1
|
Cao X, Ding L, Liang J, Zhou Y, Chen X, Li H, Liu T, Yue W, Sui J, Jiang L, Qian Y, Yang D, Wang B, Zhang H, Wu Z, Song X. LzSCL9, a Novel GRAS Transcription Factor in Lanzhou Lily ( Lilium davidii var. unicolor), Participates in Regulation of Trichokonins-Primed Heat Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:2330. [PMID: 39204766 PMCID: PMC11359455 DOI: 10.3390/plants13162330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/13/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
In our previous research, we found that trichokonins' (TKs) employment improved the thermotolerance of the Lanzhou lily, a renowned edible crop species endemic to China that is relatively susceptible to high temperatures (HTs). Here, a novel Lanzhou lily GRAS gene, LzSCL9, was identified to respond to heat stress (HS) and HS+TKs treatment based on transcriptome and RT-qPCR analysis. TKs could improve the upregulation of LzSCL9 during long-term HS. The expression profile of LzSCL9 in response to HS with or without TKs treatment showed a significant positive correlation with LzHsfA2a-1, which was previously identified as a key regulator in TKs' conferred resilience to HT. More importantly, overexpression of LzSCL9 in the lily enhanced its tolerance to HTs and silencing LzSCL9 in the lily reduced heat resistance. Taken together, this study identified the positive role of LzSCL9 in TK-induced thermotolerance, thereby preliminarily establishing a molecular mechanism on TKs regulating the thermostability of the Lanzhou lily and providing a new candidate regulator for plant heat-resistant breeding.
Collapse
Affiliation(s)
- Xing Cao
- College of Architecture, Yantai University, Yantai 264005, China; (X.C.)
| | - Liping Ding
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiahui Liang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yanrong Zhou
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiulan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
| | - Haiyan Li
- College of Architecture, Yantai University, Yantai 264005, China; (X.C.)
| | - Tao Liu
- College of Architecture, Yantai University, Yantai 264005, China; (X.C.)
| | - Wenxiu Yue
- College of Architecture, Yantai University, Yantai 264005, China; (X.C.)
| | - Juanjuan Sui
- Engineering Technology Research Center of Anti-Aging Chinese Herbal Medicine, Biology and Food Engineering College, Fuyang Normal University, Fuyang 236037, China
| | - Liangbao Jiang
- College of Architecture, Yantai University, Yantai 264005, China; (X.C.)
| | - Yulian Qian
- College of Architecture, Yantai University, Yantai 264005, China; (X.C.)
| | - Dongdong Yang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Bo Wang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Hailing Zhang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Ze Wu
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
| |
Collapse
|
2
|
Song Z, Wang R, Zhang H, Tong Z, Yuan C, Li Y, Huang C, Zhao L, Wang Y, Di Y, Sui X. Comparative transcriptome analysis reveals nicotine metabolism is a critical component for enhancing stress response intensity of innate immunity system in tobacco. FRONTIERS IN PLANT SCIENCE 2024; 15:1338169. [PMID: 38595766 PMCID: PMC11003474 DOI: 10.3389/fpls.2024.1338169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/05/2024] [Indexed: 04/11/2024]
Abstract
The pyridine alkaloid nicotine acts as one of best-studied plant resistant traits in tobacco. Previous research has shown that NtERF199 and NtERF189, acting as master regulators within the NIC1 and NIC2 locus, quantitatively contribute to nicotine accumulation levels in N. tabacum. Genome editing-created Nic1(Nterf199) and Nic2 (Nterf189) double mutant provides an ideal platform for precisely dissecting the defensive role of nicotine and the connection between the nicotine biosynthetic pathway with other putative metabolic networks. Taking this advantage, we performed a comparative transcriptomic analysis to reevaluate the potential physiological and metabolic changes in response to nicotine synthesis defect by comparing the nic1nic2 and NIC1NIC2 plants. Our findings revealed that nicotine reduction could systematically diminishes the expression intensities of genes associated with stimulus perception, signal transduction and regulation, as well as secondary metabolic flux. Consequently, this global expression reduction might compromise tobacco adaptions to environmental fitness, herbivore resistances, and plant growth and development. The up-regulation of a novel set of stress-responsive and metabolic pathway genes might signify a newly established metabolic reprogramming to tradeoff the detrimental effect of nicotine loss. These results offer additional compelling evidence regarding nicotine's critical defensive role in nature and highlights the tight link between nicotine biosynthesis and gene expression levels of quantitative resistance-related genes for better environmental adaptation.
Collapse
Affiliation(s)
- Zhongbang Song
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Ruixue Wang
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hongbo Zhang
- Plant Functional Component Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Zhijun Tong
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Cheng Yuan
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Yong Li
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Changjun Huang
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Lu Zhao
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Yuehu Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yingtong Di
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xueyi Sui
- National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| |
Collapse
|
3
|
Neves C, Ribeiro B, Amaro R, Expósito J, Grimplet J, Fortes AM. Network of GRAS transcription factors in plant development, fruit ripening and stress responses. HORTICULTURE RESEARCH 2023; 10:uhad220. [PMID: 38077496 PMCID: PMC10699852 DOI: 10.1093/hr/uhad220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/20/2023] [Indexed: 06/23/2024]
Abstract
The plant-specific family of GRAS transcription factors has been wide implicated in the regulation of transcriptional reprogramming associated with a diversity of biological functions ranging from plant development processes to stress responses. Functional analyses of GRAS transcription factors supported by in silico structural and comparative analyses are emerging and clarifying the regulatory networks associated with their biological roles. In this review, a detailed analysis of GRAS proteins' structure and biochemical features as revealed by recent discoveries indicated how these characteristics may impact subcellular location, molecular mechanisms, and function. Nomenclature issues associated with GRAS classification into different subfamilies in diverse plant species even in the presence of robust genomic resources are discussed, in particular how it affects assumptions of biological function. Insights into the mechanisms driving evolution of this gene family and how genetic and epigenetic regulation of GRAS contributes to subfunctionalization are provided. Finally, this review debates challenges and future perspectives on the application of this complex but promising gene family for crop improvement to cope with challenges of environmental transition.
Collapse
Affiliation(s)
- Catarina Neves
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Beatriz Ribeiro
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Rute Amaro
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Jesús Expósito
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Jérôme Grimplet
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Departamento de Ciencia Vegetal, Gobierno de Aragón, Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón—IA2 (CITA-Universidad de Zaragoza), Calle Miguel Servet 177, 50013 Zaragoza, Spain
| | - Ana Margarida Fortes
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| |
Collapse
|
4
|
Zhao X, Liu DK, Wang QQ, Ke S, Li Y, Zhang D, Zheng Q, Zhang C, Liu ZJ, Lan S. Genome-wide identification and expression analysis of the GRAS gene family in Dendrobium chrysotoxum. FRONTIERS IN PLANT SCIENCE 2022; 13:1058287. [PMID: 36518517 PMCID: PMC9742484 DOI: 10.3389/fpls.2022.1058287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
The GRAS gene family encodes transcription factors that participate in plant growth and development phases. They are crucial in regulating light signal transduction, plant hormone (e.g. gibberellin) signaling, meristem growth, root radial development, response to abiotic stress, etc. However, little is known about the features and functions of GRAS genes in Orchidaceae, the largest and most diverse angiosperm lineage. In this study, genome-wide analysis of the GRAS gene family was conducted in Dendrobium chrysotoxum (Epidendroideae, Orchidaceae) to investigate its physicochemical properties, phylogenetic relationships, gene structure, and expression patterns under abiotic stress in orchids. Forty-six DchGRAS genes were identified from the D. chrysotoxum genome and divided into ten subfamilies according to their phylogenetic relationships. Sequence analysis showed that most DchGRAS proteins contained conserved VHIID and SAW domains. Gene structure analysis showed that intronless genes accounted for approximately 70% of the DchGRAS genes, the gene structures of the same subfamily were the same, and the conserved motifs were also similar. The Ka/Ks ratios of 12 pairs of DchGRAS genes were all less than 1, indicating that DchGRAS genes underwent negative selection. The results of cis-acting element analysis showed that the 46 DchGRAS genes contained a large number of hormone-regulated and light-responsive elements as well as environmental stress-related elements. In addition, the real-time reverse transcription quantitative PCR (RT-qPCR) experimental results showed significant differences in the expression levels of 12 genes under high temperature, drought and salt treatment, among which two members of the LISCL subfamily (DchGRAS13 and DchGRAS15) were most sensitive to stress. Taken together, this paper provides insights into the regulatory roles of the GRAS gene family in orchids.
Collapse
Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian-Qian Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijie Ke
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
5
|
Jaiswal V, Kakkar M, Kumari P, Zinta G, Gahlaut V, Kumar S. Multifaceted Roles of GRAS Transcription Factors in Growth and Stress Responses in Plants. iScience 2022; 25:105026. [PMID: 36117995 PMCID: PMC9474926 DOI: 10.1016/j.isci.2022.105026] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Vandana Jaiswal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mrinalini Kakkar
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Priya Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Corresponding author
| | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
- Corresponding author
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| |
Collapse
|
6
|
Waseem M, Nkurikiyimfura O, Niyitanga S, Jakada BH, Shaheen I, Aslam MM. GRAS transcription factors emerging regulator in plants growth, development, and multiple stresses. Mol Biol Rep 2022; 49:9673-9685. [PMID: 35713799 DOI: 10.1007/s11033-022-07425-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/23/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
GRAS transcription factors play multifunctional roles in plant growth, development, and resistance to various biotic and abiotic stresses. The structural and functional features of GRAS TFs have been unveiled in the last two decades. A typical GRAS protein contained a C-terminal GRAS domain with a highly variable N-terminal region. Studies on these TFs increase in numbers and are reported to be involved in various important developmental processes such as flowering, root formation, and stress responses. The GRAS TFs and hormone signaling crosstalk can be implicated in plant development and to stress responses. There are relatively few reports about GRAS TFs roles in plants, and no related reviews have been published. In this review, we summarized the features of GRAS TFs, their targets, and the roles these GRAS TFs playing in plant development and multiple stresses.
Collapse
Affiliation(s)
- Muhammad Waseem
- Department of Botany, University of Narowal, Narowal, Punjab, Pakistan. .,College of Life Science, Hainan University, Hainan, P.R. China.
| | - Oswald Nkurikiyimfura
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Sylvain Niyitanga
- Department of Plant Pathology, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Bello Hassan Jakada
- College of Life Science, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Iffat Shaheen
- Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | | |
Collapse
|
7
|
Song Y, Ma B, Guo Q, Zhou L, Lv C, Liu X, Wang J, Zhou X, Zhang C. UV-B induces the expression of flavonoid biosynthetic pathways in blueberry ( Vaccinium corymbosum) calli. FRONTIERS IN PLANT SCIENCE 2022; 13:1079087. [PMID: 36483950 PMCID: PMC9722975 DOI: 10.3389/fpls.2022.1079087] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 05/20/2023]
Abstract
Ultraviolet-B (UV-B) radiation is an environmental signal that affects the accumulation of secondary metabolites in plants. In particular, UV-B promotes flavonoid biosynthesis, leading to improved fruit quality. To explore the underlying molecular mechanism, we exposed blueberry (Vaccinium corymbosum) calli to UV-B radiation and performed a transcriptome deep sequencing (RNA-seq) analysis to identify differentially expressed genes (DEGs). We detected 16,899 DEGs among different treatments, with the largest number seen after 24 h of UV-B exposure relative to controls. Functional annotation and enrichment analysis showed a significant enrichment for DEGs in pathways related to plant hormone signal transduction and phenylpropanoid and flavonoid biosynthesis. In agreement with the transcriptome data, flavonol, anthocyanin and proanthocyanidin accumulated upon UV-B radiation, and most DEGs mapping to the phenylpropanoid and flavonoid biosynthetic pathways using the KEGG mapper tool were upregulated under UV-B radiation. We also performed a weighted gene co-expression network analysis (WGCNA) to explore the relationship among genes involved in plant hormone signal transduction, encoding transcription factors or participating in flavonoid biosynthesis. The transcription factors VcMYBPA1, MYBPA2.1, MYB114, MYBA2, MYBF, and MYB102 are likely activators, whereas MYB20, VcMYB14, MYB44, and VcMYB4a are inhibitors of the flavonoid biosynthetic pathway, as evidenced by the direction of correlation between the expression of these MYBs and flavonoid biosynthesis-related genes. The transcription factors bHLH74 and bHLH25 might interact with MYB repressors or directly inhibited the expression of flavonoid biosynthetic genes to control flavonoid accumulation. We also observed the downregulation of several genes belonging to the auxin, gibberellin and brassinosteroid biosynthetic pathways, suggesting that MYB inhibitors or activators are directly or indirectly regulated to promote flavonoid biosynthesis under UV-B radiation.
Collapse
|
8
|
Zhu X, Wang B, Wei X. Genome wide identification and expression pattern analysis of the GRAS family in quinoa. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:948-962. [PMID: 34092279 DOI: 10.1071/fp21017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
GRAS, a key transcription factor in plant growth and development, has not yet been reported in quinoa. Therefore, this study used the latest quinoa genomic data to identify and analyse GRAS genes in quinoa: 52 GRAS genes were identified in quinoa, these being unevenly distributed on 19 chromosomes. Fragment duplication and tandem duplication events were the main reasons for the expansion of the GRAS gene family in quinoa. Protein sequence analysis showed that there were some differences in amino acid numbers and isoelectric points amongst different subfamilies, and the main secondary structures were α-helix and random coil. The CqGRAS gene was divided into 14 subfamilies based on results from phylogenetic analysis. The genes located in the same subfamily had similar gene structures, conserved motifs, and three-level models. Promoter region analysis showed that the GRAS family genes contained multiple homeostasis elements that responded to hormones and adversity. GO enrichment indicated that CqGRAS genes were involved in biological processes, cell components, and molecular functions. By analysing the expression of CqGRAS genes in different tissues and different treatments, it was found that GRAS genes had obvious differential expression in different tissues and stress, which indicates that GRAS genes had tissue or organ expression specificity and thus might play an important role in response to stress. These results laid a foundation for further functional research on the GRAS gene family in quinoa.
Collapse
Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; and Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Baoqiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; and Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; and Corresponding author.
| |
Collapse
|
9
|
Shukla PS, Borza T, Critchley AT, Prithiviraj B. Seaweed-Based Compounds and Products for Sustainable Protection against Plant Pathogens. Mar Drugs 2021; 19:59. [PMID: 33504049 PMCID: PMC7911005 DOI: 10.3390/md19020059] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Sustainable agricultural practices increasingly demand novel, environmentally friendly compounds which induce plant immunity against pathogens. Stimulating plant immunity using seaweed extracts is a highly viable strategy, as these formulations contain many bio-elicitors (phyco-elicitors) which can significantly boost natural plant immunity. Certain bioactive elicitors present in a multitude of extracts of seaweeds (both commercially available and bench-scale laboratory formulations) activate pathogen-associated molecular patterns (PAMPs) due to their structural similarity (i.e., analogous structure) with pathogen-derived molecules. This is achieved via the priming and/or elicitation of the defense responses of the induced systemic resistance (ISR) and systemic acquired resistance (SAR) pathways. Knowledge accumulated over the past few decades is reviewed here, aiming to explain why certain seaweed-derived bioactives have such tremendous potential to elicit plant defense responses with considerable economic significance, particularly with increasing biotic stress impacts due to climate change and the concomitant move to sustainable agriculture and away from synthetic chemistry and environmental damage. Various extracts of seaweeds display remarkably different modes of action(s) which can manipulate the plant defense responses when applied. This review focuses on both the similarities and differences amongst the modes of actions of several different seaweed extracts, as well as their individual components. Novel biotechnological approaches for the development of new commercial products for crop protection, in a sustainable manner, are also suggested.
Collapse
Affiliation(s)
- Pushp Sheel Shukla
- Marine Bio-Products Research Laboratory, Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N5E3, Canada; (P.S.S.); (T.B.)
| | - Tudor Borza
- Marine Bio-Products Research Laboratory, Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N5E3, Canada; (P.S.S.); (T.B.)
| | - Alan T. Critchley
- Verschuren Centre for Sustainability in Energy and Environment, Cape Breton University, Sydney, NS B1M1A2, Canada;
| | - Balakrishnan Prithiviraj
- Marine Bio-Products Research Laboratory, Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N5E3, Canada; (P.S.S.); (T.B.)
| |
Collapse
|
10
|
CRISPR/Cas9 Directed Mutagenesis of OsGA20ox2 in High Yielding Basmati Rice ( Oryza sativa L.) Line and Comparative Proteome Profiling of Unveiled Changes Triggered by Mutations. Int J Mol Sci 2020; 21:ijms21176170. [PMID: 32859098 PMCID: PMC7504442 DOI: 10.3390/ijms21176170] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 01/29/2023] Open
Abstract
In rice, semi-dwarfism is among the most required characteristics, as it facilitates better yields and offers lodging resistance. Here, semi-dwarf rice lines lacking any residual transgene-DNA and off-target effects were generated through CRISPR/Cas9-guided mutagenesis of the OsGA20ox2 gene in a high yielding Basmati rice line, and the isobaric tags for relative and absolute quantification (iTRAQ) strategy was utilized to elucidate the proteomic changes in mutants. The results indicated the reduced gibberellins (GA1 and GA4) levels, plant height (28.72%), and flag leaf length, while all the other traits remained unchanged. The OsGA20ox2 expression was highly suppressed, and the mutants exhibited decreased cell length, width, and restored their plant height by exogenous GA3 treatment. Comparative proteomics of the wild-type and homozygous mutant line (GXU43_9) showed an altered level of 588 proteins, 273 upregulated and 315 downregulated, respectively. The identified differentially expressed proteins (DEPs) were mainly enriched in the carbon metabolism and fixation, glycolysis/gluconeogenesis, photosynthesis, and oxidative phosphorylation pathways. The proteins (Q6AWY7, Q6AWY2, Q9FRG8, Q6EPP9, Q6AWX8) associated with growth-regulating factors (GRF2, GRF7, GRF9, GRF10, and GRF11) and GA (Q8RZ73, Q9AS97, Q69VG1, Q8LNJ6, Q0JH50, and Q5MQ85) were downregulated, while the abscisic stress-ripening protein 5 (ASR5) and abscisic acid receptor (PYL5) were upregulated in mutant lines. We integrated CRISPR/Cas9 with proteomic screening as the most reliable strategy for rapid assessment of the CRISPR experiments outcomes.
Collapse
|
11
|
Lu X, Liu W, Xiang C, Li X, Wang Q, Wang T, Liu Z, Zhang J, Gao L, Zhang W. Genome-Wide Characterization of GRAS Family and Their Potential Roles in Cold Tolerance of Cucumber ( Cucumis sativus L.). Int J Mol Sci 2020; 21:E3857. [PMID: 32485801 PMCID: PMC7312588 DOI: 10.3390/ijms21113857] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/24/2022] Open
Abstract
Cucumber (Cucumis sativus L.) is one of the most important cucurbit vegetables but is often subjected to stress during cultivation. GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) genes encode a family of transcriptional factors that regulate plant growth and development. In the model plant Arabidopsis thaliana, GRAS family genes function in formation of axillary meristem and root radial structure, phytohormone (gibberellin) signal transduction, light signal transduction and abiotic/biological stress. In this study, a gene family was comprehensively analyzed from the aspects of evolutionary tree, gene structure, chromosome location, evolutionary and expression pattern by means of bioinformatics; 37 GRAS gene family members have been screened from cucumber. We reconstructed an evolutionary tree based on multiple sequence alignment of the typical GRAS domain and conserved motif sequences with those of other species (A. thaliana and Solanum lycopersicum). Cucumber GRAS family was divided into 10 groups according to the classification of Arabidopsis and tomato genes. We conclude that tandem and segmental duplication have played important roles in the expansion and evolution of the cucumber GRAS (CsaGRAS) family. Expression patterns of CsaGRAS genes in different tissues and under cold treatment, combined with gene ontology annotation and interaction network analysis, revealed potentially different functions for CsaGRAS genes in response to cold tolerance, with members of the SHR, SCR and DELLA subfamilies likely playing important roles. In conclusion, this study provides valuable information and candidate genes for improving cucumber tolerance to cold stress.
Collapse
Affiliation(s)
- Xiaohong Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Wenqian Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Chenggang Xiang
- College of Life Science and Technology, HongHe University, Mengzi 661100, China;
| | - Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Qing Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Tao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Zixi Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Jiali Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China; (X.L.); (W.L.); (X.L.); (Q.W.); (T.W.); (Z.L.); (J.Z.); (L.G.)
| |
Collapse
|
12
|
Ferrero-Serrano Á, Cantos C, Assmann SM. The Role of Dwarfing Traits in Historical and Modern Agriculture with a Focus on Rice. Cold Spring Harb Perspect Biol 2019; 11:a034645. [PMID: 31358515 PMCID: PMC6824242 DOI: 10.1101/cshperspect.a034645] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Semidwarf stature is a valuable agronomic trait in grain crops that reduces lodging and increases harvest index. A fundamental advance during the 1960s Green Revolution was the introduction of semidwarf cultivars of rice and wheat. Essentially, all semidwarf varieties of rice under cultivation today owe their diminished stature to a specific null mutation in the gibberellic acid (GA) biosynthesis gene, SD1 However, it is now well-established that, in addition to GAs, brassinosteroids and strigolactones also control plant height. In this review, we describe the synthesis and signaling pathways of these three hormones as understood in rice and discuss the mutants and transgenics in these pathways that confer semidwarfism and other valuable architectural traits. We propose that such genes offer underexploited opportunities for broadening the genetic basis and germplasm in semidwarf rice breeding.
Collapse
Affiliation(s)
| | - Christian Cantos
- Biology Department, Penn State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
13
|
Genome-wide identification, phylogeny and function analysis of GRAS gene family in Dendrobium catenatum (Orchidaceae). Gene 2019; 705:5-15. [PMID: 30999026 DOI: 10.1016/j.gene.2019.04.038] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/20/2019] [Accepted: 04/15/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND In recent years, the molecular mechanism of plant growth and development has been reported in detail. GRAS genes, a plant-specific family of transcription factor, play critical roles in the process. GRAS transcription factors are associated with axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic or biotic stress. OBJECTIVE Here, we firstly investigated GRAS gene family in Dendrobium catenatum, an important medicinal and flowering orchid in China. METHODS The GRAS gene family in D. catenatum was cloned based on RNA-Seq data. Selected GRAS genes were introduced into Escherichia coli to express proteins. RESULTS Based on phylogenetic relationship with the Arabidopsis and Oryza GRAS family members, 47 GRAS genes from D. catenatum are identified and their deduced proteins are classified into 11 subgroups. Most of these GRAS genes contain one exon and closely related members in the phylogenetic tree have similar motif composition. Our result also reveals that GRAS genes in D. catenatum are widely distributed and expressed in different tissue. In addition, 35 GRAS genes are successfully cloned from different subgroups and 7 DoGRAS fusion proteins are induced using E. coli system. Moreover, 8 genes were up-regulated in different tissue following exposure to heat and salt stresses. CONCLUSION Our findings provide valuable information and candidate genes for future functional analysis for improving the resistance of D. catenatum growth.
Collapse
|
14
|
Wang S, Zhang N, Zhu X, Yang J, Li S, Che Y, Liu W, Si H. Identification and expression analysis of StGRAS gene family in potato (Solanum tuberosum L.). Comput Biol Chem 2019; 80:195-205. [PMID: 30978571 DOI: 10.1016/j.compbiolchem.2019.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 03/21/2019] [Accepted: 03/24/2019] [Indexed: 12/25/2022]
Abstract
The GRAS gene family is a class of plant-specific transcription factors which play pivotal roles in the regulation of plant growth and development. At present, the GRAS gene family has been completely identified in Arabidopsis thaliana, however, there are no systematic research reports in potato. In the present study, we obtained an overview of the GRAS gene family including gene structure, gene expression, chromosome mapping and phylogenetic analysis, and 52 StGRASs were identified in the potato by bioinformatics analysis, which could be divided into eight subfamilies based on phylogeny. More than 90% of genes do not contain introns and the StGRAS family major function is protein binding according to gene ontology analysis (GO).The tissue specific expression analysis showed that StGRAS3, StGRAS35 and StGRAS50 gene had the higher expression in roots, stems and leaves compared with other StGRAS, StGRAS9 and StGRAS28 genes were responded to plant hormones IAA, ABA and GA3 treatment. The result could provide a basis for further studying the function of GRAS genes and GRAS-mediated signal transduction pathways in potato.
Collapse
Affiliation(s)
- Shulin Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Ning Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xi Zhu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangwei Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Shigui Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuzhang Che
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Weigang Liu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Huaijun Si
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China.
| |
Collapse
|
15
|
Gercke D, Regel EK, Singh R, Moerschbacher BM. Rational protein design of Bacillus sp. MN chitosanase for altered substrate binding and production of specific chitosan oligomers. J Biol Eng 2019; 13:23. [PMID: 30918529 PMCID: PMC6419424 DOI: 10.1186/s13036-019-0152-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/21/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Partially acetylated chito-oligosaccharides (paCOS) have a variety of potential applications in different fields, but to harness their benefits, pure paCOS or well-defined paCOS mixtures are essential. For example, if one could produce fully acetylated (A4) and fully deacetylated (D4) tetramers in abundance, all possible variants of tetrameric paCOS could be generated reliably from them. A promising approach for generating defined paCOS is by enzymatic depolymerization of chitosan polymers using chitosanases, since these enzymes' subsite specificities directly influence the composition of the paCOS produced; however, enzymatic production of e.g. D4 is challenging because the substrate is generally hydrolyzed further by most chitosanases. To overcome this, chitosanases could potentially be engineered so that upon hydrolyzing chitosan, they are unable to hydrolyze certain substrates, leaving well-defined oligomers intact in the hydrolysate. RESULTS For this purpose, we performed rational protein engineering on the extensively studied GH 8 chitosanase CSN from Bacillus sp. MN. By specifically targeting residues with a predicted function in substrate binding, we created new muteins incapable of efficiently hydrolyzing the fully deacetylated tetramer D4, and we were able to demonstrate efficient large-scale production of D4 with an altered version of CSN. Furthermore, we were able to uncover differences in the substrate positioning and subsite specificities of the muteins, which result in altered paCOS mixtures produced from partially acetylated chitosan polymers, with possibly altered bioactivities. CONCLUSION The value of protein engineering as a tool for the more efficient production of pure oligomers and potentially bioactive paCOS mixtures was demonstrated by the results and the suitability of specific muteins for the large-scale production of strictly defined, pure paCOS in a batch process was shown using the example of D4.
Collapse
Affiliation(s)
- David Gercke
- University of Muenster, Institute for Biology and Biotechnology of Plants, Schlossplatz 8, 48143 Münster, Germany
| | - Eva K. Regel
- University of Muenster, Institute for Biology and Biotechnology of Plants, Schlossplatz 8, 48143 Münster, Germany
| | - Ratna Singh
- University of Muenster, Institute for Biology and Biotechnology of Plants, Schlossplatz 8, 48143 Münster, Germany
| | - Bruno M. Moerschbacher
- University of Muenster, Institute for Biology and Biotechnology of Plants, Schlossplatz 8, 48143 Münster, Germany
| |
Collapse
|
16
|
Zhang H, Zhu S, Liu T, Wang C, Cheng Z, Zhang X, Chen L, Sheng P, Cai M, Li C, Wang J, Zhang Z, Chai J, Zhou L, Lei C, Guo X, Wang J, Wang J, Jiang L, Wu C, Wan J. DELAYED HEADING DATE1 interacts with OsHAP5C/D, delays flowering time and enhances yield in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:531-539. [PMID: 30107076 PMCID: PMC6335081 DOI: 10.1111/pbi.12996] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/13/2018] [Accepted: 07/23/2018] [Indexed: 05/03/2023]
Abstract
Heading date is an important agronomic trait affecting crop yield. The GRAS protein family is a plant-specific super family extensively involved in plant growth and signal transduction. However, GRAS proteins are rarely reported have a role in regulating rice heading date. Here, we report a GRAS protein DHD1 (Delayed Heading Date1) delays heading and enhances yield in rice. Biochemical assays showed DHD1 physically interacts with OsHAP5C/D both in vitro and in vivo. DHD1 and OsHAP5C/D located in the nucleus and showed that rhythmic expression. Both DHD1 and OsHAP5C/D affect heading date by regulating expression of Ehd1. We propose that DHD1 interacts with OsHAP5C/D to delay heading date by inhibiting expression of Ehd1.
Collapse
Affiliation(s)
- Huan Zhang
- National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Tianzhen Liu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Chunming Wang
- National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Liping Chen
- National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Peike Sheng
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Maohong Cai
- National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jiachang Wang
- National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Zhe Zhang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Juntao Chai
- National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Liang Zhou
- National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Ling Jiang
- National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Chuanyin Wu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jianmin Wan
- National Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| |
Collapse
|
17
|
Zhou S, Hu Z, Li F, Yu X, Naeem M, Zhang Y, Chen G. Manipulation of plant architecture and flowering time by down-regulation of the GRAS transcription factor SlGRAS26 in Solanum lycopersicum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:81-93. [PMID: 29650160 DOI: 10.1016/j.plantsci.2018.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 05/03/2023]
Abstract
Previous studies suggest that GRAS transcription factors act as essential regulators, not only in plant growth and development but also in response to biotic and abiotic stresses. Recently, 53 GRAS proteins have been identified, but only a few of them have been functionally studied in tomato. Here, we isolated a novel GRAS transcription factor SlGRAS26, its down-regulation generated pleiotropic phenotypes, including reduced plant height with more lateral shoots, internode length, leaf size, even leaflets, accelerated flowering transition and decreased trichome number. Transcription analysis showed that down-regulation of SlGRAS26 altered vegetative growth by suppressing gibberellin (GA) biosynthesis genes and activating the GA inactivating genes, thereby reducing endogenous GA content in transgenic plants. SlGRAS26 may regulate the initiation of lateral buds by regulating the expression of Blind (BL) and BRC1b. The earlier initiation of flower buds in transgenic lines may be controlled by significant up-regulation of SFT, CO1, SBP3, SBP13, and SBP15 genes, related to flowering time. These results demonstrate that SlGRAS26 may play a vital role in the initiation of lateral and inflorescence meristems in tomato.
Collapse
Affiliation(s)
- Shengen Zhou
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Fenfen Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Xiaohui Yu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Muhammad Naeem
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Yanjie Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, People's Republic of China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| |
Collapse
|
18
|
Wang YX, Liu ZW, Wu ZJ, Li H, Wang WL, Cui X, Zhuang J. Genome-wide identification and expression analysis of GRAS family transcription factors in tea plant (Camellia sinensis). Sci Rep 2018; 8:3949. [PMID: 29500448 PMCID: PMC5834537 DOI: 10.1038/s41598-018-22275-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 02/20/2018] [Indexed: 12/16/2022] Open
Abstract
GRAS proteins are important transcription factors that play multifarious roles in regulating the growth and development as well as stress responses of plants. Tea plant is an economically important leaf -type beverage crop. Information concerning GRAS family transcription factors in tea plant is insufficient. In this study, 52 CsGRAS genes encoding GRAS proteins were identified from tea plant genome database. Phylogenetic analysis of the identified GRAS proteins from tea plant, Arabidopsis, and rice divided these proteins into at least 13 subgroups. Conserved motif analysis revealed that the gene structure and motif compositions of the proteins were considerably conserved among the same subgroup. Functional divergence analysis indicated that the shifted evolutionary rate might act as a major evolutionary force driving subfamily-specific functional diversification. Transcriptome analysis showed that the transcriptional levels of CsGRAS genes under non-stress conditions varied among different tea plant cultivars. qRT-PCR analysis revealed tissue and development stage-specific expression patterns of CsGRAS genes in tea plant. The expression patterns of CsGRAS genes in response to abiotic stresses and gibberellin treatment suggested the possible multiple functions of these genes. This study provides insights into the potential functions of GRAS genes.
Collapse
Affiliation(s)
- Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Wei Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Jun Wu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wen-Li Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Cui
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
19
|
Li P, Zhang B, Su T, Li P, Xin X, Wang W, Zhao X, Yu Y, Zhang D, Yu S, Zhang F. BrLAS, a GRAS Transcription Factor From Brassica rapa, Is Involved in Drought Stress Tolerance in Transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1792. [PMID: 30574156 PMCID: PMC6291521 DOI: 10.3389/fpls.2018.01792] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/19/2018] [Indexed: 05/20/2023]
Abstract
GRAS proteins belong to a plant-specific transcription factor family and play roles in diverse physiological processes and environmental signals. In this study, we identified and characterized a GRAS transcription factor gene in Brassica rapa, BrLAS, an ortholog of Arabidopsis AtLAS. BrLAS was primarily expressed in the roots and axillary meristems, and localized exclusively in the nucleus of B. rapa protoplast cells. qRT-PCR analysis indicated that BrLAS was upregulated by exogenous abscisic acid (ABA) and abiotic stress treatment [polyethylene glycol (PEG), NaCl, and H2O2]. BrLAS-overexpressing Arabidopsis plants exhibited pleiotropic characteristics, including morphological changes, delayed bolting and flowering time, reduced fertility and delayed senescence. Transgenic plants also displayed significantly enhanced drought resistance with decreased accumulation of ROS and increased antioxidant enzyme activity under drought treatment compared with the wild-type. Increased sensitivity to exogenous ABA was also observed in the transgenic plants. qRT-PCR analysis further showed that expression of several genes involved in stress responses and associated with leaf senescence were also modified. These findings suggest that BrLAS encodes a stress-responsive GRASs transcription factor that positively regulates drought stress tolerance, suggesting a role in breeding programs aimed at improving drought tolerance in plants.
Collapse
Affiliation(s)
- Pan Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Bin Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- *Correspondence: Shuancang Yu, Fenglan Zhang,
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- *Correspondence: Shuancang Yu, Fenglan Zhang,
| |
Collapse
|
20
|
Niu Y, Zhao T, Xu X, Li J. Genome-wide identification and characterization of GRAS transcription factors in tomato ( Solanum lycopersicum). PeerJ 2017; 5:e3955. [PMID: 29134140 PMCID: PMC5681854 DOI: 10.7717/peerj.3955] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/03/2017] [Indexed: 11/20/2022] Open
Abstract
Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time. The GRAS genes among tomato, Arabidopsis, rice, and grapevine were rebuilt to form a phylogenomic tree, which was divided into ten groups according to the previous classification of Arabidopsis and rice. A multiple sequence alignment exhibited the typical GRAS domain and conserved motifs similar to other gene families. Both the segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in tomato; the expression patterns across a variety of tissues and biotic conditions revealed potentially different functions of GRAS genes in tomato development and stress responses. Altogether, this study provides valuable information and robust candidate genes for future functional analysis for improving the resistance of tomato growth.
Collapse
Affiliation(s)
- Yiling Niu
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Tingting Zhao
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Xiangyang Xu
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Jingfu Li
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| |
Collapse
|
21
|
Zhang H, Cao Y, Shang C, Li J, Wang J, Wu Z, Ma L, Qi T, Fu C, Bai Z, Hu B. Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification. PLoS One 2017; 12:e0185439. [PMID: 28945786 PMCID: PMC5612761 DOI: 10.1371/journal.pone.0185439] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/12/2017] [Indexed: 12/20/2022] Open
Abstract
The GRAS gene family is a large plant-specific family of transcription factors that are involved in diverse processes during plant development. Medicago truncatula is an ideal model plant for genetic research in legumes, and specifically for studying nodulation, which is crucial for nitrogen fixation. In this study, 59 MtGRAS genes were identified and classified into eight distinct subgroups based on phylogenetic relationships. Motifs located in the C-termini were conserved across the subgroups, while motifs in the N-termini were subfamily specific. Gene duplication was the main evolutionary force for MtGRAS expansion, especially proliferation of the LISCL subgroup. Seventeen duplicated genes showed strong effects of purifying selection and diverse expression patterns, highlighting their functional importance and diversification after duplication. Thirty MtGRAS genes, including NSP1 and NSP2, were preferentially expressed in nodules, indicating possible roles in the process of nodulation. A transcriptome study, combined with gene expression analysis under different stress conditions, suggested potential functions of MtGRAS genes in various biological pathways and stress responses. Taken together, these comprehensive analyses provide basic information for understanding the potential functions of GRAS genes, and will facilitate further discovery of MtGRAS gene functions.
Collapse
Affiliation(s)
- Hailing Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yingping Cao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chen Shang
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Jikai Li
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Jianli Wang
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Zhenying Wu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Lichao Ma
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Tianxiong Qi
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Zetao Bai
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- * E-mail: (ZB); (BH)
| | - Baozhong Hu
- College of Life Science, Northeast Agricultural University, Harbin, China
- Harbin University, Harbin, China
- * E-mail: (ZB); (BH)
| |
Collapse
|
22
|
Cenci A, Rouard M. Evolutionary Analyses of GRAS Transcription Factors in Angiosperms. FRONTIERS IN PLANT SCIENCE 2017; 8:273. [PMID: 28303145 PMCID: PMC5332381 DOI: 10.3389/fpls.2017.00273] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/14/2017] [Indexed: 05/21/2023]
Abstract
GRAS transcription factors (TFs) play critical roles in plant growth and development such as gibberellin and mycorrhizal signaling. Proteins belonging to this gene family contain a typical GRAS domain in the C-terminal sequence, whereas the N-terminal region is highly variable. Although, GRAS genes have been characterized in a number of plant species, their classification is still not completely resolved. Based on a panel of eight representative species of angiosperms, we identified 29 orthologous groups or orthogroups (OGs) for the GRAS gene family, suggesting that at least 29 ancestor genes were present in the angiosperm lineage before the "Amborella" evolutionary split. Interestingly, some taxonomic groups were missing members of one or more OGs. The gene number expansion usually observed in transcription factors was not observed in GRAS while the genome triplication ancestral to the eudicots (γ hexaploidization event) was detectable in a limited number of GRAS orthogroups. We also found conserved OG-specific motifs in the variable N-terminal region. Finally, we could regroup OGs in 17 subfamilies for which names were homogenized based on a literature review and described 5 new subfamilies (DLT, RAD1, RAM1, SCLA, and SCLB). This study establishes a consistent framework for the classification of GRAS members in angiosperm species, and thereby a tool to correctly establish the orthologous relationships of GRAS genes in most of the food crops in order to facilitate any subsequent functional analyses in the GRAS gene family. The multi-fasta file containing all the sequences used in our study could be used as database to perform diagnostic BLASTp to classify GRAS genes from other non-model species.
Collapse
Affiliation(s)
- Alberto Cenci
- Bioversity InternationalMontpellier, France
- CGIAR Research Programme on Roots, Tubers and BananasMontpellier, France
- *Correspondence: Alberto Cenci
| | - Mathieu Rouard
- Bioversity InternationalMontpellier, France
- CGIAR Research Programme on Roots, Tubers and BananasMontpellier, France
- Mathieu Rouard
| |
Collapse
|
23
|
Li K, Xing R, Liu S, Li P. Advances in preparation, analysis and biological activities of single chitooligosaccharides. Carbohydr Polym 2016; 139:178-90. [DOI: 10.1016/j.carbpol.2015.12.016] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/07/2015] [Indexed: 02/07/2023]
|
24
|
Grimplet J, Agudelo-Romero P, Teixeira RT, Martinez-Zapater JM, Fortes AM. Structural and Functional Analysis of the GRAS Gene Family in Grapevine Indicates a Role of GRAS Proteins in the Control of Development and Stress Responses. FRONTIERS IN PLANT SCIENCE 2016; 7:353. [PMID: 27065316 PMCID: PMC4811876 DOI: 10.3389/fpls.2016.00353] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/07/2016] [Indexed: 05/18/2023]
Abstract
GRAS transcription factors are involved in many processes of plant growth and development (e.g., axillary shoot meristem formation, root radial patterning, nodule morphogenesis, arbuscular development) as well as in plant disease resistance and abiotic stress responses. However, little information is available concerning this gene family in grapevine (Vitis vinifera L.), an economically important woody crop. We performed a model curation of GRAS genes identified in the latest genome annotation leading to the identification of 52 genes. Gene models were improved and three new genes were identified that could be grapevine- or woody-plant specific. Phylogenetic analysis showed that GRAS genes could be classified into 13 groups that mapped on the 19 V. vinifera chromosomes. Five new subfamilies, previously not characterized in other species, were identified. Multiple sequence alignment showed typical GRAS domain in the proteins and new motifs were also described. As observed in other species, both segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in grapevine. Expression patterns across a variety of tissues and upon abiotic and biotic conditions revealed possible divergent functions of GRAS genes in grapevine development and stress responses. By comparing the information available for tomato and grapevine GRAS genes, we identified candidate genes that might constitute conserved transcriptional regulators of both climacteric and non-climacteric fruit ripening. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming at improving the quality of fleshy fruits.
Collapse
Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | | | - Rita T. Teixeira
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
| | - Jose M. Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | - Ana M. Fortes
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
- Instituto de Tecnologia de Química Biológica, Biotecnologia de Células VegetaisOeiras, Portugal
- *Correspondence: Ana M. Fortes
| |
Collapse
|
25
|
Huang W, Xian Z, Kang X, Tang N, Li Z. Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato. BMC PLANT BIOLOGY 2015; 15:209. [PMID: 26302743 PMCID: PMC4549011 DOI: 10.1186/s12870-015-0590-6] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/11/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits. RESULTS In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated. CONCLUSIONS This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.
Collapse
Affiliation(s)
- Wei Huang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Zhiqiang Xian
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Xia Kang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Ning Tang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Zhengguo Li
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| |
Collapse
|
26
|
Rice osa-miR171c Mediates Phase Change from Vegetative to Reproductive Development and Shoot Apical Meristem Maintenance by Repressing Four OsHAM Transcription Factors. PLoS One 2015; 10:e0125833. [PMID: 26023934 PMCID: PMC4449180 DOI: 10.1371/journal.pone.0125833] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/25/2015] [Indexed: 12/20/2022] Open
Abstract
Phase change from vegetative to reproductive development is one of the critical developmental steps in plants, and it is regulated by both environmental and endogenous factors. The maintenance of shoot apical meristem (SAM) identity, miRNAs and flowering integrators are involved in this phase change process. Here, we report that the miRNA osa-miR171c targets four GRAS (GAI-RGA-SCR) plant-specific transcription factors (OsHAM1, OsHAM2, OsHAM3, and OsHAM4) to control the floral transition and maintenance of SAM indeterminacy in rice (Oryza sativa). We characterized a rice T-DNA insertion delayed heading (dh) mutant, where the expression of OsMIR171c gene is up-regulated. This mutant showed pleiotropic phenotypic defects, including especially prolonged vegetative phase, delayed heading date, and bigger shoot apex. Parallel expression analysis showed that osa-miR171c controlled the expression change of four OsHAMs in the shoot apex during floral transition, and responded to light. In the dh mutant, the expression of the juvenile-adult phase change negative regulator osa-miR156 was up-regulated, expression of the flowering integrators Hd3a and RFT1 was inhibited, and expression of FON4 negative regulators involved in the maintenance of SAM indeterminacy was also inhibited. From these data, we propose that the inhibition of osa-miR171c-mediated OsHAM transcription factors regulates the phase transition from vegetative to reproductive development by maintaining SAM indeterminacy and inhibiting flowering integrators.
Collapse
|
27
|
Thieulin-Pardo G, Avilan L, Kojadinovic M, Gontero B. Fairy "tails": flexibility and function of intrinsically disordered extensions in the photosynthetic world. Front Mol Biosci 2015; 2:23. [PMID: 26042223 PMCID: PMC4436894 DOI: 10.3389/fmolb.2015.00023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/04/2015] [Indexed: 12/22/2022] Open
Abstract
Intrinsically Disordered Proteins (IDPs), or protein fragments also called Intrinsically Disordered Regions (IDRs), display high flexibility as the result of their amino acid composition. They can adopt multiple roles. In globular proteins, IDRs are usually found as loops and linkers between secondary structure elements. However, not all disordered fragments are loops: some proteins bear an intrinsically disordered extension at their C- or N-terminus, and this flexibility can affect the protein as a whole. In this review, we focus on the disordered N- and C-terminal extensions of globular proteins from photosynthetic organisms. Using the examples of the A2B2-GAPDH and the α Rubisco activase isoform, we show that intrinsically disordered extensions can help regulate their “host” protein in response to changes in light, thereby participating in photosynthesis regulation. As IDPs are famous for their large number of protein partners, we used the examples of the NAC, bZIP, TCP, and GRAS transcription factor families to illustrate the fact that intrinsically disordered extremities can allow a protein to have an increased number of partners, which directly affects its regulation. Finally, for proteins from the cryptochrome light receptor family, we describe how a new role for the photolyase proteins may emerge by the addition of an intrinsically disordered extension, while still allowing the protein to absorb blue light. This review has highlighted the diverse repercussions of the disordered extension on the regulation and function of their host protein and outlined possible future research avenues.
Collapse
Affiliation(s)
- Gabriel Thieulin-Pardo
- UMR 7281, Centre National de la Recherche Scientifique, Aix-Marseille Université Marseille, France
| | - Luisana Avilan
- UMR 7281, Centre National de la Recherche Scientifique, Aix-Marseille Université Marseille, France
| | - Mila Kojadinovic
- UMR 7281, Centre National de la Recherche Scientifique, Aix-Marseille Université Marseille, France
| | - Brigitte Gontero
- UMR 7281, Centre National de la Recherche Scientifique, Aix-Marseille Université Marseille, France
| |
Collapse
|
28
|
Wang GL, Xiong F, Que F, Xu ZS, Wang F, Xiong AS. Morphological characteristics, anatomical structure, and gene expression: novel insights into gibberellin biosynthesis and perception during carrot growth and development. HORTICULTURE RESEARCH 2015; 2:15028. [PMID: 26504574 PMCID: PMC4595985 DOI: 10.1038/hortres.2015.28] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/23/2015] [Accepted: 05/24/2015] [Indexed: 05/08/2023]
Abstract
Gibberellins (GAs) are considered potentially important regulators of cell elongation and expansion in plants. Carrot undergoes significant alteration in organ size during its growth and development. However, the molecular mechanisms underlying gibberellin accumulation and perception during carrot growth and development remain unclear. In this study, five stages of carrot growth and development were investigated using morphological and anatomical structural techniques. Gibberellin levels in leaf, petiole, and taproot tissues were also investigated for all five stages. Gibberellin levels in the roots initially increased and then decreased, but these levels were lower than those in the petioles and leaves. Genes involved in gibberellin biosynthesis and signaling were identified from the carrotDB, and their expression was analyzed. All of the genes were evidently responsive to carrot growth and development, and some of them showed tissue-specific expression. The results suggested that gibberellin level may play a vital role in carrot elongation and expansion. The relative transcription levels of gibberellin pathway-related genes may be the main cause of the different bioactive GAs levels, thus exerting influences on gibberellin perception and signals. Carrot growth and development may be regulated by modification of the genes involved in gibberellin biosynthesis, catabolism, and perception.
Collapse
Affiliation(s)
- Guang-Long Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Xiong
- Key Laboratories of Crop Genetics and Physiology of the Jiangsu Province and Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Feng Que
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- ()
| |
Collapse
|
29
|
Abarca D, Pizarro A, Hernández I, Sánchez C, Solana SP, del Amo A, Carneros E, Díaz-Sala C. The GRAS gene family in pine: transcript expression patterns associated with the maturation-related decline of competence to form adventitious roots. BMC PLANT BIOLOGY 2014; 14:354. [PMID: 25547982 PMCID: PMC4302573 DOI: 10.1186/s12870-014-0354-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 11/27/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND Adventitious rooting is an organogenic process by which roots are induced from differentiated cells other than those specified to develop roots. In forest tree species, age and maturation are barriers to adventitious root formation by stem cuttings. The mechanisms behind the respecification of fully differentiated progenitor cells, which underlies adventitious root formation, are unknown. RESULTS Here, the GRAS gene family in pine is characterized and the expression of a subset of these genes during adventitious rooting is reported. Comparative analyses of protein structures showed that pine GRAS members are conserved compared with their relatives in angiosperms. Relatively high GRAS mRNA levels were measured in non-differentiated proliferating embryogenic cultures and during embryo development. The mRNA levels of putative GRAS family transcription factors, including Pinus radiata's SCARECROW (SCR), PrSCR, and SCARECROW-LIKE (SCL) 6, PrSCL6, were significantly reduced or non-existent in adult tissues that no longer had the capacity to form adventitious roots, but were maintained or induced after the reprogramming of adult cells in rooting-competent tissues. A subset of genes, SHORT-ROOT (PrSHR), PrSCL1, PrSCL2, PrSCL10 and PrSCL12, was also expressed in an auxin-, age- or developmental-dependent manner during adventitious root formation. CONCLUSIONS The GRAS family of pine has been characterized by analyzing protein structures, phylogenetic relationships, conserved motifs and gene expression patterns. Individual genes within each group have acquired different and specialized functions, some of which could be related to the competence and reprogramming of adult cells to form adventitious roots.
Collapse
Affiliation(s)
- Dolores Abarca
- />Department of Life Sciences, University of Alcalá, Ctra. de Barcelona Km 33.600, 28805 Alcalá de Henares, Madrid Spain
| | - Alberto Pizarro
- />Department of Life Sciences, University of Alcalá, Ctra. de Barcelona Km 33.600, 28805 Alcalá de Henares, Madrid Spain
| | - Inmaculada Hernández
- />Department of Life Sciences, University of Alcalá, Ctra. de Barcelona Km 33.600, 28805 Alcalá de Henares, Madrid Spain
| | - Conchi Sánchez
- />Department of Plant Physiology, Instituto de Investigaciones Agrobiológicas de Galicia (CSIC), Apartado 122, 15080 Santiago de Compostela, Spain
| | - Silvia P Solana
- />Department of Life Sciences, University of Alcalá, Ctra. de Barcelona Km 33.600, 28805 Alcalá de Henares, Madrid Spain
| | - Alicia del Amo
- />Department of Life Sciences, University of Alcalá, Ctra. de Barcelona Km 33.600, 28805 Alcalá de Henares, Madrid Spain
| | - Elena Carneros
- />Department of Life Sciences, University of Alcalá, Ctra. de Barcelona Km 33.600, 28805 Alcalá de Henares, Madrid Spain
| | - Carmen Díaz-Sala
- />Department of Life Sciences, University of Alcalá, Ctra. de Barcelona Km 33.600, 28805 Alcalá de Henares, Madrid Spain
| |
Collapse
|
30
|
Song XM, Liu TK, Duan WK, Ma QH, Ren J, Wang Z, Li Y, Hou XL. Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis). Genomics 2013; 103:135-46. [PMID: 24365788 DOI: 10.1016/j.ygeno.2013.12.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 11/08/2013] [Accepted: 12/16/2013] [Indexed: 12/23/2022]
Abstract
The GRAS gene family is one of the most important families of transcriptional regulators. In this study, 48 GRAS genes are identified from Chinese cabbage, and they are classified into eight groups according to the classification of Arabidopsis. The characterization, classification, gene structure and phylogenetic construction of GRAS proteins are performed. Distribution mapping shows that GRAS proteins are nonrandomly localized in 10 chromosomes. Fifty-five orthologous gene pairs are shared by Chinese cabbage and Arabidopsis, and interaction networks of these orthologous genes are constructed. The expansion of GRAS genes in Chinese cabbage results from genome triplication. Among the 17 species examined, 14 higher plants carry the GRAS genes, whereas two lower plants and one fungi species do not. Furthermore, the expression patterns of GRAS genes exhibit differences in three tissues based on RNA-seq data. Taken together, this comprehensive analysis will provide rich resources for studying GRAS protein functions in Chinese cabbage.
Collapse
Affiliation(s)
- Xiao-Ming Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tong-Kun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei-Ke Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing-Hua Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
31
|
Torres-Galea P, Hirtreiter B, Bolle C. Two GRAS proteins, SCARECROW-LIKE21 and PHYTOCHROME A SIGNAL TRANSDUCTION1, function cooperatively in phytochrome A signal transduction. PLANT PHYSIOLOGY 2013; 161:291-304. [PMID: 23109688 PMCID: PMC3532260 DOI: 10.1104/pp.112.206607] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Photoreceptors, especially the far-red light-absorbing phytochrome A, play a crucial role in early seedling development, triggering the transition from etiolated to photomorphogenic growth. Here, we describe the biological functions of two GRAS proteins from Arabidopsis (Arabidopsis thaliana), SCARECROW-LIKE21 (SCL21) and PHYTOCHROME A SIGNAL TRANSDUCTION1 (PAT1), which are specifically involved in phytochrome A signal transduction. Loss-of-function mutants show an elongated hypocotyl under far-red light and are impaired in other far-red high-irradiance responses. The SCL21 transcript itself is down-regulated by far-red light in a phytochrome A- and PAT1-dependent manner. Our results demonstrate that both SCL21 and PAT1 are positive regulators of phytochrome A signal transduction for several high-irradiance responses. Genetic and biochemical evidence suggest a direct interaction of the two proteins.
Collapse
|
32
|
GRAS proteins: the versatile roles of intrinsically disordered proteins in plant signalling. Biochem J 2012; 442:1-12. [PMID: 22280012 DOI: 10.1042/bj20111766] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
IDPs (intrinsically disordered proteins) are highly abundant in eukaryotic proteomes and important for cellular functions, especially in cell signalling and transcriptional regulation. An IDR (intrinsically disordered region) within an IDP often undergoes disorder-to-order transitions upon binding to various partners, allowing an IDP to recognize and bind different partners at various binding interfaces. Plant-specific GRAS proteins play critical and diverse roles in plant development and signalling, and act as integrators of signals from multiple plant growth regulatory and environmental inputs. Possessing an intrinsically disordered N-terminal domain, the GRAS proteins constitute the first functionally required unfoldome from the plant kingdom. Furthermore, the N-terminal domains of GRAS proteins contain MoRFs (molecular recognition features), short interaction-prone segments that are located within IDRs and are able to recognize their interacting partners by undergoing disorder-to-order transitions upon binding to these specific partners. These MoRFs represent potential protein-protein binding sites and may be acting as molecular bait in recognition events during plant development. Intrinsic disorder provides GRAS proteins with a degree of binding plasticity that may be linked to their functional versatility. As an overview of structure-function relationships for GRAS proteins, the present review covers the main biological functions of the GRAS family, the IDRs within these proteins and their implications for understanding mode-of-action.
Collapse
|
33
|
Kovi MR, Zhang Y, Yu S, Yang G, Yan W, Xing Y. Candidacy of a chitin-inducible gibberellin-responsive gene for a major locus affecting plant height in rice that is closely linked to Green Revolution gene sd1. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:705-14. [PMID: 21637999 DOI: 10.1007/s00122-011-1620-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 05/14/2011] [Indexed: 05/03/2023]
Abstract
Appropriate plant height is crucial for lodging resistance to improve the rice crop yield. The application of semi-dwarf 1 led to the green revolution in the 1960s, by predominantly increasing the rice yield. However, the frequent use of single sd1 gene sources may cause genetic vulnerability to pests and diseases. Identifying useful novel semi-dwarf genes is important for the genetic manipulation of plant architecture in practical rice breeding. In this study, introgression lines derived from two parents contrasting in plant height, Zhenshan 97 and Pokkali were employed to locate a gene with a large effect on plant height by the bulk segregant analysis method. A major gene, ph1, was mapped to a region closely linked to sd1 on chromosome 1; the additive effects of ph1 were more than 50 cm on the plant height and 2 days on the heading date in a BC(4)F(2) population and its progeny. ph1 was then fine mapped to BAC AP003227. Gene annotation indicated that LOC_OS01g65990 encoding a chitin-inducible gibberellin-responsive protein (CIGR), which belongs to the GRAS family, might be the right candidate gene of ph1. Co-segregation analysis of the candidate gene-derived marker finally confirmed its identity as the candidate gene. A higher expression level of the CIGR was detected in all the tested tissues in tall plants compared to those of short plants, especially in the young leaf sheath containing elongating tissues, which indicated its importance role in regulating plant height. ph1 showed a tremendous genetic effect on plant height, which is distinct from sd1 and could be a new resource for breeding semi-dwarf varieties.
Collapse
Affiliation(s)
- Mallikarjuna Rao Kovi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | | | | | | | | | | |
Collapse
|
34
|
Krugman T, Peleg Z, Quansah L, Chagué V, Korol AB, Nevo E, Saranga Y, Fait A, Chalhoub B, Fahima T. Alteration in expression of hormone-related genes in wild emmer wheat roots associated with drought adaptation mechanisms. Funct Integr Genomics 2011; 11:565-83. [PMID: 21656015 DOI: 10.1007/s10142-011-0231-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 05/03/2011] [Accepted: 05/05/2011] [Indexed: 12/27/2022]
Abstract
Transcriptomic and metabolomic profiles were used to unravel drought adaptation mechanisms in wild emmer wheat (Triticum turgidum ssp. dicoccoides), the progenitor of cultivated wheat, by comparing the response to drought stress in roots of genotypes contrasting in drought tolerance. The differences between the drought resistant (R) and drought susceptible (S) genotypes were characterized mainly by shifts in expression of hormone-related genes (e.g., gibberellins, abscisic acid (ABA) and auxin), including biosynthesis, signalling and response; RNA binding; calcium (calmodulin, caleosin and annexin) and phosphatidylinositol signalling, in the R genotype. ABA content in the roots of the R genotype was higher in the well-watered treatment and increased in response to drought, while in the S genotype ABA was invariant. The metabolomic profiling revealed in the R genotype a higher accumulation of tricarboxylic acid cycle intermediates and drought-related metabolites, including glucose, trehalose, proline and glycine. The integration of transcriptomics and metabolomics results indicated that adaptation to drought included efficient regulation and signalling pathways leading to effective bio-energetic processes, carbon metabolism and cell homeostasis. In conclusion, mechanisms of drought tolerance were identified in roots of wild emmer wheat, supporting our previous studies on the potential of this genepool as a valuable source for novel candidate genes to improve drought tolerance in cultivated wheat.
Collapse
Affiliation(s)
- Tamar Krugman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Mt. Carmel, Haifa, Israel
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Vergne E, Grand X, Ballini E, Chalvon V, Saindrenan P, Tharreau D, Nottéghem JL, Morel JB. Preformed expression of defense is a hallmark of partial resistance to rice blast fungal pathogen Magnaporthe oryzae. BMC PLANT BIOLOGY 2010; 10:206. [PMID: 20849575 PMCID: PMC2956555 DOI: 10.1186/1471-2229-10-206] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 09/17/2010] [Indexed: 05/09/2023]
Abstract
BACKGROUND Partial resistance to plant pathogens is extensively used in breeding programs since it could contribute to resistance durability. Partial resistance often builds up during plant development and confers quantitative and usually broad-spectrum resistance. However, very little is known on the mechanisms underlying partial resistance. Partial resistance is often explained by poorly effective induction of plant defense systems. By exploring rice natural diversity, we asked whether expression of defense systems before infection could explain partial resistance towards the major fungal pathogen Magnaporthe oryzae. The constitutive expression of 21 defense-related genes belonging to the defense system was monitored in 23 randomly sampled rice cultivars for which partial resistance was measured. RESULTS We identified a strong correlation between the expression of defense-related genes before infection and partial resistance. Only a weak correlation was found between the induction of defense genes and partial resistance. Increasing constitutive expression of defense-related genes also correlated with the establishment of partial resistance during plant development. Some rice genetic sub-groups displayed a particular pattern of constitutive expression, suggesting a strong natural polymorphism for constitutive expression of defense. Constitutive levels of hormones like salicylic acid and ethylene cannot explain constitutive expression of defense. We could identify an area of the genome that contributes to explain both preformed defense and partial resistance. CONCLUSION These results indicate that constitutive expression of defense-related genes is likely responsible for a large part of partial resistance in rice. The finding of this preformed defense system should help guide future breeding programs and open the possibility to identify the molecular mechanisms behind partial resistance.
Collapse
Affiliation(s)
- Emilie Vergne
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - Xavier Grand
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - Elsa Ballini
- Montpellier SUPAGRO, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - Véronique Chalvon
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - P Saindrenan
- CNRS-Université Paris-Sud, Institut de Biotechnologie des Plantes, Physiopathologie Moléculaire Végétale, Bâtiment 630, 91405 Orsay Cedex, France
| | - D Tharreau
- CIRAD, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - J-L Nottéghem
- Montpellier SUPAGRO, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| | - J-B Morel
- INRA, UMR BGPI INRA/CIRAD/SupAgro, Campus International de Baillarguet, TA A 54/K, 34398 Montpellier, France
| |
Collapse
|
36
|
Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley. Funct Integr Genomics 2010; 10:509-21. [PMID: 20464438 DOI: 10.1007/s10142-010-0173-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 04/04/2010] [Accepted: 04/20/2010] [Indexed: 10/19/2022]
Abstract
The barley mutant allele sdw3 confers a gibberellin-insensitive, semi-dwarf phenotype with potential for breeding of new semi-dwarfed barley cultivars. Towards map-based cloning, sdw3 was delimited by high-resolution genetic mapping to a 0.04 cM interval in a "cold spot" of recombination of the proximal region of the short arm of barley chromosome 2H. Extensive synteny between the barley Sdw3 locus (Hvu_sdw3) and the orthologous regions (Osa_sdw3, Sbi_sdw3, Bsy_sdw3) of three other grass species (Oryza sativa, Sorghum bicolor, Brachypodium sylvaticum) allowed for efficient synteny-based marker saturation in the target interval. Comparative sequence analysis revealed colinearity for 23 out of the 38, 35, and 29 genes identified in Brachypodium, rice, and Sorghum, respectively. Markers co-segregating with Hvu_sdw3 were generated from two of these genes. Initial attempts at chromosome walking in barley were performed with seven orthologous gene probes which were delimiting physical distances of 223, 123, and 127 kb in Brachypodium, rice, and Sorghum, respectively. Six non-overlapping small bacterial artificial chromosome (BAC) clone contigs (cumulative length of 670 kb) were obtained, which indicated a considerably larger physical size of Hvu_sdw3. Low-pass sequencing of selected BAC clones from these barley contigs exhibited a substantially lower gene frequency per physical distance and the presence of additional non-colinear genes. Four candidate genes for sdw3 were identified within barley BAC sequences that either co-segregated with the gene sdw3 or were located adjacent to these co-segregating genes. Identification of genic sequences in the sdw3 context provides tools for marker-assisted selection. Eventual identification of the actual gene will contribute new information for a basic understanding of the mechanisms underlying growth regulation in barley.
Collapse
|
37
|
Ulvan, a sulfated polysaccharide from green algae, activates plant immunity through the jasmonic acid signaling pathway. J Biomed Biotechnol 2010; 2010:525291. [PMID: 20445752 PMCID: PMC2860583 DOI: 10.1155/2010/525291] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 02/08/2010] [Indexed: 11/17/2022] Open
Abstract
The industrial use of elicitors as alternative tools for disease control needs the identification of abundant sources of them. We report on an elicitor obtained from the green algae Ulva spp. A fraction containing most exclusively the sulfated polysaccharide known as ulvan-induced expression of a GUS gene placed under the control of a lipoxygenase gene promoter. Gene expression profiling was performed upon ulvan treatments on Medicago truncatula and compared to phytohormone effects. Ulvan induced a gene expression signature similar to that observed upon methyl jasmonate treatment (MeJA). Involvement of jasmonic acid (JA) in ulvan response was confirmed by detecting induction of protease inhibitory activity and by hormonal profiling of JA, salicylic acid (SA) and abscisic acid (ABA). Ulvan activity on the hormonal pathway was further consolidated by using Arabidopsis hormonal mutants. Altogether, our results demonstrate that green algae are a potential reservoir of ulvan elicitor which acts through the JA pathway.
Collapse
|
38
|
El Hadrami A, Adam LR, El Hadrami I, Daayf F. Chitosan in plant protection. Mar Drugs 2010; 8:968-87. [PMID: 20479963 PMCID: PMC2866471 DOI: 10.3390/md8040968] [Citation(s) in RCA: 284] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 03/24/2010] [Accepted: 03/29/2010] [Indexed: 11/16/2022] Open
Abstract
Chitin and chitosan are naturally-occurring compounds that have potential in agriculture with regard to controlling plant diseases. These molecules were shown to display toxicity and inhibit fungal growth and development. They were reported to be active against viruses, bacteria and other pests. Fragments from chitin and chitosan are known to have eliciting activities leading to a variety of defense responses in host plants in response to microbial infections, including the accumulation of phytoalexins, pathogen-related (PR) proteins and proteinase inhibitors, lignin synthesis, and callose formation. Based on these and other proprieties that help strengthen host plant defenses, interest has been growing in using them in agricultural systems to reduce the negative impact of diseases on yield and quality of crops. This review recapitulates the properties and uses of chitin, chitosan, and their derivatives, and will focus on their applications and mechanisms of action during plant-pathogen interactions.
Collapse
Affiliation(s)
- Abdelbasset El Hadrami
- University of Manitoba, Department of Plant Science, 222, Agriculture Building, Winnipeg, Manitoba, R3T 2N2, Canada; E-Mail:
(A.E.);
(L.R.A.)
| | - Lorne R. Adam
- University of Manitoba, Department of Plant Science, 222, Agriculture Building, Winnipeg, Manitoba, R3T 2N2, Canada; E-Mail:
(A.E.);
(L.R.A.)
| | - Ismail El Hadrami
- Laboratoire de Biotechnologies, Protection et Valorisation des Ressources Végétales (Biotec-VRV), Faculté des Sciences Semlalia, B.P. 2390, 40 000, Marrakech, Morocco; E-Mail:
(I.E.)
| | - Fouad Daayf
- University of Manitoba, Department of Plant Science, 222, Agriculture Building, Winnipeg, Manitoba, R3T 2N2, Canada; E-Mail:
(A.E.);
(L.R.A.)
| |
Collapse
|
39
|
Li Y, Yin H, Wang Q, Zhao X, Du Y, Li F. Oligochitosan induced Brassica napus L. production of NO and H2O2 and their physiological function. Carbohydr Polym 2009. [DOI: 10.1016/j.carbpol.2008.09.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
40
|
Berrocal-Lobo M, Molina A. Arabidopsis defense response against Fusarium oxysporum. TRENDS IN PLANT SCIENCE 2008; 13:145-50. [PMID: 18289920 DOI: 10.1016/j.tplants.2007.12.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 12/11/2007] [Accepted: 12/17/2007] [Indexed: 05/07/2023]
Abstract
The plant fungal pathogen Fusarium oxysporum (Fox) is the causal agent of root rot or wilt diseases in several plant species, including crops such as tomato (Solanum lycopersicum), banana (Musa sapientum) and asparagus (Asparagus officinalis). Colonization of plants by Fox leads to the necrosis of the infected tissues, a subsequent collapse of vascular vessels and decay of the plant. Plant resistance to Fox appears to be monogenic or oligogenic depending on the host. Perception of Fox by plants follows the concept of elicitor-induced immune response, which in turn activates several plant defense signaling pathways. Here, we review the Fox-derived elicitors identified so far and the interaction among the different signaling pathways mediating plant resistance to Fox.
Collapse
Affiliation(s)
- Marta Berrocal-Lobo
- Centro de Biotecnología Genómica Plantas, ETSI Montes, Ciudad Universitaria s/n, 28040, Madrid, Spain.
| | | |
Collapse
|
41
|
Mallard S, Nègre S, Pouya S, Gaudet D, Lu ZX, Dedryver F. Adult plant resistance-related gene expression in 'Camp Remy' wheat inoculated with Puccinia striiformis. MOLECULAR PLANT PATHOLOGY 2008; 9:213-25. [PMID: 18705853 PMCID: PMC6640271 DOI: 10.1111/j.1364-3703.2007.00459.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The French wheat variety 'Camp Remy' (CR) possesses a durable, adult plant resistance to yellow rust (YR), caused by the pathogen Puccinia striiformis. Using cDNA-AFLP on different sets of heterogeneous inbred families (HIFs) derived from the cross CR x Récital, we compared gene expression profiles during one seedling and two adult developmental stages following inoculation with P. striiformis. Transcripts differentially expressed in response to YR infection were isolated and cloned. Sequence analysis of the resultant clones revealed several classes of putative genes, including those related to resistance/defence responses, transcription and signal transduction, and primary metabolism. The expression profiles of seven selected genes were obtained using real-time PCR in CR leaves at the same three stages of development. The results confirmed the stage-specific expression of the genes at one or two specific stages in response to P. striiformis infection and demonstrated that CR modifies the expression of some resistance/defence-related genes during its transition from the seedling to adult growth stages. These results provided the first clue to understand the molecular basis of quantitative trait loci for adult plant resistance to YR and connect it with durability.
Collapse
Affiliation(s)
- Stéphanie Mallard
- INRA, Agrocampus Rennes, UMR118, Amélioration des Plantes et Biotechnologies Végétales, 35650 Le Rheu, France
| | | | | | | | | | | |
Collapse
|
42
|
Libault M, Wan J, Czechowski T, Udvardi M, Stacey G. Identification of 118 Arabidopsis transcription factor and 30 ubiquitin-ligase genes responding to chitin, a plant-defense elicitor. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:900-11. [PMID: 17722694 DOI: 10.1094/mpmi-20-8-0900] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Chitin, found in the cell walls of true fungi and the exoskeleton of insects and nematodes, is a well-established elicitor of plant defense responses. In this study, we analyzed the expression patterns of Arabidopsis thaliana transcription factor (TF) and ubiquitin-ligase genes in response to purified chitooctaose at different treatment times (15, 30, 60, 90, and 120 min after treatment), using both quantitative polymerase chain reaction and the Affymetrix Arabidopsis whole-genome array. A total of 118 TF genes and 30 ubiquitin-ligase genes were responsive to the chitin treatment. Among these genes, members from the following four TF families were overrepresented: APETALA2/ethylene-reponsive element binding proteins (27), C2H2 zinc finger proteins (14), MYB domain-containing proteins (11), and WRKY domain transcription factors (14). Transcript variants from a few of these genes were found to respond differentially to chitin, suggesting transcript-specific regulation of these TF genes.
Collapse
Affiliation(s)
- Marc Libault
- National Center for Soybean Biotechnology, Division of Plant Science, Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | | | | | | | | |
Collapse
|
43
|
Tanabe S, Okada M, Jikumaru Y, Yamane H, Kaku H, Shibuya N, Minami E. Induction of resistance against rice blast fungus in rice plants treated with a potent elicitor, N-acetylchitooligosaccharide. Biosci Biotechnol Biochem 2006; 70:1599-605. [PMID: 16861793 DOI: 10.1271/bbb.50677] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The mode of action of a potent elicitor, N-acetylchitooligosaccharide, in rice plants was examined. In intact seedlings, no significant uptake of the elicitor via the roots was observed within 3 h, whereas rapid uptake was observed in excised leaves. Rapid and transient expression of an elicitor-responsive gene, EL2, was induced in the leaves of intact seedlings sprayed with the elicitor or in the roots and leaves of intact seedlings by immersing roots in the elicitor solution. Histochemical analysis indicated that EL2 was expressed in cells exposed to the elicitor of root and leaves. In seedlings treated with the elicitor for 1 d or longer, hyphal growth of rice blast fungus was significantly delayed, and an accumulation of auto-fluorescence around the infection site was observed. Two defense-related genes, PR-1 and PR-10 (PBZ1), were induced in a systemic and local manner by elicitor treatment, in correlation with the induction of resistance against rice blast fungus. N-Acetylchitoheptaose did not inhibit the hyphal growth of the fungi. These results indicate the occurrence of systemic signal transmission from N-acetylchitooligosaccharide in rice plants.
Collapse
Affiliation(s)
- Shigeru Tanabe
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | | | | | | | | | | | | |
Collapse
|
44
|
Kaku H, Nishizawa Y, Ishii-Minami N, Akimoto-Tomiyama C, Dohmae N, Takio K, Minami E, Shibuya N. Plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor. Proc Natl Acad Sci U S A 2006; 103:11086-91. [PMID: 16829581 PMCID: PMC1636686 DOI: 10.1073/pnas.0508882103] [Citation(s) in RCA: 729] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Indexed: 11/18/2022] Open
Abstract
Chitin is a major component of fungal cell walls and serves as a molecular pattern for the recognition of potential pathogens in the innate immune systems of both plants and animals. In plants, chitin oligosaccharides have been known to induce various defense responses in a wide range of plant cells including both monocots and dicots. To clarify the molecular machinery involved in the perception and transduction of chitin oligosaccharide elicitor, a high-affinity binding protein for this elicitor was isolated from the plasma membrane of suspension-cultured rice cells. Characterization of the purified protein, CEBiP, as well as the cloning of the corresponding gene revealed that CEBiP is actually a glycoprotein consisting of 328 amino acid residues and glycan chains. CEBiP was predicted to have a short membrane spanning domain at the C terminus. Knockdown of CEBiP gene by RNA interference resulted in the suppression of the elicitor-induced oxidative burst as well as the gene responses, showing that CEBiP plays a key role in the perception and transduction of chitin oligosaccharide elicitor in the rice cells. Structural analysis of CEBiP also indicated the presence of two LysM motifs in the extracellular portion of CEBiP. As the LysM motif has been known to exist in the putative Nod-factor receptor kinases involved in the symbiotic signaling between leguminous plants and rhizobial bacteria, the result indicates the involvement of partially homologous plasma membrane proteins both in defense and symbiotic signaling in plant cells.
Collapse
Affiliation(s)
- Hanae Kaku
- Department of Biochemistry, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Yamaguchi T, Minami E, Ueki J, Shibuya N. Elicitor-induced Activation of Phospholipases Plays an Important Role for the Induction of Defense Responses in Suspension-cultured Rice Cells. ACTA ACUST UNITED AC 2005; 46:579-87. [PMID: 15695430 DOI: 10.1093/pcp/pci065] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Biphasic generation of reactive oxygen species (ROS) induced by N-acetylchitooligosaccharide elicitor in rice cells was associated with the activation of phopholipase C (PLC) and phospholipase D (PLD). The activation of both enzymes was observed for the first phase of ROS generation, but only the activation of PLD was evident for the second response. Activation of PLD was associated with its recruitment to the membrane. Enzymatic products of these phospholipases, diacylglycerol (DG) and phosphatidic acid (PA), could induce ROS generation by themselves. Moreover, the addition of these lipids compensated the inhibition of the second phase of ROS generation by cycloheximide, indicating the involvement of the synthesis of PLD or related proteins in the second phase of ROS generation. DG and PA also induced the expression of elicitor-responsive genes in the absence of the elicitor. They could not induce phytoalexin biosynthesis by themselves but greatly enhanced the elicitor-induced phytoalexin accumulation. Further, the inhibition of PLD by 1-butanol inhibited the elicitor-induced phytoalexin accumulation, indicating the involvement of PLD and its reaction product, PA, in the induction of phytoalexin biosynthesis. These results indicated the importance of phospholipid signaling, especially by PLD and its product PA, in plant defense responses.
Collapse
Affiliation(s)
- Takeshi Yamaguchi
- Department of Rice Research, National Agricultural Research Center, National Agricultural Bio-oriented Research Organization, Joetsu, Niigata, 943-0193 Japan
| | | | | | | |
Collapse
|