidial Localization and Turnover of Enzymes Involved in Isoprenoid Biosynthesis in Chloroplasts. PLoS One 2016; 11:e0150539. [PMID: 26919668 PMCID: PMC4769067 DOI: 10.1371/journal.pone.0150539] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/15/2016] [Indexed: 11/23/2022] Open
Abstract
Plastidial isoprenoids are a diverse group of metabolites with roles in photosynthesis, growth regulation, and interaction with the environment. The methylerythritol 4-phosphate (MEP) pathway produces the metabolic precursors of all types of plastidial isoprenoids. Proteomics studies in Arabidopsis thaliana have shown that all the enzymes of the MEP pathway are localized in the plastid stroma. However, immunoblot analysis of chloroplast subfractions showed that the first two enzymes of the pathway, deoxyxylulose 5-phosphate synthase (DXS) and reductoisomerase (DXR), can also be found in non-stromal fractions. Both transient and stable expression of GFP-tagged DXS and DXR proteins confirmed the presence of the fusion proteins in distinct subplastidial compartments. In particular, DXR-GFP was found to accumulate in relatively large vesicles that could eventually be released from chloroplasts, presumably to be degraded by an autophagy-independent process. Together, we propose that protein-specific mechanisms control the localization and turnover of the first two enzymes of the MEP pathway in Arabidopsis chloroplasts.
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Affiliation(s)
- Catalina Perello
- Program of Plant Metabolism and Metabolic Engineering, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Ernesto Llamas
- Program of Plant Metabolism and Metabolic Engineering, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Vincent Burlat
- Université de Toulouse, CNRS, UMR 5546, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
| | - Miriam Ortiz-Alcaide
- Program of Plant Metabolism and Metabolic Engineering, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Michael A. Phillips
- Program of Plant Metabolism and Metabolic Engineering, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Pablo Pulido
- Program of Plant Metabolism and Metabolic Engineering, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Manuel Rodriguez-Concepcion
- Program of Plant Metabolism and Metabolic Engineering, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
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Jones DC, Zheng W, Huang S, Du C, Zhao X, Yennamalli RM, Sen TZ, Nettleton D, Wurtele ES, Li L. A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence. FRONTIERS IN PLANT SCIENCE 2016; 7:983. [PMID: 27462324 PMCID: PMC4940393 DOI: 10.3389/fpls.2016.00983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/21/2016] [Indexed: 05/05/2023]
Abstract
Nearly immobile, plants have evolved new components to be able to respond to changing environments. One example is Qua Quine Starch (QQS, AT3G30720), an Arabidopsis thaliana-specific orphan gene that integrates primary metabolism with adaptation to environment changes. SAQR (Senescence-Associated and QQS-Related, AT1G64360), is unique to a clade within the family Brassicaceae; as such, the gene may have arisen about 20 million years ago. SAQR is up-regulated in QQS RNAi mutant and in the apx1 mutant under light-induced oxidative stress. SAQR plays a role in carbon allocation: overexpression lines of SAQR have significantly decreased starch content; conversely, in a saqr T-DNA knockout (KO) line, starch accumulation is increased. Meta-analysis of public microarray data indicates that SAQR expression is correlated with expression of a subset of genes involved in senescence, defense, and stress responses. SAQR promoter::GUS expression analysis reveals that SAQR expression increases after leaf expansion and photosynthetic capacity have peaked, just prior to visible natural senescence. SAQR is expressed predominantly within leaf and cotyledon vasculature, increasing in intensity as natural senescence continues, and then decreasing prior to death. In contrast, under experimentally induced senescence, SAQR expression increases in vasculature of cotyledons but not in true leaves. In SAQR KO line, the transcript level of the dirigent-like disease resistance gene (AT1G22900) is increased, while that of the Early Light Induced Protein 1 gene (ELIP1, AT3G22840) is decreased. Taken together, these data indicate that SAQR may function in the QQS network, playing a role in integration of primary metabolism with adaptation to internal and environmental changes, specifically those that affect the process of senescence.
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Affiliation(s)
- Dallas C. Jones
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Wenguang Zheng
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Sheng Huang
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
| | - Chuanlong Du
- Department of Statistics, Iowa State University, AmesIA, USA
| | - Xuefeng Zhao
- Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, AmesIA, USA
| | - Ragothaman M. Yennamalli
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agriculture Research Service, AmesIA, USA
| | - Taner Z. Sen
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agriculture Research Service, AmesIA, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, AmesIA, USA
| | - Eve S. Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Center for Metabolic Biology, Iowa State University, AmesIA, USA
| | - Ling Li
- Department of Genetics, Development and Cell Biology, Iowa State University, AmesIA, USA
- Center for Metabolic Biology, Iowa State University, AmesIA, USA
- *Correspondence: Ling Li,
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