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Dokka N, Tyagi S, Ramkumar MK, Rathinam M, Senthil K, Sreevathsa R. Genome-wide identification and characterization of DIRIGENT gene family (CcDIR) in pigeonpea (Cajanus cajan L.) provide insights on their spatial expression pattern and relevance to stress response. Gene 2024; 914:148417. [PMID: 38555003 DOI: 10.1016/j.gene.2024.148417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/20/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
This study is a thorough characterization of pigeonpea dirigent gene (CcDIR) family, an important component of the lignin biosynthesis pathway. Genome-wide analysis identified 25 CcDIR genes followed by a range of analytical approaches employed to unravel their structural and functional characteristics. Structural examination revealed a classic single exon and no intron arrangement in CcDIRs contributing to our understanding on evolutionary dynamics. Phylogenetic analysis elucidated evolutionary relationships among CcDIR genes with six DIR sub-families, while motif distribution analysis displayed and highlighted ten conserved protein motifs in CcDIRs. Promoter analyses of all the dirigent genes detected 18 stress responsive cis-acting elements offering insights into transcriptional regulation. While spatial expression analyses across six plant tissues showed preferential expression of CcDIR genes, exposure to salt (CcDIR2 and CcDIR9) and herbivory (CcDIR1, CcDIR2, CcDIR3 and CcDIR11), demonstrated potential roles of specific DIRs in plant defense. Interestingly, increased gene expression during herbivory, also correlated with increased lignin content authenticating the specific response. Furthermore, exogenous application of stress hormones, SA and MeJA on leaves significantly induced the expression of CcDIRs that responded to herbivory. Taken together, these findings contribute to a comprehensive understanding of CcDIR genes impacting development and stress response in the important legume pigeonpea.
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Affiliation(s)
- Narasimham Dokka
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Shaily Tyagi
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - M K Ramkumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Maniraj Rathinam
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Kameshwaran Senthil
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India.
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Castañón-Suárez CA, Arrizubieta M, Castelán-Muñoz N, Sánchez-Rodríguez DB, Caballero-Cordero C, Zluhan-Martínez E, Patiño-Olvera SC, Arciniega-González J, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. The MADS-box genes SOC1 and AGL24 antagonize XAL2 functions in Arabidopsis thaliana root development. FRONTIERS IN PLANT SCIENCE 2024; 15:1331269. [PMID: 38576790 PMCID: PMC10994003 DOI: 10.3389/fpls.2024.1331269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/06/2024] [Indexed: 04/06/2024]
Abstract
MADS-domain transcription factors play pivotal roles in numerous developmental processes in Arabidopsis thaliana. While their involvement in flowering transition and floral development has been extensively examined, their functions in root development remain relatively unexplored. Here, we explored the function and genetic interaction of three MADS-box genes (XAL2, SOC1 and AGL24) in primary root development. By analyzing loss-of-function and overexpression lines, we found that SOC1 and AGL24, both critical components in flowering transition, redundantly act as repressors of primary root growth as the loss of function of either SOC1 or AGL24 partially recovers the primary root growth, meristem cell number, cell production rate, and the length of fully elongated cells of the short-root mutant xal2-2. Furthermore, we observed that the simultaneous overexpression of AGL24 and SOC1 leads to short-root phenotypes, affecting meristem cell number and fully elongated cell size, whereas SOC1 overexpression is sufficient to affect columella stem cell differentiation. Additionally, qPCR analyses revealed that these genes exhibit distinct modes of transcriptional regulation in roots compared to what has been previously reported for aerial tissues. We identified 100 differentially expressed genes in xal2-2 roots by RNA-seq. Moreover, our findings revealed that the expression of certain genes involved in cell differentiation, as well as stress responses, which are either upregulated or downregulated in the xal2-2 mutant, reverted to WT levels in the absence of SOC1 or AGL24.
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Affiliation(s)
- Claudio A. Castañón-Suárez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Maite Arrizubieta
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Natalia Castelán-Muñoz
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Postgrado en Recursos Genéticos y Productividad-Fisiología Vegetal, Colegio de Postgraduados, Texcoco, Estado de México, Mexico
| | - Diana Belén Sánchez-Rodríguez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Carolina Caballero-Cordero
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sandra C. Patiño-Olvera
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - J.Arturo Arciniega-González
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Dharni JS, Shi Y, Zhang C, Petersen C, Walia H, Staswick P. Growth and transcriptional response of wheat and rice to the tertiary amine BMVE. FRONTIERS IN PLANT SCIENCE 2024; 14:1273620. [PMID: 38269141 PMCID: PMC10806070 DOI: 10.3389/fpls.2023.1273620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Introduction Seed vigor is largely a product of sound seed development, maturation processes, genetics, and storage conditions. It is a crucial factor impacting plant growth and crop yield and is negatively affected by unfavorable environmental conditions, which can include drought and heat as well as cold wet conditions. The latter leads to slow germination and increased seedling susceptibility to pathogens. Prior research has shown that a class of plant growth regulators called substituted tertiary amines (STAs) can enhance seed germination, seedling growth, and crop productivity. However, inconsistent benefits have limited STA adoption on a commercial scale. Methods We developed a novel seed treatment protocol to evaluate the efficacy of 2-(N-methyl benzyl aminoethyl)-3-methyl butanoate (BMVE), which has shown promise as a crop seed treatment in field trials. Transcriptomic analysis of rice seedlings 24 h after BMVE treatment was done to identify the molecular basis for the improved seedling growth. The impact of BMVE on seed development was also evaluated by spraying rice panicles shortly after flower fertilization and subsequently monitoring the impact on seed traits. Results BMVE treatment of seeds 24 h after imbibition consistently improved wheat and rice seedling shoot and root growth in lab conditions. Treated wheat seedlings grown to maturity in a greenhouse also resulted in higher biomass than controls, though only under drought conditions. Treated seedlings had increased levels of transcripts involved in reactive oxygen species scavenging and auxin and gibberellic acid signaling. Conversely, several genes associated with increased reactive oxygen species/ROS load, abiotic stress responses, and germination hindering processes were reduced. BMVE spray increased both fresh and mature seed weights relative to the control for plants exposed to 96 h of heat stress. BMVE treatment during seed development also benefited germination and seedling growth in the next generation, under both ambient and heat stress conditions. Discussion The optimized experimental conditions we developed provide convincing evidence that BMVE does indeed have efficacy in plant growth enhancement. The results advance our understanding of how STAs work at the molecular level and provide insights for their practical application to improve crop growth.
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Affiliation(s)
- Jaspinder Singh Dharni
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Yu Shi
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | | | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
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Muthusamy M, Lee SI. Abiotic stress-induced secondary metabolite production in Brassica: opportunities and challenges. FRONTIERS IN PLANT SCIENCE 2024; 14:1323085. [PMID: 38239210 PMCID: PMC10794482 DOI: 10.3389/fpls.2023.1323085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/13/2023] [Indexed: 01/22/2024]
Abstract
Over the decades, extensive research efforts have been undertaken to understand how secondary plant metabolites are affected by genetic, environmental, and agronomic factors. Understanding the genetic basis of stress-response metabolite biosynthesis is crucial for sustainable agriculture production amidst frequent occurrence of climatic anomalies. Although it is known that environmental factors influence phytochemical profiles and their content, studies of plant compounds in relation to stress mitigation are only emerging and largely hindered by phytochemical diversities and technical shortcomings in measurement techniques. Despite these challenges, considerable success has been achieved in profiling of secondary metabolites such as glucosinolates, flavonoids, carotenoids, phenolic acids and alkaloids. In this study, we aimed to understand the roles of glucosinolates, flavonoids, carotenoids, phenolic acids and alkaloids in relation to their abiotic stress response, with a focus on the developing of stress-resilient crops. The focal genus is the Brassica since it (i) possesses variety of specialized phytochemicals that are important for its plant defense against major abiotic stresses, and (ii) hosts many economically important crops that are sensitive to adverse growth conditions. We summarize that augmented levels of specialized metabolites in Brassica primarily function as stress mitigators against oxidative stress, which is a secondary stressor in many abiotic stresses. Furthermore, it is clear that functional characterization of stress-response metabolites or their genetic pathways describing biosynthesis is essential for developing stress-resilient Brassica crops.
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Affiliation(s)
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), Rural Development Administration, Jeonju, Republic of Korea
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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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Alejo-Jacuinde G, Nájera-González HR, Chávez Montes RA, Gutierrez Reyes CD, Barragán-Rosillo AC, Perez Sanchez B, Mechref Y, López-Arredondo D, Yong-Villalobos L, Herrera-Estrella L. Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism. Commun Biol 2023; 6:820. [PMID: 37550387 PMCID: PMC10406817 DOI: 10.1038/s42003-023-05192-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
Chia (Salvia hispanica) is an emerging crop considered a functional food containing important substances with multiple potential applications. However, the molecular basis of some relevant chia traits, such as seed mucilage and polyphenol content, remains to be discovered. This study generates an improved chromosome-level reference of the chia genome, resolving some highly repetitive regions, describing methylation patterns, and refining genome annotation. Transcriptomic analysis shows that seeds exhibit a unique expression pattern compared to other organs and tissues. Thus, a metabolic and proteomic approach is implemented to study seed composition and seed-produced mucilage. The chia genome exhibits a significant expansion in mucilage synthesis genes (compared to Arabidopsis), and gene network analysis reveals potential regulators controlling seed mucilage production. Rosmarinic acid, a compound with enormous therapeutic potential, was classified as the most abundant polyphenol in seeds, and candidate genes for its complex pathway are described. Overall, this study provides important insights into the molecular basis for the unique characteristics of chia seeds.
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Affiliation(s)
- Gerardo Alejo-Jacuinde
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Héctor-Rogelio Nájera-González
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Ricardo A Chávez Montes
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | | | - Alfonso Carlos Barragán-Rosillo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Benjamin Perez Sanchez
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Damar López-Arredondo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Lenin Yong-Villalobos
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA.
| | - Luis Herrera-Estrella
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA.
- Unidad de Genómica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto., 36821, Mexico.
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Quezada M, Giorello FM, Da Silva CC, Aguilar I, Balmelli G. Single-step genome-wide association study for susceptibility to Teratosphaeria nubilosa and precocity of vegetative phase change in Eucalyptus globulus. FRONTIERS IN PLANT SCIENCE 2023; 14:1124768. [PMID: 37465383 PMCID: PMC10350686 DOI: 10.3389/fpls.2023.1124768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/24/2023] [Indexed: 07/20/2023]
Abstract
Introduction Mycosphaerella leaf disease (MLD) is one of the most prevalent foliar diseases of Eucalyptus globulus plantations around the world. Since resistance management strategies have not been effective in commercial plantations, breeding to develop more resistant genotypes is the most promising strategy. Available genomic information can be used to detect genomic regions associated with resistance to MLD, which could significantly speed up the process of genetic improvement. Methods We investigated the genetic basis of MLD resistance in a breeding population of E. globulus which was genotyped with the EUChip60K SNP array. Resistance to MLD was evaluated through resistance of the juvenile foliage, as defoliation and leaf spot severity, and through precocity of change to resistant adult foliage. Genome-wide association studies (GWAS) were carried out applying four Single-SNP models, a Genomic Best Linear Unbiased Prediction (GBLUP-GWAS) approach, and a Single-step genome-wide association study (ssGWAS). Results The Single-SNP (model K) and GBLUP-GWAS models detected 13 and 16 SNP-trait associations in chromosomes 2, 3 y 11; whereas the ssGWAS detected 66 SNP-trait associations in the same chromosomes, and additional significant SNP-trait associations in chromosomes 5 to 9 for the precocity of phase change (proportion of adult foliage). For this trait, the two main regions in chromosomes 3 and 11 were identified for the three approaches. The SNPs identified in these regions were positioned near the key miRNA genes, miR156.5 and miR157.4, which have a main role in the regulation of the timing of vegetative change, and also in the response to environmental stresses in plants. Discussion Our results demonstrated that ssGWAS was more powerful in detecting regions that affect resistance than conventional GWAS approaches. Additionally, the results suggest a polygenic genetic architecture for the heteroblastic transition in E. globulus and identified useful SNP markers for the development of marker-assisted selection strategies for resistance to MLD.
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Affiliation(s)
- Marianella Quezada
- Programa Nacional de Investigación en Producción de Leche, Estación Experimental “Wilson Ferreira Adulnate”, Instituto Nacional de Investigación Agropecuaria, Canelones, Uruguay
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Facundo Matias Giorello
- PDU Espacio de Biología Vegetal del Noreste, sede Tacuarembó, CENUR Noreste, Universidad de la República, Tacuarembó, Uruguay
| | - Cecilia Corina Da Silva
- PDU Espacio de Biología Vegetal del Noreste, sede Tacuarembó, CENUR Noreste, Universidad de la República, Tacuarembó, Uruguay
| | - Ignacio Aguilar
- Programa Nacional de Investigación en Producción de Leche, Estación Experimental “Wilson Ferreira Adulnate”, Instituto Nacional de Investigación Agropecuaria, Canelones, Uruguay
| | - Gustavo Balmelli
- Programa Nacional de Investigación en Producción Forestal, Estación Experimental del Norte, Instituto Nacional de Investigación Agropecuaria, Tacuarembó, Uruguay
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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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Ajayi OO, Bregitzer P, Klos K, Hu G, Walling JG, Mahalingam R. QTL mapping of shoot and seed traits impacted by Drought in Barley using a recombinant inbred line Population. BMC PLANT BIOLOGY 2023; 23:283. [PMID: 37245001 DOI: 10.1186/s12870-023-04292-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/17/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND With ongoing climate change, drought events are severely limiting barley production worldwide and pose a significant risk to the malting, brewing and food industry. The genetic diversity inherent in the barley germplasm offers an important resource to develop stress resiliency. The purpose of this study was to identify novel, stable, and adaptive Quantitative Trait Loci (QTL), and candidate genes associated with drought tolerance. A recombinant inbred line (RIL) population (n = 192) developed from a cross between the drought tolerant 'Otis' barley variety, and susceptible 'Golden Promise'(GP) was subjected to short-term progressive drought during heading in the biotron. This population was also evaluated under irrigated and rainfed conditions in the field for yields and seed protein content. RESULTS Barley 50k iSelect SNP Array was used to genotype the RIL population to elucidate drought-adaptive QTL. Twenty-three QTL (eleven for seed weight, eight for shoot dry weight and four for protein content) were identified across several barley chromosomes. QTL analysis identified genomic regions on chromosome 2 and 5 H that appear to be stable across both environments and accounted for nearly 60% variation in shoot weight and 17.6% variation in seed protein content. QTL at approximately 29 Mbp on chromosome 2 H and 488 Mbp on chromosome 5 H are in very close proximity to ascorbate peroxidase (APX) and in the coding sequence of the Dirigent (DIR) gene, respectively. Both APX and DIR are well-known key players in abiotic stress tolerance in several plants. In the quest to identify key recombinants with improved tolerance to drought (like Otis) and good malting profiles (like GP), five drought tolerant RILs were selected for malt quality analysis. The selected drought tolerant RILs exhibited one or more traits that were outside the realms of the suggested limits for acceptable commercial malting quality. CONCLUSIONS The candidate genes can be used for marker assisted selection and/or genetic manipulation to develop barley cultivars with improved tolerance to drought. RILs with genetic network reshuffling necessary to generate drought tolerance of Otis and favorable malting quality attributes of GP may be realized by screening a larger population.
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Affiliation(s)
- Oyeyemi O Ajayi
- Cereal Crops Research Unit, USDA-ARS, 502 Walnut Street, Madison, WI, 53762, USA
| | - Phil Bregitzer
- Small Grains and Potato Germplasm Research, USDA-ARS, Aberdeen, ID, USA
| | - Kathy Klos
- Small Grains and Potato Germplasm Research, USDA-ARS, Aberdeen, ID, USA
| | - Gongshe Hu
- Small Grains and Potato Germplasm Research, USDA-ARS, Aberdeen, ID, USA
| | - Jason G Walling
- Cereal Crops Research Unit, USDA-ARS, 502 Walnut Street, Madison, WI, 53762, USA
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Kapoor P, Rakhra G, Kumar V, Joshi R, Gupta M, Rakhra G. Insights into the functional characterization of DIR proteins through genome-wide in silico and evolutionary studies: a systematic review. Funct Integr Genomics 2023; 23:166. [PMID: 37202648 DOI: 10.1007/s10142-023-01095-z] [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: 03/22/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Dirigent proteins (DIRs) are a new class of proteins that were identified during the 8-8' lignan biosynthetic pathway and involves the formation of ( +) or ( -)-pinoresinol through stereoselective coupling from E-coniferyl alcohol. These proteins are known to play a vital role in the development and stress response in plants. Various studies have reported the functional and structural characterization of dirigent gene family in different plants using in silico approaches. Here, we have summarized the importance of dirigent proteins in plants and their role in plant stress tolerance by analyzing the genome-wide analysis including gene structure, mapping of chromosomes, phylogenetic evolution, conserved motifs, gene structure, and gene duplications in important plants. Overall, this review would help to compare and clarify the molecular and evolutionary characteristics of dirigent gene family in different plants.
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Affiliation(s)
- Preedhi Kapoor
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Gurseen Rakhra
- Department of Nutrition and Dietetics, Faculty of Allied Health Sciences, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | - Vineet Kumar
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Ridhi Joshi
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Mahiti Gupta
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, 133207, India
| | - Gurmeen Rakhra
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India.
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, 133207, India.
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11
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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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12
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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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13
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Harith-Fadzilah N, Lam SD, Haris-Hussain M, Ghani IA, Zainal Z, Jalinas J, Hassan M. Proteomics and Interspecies Interaction Analysis Revealed Abscisic Acid Signalling to Be the Primary Driver for Oil Palm's Response against Red Palm Weevil Infestation. PLANTS (BASEL, SWITZERLAND) 2021; 10:2574. [PMID: 34961045 PMCID: PMC8709180 DOI: 10.3390/plants10122574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
The red palm weevil (RPW; Rhynchophorus ferrugineus Olivier (Coleoptera Curculionidae)) is an invasive insect pest that is difficult to manage due to its nature of infesting the host palm trees from within. A holistic, molecular-based approach to identify proteins that correlate with RPW infestation could give useful insights into the vital processes that are prevalent to the host's infestation response and identify the potential biomarkers for an early detection technique. Here, a shotgun proteomic analysis was performed on oil palm (Elaeis guineensis; OP) under untreated (control), wounding by drilling (wounded), and artificial larval infestation (infested) conditions at three different time points to characterise the RPW infestation response at three different stages. KEGG pathway enrichment analysis revealed many overlapping pathways between the control, wounded, and infested groups. Further analysis via literature searches narrowed down biologically relevant proteins into categories, which were photosynthesis, growth, and stress response. Overall, the patterns of protein expression suggested abscisic acid (ABA) hormone signalling to be the primary driver of insect herbivory response. Interspecies molecular docking analysis between RPW ligands and OP receptor proteins provided putative interactions that result in ABA signalling activation. Seven proteins were selected as candidate biomarkers for early infestation detection based on their relevance and association with ABA signalling. The MS data are available via ProteomeXchange with identifier PXD028986. This study provided a deeper insight into the mechanism of stress response in OP in order to develop a novel detection method or improve crop management.
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Affiliation(s)
- Nazmi Harith-Fadzilah
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.H.-F.); (Z.Z.)
| | - Su Datt Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Mohammad Haris-Hussain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (M.H.-H.); (I.A.G.); (J.J.)
| | - Idris Abd Ghani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (M.H.-H.); (I.A.G.); (J.J.)
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.H.-F.); (Z.Z.)
| | - Johari Jalinas
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (M.H.-H.); (I.A.G.); (J.J.)
| | - Maizom Hassan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.H.-F.); (Z.Z.)
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Xu W, Liu T, Zhang H, Zhu H. Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses. Front Genet 2021; 12:658148. [PMID: 34630501 PMCID: PMC8493098 DOI: 10.3389/fgene.2021.658148] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
DIRIGENT (DIR) genes are key players in environmental stress responses that have been identified in many vascular plant species. However, few studies have examined the VrDIR genes in mungbean. In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method. VrDIRs were distributed on seven of the 11 mungbean chromosomes, and chromosome three contained the most VrDIR genes, with seven members. Thirty-two of the 37 VrDIRs contained a typical DIR gene structure, with one exon; the conserved DIR domain (i.e., Pfam domain) occupied most of the protein in 33 of the 37 VrDIRs. The gene structures of VrDIR genes were analyzed, and a total of 19 distinct motifs were detected. VrDIR genes were classified into five groups based on their phylogenetic relationships, and 13 duplicated gene pairs were identified. In addition, a total of 92 cis-acting elements were detected in all 37 VrDIR promoter regions, and VrDIR genes contained different numbers and types of cis-acting elements. As a result, VrDIR genes showed distinct expression patterns in different tissues and in response to salt and drought stress.
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Affiliation(s)
- Wenying Xu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Tong Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Huiying Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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15
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Cox LD, Munholland S, Mats L, Zhu H, Crosby WL, Lukens L, Pauls KP, Bozzo GG. The Induction of the Isoflavone Biosynthesis Pathway Is Associated with Resistance to Common Bacterial Blight in Phaseolus vulgaris L. Metabolites 2021; 11:433. [PMID: 34357327 PMCID: PMC8306140 DOI: 10.3390/metabo11070433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 11/17/2022] Open
Abstract
Xanthomonas axonopodis infects common bean (Phaseolus vulgaris L.) causing the disease common bacterial blight (CBB). The aim of this study was to investigate the molecular and metabolic mechanisms underlying CBB resistance in P. vulgaris. Trifoliate leaves of plants of a CBB-resistant P. vulgaris recombinant inbred line (RIL) and a CBB-susceptible RIL were inoculated with X. axonopodis or water (mock treatment). Leaves sampled at defined intervals over a 48-h post-inoculation (PI) period were monitored for alterations in global transcript profiles. A total of 800 genes were differentially expressed between pathogen and mock treatments across both RILs; approximately half were differentially expressed in the CBB-resistant RIL at 48 h PI. Notably, there was a 4- to 32-fold increased transcript abundance for isoflavone biosynthesis genes, including several isoflavone synthases, isoflavone 2'-hydroxylases and isoflavone reductases. Ultra-high performance liquid chromatography-tandem mass spectrometry assessed leaf metabolite levels as a function of the PI period. The concentrations of the isoflavones daidzein and genistein and related metabolites coumestrol and phaseollinisoflavan were increased in CBB-resistant RIL plant leaves after exposure to the pathogen. Isoflavone pathway transcripts and metabolite profiles were unaffected in the CBB-susceptible RIL. Thus, induction of the isoflavone pathway is associated with CBB-resistance in P. vulgaris.
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Affiliation(s)
- Laura D. Cox
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.D.C.); (L.L.); (K.P.P.)
| | - Seth Munholland
- Department of Biological Sciences, University of Windsor, 401 Sunset Ave, Windsor, ON N9B 3P4, Canada; (S.M.); (W.L.C.)
| | - Lili Mats
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, ON N1G 5C9, Canada; (L.M.); (H.Z.)
| | - Honghui Zhu
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, ON N1G 5C9, Canada; (L.M.); (H.Z.)
| | - William L. Crosby
- Department of Biological Sciences, University of Windsor, 401 Sunset Ave, Windsor, ON N9B 3P4, Canada; (S.M.); (W.L.C.)
| | - Lewis Lukens
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.D.C.); (L.L.); (K.P.P.)
| | - Karl Peter Pauls
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.D.C.); (L.L.); (K.P.P.)
| | - Gale G. Bozzo
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.D.C.); (L.L.); (K.P.P.)
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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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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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18
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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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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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Davies KM, Jibran R, Zhou Y, Albert NW, Brummell DA, Jordan BR, Bowman JL, Schwinn KE. The Evolution of Flavonoid Biosynthesis: A Bryophyte Perspective. FRONTIERS IN PLANT SCIENCE 2020; 11:7. [PMID: 32117358 PMCID: PMC7010833 DOI: 10.3389/fpls.2020.00007] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/07/2020] [Indexed: 05/04/2023]
Abstract
The flavonoid pathway is one of the best characterized specialized metabolite pathways of plants. In angiosperms, the flavonoids have varied roles in assisting with tolerance to abiotic stress and are also key for signaling to pollinators and seed dispersal agents. The pathway is thought to be specific to land plants and to have arisen during the period of land colonization around 550-470 million years ago. In this review we consider current knowledge of the flavonoid pathway in the bryophytes, consisting of the liverworts, hornworts, and mosses. The pathway is less characterized for bryophytes than angiosperms, and the first genetic and molecular studies on bryophytes are finding both commonalities and significant differences in flavonoid biosynthesis and pathway regulation between angiosperms and bryophytes. This includes biosynthetic pathway branches specific to each plant group and the apparent complete absence of flavonoids from the hornworts.
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Affiliation(s)
- Kevin M. Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Yanfei Zhou
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - David A. Brummell
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Brian R. Jordan
- Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Kathy E. Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
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Knockdown of the chitin-binding protein family gene CaChiIV1 increased sensitivity to Phytophthora capsici and drought stress in pepper plants. Mol Genet Genomics 2019; 294:1311-1326. [PMID: 31175439 DOI: 10.1007/s00438-019-01583-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 12/31/2022]
Abstract
Phytophthora capsici has been the most destructive pathogen of pepper plants (Capsicum annuum L.), possessing the ability to quickly overcome the host defense system. In this context, the chitin-binding protein (CBP) family member CaChiIV1 regulates the response to P. capsici and abiotic stresses. The relevance of functional characterization and regulation of CaChiIV1 has not been explored in horticultural crops, especially pepper plants. The target gene (CaChiIV1) was isolated from pepper plants and cloned; the encoded protein carries a chitin-binding domain (CBD) that is rich in cysteine residues and has a hinge region with an abundance of proline and glycine residues. Additionally, the conserved regions in the promoter have a remarkable motif, "TTGACC". The expression of CaChiIV1 was markedly regulated by methyl-jasmonate (MeJA), hydrogen peroxide (H2O2), melatonin, mannitol and P. capsici (PC and HX-9) infection. Knockdown of CaChiIV1 in pepper plants increased sensitivity to P. capsici (PC strain). Higher malondialdehyde (MDA) content and relative electrolyte leakage (REL) but lower antioxidant enzyme activities, chlorophyll content, root activity, and proline content were observed in CaChiIV1-silenced plants than in control plants. In conclusion, CaChiIV1-silenced pepper plants displayed increased susceptibility to P. capsici infection due to changes in expression of defense-related genes, thus showing its coregulation affect in particular conditions. Furthermore, antioxidant enzymes and proline content were largely diminished in CaChiIV1-silenced plants. Therefore, this evidence suggests that the CaChiIV1 gene plays a prominent role in the defense mechanism of pepper plants against P. capsici infection. In the future, the potential role of the CaChiIV1 gene in defense regulatory pathways and its coregulation with other pathogen-related genes should be identified.
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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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23
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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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24
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Haile ZM, Nagpala-De Guzman EG, Moretto M, Sonego P, Engelen K, Zoli L, Moser C, Baraldi E. Transcriptome Profiles of Strawberry ( Fragaria vesca) Fruit Interacting With Botrytis cinerea at Different Ripening Stages. FRONTIERS IN PLANT SCIENCE 2019; 10:1131. [PMID: 31620156 PMCID: PMC6759788 DOI: 10.3389/fpls.2019.01131] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 08/15/2019] [Indexed: 05/04/2023]
Abstract
Gray mold caused by Botrytis cinerea is a major cause of economic losses in strawberry fruit production, limiting fruit shelf life and commercialization. When the fungus infects Fragaria × ananassa strawberry at flowering or unripe fruit stages, symptoms develop after an extended latent phase on ripe fruits before or after harvesting. To elucidate the growth kinetics of B. cinerea on flower/fruit and the molecular responses associated with low susceptibility of unripe fruit stages, woodland strawberry Fragaria vesca flowers and fruits, at unripe white and ripe red stages, were inoculated with B. cinerea. Quantification of fungal genomic DNA within 72 h postinoculation (hpi) showed limited fungal growth on open flower and white fruit, while on red fruit, the growth was exponential starting from 24 hpi and sporulation was observed within 48 hpi. RNA sequencing applied to white and red fruit at 24 hpi showed that a total of 2,141 genes (12.5% of the total expressed genes) were differentially expressed due to B. cinerea infection. A broad transcriptional reprogramming was observed in both unripe and ripe fruits, involving in particular receptor and signaling, secondary metabolites, and defense response pathways. Membrane-localized receptor-like kinases and nucleotide-binding site leucine-rich repeat genes were predominant in the surveillance system of the fruits, most of them being downregulated in white fruits and upregulated in red fruits. In general, unripe fruits exhibited a stronger defense response than red fruits. Genes encoding for pathogenesis-related proteins and flavonoid polyphenols as well as genes involved in cell-wall strengthening were upregulated, while cell-softening genes appeared to be switched off. As a result, B. cinerea remained quiescent in white fruits, while it was able to colonize ripe red fruits.
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Affiliation(s)
- Zeraye Mehari Haile
- Laboratory of Biotechnology and Plant Pathology, DISTAL, University of Bologna, Bologna, Italy
- Plant Protection Research Division of Melkasa Agricultural Research Center, Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa, Ethiopia
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | | | - Marco Moretto
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Paolo Sonego
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Kristof Engelen
- ESAT-ELECTA, Electrical Energy and Computer Architectures, Leuven, Belgium
| | - Lisa Zoli
- Laboratory of Biotechnology and Plant Pathology, DISTAL, University of Bologna, Bologna, Italy
| | - Claudio Moser
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Elena Baraldi
- Laboratory of Biotechnology and Plant Pathology, DISTAL, University of Bologna, Bologna, Italy
- *Correspondence: Elena Baraldi,
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25
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Marquez N, Giachero ML, Gallou A, Debat HJ, Cranenbrouck S, Di Rienzo JA, Pozo MJ, Ducasse DA, Declerck S. Transcriptional Changes in Mycorrhizal and Nonmycorrhizal Soybean Plants upon Infection with the Fungal Pathogen Macrophomina phaseolina. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:842-855. [PMID: 29498566 DOI: 10.1094/mpmi-11-17-0282-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Macrophomina phaseolina is a soil-borne fungal pathogen with a wide host range that causes charcoal rot in soybean [Glycine max (L.) Merr.]. Control of the disease is a challenge, due to the absence of genetic resistance and effective chemical control. Alternative or complementary measures are needed, such as the use of biological control agents, in an integrated approach. Several studies have demonstrated the role of arbuscular mycorrhizal fungi (AMF) in enhancing plant resistance or tolerance to biotic stresses, decreasing the symptoms and pressure caused by various pests and diseases, including M. phaseolina in soybean. However, the specific contribution of AMF in the regulation of the plant response to M. phaseolina remains unclear. Therefore, the objective of the present study was to investigate, under strict in-vitro culture conditions, the global transcriptional changes in roots of premycorrhized soybean plantlets challenged by M. phaseolina (+AMF+Mp) as compared with nonmycorrhizal soybean plantlets (-AMF+Mp). MapMan software was used to distinguish transcriptional changes, with special emphasis on those related to plant defense responses. Soybean genes identified as strongly upregulated during infection by the pathogen included pathogenesis-related proteins, disease-resistance proteins, transcription factors, and secondary metabolism-related genes, as well as those encoding for signaling hormones. Remarkably, the +AMF+Mp treatment displayed a lower number of upregulated genes as compared with the -AMF+Mp treatment. AMF seemed to counteract or balance costs upon M. phaseolina infection, which could be associated to a negative impact on biomass and seed production. These detailed insights in soybean-AMF interaction help us to understand the complex underlying mechanisms involved in AMF-mediated biocontrol and support the importance of preserving and stimulating the existing plant-AMF associates, via adequate agricultural practices, to optimize their agro-ecological potential.
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Affiliation(s)
- Nathalie Marquez
- 1 Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Camino 60 cuadras km 5.5, 5119. Córdoba, Argentina
- 2 Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - María L Giachero
- 1 Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Camino 60 cuadras km 5.5, 5119. Córdoba, Argentina
| | - Adrien Gallou
- 3 Centro Nacional de Referencia de Control Biológico, Km 1.5 Carretera Tecomán-Estación FFCC. Apdo. Postal 67, Tecomán, Colima, México
| | - Humberto J Debat
- 1 Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Camino 60 cuadras km 5.5, 5119. Córdoba, Argentina
| | - Sylvie Cranenbrouck
- 4 Université catholique de Louvain, Earth and Life Institute, Applied Microbiology, Mycology, Mycothèque de l'Université catholique de Louvain (MUCL), Part of the Belgian Coordinated Collections of Microorganisms (BCCM), Croix du Sud 2, bte L7.05.06, B-1358, Louvain-la-Neuve, Belgium
| | - Julio A Di Rienzo
- 5 Cátedra de Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ing Agr; Felix Aldo Marrone 746, 5000 Córdoba, Argentina
| | - María J Pozo
- 6 Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Prof. Albareda 1, 18008, Granada, Spain
| | - Daniel A Ducasse
- 1 Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Camino 60 cuadras km 5.5, 5119. Córdoba, Argentina
| | - Stéphane Declerck
- 7 Université catholique de Louvain, Earth and Life Institute, Applied Microbiology, Mycology, Croix du Sud 2, bte L7.05.06, B-1358, Louvain-la-Neuve, Belgium
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26
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Ali M, Luo DX, Khan A, Haq SU, Gai WX, Zhang HX, Cheng GX, Muhammad I, Gong ZH. Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (Capsicum annuum L.) and Transcriptional Regulation to Phytophthora capsici, Abiotic Stresses and Hormonal Applications. Int J Mol Sci 2018; 19:E2216. [PMID: 30060631 PMCID: PMC6121964 DOI: 10.3390/ijms19082216] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 11/26/2022] Open
Abstract
Chitin-binding proteins are pathogenesis-related gene family, which play a key role in the defense response of plants. However, thus far, little is known about the chitin-binding family genes in pepper (Capsicum annuum L.). In current study, 16 putative chitin genes (CaChi) were retrieved from the latest pepper genome database, and were classified into four distinct classes (I, III, IV and VI) based on their sequence structure and domain architectures. Furthermore, the structure of gene, genome location, gene duplication and phylogenetic relationship were examined to clarify a comprehensive background of the CaChi genes in pepper. The tissue-specific expression analysis of the CaChi showed the highest transcript levels in seed followed by stem, flower, leaf and root, whereas the lowest transcript levels were noted in red-fruit. Phytophthora capsici post inoculation, most of the CaChi (CaChiI3, CaChiIII1, CaChiIII2, CaChiIII4, CaChiIII6, CaChiIII7, CaChiIV1, CaChiVI1 and CaChiVI2) were induced by both strains (PC and HX-9). Under abiotic and exogenous hormonal treatments, the CaChiIII2, CaChiIII7, CaChiVI1 and CaChiVI2 were upregulated by abiotic stress, while CaChiI1, CaChiIII7, CaChiIV1 and CaChiIV2 responded to hormonal treatments. Furthermore, CaChiIV1-silenced plants display weakened defense by reducing (60%) root activity and increase susceptibility to NaCl stress. Gene ontology (GO) enrichment analysis revealed that CaChi genes primarily contribute in response to biotic, abiotic stresses and metabolic/catabolic process within the biological process category. These results exposed that CaChi genes are involved in defense response and signal transduction, suggesting their vital roles in growth regulation as well as response to stresses in pepper plant. In conclusion, these finding provide basic insights for functional validation of the CaChi genes in different biotic and abiotic stresses.
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Affiliation(s)
- Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - De-Xu Luo
- Xuhuai Region Huaiyin Institute of Agricultural Sciences, Huaian 223001, China.
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Saeed Ul Haq
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Guo-Xin Cheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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Byun MY, Cui LH, Lee J, Park H, Lee A, Kim WT, Lee H. Identification of Rice Genes Associated With Enhanced Cold Tolerance by Comparative Transcriptome Analysis With Two Transgenic Rice Plants Overexpressing DaCBF4 or DaCBF7, Isolated From Antarctic Flowering Plant Deschampsia antarctica. FRONTIERS IN PLANT SCIENCE 2018; 9:601. [PMID: 29774046 PMCID: PMC5943562 DOI: 10.3389/fpls.2018.00601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/16/2018] [Indexed: 05/25/2023]
Abstract
Few plant species can survive in Antarctica, the harshest environment for living organisms. Deschampsia antarctica is the only natural grass species to have adapted to and colonized the maritime Antarctic. To investigate the molecular mechanism of the Antarctic adaptation of this plant, we identified and characterized D. antarctica C-repeat binding factor 4 (DaCBF4), which belongs to monocot CBF group IV. The transcript level of DaCBF4 in D. antarctica was markedly increased by cold and dehydration stress. To assess the roles of DaCBF4 in plants, we generated a DaCBF4-overexpressing transgenic rice plant (Ubi:DaCBF4) and analyzed its abiotic stress response phenotype. Ubi:DaCBF4 displayed enhanced tolerance to cold stress without growth retardation under any condition compared to wild-type plants. Because the cold-specific phenotype of Ubi:DaCBF4 was similar to that of Ubi:DaCBF7 (Byun et al., 2015), we screened for the genes responsible for the improved cold tolerance in rice by selecting differentially regulated genes in both transgenic rice lines. By comparative transcriptome analysis using RNA-seq, we identified 9 and 15 genes under normal and cold-stress conditions, respectively, as putative downstream targets of the two D. antarctica CBFs. Overall, our results suggest that Antarctic hairgrass DaCBF4 mediates the cold-stress response of transgenic rice plants by adjusting the expression levels of a set of stress-responsive genes in transgenic rice plants. Moreover, selected downstream target genes will be useful for genetic engineering to enhance the cold tolerance of cereal plants, including rice.
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Affiliation(s)
- Mi Young Byun
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Li Hua Cui
- Department of Systems Biology, Yonsei University, Seoul, South Korea
| | - Jungeun Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
- Polar Science, University of Science & Technology, Daejeon, South Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
- Polar Science, University of Science & Technology, Daejeon, South Korea
| | - Andosung Lee
- Department of Systems Biology, Yonsei University, Seoul, South Korea
| | - Woo Taek Kim
- Department of Systems Biology, Yonsei University, Seoul, South Korea
| | - Hyoungseok Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
- Polar Science, University of Science & Technology, Daejeon, South Korea
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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: 35] [Impact Index Per Article: 5.8] [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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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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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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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: 114] [Impact Index Per Article: 16.3] [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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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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Lu K, Guo W, Lu J, Yu H, Qu C, Tang Z, Li J, Chai Y, Liang Y. Genome-Wide Survey and Expression Profile Analysis of the Mitogen-Activated Protein Kinase (MAPK) Gene Family in Brassica rapa. PLoS One 2015; 10:e0132051. [PMID: 26173020 PMCID: PMC4501733 DOI: 10.1371/journal.pone.0132051] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 06/09/2015] [Indexed: 12/29/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are fundamental signal transduction modules in plants, controlling cell division, development, hormone signaling, and biotic and abiotic stress responses. Although MAPKs have been investigated in several plant species, a comprehensive analysis of the MAPK gene family has hitherto not been performed in Brassica rapa. In this study, we identified 32 MAPKs in the B. rapa genome by conducting BLASTP and syntenic block analyses, and screening for the essential signature motif (TDY or TEY) of plant MAPK proteins. Of the 32 BraMAPK genes retrieved from the Brassica Database, 13 exhibited exon splicing errors, excessive splicing of the 5' sequence, excessive retention of the 5' sequence, and sequencing errors of the 3' end. Phylogenetic trees of the 32 corrected MAPKs from B. rapa and of MAPKs from other plants generated by the neighbor-joining and maximum likelihood methods suggested that BraMAPKs could be divided into four groups (groups A, B, C, and D). Gene number expansion was observed for BraMAPK genes in groups A and D, which may have been caused by the tandem duplication and genome triplication of the ancestral genome of the Brassica progenitor. Except for five members of the BraMAPK10 subfamily, the identified BraMAPKs were expressed in most of the tissues examined, including callus, root, stem, leaf, flower, and silique. Quantitative real-time PCR demonstrated that at least six and five BraMAPKs were induced or repressed by various abiotic stresses and hormone treatments, respectively, suggesting their potential roles in the abiotic stress response and various hormone signal transduction pathways in B. rapa. This study provides valuable insight into the putative physiological and biochemical functions of MAPK genes in B. rapa.
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Affiliation(s)
- Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
- * E-mail: (KL); (YL)
| | - Wenjin Guo
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
| | - Junxing Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Hao Yu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
| | - Zhanglin Tang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
| | - Yourong Chai
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
| | - Ying Liang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, PR China
- Chongqing Rapeseed Engineering Research Center, Southwest University, Beibei, Chongqing 400715, PR China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Beibei, Chongqing 400715, PR China
- * E-mail: (KL); (YL)
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Ying L, Chen H, Cai W. BnNAC485 is involved in abiotic stress responses and flowering time in Brassica napus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 79:77-87. [PMID: 24690671 DOI: 10.1016/j.plaphy.2014.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 03/03/2014] [Indexed: 05/11/2023]
Abstract
NAC domain proteins are plant-specific transcription factors that play important roles in plant growth and development. In this present study, we isolated BnNAC485 from Brassica napus L. (cv. HuYou15) and found that it showed high homology (84% at the amino acid level) with a NAC protein called AtRD26/ANAC072. BnNAC485 was specifically expressed in cotyledons and leaves of young seedlings, and expression was induced by abiotic stress and abscisic acid (ABA) treatment. The BnNAC485 protein localized to the nucleus. Over-expression of BnNAC485 enhanced tolerance to abiotic stress compared with wild-type plants in both B. napus and Arabidopsis thaliana. Furthermore, under exogenous ABA stress, BnNAC485 over-expression lines showed hypersensitivity to this treatment compared with wild-type B. napus and A. thaliana plants. Moreover, exogenous ABA treatment enhanced stomatal closing in B. napus plants over-expressing BnNAC485. Real-time RT-PCR assays showed that some abiotic- or ABA-responsive genes were up-regulated in A. thaliana plants over-expressing BnNAC485. Additionally, the transgenic lines flowered earlier than the wild-type B. napus and A. thaliana plants and the expression patterns of certain circadian clock genes were found to have changed. These results suggest that BnNAC485 acts in response to abiotic stress in plants via an ABA-mediated pathway and this gene can also alter plant flowering time.
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Affiliation(s)
- Lu Ying
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Graduate School of Chinese Academy of Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Haiying Chen
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Graduate School of Chinese Academy of Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Weiming Cai
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Graduate School of Chinese Academy of Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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Li Q, Chen J, Xiao Y, Di P, Zhang L, Chen W. The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance. BMC Genomics 2014; 15:388. [PMID: 24885106 PMCID: PMC4052678 DOI: 10.1186/1471-2164-15-388] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Isatis indigotica Fort. is one of the most commonly used traditional Chinese medicines. Its antiviral compound is a kind of lignan, which is formed with the action of dirigent proteins (DIR). DIR proteins are members of a large family of proteins which impart stereoselectivity on the phenoxy radical-coupling reaction, yielding optically active lignans from two molecules of E-coniferyl alcohol. They exist in almost every vascular plant. However, the DIR and DIR-like protein gene family in I. indigotica has not been analyzed in detail yet. This study focuses on discovery and analysis of this protein gene family in I. indigotica for the first time. RESULTS Analysis of transcription profiling database from I. indigotica revealed a family of 19 full-length unique DIR and DIR-like proteins. Sequence analysis found that I. indigotica DIR and DIR-like proteins (IiDIR) were all-beta strand proteins, with a signal peptide at the N-terminus. Phylogenetic analysis of the 19 proteins indicated that the IiDIR genes cluster into three distinct subfamilies, DIR-a, DIR-b/d, and DIR-e, of a larger plant DIR and DIR-like gene family. Gene-specific primers were designed for 19 unique IiDIRs and were used to evaluate patterns of constitutive expression in different organs. It showed that most IiDIR genes were expressed comparatively higher in roots and flowers than stems and leaves. CONCLUSIONS New DIR and DIR-like proteins were discovered from the transcription profiling database of I. indigotica through bioinformatics methods for the first time. Sequence characteristics and transcript abundance of these new genes were analyzed. This study will provide basic data necessary for further studies.
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Affiliation(s)
| | | | | | | | - Lei Zhang
- Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, No, 415 Fengyang Road, Huangpu District, Shanghai 200003, China.
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