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Chen C, Cai Y, He B, Zhang Q, Liang D, Wang Y, Chen H, Yao J. Genome-Wide Identification, Evolution, and Expression Analysis of the DIR Gene Family in Schima superba. Int J Mol Sci 2024; 25:7467. [PMID: 39000574 PMCID: PMC11242867 DOI: 10.3390/ijms25137467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Schima superba, commonly known as the Chinese guger tree, is highly adaptable and tolerant of poor soil conditions. It is one of the primary species forming the evergreen broad-leaved forests in southern China. Dirigent proteins (DIRs) play crucial roles in the synthesis of plant lignin and lignans, secondary metabolism, and response to adversity stress. However, research on the DIR gene family in S. superba is currently limited. This study identified 24 SsDIR genes, categorizing them into three subfamilies. These genes are unevenly distributed across 13 chromosomes, with 83% being intronless. Collinearity analysis indicated that tandem duplication played a more significant role in the expansion of the gene family compared to segmental duplication. Additionally, we analyzed the expression patterns of SsDIRs in different tissues of S. superba. The SsDIR genes exhibited distinct expression patterns across various tissues, with most being specifically expressed in the roots. Further screening identified SsDIR genes that may regulate drought stress, with many showing differential expression under drought stress conditions. In the promoter regions of SsDIRs, various cis-regulatory elements involved in developmental regulation, hormone response, and stress response were identified, which may be closely related to their diverse regulatory functions. This study will contribute to the further functional identification of SsDIR genes, providing insights into the biosynthetic pathways of lignin and lignans and the mechanisms of plant stress resistance.
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Affiliation(s)
- Changya Chen
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Yanling Cai
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Boxiang He
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Qian Zhang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Dongcheng Liang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Yingli Wang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Hongpeng Chen
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jun Yao
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
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Li T, Luo W, Du C, Lin X, Lin G, Chen R, He H, Wang R, Lu L, Xie X. Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L. BMC Genomics 2024; 25:671. [PMID: 38970011 PMCID: PMC11229024 DOI: 10.1186/s12864-024-10577-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND The dirigent (DIR) genes encode proteins that act as crucial regulators of plant lignin biosynthesis. In Solanaceae species, members of the DIR gene family are intricately related to plant growth and development, playing a key role in responding to various biotic and abiotic stresses. It will be of great application significance to analyze the DIR gene family and expression profile under various pathogen stresses in Solanaceae species. RESULTS A total of 57 tobacco NtDIRs and 33 potato StDIRs were identified based on their respective genome sequences. Phylogenetic analysis of DIR genes in tobacco, potato, eggplant and Arabidopsis thaliana revealed three distinct subgroups (DIR-a, DIR-b/d and DIR-e). Gene structure and conserved motif analysis showed that a high degree of conservation in both exon/intron organization and protein motifs among tobacco and potato DIR genes, especially within members of the same subfamily. Total 8 pairs of tandem duplication genes (3 pairs in tobacco, 5 pairs in potato) and 13 pairs of segmental duplication genes (6 pairs in tobacco, 7 pairs in potato) were identified based on the analysis of gene duplication events. Cis-regulatory elements of the DIR promoters participated in hormone response, stress responses, circadian control, endosperm expression, and meristem expression. Transcriptomic data analysis under biotic stress revealed diverse response patterns among DIR gene family members to pathogens, indicating their functional divergence. After 96 h post-inoculation with Ralstonia solanacearum L. (Ras), tobacco seedlings exhibited typical symptoms of tobacco bacterial wilt. The qRT-PCR analysis of 11 selected NtDIR genes displayed differential expression pattern in response to the bacterial pathogen Ras infection. Using line 392278 of potato as material, typical symptoms of potato late blight manifested on the seedling leaves under Phytophthora infestans infection. The qRT-PCR analysis of 5 selected StDIR genes showed up-regulation in response to pathogen infection. Notably, three clustered genes (NtDIR2, NtDIR4, StDIR3) exhibited a robust response to pathogen infection, highlighting their essential roles in disease resistance. CONCLUSION The genome-wide identification, evolutionary analysis, and expression profiling of DIR genes in response to various pathogen infection in tobacco and potato have provided valuable insights into the roles of these genes under various stress conditions. Our results could provide a basis for further functional analysis of the DIR gene family under pathogen infection conditions.
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Affiliation(s)
- Tong Li
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Wenbin Luo
- Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Chaofan Du
- Longyan Tobacco Company, Longyan, 364000, China
| | - Xiaolu Lin
- Longyan Tobacco Company, Longyan, 364000, China
| | - Guojian Lin
- Longyan Tobacco Company, Longyan, 364000, China
| | - Rui Chen
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Huaqin He
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Ruiqi Wang
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Libin Lu
- Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China.
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China.
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou, 350002, China.
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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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4
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Pečenková T, Potocký M, Stegmann M. More than meets the eye: knowns and unknowns of the trafficking of small secreted proteins in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3713-3730. [PMID: 38693754 DOI: 10.1093/jxb/erae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/01/2024] [Indexed: 05/03/2024]
Abstract
Small proteins represent a significant portion of the cargo transported through plant secretory pathways, playing crucial roles in developmental processes, fertilization, and responses to environmental stresses. Despite the importance of small secreted proteins, substantial knowledge gaps persist regarding the regulatory mechanisms governing their trafficking along the secretory pathway, and their ultimate localization or destination. To address these gaps, we conducted a comprehensive literature review, focusing particularly on trafficking and localization of Arabidopsis small secreted proteins with potential biochemical and/or signaling roles in the extracellular space, typically those within the size range of 101-200 amino acids. Our investigation reveals that while at least six members of the 21 mentioned families have a confirmed extracellular localization, eight exhibit intracellular localization, including cytoplasmic, nuclear, and chloroplastic locations, despite the presence of N-terminal signal peptides. Further investigation into the trafficking and secretion mechanisms of small protein cargo could not only deepen our understanding of plant cell biology and physiology but also provide a foundation for genetic manipulation strategies leading to more efficient plant cultivation.
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Affiliation(s)
- Tamara Pečenková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Martin Potocký
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Martin Stegmann
- Technical University Munich, School of Life Sciences, Phytopathology, Emil-Ramann-Str. 2, 85354 Freising, Germany
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5
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Chen R, Yu J, Yu L, Xiao L, Xiao Y, Chen J, Gao S, Chen X, Li Q, Zhang H, Chen W, Zhang L. The ERF transcription factor LTF1 activates DIR1 to control stereoselective synthesis of antiviral lignans and stress defense in Isatis indigotica roots. Acta Pharm Sin B 2024; 14:405-420. [PMID: 38261810 PMCID: PMC10792966 DOI: 10.1016/j.apsb.2023.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/13/2023] [Accepted: 08/07/2023] [Indexed: 01/25/2024] Open
Abstract
Lignans are a powerful weapon for plants to resist stresses and have diverse bioactive functions to protect human health. Elucidating the mechanisms of stereoselective biosynthesis and response to stresses of lignans is important for the guidance of plant improvement. Here, we identified the complete pathway to stereoselectively synthesize antiviral (-)-lariciresinol glucosides in Isatis indigotica roots, which consists of three-step sequential stereoselective enzymes DIR1/2, PLR, and UGT71B2. DIR1 was further identified as the key gene in respoJanuary 2024nse to stresses and was able to trigger stress defenses by mediating the elevation in lignan content. Mechanistically, the phytohormone-responsive ERF transcription factor LTF1 colocalized with DIR1 in the cell periphery of the vascular regions in mature roots and helped resist biotic and abiotic stresses by directly regulating the expression of DIR1. These systematic results suggest that DIR1 as the first common step of the lignan pathway cooperates with PLR and UGT71B2 to stereoselectively synthesize (-)-lariciresinol derived antiviral lignans in I. indigotica roots and is also a part of the LTF1-mediated regulatory network to resist stresses. In conclusion, the LTF1-DIR1 module is an ideal engineering target to improve plant Defenses while increasing the content of valuable lignans in plants.
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Affiliation(s)
- Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China
- State Key Laboratory of Dao-di Herbs, Beijing 100700, China
| | - Jian Yu
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Luyao Yu
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Liang Xiao
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Ying Xiao
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Junfeng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shouhong Gao
- Department of Pharmacy, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Xianghui Chen
- School of Medicine, Shanghai University, Shanghai 200433, China
| | - Qing Li
- Department of Pharmacy, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Henan Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai 201403, China
| | - Wansheng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacy, Shanghai Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
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6
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Li W, Lin YCJ, Chen YL, Zhou C, Li S, De Ridder N, Oliveira DM, Zhang L, Zhang B, Wang JP, Xu C, Fu X, Luo K, Wu AM, Demura T, Lu MZ, Zhou Y, Li L, Umezawa T, Boerjan W, Chiang VL. Woody plant cell walls: Fundamentals and utilization. MOLECULAR PLANT 2024; 17:112-140. [PMID: 38102833 DOI: 10.1016/j.molp.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Cell walls in plants, particularly forest trees, are the major carbon sink of the terrestrial ecosystem. Chemical and biosynthetic features of plant cell walls were revealed early on, focusing mostly on herbaceous model species. Recent developments in genomics, transcriptomics, epigenomics, transgenesis, and associated analytical techniques are enabling novel insights into formation of woody cell walls. Here, we review multilevel regulation of cell wall biosynthesis in forest tree species. We highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic trees. We outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | | | - Ying-Lan Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Nette De Ridder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dyoni M Oliveira
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaokang Fu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Taku Demura
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Laigeng Li
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Toshiaki Umezawa
- Laboratory of Metabolic Science of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
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7
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Guo Z, Xu W, Wei D, Zheng S, Liu L, Cai Y. Functional analysis of a dirigent protein AtsDIR23 in Acorustatarinowii. JOURNAL OF PLANT PHYSIOLOGY 2023; 290:154098. [PMID: 37774564 DOI: 10.1016/j.jplph.2023.154098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/17/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
Abstract
Acorus tatarinowii (A. tatarinowii) is a medicinal plant of the Araceae family. Currently, pharmacology focuses on the study of volatile oils, but there are few reports of another important secondary metabolite, lignan. Dirigent protein is thought to play an important role in plant secondary metabolism and responds to a variety of biotic and abiotic stresses. However, the DIR gene family of A. tatarinowii has not been systematically analyzed, and it is unknown whether it affects lignan synthesis. In this study, a total of 27 AtsDIRs were identified by comprehensive analysis of the genome of the medicinal plant A. tatarinowii, and the candidate gene AtsDIR23 that may be involved in lignan synthesis was screened through bioinformatics and transcriptome analysis. It is worth noting that AtsDIR23 is significantly expressed in rhizomes and is a member of the DIR-a subfamily. Subsequently, subcellular localization revealed that AtsDIR23 was localized in chloroplasts. The functional verification of AtsDIR23 b y the transient transformation of A. tatarinowii and the stable transformation of Arabidopsis thaliana showed that the content of lignans in overexpressed plants increased. Co-expression analysis screening revealed the MYB transcription factor (AtsMYB91) that is highly correlated with AtsDIR23 expression, while yeast one-hybrid assays and double luciferase experiments showed that AtsMYB91 negatively regulated the expression of AtsDIR23 b y binding to the AtsDIR23 promoter. In conclusion, AtsDIR23 can promote the accumulation of lignans, which provides a reference for further research on the regulation of lignans by DIR genes.
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Affiliation(s)
- Zihui Guo
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Dongyi Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Siyan Zheng
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Lin Liu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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8
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Gao YQ, Huang JQ, Reyt G, Song T, Love A, Tiemessen D, Xue PY, Wu WK, George MW, Chen XY, Chao DY, Castrillo G, Salt DE. A dirigent protein complex directs lignin polymerization and assembly of the root diffusion barrier. Science 2023; 382:464-471. [PMID: 37883539 DOI: 10.1126/science.adi5032] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023]
Abstract
Functionally similar to the tight junctions present in animal guts, plant roots have evolved a lignified Casparian strip as an extracellular diffusion barrier in the endodermis to seal the root apoplast and maintain nutrient homeostasis. How this diffusion barrier is structured has been partially defined, but its lignin polymerization and assembly steps remain elusive. Here, we characterize a family of dirigent proteins (DPs) essential for both the localized polymerization of lignin required for Casparian strip biogenesis in the cell wall and for attachment of the strip to the plasma membrane to seal the apoplast. We reveal a Casparian strip lignification mechanism that requires cooperation between DPs and the Schengen pathway. Furthermore, we demonstrate that DPs directly mediate lignin polymerization as part of this mechanism.
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Affiliation(s)
- Yi-Qun Gao
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Jin-Quan Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guilhem Reyt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Tao Song
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ashley Love
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - David Tiemessen
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Pei-Ying Xue
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Farmland Eco-environment of Hebei Province, College of Resources and Environmental Sciences, Hebei Agricultural University, Hebei, Baoding 071000, China
| | - Wen-Kai Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Gabriel Castrillo
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
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9
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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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10
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Ube N, Ishihara A, Yabuta Y, Taketa S, Kato Y, Nomura T. Molecular identification of a laccase that catalyzes the oxidative coupling of a hydroxycinnamic acid amide for hordatine biosynthesis in barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1037-1050. [PMID: 37163295 DOI: 10.1111/tpj.16278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/11/2023]
Abstract
Plants produce dimerized phenolic compounds as secondary metabolites. Hordatine A (HA), a dehydrodimer of p-coumaroylagmatine (pCA), is an antifungal compound accumulated at high levels in young barley (Hordeum vulgare) seedlings. The enzyme responsible for the oxidative dimerization of pCA, which is the final step of the hordatine biosynthetic pathway, has not been identified. In this study, we first verified the presence of this enzyme activity in the crude extract of barley seedlings. Because the enzyme activity was not dependent on H2 O2 , the responsible enzyme was not peroxidase, which was previously implicated in HA biosynthesis. The analysis of the dissection lines of wheat (Triticum aestivum) carrying aberrant barley 2H chromosomes detected HA in the wheat lines carrying the distal part of the 2H short arm. This chromosomal region contains two laccase genes (HvLAC1 and HvLAC2) that are highly expressed at the seedling stage and may encode enzymes that oxidize pCA during the formation of HA. Changes in the HvLAC transcript levels coincided with the changes in the HA biosynthesis-related enzyme activities in the crude extract and the HA content in barley seedlings. Moreover, HvLAC genes were heterologously expressed in Nicotiana benthamiana leaves and in bamboo (Phyllostachys nigra) suspension cells and HA biosynthetic activities were detected in the crude extract of transformed N. benthamiana leaves and bamboo suspension cells. The HA formed by the enzymatic reaction had the same stereo-configuration as the naturally occurring HA. These results demonstrate that HvLAC enzymes mediate the oxidative coupling of pCA during HA biosynthesis.
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Affiliation(s)
- Naoki Ube
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Atsushi Ishihara
- Faculty of Agriculture, Tottori University, 4-101 Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Yukinori Yabuta
- Faculty of Agriculture, Tottori University, 4-101 Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Shin Taketa
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Yasuo Kato
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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11
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Balk M, Sofia P, Neffe AT, Tirelli N. Lignin, the Lignification Process, and Advanced, Lignin-Based Materials. Int J Mol Sci 2023; 24:11668. [PMID: 37511430 PMCID: PMC10380785 DOI: 10.3390/ijms241411668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
At a time when environmental considerations are increasingly pushing for the application of circular economy concepts in materials science, lignin stands out as an under-used but promising and environmentally benign building block. This review focuses (A) on understanding what we mean with lignin, i.e., where it can be found and how it is produced in plants, devoting particular attention to the identity of lignols (including ferulates that are instrumental for integrating lignin with cell wall polysaccharides) and to the details of their coupling reactions and (B) on providing an overview how lignin can actually be employed as a component of materials in healthcare and energy applications, finally paying specific attention to the use of lignin in the development of organic shape-memory materials.
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Affiliation(s)
- Maria Balk
- Institute of Functional Materials for Sustainability, Helmholtz-Zentrum Hereon, Kantstrasse 55, 14513 Teltow, Germany
| | - Pietro Sofia
- Laboratory of Polymers and Biomaterials, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- The Open University Affiliated Research Centre at the Istituto Italiano di Tecnologia (ARC@IIT), Via Morego 30, 16163 Genova, Italy
| | - Axel T Neffe
- Institute of Functional Materials for Sustainability, Helmholtz-Zentrum Hereon, Kantstrasse 55, 14513 Teltow, Germany
| | - Nicola Tirelli
- Laboratory of Polymers and Biomaterials, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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12
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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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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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Zheng Z, Chen S, Wei P, Guo S, Yu G, Wu J. The proteomics and metabolomics studies of GZU001 on promoting the Merisis of maize (Zea mays L.) roots. BMC PLANT BIOLOGY 2023; 23:103. [PMID: 36803498 PMCID: PMC9942296 DOI: 10.1186/s12870-023-04130-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Plant growth regulators are chemicals that regulate plant growth and development, which can regulate hormonal balance and affect plant growth, thereby increasing crop yield and improving crop quality. Our studies have revealed a new compound, GZU001, which could be used as a plant growth regulator. This compound has been observed to affect root elongation in maize significantly. However, the exact mechanism of this phenomenon is still being investigated. RESULTS Metabolomics and proteomics were used in unison in this study to explore the response pathway and regulation mechanism of GZU001 in promoting maize root elongation. From the appearance, we can see that both roots and plants of maize treated with GZU001 are significantly improved. Maize root metabolism revealed 101 differentially abundant proteins and 79 differentially expressed metabolites. The current study identified altered proteins and metabolites associated with physiological and biochemical processes. GZU001 treatment has been demonstrated to promote primary metabolism, essential for carbohydrates, amino acids, energy, and secondary metabolism. The result suggests that the stimulation of primary metabolism is beneficial for the growth and development of maize and plays a significant role in sustaining metabolism and growth. CONCLUSIONS This study recorded the changes of related proteins and metabolites in maize roots after GZU001 treatment and provided evidence for this compound's action mode and mechanism in plants.
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Affiliation(s)
- Zhiguo Zheng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
| | - Shunhong Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
| | - Panpan Wei
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
| | - Shengxin Guo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
| | - Gang Yu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang, 550014, China
| | - Jian Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China.
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15
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Wei J, Luo B, Kong S, Liu W, Zhang C, Wei Z, Min X. Screening and identification of multiple abiotic stress responsive candidate genes based on hybrid-sequencing in Vicia sativa. Heliyon 2023; 9:e13536. [PMID: 36816321 PMCID: PMC9929474 DOI: 10.1016/j.heliyon.2023.e13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Common vetch is an important leguminous forage for both livestock fodder and green manure and has a tremendous latent capacity in a sustainable agroecosystem. In the present study, a comprehensive transcriptome analysis of the aboveground leaves and underground roots of common vetch under multiple abiotic stress treatments, including NaCl, drought, cold, and cold drought, was performed using hybrid-sequencing technology, i. e. single-molecule real-time sequencing technology (SMRT) and supplemented by next-generation sequencing (NGS) technology. A total of 485,038 reads of insert (ROIs) with a mean length of 2606 bp and 228,261 full-length nonchimeric (FLNC) reads were generated. After deduplication, 39,709 transcripts were generated. Of these transcripts, we identified 1059 alternative splicing (AS) events, 17,227 simple sequence repeats (SSRs), and 1647 putative transcription factors (TFs). Furthermore, 640 candidates long noncoding RNAs (lncRNAs) and 28,256 complete coding sequences (CDSs) were identified. In gene annotation analyses, a total of 38,826 transcripts (97.78%) were annotated in eight public databases. Finally, seven multiple abiotic stress-responsive candidate genes were obtained through gene expression, annotation information, and protein-protein interaction (PPI) networks. Our research not only enriched the structural information of FL transcripts in common vetch, but also provided useful information for exploring the molecular mechanism of multiple abiotic stress tolerance between aboveground and underground tissues in common vetch and related legumes.
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Affiliation(s)
- Jia Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Bo Luo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Shiyi Kong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People’s Republic of China
| | - Chuanjie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
| | - Xueyang Min
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
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16
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Luo R, Pan W, Liu W, Tian Y, Zeng Y, Li Y, Li Z, Cui L. The barley DIR gene family: An expanded gene family that is involved in stress responses. Front Genet 2022; 13:1042772. [PMID: 36406120 PMCID: PMC9667096 DOI: 10.3389/fgene.2022.1042772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/24/2022] [Indexed: 09/09/2023] Open
Abstract
Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.
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Affiliation(s)
- Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenqiang Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yuan Tian
- Xintai Urban and Rural Development Group Co., Ltd., Taian, Shandong, China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zhimin Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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Bardin M, Rousselot-Pailley P, Tron T, Robert V. Investigation of dirigent like domains from bacterial genomes. BMC Bioinformatics 2022; 23:313. [PMID: 35918655 PMCID: PMC9344732 DOI: 10.1186/s12859-022-04832-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DIRs are mysterious protein that have the ability to scavenge free radicals, which, are highly reactive with molecules in their vicinity. What is even more fascinating is that they carry out from these highly unstable species, a selective reaction (i.e., stereoenantioselective) from a well-defined substrate to give a very precise product. Unfortunately, to date, only three products have been demonstrated following studies on DIRs from the plant world, which until now was the kingdom where these proteins had been demonstrated. Within this kingdom, each DIR protein has its own type of substrate. The products identified to date, have on the other hand, a strong economic impact: in agriculture for example, the biosynthesis of (+)-gossypol could be highlighted (a repellent antifood produced by the cotton plant) by the DIRs of cotton. In forsythia plant species, it is the biosynthesis of (-)-pinoresinol, an intermediate leading to the synthesis of podophyllotoxine (a powerful anicancerous agent) which has been revealed. Recently, a clear path of study, potentially with strong impact, appeared by the hypothesis of the potential existence of protein DIR within the genomes of prokaryotes. The possibility of working with this type of organism is an undeniable advantage: since many sequenced genomes are available and the molecular tools are already developed. Even easier to implement and working on microbes, of less complex composition, offers many opportunities for laboratory studies. On the other hand, the diversity of their environment (e.g., soil, aquatic environments, extreme environmental conditions (pH, temperature, pressure) make them very diverse and varied subjects of study. Identifying new DIR proteins from bacteria means identifying new substrate or product molecules from these organisms. It is the promise of going further in understanding the mechanism of action of these proteins and this will most likely have a strong impact in the fields of agricultural, pharmaceutical and/or food chemistry. RESULTS Our goal is to obtain as much information as possible about these proteins to unlock the secrets of their exceptional functioning. Analyzes of structural and functional genomic data led to the identification of the Pfam PF03018 domain as characteristic of DIR proteins. This domain has been further identified in the sequence of bacterial proteins therefore named as DIR-like (DIRL). We have chosen a multidisciplinary bioinformatic approach centered on bacterial genome identification, gene expression and regulation signals, protein structures, and their molecular information content. The objective of this study was to perform a thorough bioinformatic analysis on these DIRLs to highlight any information leading to the selection of candidate bacteria for further cloning, purification, and characterization of bacterial DIRs. CONCLUSIONS From studies of DIRL genes identification, primary structures, predictions of their secondary and tertiary structures, prediction of DIRL signals sequences, analysis of their gene organization and potential regulation, a list of primary bacterial candidates is proposed.
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Affiliation(s)
- Merlin Bardin
- CNRS, Centrale Marseille, iSm2, Aix Marseille Univ, Marseille, France
| | | | - Thierry Tron
- CNRS, Centrale Marseille, iSm2, Aix Marseille Univ, Marseille, France
| | - Viviane Robert
- CNRS, Centrale Marseille, iSm2, Aix Marseille Univ, Marseille, France.
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Secondary metabolite pathway of SDG (secoisolariciresinol) was observed to trigger ROS scavenging system in response to Ca2+ stress in cotton. Genomics 2022; 114:110398. [DOI: 10.1016/j.ygeno.2022.110398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/12/2022] [Accepted: 06/01/2022] [Indexed: 11/21/2022]
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19
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Songsomboon K, Crawford R, Crawford J, Hansen J, Cummings J, Mattson N, Bergstrom GC, Viands DR. Genome-Wide Associations with Resistance to Bipolaris Leaf Spot (Bipolaris oryzae (Breda de Haan) Shoemaker) in a Northern Switchgrass Population (Panicum virgatum L.). PLANTS 2022; 11:plants11101362. [PMID: 35631787 PMCID: PMC9144872 DOI: 10.3390/plants11101362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022]
Abstract
Switchgrass (Panicum virgatum L.), a northern native perennial grass, suffers from yield reduction from Bipolaris leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoemaker. This study aimed to determine the resistant populations via multiple phenotyping approaches and identify potential resistance genes from genome-wide association studies (GWAS) in the switchgrass northern association panel. The disease resistance was evaluated from both natural (field evaluations in Ithaca, New York and Phillipsburg, Philadelphia) and artificial inoculations (detached leaf and leaf disk assays). The most resistant populations based on a combination of three phenotyping approaches—detached leaf, leaf disk, and mean from two locations—were ‘SW788’, ‘SW806’, ‘SW802’, ‘SW793’, ‘SW781’, ‘SW797’, ‘SW798’, ‘SW803’, ‘SW795’, ‘SW805’. The GWAS from the association panel showed 27 significant SNPs on 12 chromosomes: 1K, 2K, 2N, 3K, 3N, 4N, 5K, 5N, 6N, 7K, 7N, and 9N. These markers accumulatively explained the phenotypic variance of the resistance ranging from 3.28 to 26.52%. Within linkage disequilibrium of 20 kb, these SNP markers linked with the potential resistance genes included the genes encoding for NBS-LRR, PPR, cell-wall related proteins, homeostatic proteins, anti-apoptotic proteins, and ABC transporter.
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Affiliation(s)
- Kittikun Songsomboon
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
- Correspondence:
| | - Ryan Crawford
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
| | - Jamie Crawford
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
| | - Julie Hansen
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
| | | | - Neil Mattson
- Section of Horticulture, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA;
| | - Gary C. Bergstrom
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA;
| | - Donald R. Viands
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; (R.C.); (J.C.); (J.H.); (D.R.V.)
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Li X, Liu Z, Zhao H, Deng X, Su Y, Li R, Chen B. Overexpression of Sugarcane ScDIR Genes Enhances Drought Tolerance in Nicotiana benthamiana. Int J Mol Sci 2022; 23:5340. [PMID: 35628151 PMCID: PMC9141896 DOI: 10.3390/ijms23105340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Dirigent proteins (DIRs) are known to function in lignin biogenesis and to be involved in stress resistance in plants. However, the sugarcane DIRs have not been functionally characterized. In this study, we investigated the DIR-protein-encoding genes in Saccharum spp. (ScDIR) by screening collections of sugarcane databases, monitoring the responses of these genes to drought stress by real-time quantitative PCR, and identifying their heterologous expression in tobacco. Of the 64 ScDIRs identified, four belonging to the DIR-b/d (ScDIR5 and ScDIR11) and DIR-c (ScDIR7 and ScDIR40) subfamilies showed a significant transcriptional response when subjected to drought stress. ScDIR5, ScDIR7, and ScDIR11 are localized in the cell membrane, whereas ScDIR40 is found in the cell wall. The overexpression of these ScDIR genes in tobacco generally increased the drought tolerance of the transgenic lines, with ScDIR7 conferring the highest degree of drought tolerance. The characterization of the physiological and biochemical indicators (superoxide dismutase, catalase, malondialdehyde, and H2O2) confirmed that the ScDIR-overexpressing lines outperformed the wild type. These results demonstrated that specific ScDIRs in sugarcane respond and contribute to tolerance of drought stress, shedding light on potential means of improving drought tolerance in this crop.
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Affiliation(s)
- Xiufang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Zongling Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Haiyun Zhao
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China;
| | - Xingli Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Yizu Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China;
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21
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Pilati S, Malacarne G, Navarro-Payá D, Tomè G, Riscica L, Cavecchia V, Matus JT, Moser C, Blanzieri E. Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families. Biomolecules 2021; 11:1744. [PMID: 34944388 PMCID: PMC8698957 DOI: 10.3390/biom11121744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022] Open
Abstract
The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.
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Affiliation(s)
- Stefania Pilati
- Research and Innovation Centre, Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (G.M.); (C.M.)
| | - Giulia Malacarne
- Research and Innovation Centre, Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (G.M.); (C.M.)
| | - David Navarro-Payá
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46908 Paterna, Valencia, Spain; (D.N.-P.); (J.T.M.)
| | - Gabriele Tomè
- Centre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy;
| | - Laura Riscica
- Department of Information Engineering and Computer Science, University of Trento, 38123 Trento, Italy; (L.R.); (E.B.)
| | - Valter Cavecchia
- CNR-Institute of Materials for Electronics and Magnetism, 38123 Trento, Italy;
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46908 Paterna, Valencia, Spain; (D.N.-P.); (J.T.M.)
| | - Claudio Moser
- Research and Innovation Centre, Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy; (G.M.); (C.M.)
| | - Enrico Blanzieri
- Department of Information Engineering and Computer Science, University of Trento, 38123 Trento, Italy; (L.R.); (E.B.)
- CNR-Institute of Materials for Electronics and Magnetism, 38123 Trento, Italy;
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22
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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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23
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Cervantes S, Vuosku J, Pyhäjärvi T. Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris. PeerJ 2021; 9:e11781. [PMID: 34466281 PMCID: PMC8380025 DOI: 10.7717/peerj.11781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Despite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.
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Affiliation(s)
- Sandra Cervantes
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Jaana Vuosku
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Tanja Pyhäjärvi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
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Yang X, Zhong S, Zhang Q, Ren Y, Sun C, Chen F. A loss-of-function of the dirigent gene TaDIR-B1 improves resistance to Fusarium crown rot in wheat. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:866-868. [PMID: 33567136 PMCID: PMC8131038 DOI: 10.1111/pbi.13554] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/24/2020] [Accepted: 01/08/2021] [Indexed: 05/06/2023]
Affiliation(s)
- Xia Yang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/CIMMYT‐China (Henan) Joint Center of Wheat and MaizeHenan Agricultural UniversityZhengzhouChina
| | - Shaobin Zhong
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
| | - Qijun Zhang
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
| | - Yan Ren
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/CIMMYT‐China (Henan) Joint Center of Wheat and MaizeHenan Agricultural UniversityZhengzhouChina
| | - Congwei Sun
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/CIMMYT‐China (Henan) Joint Center of Wheat and MaizeHenan Agricultural UniversityZhengzhouChina
| | - Feng Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/CIMMYT‐China (Henan) Joint Center of Wheat and MaizeHenan Agricultural UniversityZhengzhouChina
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25
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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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26
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Noman A, Aqeel M, Islam W, Khalid N, Akhtar N, Qasim M, Yasin G, Hashem M, Alamri S, Al-Zoubi OM, Jalees MM, Al-Sadi A. Insects-plants-pathogens: Toxicity, dependence and defense dynamics. Toxicon 2021; 197:87-98. [PMID: 33848517 DOI: 10.1016/j.toxicon.2021.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
In a natural ecosystem, the pathogen-plant-insect relationship has diverse implications for each other. The pathogens as well as insect-pests consume plant tissues as their feed that mostly results in damage. In turn, plant species have evolved specialized defense system to not only protect themselves but reduce the damage also. Such tripartite interactions involve toxicity, metabolic modulations, resistance etc. among all participants of interaction. These attributes result in selection pressure among participants. Coevolution of such traits reveals need to focus and unravel multiple hidden aspects of insect-plant-pathogen interactions. The definite modulations during plant responses to biotic stress and the operating defense network against herbivores are vital to research areas. Different types of plant pathogens and herbivores are tackled with various changes in plants, e.g. changes in genes expression, glucosinolate metabolism detoxification, signal transduction, cell wall modifications, Ca2+dependent signaling. It is essential to clarify which chemical in plants can work as a defense signal or weapon in plant-pathogen-herbivore interactions. In spite of increased knowledge regarding signal transduction pathways regulating growth-defense balance, much more is needed to unveil the coordination of growth rate with metabolic modulations in bi-trophic interactions. Here, we addressed plant-pathogen-insect interaction for toxicity as well as dependnce along with plant defense dynamics against pathogens and insects with broad range effects at the physio-biochemical and molecular level. We have reviewed interfaces in plant-pathogen-insect research to show pulsating regulation of plant immunity for attuning survival and ecological equilibrium. An improved understanding of the systematic foundation of growth-defense stability has vital repercussions for enhancing crop yield, including insights into uncoupling of host-parasite tradeoffs for ecological and environmental sustainability.
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Affiliation(s)
- Ali Noman
- Department of Botany, Government College University, Faisalabad, 38040, Pakistan.
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Waqar Islam
- College of Geography, Fujian Normal University, Fuzhou, PR China
| | - Noreen Khalid
- Department of Botany, Government College Women University, Sialkot, Pakistan
| | - Noreen Akhtar
- Department of Botany, Government College for Women University, Faisalabad, Pakistan
| | - Muhammad Qasim
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, PR China
| | - Ghulam Yasin
- Institute of Pure and Applied Biology, Bahau Din Zakria University Multan Pakistan, Pakistan
| | - Mohamed Hashem
- King Khalid University, College of Science, Department of Biology, Abha, 61413, Saudi Arabia; Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut, 71516, Egypt.
| | - Saad Alamri
- King Khalid University, College of Science, Department of Biology, Abha, 61413, Saudi Arabia
| | | | - Muhammad Moazam Jalees
- Department of Microbiology, Cholistan University of Veterinary and Animal Sciences. Bahawalpur, Pakistan
| | - Abdullah Al-Sadi
- College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat. Sultanate of Oman, Oman
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27
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Ma R, Huang B, Chen J, Huang Z, Yu P, Ruan S, Zhang Z. Genome-wide identification and expression analysis of dirigent-jacalin genes from plant chimeric lectins in Moso bamboo (Phyllostachys edulis). PLoS One 2021; 16:e0248318. [PMID: 33724993 PMCID: PMC7963094 DOI: 10.1371/journal.pone.0248318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/24/2021] [Indexed: 12/02/2022] Open
Abstract
Dirigent-jacalin (D-J) genes belong to the plant chimeric lectin family, and play vital roles in plant growth and resistance to abiotic and biotic stresses. To explore the functions of the D-J family in the growth and development of Moso bamboo (Phyllostachys edulis), their physicochemical properties, phylogenetic relationships, gene and protein structures, and expression patterns were analyzed in detail. Four putative PeD-J genes were identified in the Moso bamboo genome, and microsynteny and phylogenetic analyses indicated that they represent a new branch in the evolution of plant lectins. PeD-J proteins were found to be composed of a dirigent domain and a jacalin-related lectin domain, each of which contained two different motifs. Multiple sequence alignment and homologous modeling analysis indicated that the three-dimensional structure of the PeD-J proteins was significantly different compared to other plant lectins, primarily due to the tandem dirigent and jacalin domains. We surveyed the upstream putative promoter regions of the PeD-Js and found that they mainly contained cis-acting elements related to hormone and abiotic stress response. An analysis of the expression patterns of root, leaf, rhizome and panicle revealed that four PeD-J genes were highly expressed in the panicle, indicating that they may be required during the formation and development of several different tissue types in Moso bamboo. Moreover, PeD-J genes were shown to be involved in the rapid growth and development of bamboo shoots. Quantitative Real-time PCR (qRT PCR) assays further verified that D-J family genes were responsive to hormones and stresses. The results of this study will help to elucidate the biological functions of PeD-Js during bamboo growth, development and stress response.
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Affiliation(s)
- Ruifang Ma
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
| | - Bin Huang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
| | - Jialu Chen
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
| | - Zhinuo Huang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
| | - Peiyao Yu
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
| | - Shiyu Ruan
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
| | - Zhijun Zhang
- State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou, Zhejiang, China
- * E-mail:
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28
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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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A transcriptomic view to wounding response in young Scots pine stems. Sci Rep 2021; 11:3778. [PMID: 33580160 PMCID: PMC7881122 DOI: 10.1038/s41598-021-82848-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
We studied the stress response of five-year-old Scots pine xylem to mechanical wounding using RNA sequencing. In general, we observed a bimodal response in pine xylem after wounding. Transcripts associated with water deficit stress, defence, and cell wall modification were induced at the earliest time point of three hours; at the same time, growth-related processes were down-regulated. A second temporal wave was triggered either at the middle and/or at the late time points (one and four days). Secondary metabolism, such as stilbene and lignan biosynthesis started one day after wounding. Scots pine synthesises the stilbenes pinosylvin and its monomethyl ether both as constitutive and induced defence compounds. Stilbene biosynthesis is induced by wounding, pathogens and UV stress, but is also developmentally regulated when heartwood is formed. Comparison of wounding responses to heartwood formation shows that many induced processes (in addition to stilbene biosynthesis) are similar and relate to defence or desiccation stress, but often specific transcripts are up-regulated in the developmental and wounding induced contexts. Pine resin biosynthesis was not induced in response to wounding, at least not during the first four days.
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30
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Ma X, Xu W, Liu T, Chen R, Zhu H, Zhang H, Cai C, Li S. Functional characterization of soybean (Glycine max) DIRIGENT genes reveals an important role of GmDIR27 in the regulation of pod dehiscence. Genomics 2021; 113:979-990. [PMID: 33144217 DOI: 10.1016/j.ygeno.2020.10.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/02/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022]
Abstract
DIRIGENT (DIR) genes play important roles in regulating plant growth and development and have been studied in many plant species. However, information on DIR genes in soybean is limited. Here, we identified and characterized 54 GmDIRs and studied the characteristics of GmDIRs. Most of the GmDIRs contained a classical gene structure, one exon; 26 conserved motifs were found among these GmDIRs. The GmDIRs were grouped into four subfamilies, DIR-a, DIR-b, DIR-e and DIR-f, based on a phylogenetic analysis, and 24 duplicated gene pairs were identified. Differences in the cis-acting elements in the GmDIR promoter regions might result in distinct expression patterns of GmDIRs in different tissues. In addition, GmDIR27 had a close relationship with the pod dehiscence gene GmPdh1, and overexpression of GmDIR27 increased pod dehiscence by affecting several pod dehiscence-related gene expressions. Generally, our results provide essential information that aids future efforts to functionally characterize soybean GmDIR genes.
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Affiliation(s)
- Xiaofei Ma
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenying Xu
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Tong Liu
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Ruying Chen
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Huiying Zhang
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Chunmei Cai
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuai Li
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China.
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Laoué J, Depardieu C, Gérardi S, Lamothe M, Bomal C, Azaiez A, Gros-Louis MC, Laroche J, Boyle B, Hammerbacher A, Isabel N, Bousquet J. Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce. FRONTIERS IN PLANT SCIENCE 2021; 12:675108. [PMID: 34079574 PMCID: PMC8166253 DOI: 10.3389/fpls.2021.675108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/08/2021] [Indexed: 05/05/2023]
Abstract
Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.
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Affiliation(s)
- Justine Laoué
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- *Correspondence: Justine Laoué
| | - Claire Depardieu
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Claude Bomal
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Aïda Azaiez
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Marie-Claude Gros-Louis
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Almuth Hammerbacher
- Department of Zoology, Entomology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
- Jean Bousquet
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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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Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum. PLANTS 2020; 9:plants9060780. [PMID: 32580425 PMCID: PMC7356841 DOI: 10.3390/plants9060780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 11/29/2022]
Abstract
For forage and turf grasses, wounding is a predominant stress that often results in extensive loss of vegetative tissues followed by rapid regrowth. Currently, little is known concerning the perception, signaling, or molecular responses associated with wound stress in forage- and turf-related grasses. A transcriptome analysis of Lolium temulentum plants subjected to severe wounding revealed 9413 upregulated and 7704 downregulated, distinct, differentially expressed genes (DEGs). Categories related to signaling, transcription, and response to stimuli were enriched in the upregulated DEGs. Specifically, sequences annotated as enzymes involved in hormone biosynthesis/action and cell wall modifications, mitogen-activated protein kinases, WRKY transcription factors, proteinase inhibitors, and pathogen defense-related DEGs were identified. Surprisingly, DEGs related to heat shock and chaperones were more prevalent in the downregulated DEGs when compared with the upregulated DEGs. This wound transcriptome analysis is the first step in identifying the molecular components and pathways used by grasses in response to wounding. The information gained from the analysis will provide a valuable molecular resource that will be used to develop approaches that can improve the recovery, regrowth, and long-term fitness of forage and turf grasses before/after cutting or grazing.
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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Liu Y, Lu S, Liu K, Wang S, Huang L, Guo L. Proteomics: a powerful tool to study plant responses to biotic stress. PLANT METHODS 2019; 15:135. [PMID: 31832077 PMCID: PMC6859632 DOI: 10.1186/s13007-019-0515-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/29/2019] [Indexed: 05/08/2023]
Abstract
In recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed from an isolated field into a comprehensive tool for biological research that can be used to explain biological functions. Several studies have successfully used the power of proteomics as a discovery tool to uncover plant resistance mechanisms. There is growing evidence that indicates that the spatial proteome and post-translational modifications (PTMs) of proteins directly participate in the plant immune response. Therefore, understanding the subcellular localization and PTMs of proteins is crucial for a comprehensive understanding of plant responses to biotic stress. In this review, we discuss current approaches to plant proteomics that use mass spectrometry, with particular emphasis on the application of spatial proteomics and PTMs. The purpose of this paper is to investigate the current status of the field, discuss recent research challenges, and encourage the application of proteomics techniques to further research.
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Affiliation(s)
- Yahui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- National Institute of Metrology, Beijing, China
| | - Song Lu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Kefu Liu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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The Resurgence of Dirigent Story: Time for a Bacterial Chapter. Curr Microbiol 2019; 77:517-521. [PMID: 31728698 DOI: 10.1007/s00284-019-01809-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/04/2019] [Indexed: 01/16/2023]
Abstract
For several decades, dirigent (DIR) domain-containing proteins have been assumed to be green lineage-specific, responsible for the defence response and lignan/lignin biosynthesis. Despite their high potential in terms of biotechnology and chemistry, to date there have been very few well-studied plant DIRs. However, recent achievements in sequencing technologies have allowed for discovery of DIR genes in bacteria. This prospective study suggests expansion of the focus of research to consider the existence of bacterial DIRs. It also considers the outlook for understanding DIR functioning with respect to the fields of green lineage evolution, organic synthesis, and biotechnology.
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37
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Whitehill JG, Bohlmann J. A molecular and genomic reference system for conifer defence against insects. PLANT, CELL & ENVIRONMENT 2019; 42:2844-2859. [PMID: 31042808 PMCID: PMC6852437 DOI: 10.1111/pce.13571] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/24/2019] [Accepted: 04/27/2019] [Indexed: 05/29/2023]
Abstract
Insect pests are part of natural forest ecosystems contributing to forest rejuvenation but can also cause ecological disturbance and economic losses that are expected to increase with climate change. The white pine or spruce weevil (Pissodes strobi) is a pest of conifer forests in North America. Weevil-host interactions with various spruce (Picea) species have been explored as a genomic and molecular reference system for conifer defence against insects. Interactions occur in two major phases of the insect life cycle. In the exophase, adult weevils are free-moving and display behaviour of host selection for oviposition that is affected by host traits. In the endophase, insects live within the host where mobility and development from eggs to young adults are affected by a complex system of host defences. Genetic resistance exists in several spruce species and involves synergism of constitutive and induced chemical and physical defences that comprise the conifer defence syndrome. Here, we review conifer defences that disrupt the weevil life cycle and mechanisms by which trees resist weevil attack. We highlight molecular and genomic aspects and a possible role for the weevil microbiome. Knowledge of this conifer defence system is supporting forest health strategies and tree breeding for insect resistance.
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Affiliation(s)
| | - Jörg Bohlmann
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Department of BotanyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
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Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela. Proc Natl Acad Sci U S A 2019; 116:18893-18899. [PMID: 31484765 DOI: 10.1073/pnas.1910401116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aquatic plants have to adapt to the environments distinct from where land plants grow. A critical aspect of adaptation is the dynamics of sequence repeats, not resolved in older sequencing platforms due to incomplete and fragmented genome assemblies from short reads. Therefore, we used PacBio long-read sequencing of the Spirodela polyrhiza genome, reaching a 44-fold increase of contiguity with an N50 (a median of contig lengths) of 831 kb and filling 95.4% of gaps left from the previous version. Reconstruction of repeat regions indicates that sequentially nested long terminal repeat (LTR) retrotranspositions occur early in monocot evolution, featured with both prokaryote-like gene-rich regions and eukaryotic repeat islands. Protein-coding genes are reduced to 18,708 gene models supported by 492,435 high-quality full-length PacBio complementary DNA (cDNA) sequences. Different from land plants, the primitive architecture of Spirodela's adventitious roots and lack of lateral roots and root hairs are consistent with dispensable functions of nutrient absorption. Disease-resistant genes encoding antimicrobial peptides and dirigent proteins are expanded by tandem duplications. Remarkably, disease-resistant genes are not only amplified, but also highly expressed, consistent with low levels of 24-nucleotide (nt) small interfering RNA (siRNA) that silence the immune system of land plants, thereby protecting Spirodela against a wide spectrum of pathogens and pests. The long-read sequence information not only sheds light on plant evolution and adaptation to the environment, but also facilitates applications in bioenergy and phytoremediation.
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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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40
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Chu Y, Chee P, Culbreath A, Isleib TG, Holbrook CC, Ozias-Akins P. Major QTLs for Resistance to Early and Late Leaf Spot Diseases Are Identified on Chromosomes 3 and 5 in Peanut ( Arachis hypogaea). FRONTIERS IN PLANT SCIENCE 2019; 10:883. [PMID: 31333711 PMCID: PMC6625158 DOI: 10.3389/fpls.2019.00883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 06/20/2019] [Indexed: 05/21/2023]
Abstract
Early and late leaf spots (LLSs) are the major foliar diseases of peanut responsible for severely decreased yield in the absence of intensive fungicide spray programs. Pyramiding host resistance to leaf spots in elite cultivars is a sustainable solution to mitigate the diseases. In order to determine the genetic control of leaf spot disease resistance in peanut, a recombinant inbred line population (Florida-07 × GP-NC WS16) segregating for resistance to both diseases was used to construct a SNP-based linkage map consisting of 855 loci. QTL mapping revealed three resistance QTLs for LLS qLLSA05 (phenotypic variation explained, PVE = 7-10%), qLLSB03 (PVE = 5-7%), and qLLSB05 (PVE = 15-41%) that were consistently expressed over multi-year analysis. Two QTL, qLLSA05 and qLLSB05, confirmed our previously published QTL-seq results. For early leaf spot, three resistance QTLs were identified in multiple years, two on chromosome A03 (PVE = 8-12%) and one on chromosome B03 (PVE = 13-20%), with the locus qELSA03_1.1 coinciding with the previously published genomic region for LLS resistance in GPBD4. Comparative analysis of the genomic regions spanning the QTLs suggests that resistance to early and LLSs are largely genetically independent. In addition, QTL analysis on yield showed that the presence of resistance allele in qLLSB03 and qLLSB05 loci might result in protection from yield loss caused by LLS disease damage. Finally, post hoc analysis of the RIL subpopulation that was not utilized in the QTL mapping revealed that the flanking markers for these QTLs can successfully select for resistant and susceptible lines, confirming the effectiveness of pyramiding these resistance loci to improve host-plant resistance in peanut breeding programs using marker-assisted selection.
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Affiliation(s)
- Ye Chu
- Department of Horticulture, The University of Georgia Tifton Campus, Tifton, GA, United States
| | - Peng Chee
- Department of Crop and Soil Sciences, The University of Georgia Tifton Campus, Tifton, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, The University of Georgia Tifton Campus, Tifton, GA, United States
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Thomas G. Isleib
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - C. Corley Holbrook
- Institute of Plant Breeding, Genetics and Genomics, The University of Georgia Tifton Campus, Tifton, GA, United States
- United States Department of Agriculture (USDA), Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Peggy Ozias-Akins
- Department of Horticulture, The University of Georgia Tifton Campus, Tifton, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, The University of Georgia Tifton Campus, Tifton, GA, United States
- *Correspondence: Peggy Ozias-Akins,
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Patwa N, Nithin C, Bahadur RP, Basak J. Identification and characterization of differentially expressed Phaseolus vulgaris miRNAs and their targets during mungbean yellow mosaic India virus infection reveals new insight into Phaseolus-MYMIV interaction. Genomics 2018; 111:1333-1342. [PMID: 30237075 DOI: 10.1016/j.ygeno.2018.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/17/2018] [Accepted: 09/09/2018] [Indexed: 02/06/2023]
Abstract
Phaseolus vulgaris is an economically important legume in tropical and subtropical regions of Asia, Africa, Latin-America and parts of USA and Europe. However, its production gets severely affected by mungbean yellow mosaic India virus (MYMIV). We aim to identify and characterize differentially expressed miRNAs during MYMIV-infection in P. vulgaris. A total of 422 miRNAs are identified of which 292 are expressed in both MYMIV-treated and mock-treated samples, 109 are expressed only in MYMIV-treated and 21 are expressed only in mock-treated samples. Selected up- and down-regulated miRNAs are validated by RT-qPCR. 3367 target ORFs are identified for 270 miRNAs. Selected targets are validated by 5' RLM-RACE. Differentially expressed miRNAs regulate transcription factors and are involved in improving stress tolerance to MYMIV. These findings will provide an insight into the role of miRNAs during MYMIV infection in P. vulgaris in particular and during any biotic stress conditions in Leguminosae family in general.
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Affiliation(s)
- Nisha Patwa
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan 731235, India
| | - Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India
| | - Jolly Basak
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan 731235, India.
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Juliana P, Singh RP, Singh PK, Poland JA, Bergstrom GC, Huerta-Espino J, Bhavani S, Crossa J, Sorrells ME. Genome-wide association mapping for resistance to leaf rust, stripe rust and tan spot in wheat reveals potential candidate genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1405-1422. [PMID: 29589041 PMCID: PMC6004277 DOI: 10.1007/s00122-018-3086-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 03/12/2018] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE Genome-wide association mapping in conjunction with population sequencing map and Ensembl plants was used to identify markers/candidate genes linked to leaf rust, stripe rust and tan spot resistance in wheat. Leaf rust (LR), stripe rust (YR) and tan spot (TS) are some of the important foliar diseases in wheat (Triticum aestivum L.). To identify candidate resistance genes for these diseases in CIMMYT's (International Maize and Wheat Improvement Center) International bread wheat screening nurseries, we used genome-wide association studies (GWAS) in conjunction with information from the population sequencing map and Ensembl plants. Wheat entries were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. Using a mixed linear model, we observed that seedling resistance to LR was associated with 12 markers on chromosomes 1DS, 2AS, 2BL, 3B, 4AL, 6AS and 6AL, and seedling resistance to TS was associated with 14 markers on chromosomes 1AS, 2AL, 2BL, 3AS, 3AL, 3B, 6AS and 6AL. Seedling and adult plant resistance (APR) to YR were associated with several markers at the distal end of chromosome 2AS. In addition, YR APR was also associated with markers on chromosomes 2DL, 3B and 7DS. The potential candidate genes for these diseases included several resistance genes, receptor-like serine/threonine-protein kinases and defense-related enzymes. However, extensive LD in wheat that decays at about 5 × 107 bps, poses a huge challenge for delineating candidate gene intervals and candidates should be further mapped, functionally characterized and validated. We also explored a segment on chromosome 2AS associated with multiple disease resistance and identified seventeen disease resistance linked genes. We conclude that identifying candidate genes linked to significant markers in GWAS is feasible in wheat, thus creating opportunities for accelerating molecular breeding.
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Affiliation(s)
- Philomin Juliana
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico
| | - Pawan K Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico
| | - Jesse A Poland
- Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Gary C Bergstrom
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, 56230, Chapingo, Edo. de México, Mexico
| | - Sridhar Bhavani
- CIMMYT, ICRAF house, United Nations Avenue, Gigiri, Village Market, Nairobi, 00621, Kenya
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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Wang J, Wang J, Wang X, Li R, Chen B. Proteomic response of hybrid wild rice to cold stress at the seedling stage. PLoS One 2018; 13:e0198675. [PMID: 29879216 PMCID: PMC5991693 DOI: 10.1371/journal.pone.0198675] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022] Open
Abstract
Low temperature at the seedling stage is a major damaging factor for rice production in southern China. To better understand the cold response of cultivated and wild rice, cold-sensitive cultivar 93–11 (Oryza sativa L. ssp. Indica) and cold-resistant hybrid wild rice DC907 with a 93–11 genetic background were used for a quantitative proteomic analysis with tandem mass tags (TMT) in parallel. Rice seedlings grown for four weeks at a normal temperature (25°C) were treated at 8–10°C for 24, 72 and 120 h. The number of differentially expressed proteins increased gradually over time in the cold-exposed rice in comparison with the untreated rice. A total of 366 unique proteins involved in ATP synthesis, photosystem, reactive oxygen species, stress response, cell growth and integrity were identified as responding to cold stress in DC907. While both DC907 and 93–11 underwent similar alterations in proteomic profiles in response to cold stress, DC907 responded in a prompter manner in terms of expressing cold-responding proteins, maintained a higher level of photosynthesis to power the cells, and possessed a stable and higher level of DIR proteins to prevent the plant from obtaining irreversible cell structure damage. The observations made in this study may lay a new foundation for further investigation of cold sensitivity or tolerance mechanisms in rice.
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Affiliation(s)
- Jinzi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
| | - Jun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xin Wang
- College of Agriculture, Guangxi University, Nanning, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
- * E-mail: (BC); (RL)
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, China
- * E-mail: (BC); (RL)
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Corbin C, Drouet S, Markulin L, Auguin D, Lainé É, Davin LB, Cort JR, Lewis NG, Hano C. A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation. PLANT MOLECULAR BIOLOGY 2018; 97:73-101. [PMID: 29713868 DOI: 10.1007/s11103-018-0725-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/02/2018] [Indexed: 05/21/2023]
Abstract
Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset of genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.
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Affiliation(s)
- Cyrielle Corbin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Lucija Markulin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Éric Lainé
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - John R Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA.
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France.
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France.
- Pôle Universitaire d'Eure et Loir, 21 Rue de Loigny la Bataille, 28000, Chartres, France.
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Cheng X, Su X, Muhammad A, Li M, Zhang J, Sun Y, Li G, Jin Q, Cai Y, Lin Y. Molecular Characterization, Evolution, and Expression Profiling of the Dirigent ( DIR) Family Genes in Chinese White Pear ( Pyrus bretschneideri). Front Genet 2018; 9:136. [PMID: 29713336 PMCID: PMC5911567 DOI: 10.3389/fgene.2018.00136] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/03/2018] [Indexed: 01/24/2023] Open
Abstract
Stone cells content and size are the key factors determining the internal quality of the pear fruit. Synthesis of lignin and thickening of secondary cell wall are the keys to the development of stone cells. The polymerization of monolignols and secondary cell wall formation requires the participation of dirigent proteins (DIRs). In recent years, DIR family have been studied in higher plants, but lack of comprehensive study in the pear DIR (PbDIR) family. This study focuses on the identification and analysis of PbDIR family for the first time. We identified 35 PbDIRs from the pear genome, 89% of which are intronless genes. Phylogenetic tree and chromosome localization analysis showed that 35 PbDIRs were divided into four subfamilies (DIR-a, -b/d, -e, and -g) and irregularly distributed among 10 chromosomes. In addition, we identified 29, 26, and 14 DIRs from the other three Rosids (peach, Mei, and grape), respectively. Interspecies microsynteny analysis revealed the collinear gene pairs between pear and peach are the most. Temporal expression analysis showed that the expression changes of seven PbDIRs (DIR-a subfamily: PbDIR4 and PbDIR5; DIR-b/d subfamily: PbDIR11; DIR-g subfamily: PbDIR19; DIR-e subfamily: PbDIR23, 25 and 26) in fruits were consistent with the changes of fruit lignin and stone cells contents. In addition, the subfamily of PbDIRs in fruits showed significant responses after treatment with ABA, SA, and MeJA. According to the protein tertiary structure, key amino acid residues and expression patterns analysis found that PbDIR4 might be involved in the metabolism of lignin and related to stone cells contents in pear fruits. In this study, we systematically analyzed the structure, evolution, function and expression of PbDIR family, which not only confirmed the characteristics of PbDIR family, but also laid the foundation for revealing the role of DIR in pear stone cell development and lignin polymerization.
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Affiliation(s)
- Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Manli Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Jinyun Zhang
- School of Life Science, Anhui Agricultural University, Hefei, China.,Institute of Horticultural, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yanming Sun
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
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Genome-wide analysis of dirigent gene family in pepper (Capsicum annuum L.) and characterization of CaDIR7 in biotic and abiotic stresses. Sci Rep 2018; 8:5500. [PMID: 29615685 PMCID: PMC5883049 DOI: 10.1038/s41598-018-23761-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 03/19/2018] [Indexed: 11/22/2022] Open
Abstract
The dirigent (DIR and DIR-like) proteins involved in lignification, play a pivotal role against biotic and abiotic stresses in plants. However, no information is available about DIR gene family in pepper (Capsicum annuum L.). In this study, 24 putative dirigent genes (CaDIRs) were identified, their gene structure, genome location, gene duplication and phylogenetic relationship were elucidated. Tissue-specific expression analysis displayed the highest transcription levels in flower, stem and leaf. Some CaDIRs were up-regulated by virulent (CaDIR2, 3, 6, 7, 11, 14, 16, 22 and 23) and avirulent (CaDIR3, 5, 7, 16, 20, 22, 23 and 24) Phytophthora capsici strains, as well as by Methyl jasmonate, salicylic acid, NaCl and mannitol stresses. Acid-soluble lignin content increased (103.21%) after P. capsici inoculation (48-hour). Silencing of CaDIR7 weakened plant defense by reducing (~50%) root activity and made plants more susceptible (35.7%) to P. capsici and NaCl (300 mM). Leaf discs of the CaDIR7:silenced plants exposed to NaCl and mannitol (300 mM each), exhibited a significant decrease (56.25% and 48% respectively) in the chlorophyll content. These results suggested that CaDIR7 is involved in pepper defense response against pathogen and abiotic stresses and the study will provide basic insights for future research regarding CaDIRs.
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Behr M, Sergeant K, Leclercq CC, Planchon S, Guignard C, Lenouvel A, Renaut J, Hausman JF, Lutts S, Guerriero G. Insights into the molecular regulation of monolignol-derived product biosynthesis in the growing hemp hypocotyl. BMC PLANT BIOLOGY 2018; 18:1. [PMID: 29291729 PMCID: PMC5749015 DOI: 10.1186/s12870-017-1213-1] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/12/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Lignin and lignans are both derived from the monolignol pathway. Despite the similarity of their building blocks, they fulfil different functions in planta. Lignin strengthens the tissues of the plant, while lignans are involved in plant defence and growth regulation. Their biosyntheses are tuned both spatially and temporally to suit the development of the plant (water conduction, reaction to stresses). We propose to study the general molecular events related to monolignol-derived product biosynthesis, especially lignin. It was previously shown that the growing hemp hypocotyl (between 6 and 20 days after sowing) is a valid system to study secondary growth and the molecular events accompanying lignification. The present work confirms the validity of this system, by using it to study the regulation of lignin and lignan biosynthesis. Microscopic observations, lignin analysis, proteomics, together with in situ laccase and peroxidase activity assays were carried out to understand the dynamics of lignin synthesis during the development of the hemp hypocotyl. RESULTS Based on phylogenetic analysis and targeted gene expression, we suggest a role for the hemp dirigent and dirigent-like proteins in lignan biosynthesis. The transdisciplinary approach adopted resulted in the gene- and protein-level quantification of the main enzymes involved in the biosynthesis of monolignols and their oxidative coupling (laccases and class III peroxidases), in lignin deposition (dirigent-like proteins) and in the determination of the stereoconformation of lignans (dirigent proteins). CONCLUSIONS Our work sheds light on how, in the growing hemp hypocotyl, the provision of the precursors needed to synthesize the aromatic biomolecules lignin and lignans is regulated at the transcriptional and proteomic level.
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Affiliation(s)
- Marc Behr
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute - Agronomy (ELI-A), Université catholique de Louvain (UcL), 1348 Louvain-la-Neuve, Belgium
| | - Kjell Sergeant
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg
| | - Céline C. Leclercq
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg
| | - Sébastien Planchon
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg
| | - Cédric Guignard
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg
| | - Audrey Lenouvel
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg
| | - Jean-Francois Hausman
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg
| | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute - Agronomy (ELI-A), Université catholique de Louvain (UcL), 1348 Louvain-la-Neuve, Belgium
| | - Gea Guerriero
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4362 Esch/Alzette, Luxembourg
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Regente M, Pinedo M, San Clemente H, Balliau T, Jamet E, de la Canal L. Plant extracellular vesicles are incorporated by a fungal pathogen and inhibit its growth. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5485-5495. [PMID: 29145622 DOI: 10.1093/jxb/erx355] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Extracellular vesicles (EV) are membrane particles released by cells into their environment and are considered to be key players in intercellular communication. EV are produced by all domains of life but limited knowledge about EV in plants is available, although their implication in plant defense has been suggested. We have characterized sunflower EV and tested whether they could interact with fungal cells. EV were isolated from extracellular fluids of seedlings and characterized by transmission electron microscopy and proteomic analysis. These nanovesicles appeared to be enriched in cell wall remodeling enzymes and defense proteins. Membrane-labeled EV were prepared and their uptake by the phytopathogenic fungus Sclerotinia sclerotiorum was verified. Functional tests further evaluated the ability of EV to affect fungal growth. Spores treated with plant EV showed growth inhibition, morphological changes, and cell death. Conclusive evidence on the existence of plant EV is presented and we demonstrate their ability to interact with and kill fungal cells. Our results introduce the concept of cell-to-cell communication through EV in plants.
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Affiliation(s)
- Mariana Regente
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Funes 3250, 7600 Mar del Plata, Argentina
| | - Marcela Pinedo
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Funes 3250, 7600 Mar del Plata, Argentina
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP 42617, 31326 Castanet-Tolosan, France
| | - Thierry Balliau
- PAPPSO, GQE - Le Moulon, INRA, Université de Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP 42617, 31326 Castanet-Tolosan, France
| | - Laura de la Canal
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Funes 3250, 7600 Mar del Plata, Argentina
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49
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Corbin C, Drouet S, Mateljak I, Markulin L, Decourtil C, Renouard S, Lopez T, Doussot J, Lamblin F, Auguin D, Lainé E, Fuss E, Hano C. Functional characterization of the pinoresinol-lariciresinol reductase-2 gene reveals its roles in yatein biosynthesis and flax defense response. PLANTA 2017; 246:405-420. [PMID: 28451749 DOI: 10.1007/s00425-017-2701-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/20/2017] [Indexed: 05/23/2023]
Abstract
MAIN CONCLUSION This study provides new insights into the biosynthesis regulation and in planta function of the lignan yatein in flax leaves. Pinoresinol-lariciresinol reductases (PLR) catalyze the conversion of pinoresinol into secoisolariciresinol (SECO) in lignan biosynthesis. Several lignans are accumulated in high concentrations, such as SECO accumulated as secoisolariciresinol diglucoside (SDG) in seeds and yatein in aerial parts, in the flax plant (Linum usitatissimum L.) from which two PLR enzymes of opposite enantioselectivity have been isolated. While LuPLR1 catalyzes the biosynthesis of (+)-SECO leading to (+)-SDG in seeds, the role(s) of the second PLR (LuPLR2) is not completely elucidated. This study provides new insights into the in planta regulation and function of the lignan yatein in flax leaves: its biosynthesis relies on a different PLR with opposite stereospecificity but also on a distinct expression regulation. RNAi technology provided evidence for the in vivo involvement of the LuPLR2 gene in the biosynthesis of (-)-yatein accumulated in flax leaves. LuPLR2 expression in different tissues and in response to stress was studied by RT-qPCR and promoter-reporter transgenesis showing that the spatio-temporal expression of the LuPLR2 gene in leaves perfectly matches the (-)-yatein accumulation and that LuPLR2 expression and yatein production are increased by methyl jasmonate and wounding. A promoter deletion approach yielded putative regulatory elements. This expression pattern in relation to a possible role for this lignan in flax defense is discussed.
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Affiliation(s)
- Cyrielle Corbin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Ivan Mateljak
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Lucija Markulin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Cédric Decourtil
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Sullivan Renouard
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Tatiana Lopez
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Joël Doussot
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
- Ecole SITI, Département CASER, Le CNAM, Paris, France
| | - Frédéric Lamblin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Eric Lainé
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France
| | - Elisabeth Fuss
- Interfaculty Institute of Biochemistry, Hoppe-Seyler-St. 4, 72076, Tübingen, Germany
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRA USC1328, Université d'Orléans, 21 rue de Loigny la Bataille, 28000, Chartres, France.
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50
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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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