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Zhou X, Zhong T, Wu M, Li Q, Yu W, Gan L, Xiang X, Zhang Y, Shi Y, Zhou Y, Chen P, Zhang C. Multiomics analysis of a resistant European turnip ECD04 during clubroot infection reveals key hub genes underlying resistance mechanism. FRONTIERS IN PLANT SCIENCE 2024; 15:1396602. [PMID: 38845850 PMCID: PMC11153729 DOI: 10.3389/fpls.2024.1396602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024]
Abstract
The clubroot disease has become a worldwide threat for crucifer crop production, due to its soil-borne nature and difficulty to eradicate completely from contaminated field. In this study we used an elite resistant European fodder turnip ECD04 and investigated its resistance mechanism using transcriptome, sRNA-seq, degradome and gene editing. A total of 1751 DEGs were identified from three time points after infection, among which 7 hub genes including XTH23 for cell wall assembly and two CPK28 genes in PTI pathways. On microRNA, we identified 17 DEMs and predicted 15 miRNA-target pairs (DEM-DEG). We validated two pairs (miR395-APS4 and miR160-ARF) by degradome sequencing. We investigated the miR395-APS4 pair by CRISPR-Cas9 mediated gene editing, the result showed that knocking-out APS4 could lead to elevated clubroot resistance in B. napus. In summary, the data acquired on transcriptional response and microRNA as well as target genes provide future direction especially gene candidates for genetic improvement of clubroot resistance on Brassica species.
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Affiliation(s)
- Xueqing Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ting Zhong
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meixiu Wu
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qian Li
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Wenlin Yu
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Longcai Gan
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianyu Xiang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yunyun Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yaru Shi
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuanwei Zhou
- Rice and Oil Research Institute, Yichang Academy of Agricultural Science, Yichang, China
| | - Peng Chen
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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2
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Del Corpo D, Coculo D, Greco M, De Lorenzo G, Lionetti V. Pull the fuzes: Processing protein precursors to generate apoplastic danger signals for triggering plant immunity. PLANT COMMUNICATIONS 2024:100931. [PMID: 38689495 DOI: 10.1016/j.xplc.2024.100931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/29/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
The apoplast is one of the first cellular compartments outside the plasma membrane encountered by phytopathogenic microbes in the early stages of plant tissue invasion. Plants have developed sophisticated surveillance mechanisms to sense danger events at the cell surface and promptly activate immunity. However, a fine tuning of the activation of immune pathways is necessary to mount a robust and effective defense response. Several endogenous proteins and enzymes are synthesized as inactive precursors, and their post-translational processing has emerged as a critical mechanism for triggering alarms in the apoplast. In this review, we focus on the precursors of phytocytokines, cell wall remodeling enzymes, and proteases. The physiological events that convert inactive precursors into immunomodulatory active peptides or enzymes are described. This review also explores the functional synergies among phytocytokines, cell wall damage-associated molecular patterns, and remodeling, highlighting their roles in boosting extracellular immunity and reinforcing defenses against pests.
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Affiliation(s)
- Daniele Del Corpo
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Daniele Coculo
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Marco Greco
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Giulia De Lorenzo
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Vincenzo Lionetti
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy.
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3
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Tan W, Nian H, Tran LSP, Jin J, Lian T. Small peptides: novel targets for modulating plant-rhizosphere microbe interactions. Trends Microbiol 2024:S0966-842X(24)00085-4. [PMID: 38670883 DOI: 10.1016/j.tim.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The crucial role of rhizosphere microbes in plant growth and their resilience to environmental stresses underscores the intricate communication between microbes and plants. Plants are equipped with a diverse set of signaling molecules that facilitate communication across different biological kingdoms, although our comprehension of these mechanisms is still evolving. Small peptides produced by plants (SPPs) and microbes (SPMs) play a pivotal role in intracellular signaling and are essential in orchestrating various plant development stages. In this review, we posit that SPPs and SPMs serve as crucial signaling agents for the bidirectional cross-kingdom communication between plants and rhizosphere microbes. We explore several potential mechanistic pathways through which this communication occurs. Additionally, we propose that leveraging small peptides, inspired by plant-rhizosphere microbe interactions, represents an innovative approach in the field of holobiont engineering.
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Affiliation(s)
- Weiyi Tan
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA.
| | - Jing Jin
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.
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4
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Asadi M, Millar AA. Review: Plant microRNAs in pathogen defense: A panacea or a piece of the puzzle? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111993. [PMID: 38266718 DOI: 10.1016/j.plantsci.2024.111993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Plant microRNAs (miRNAs) control key agronomic traits that are associated with their conserved role(s) in development. However, despite a multitude of studies, the utility of miRNAs in plant-pathogen resistance remains less certain. Reviewing the literature identifies three general classes of miRNAs regarding plant pathogen defense. Firstly, a number of evolutionary dynamic 22 nucleotide miRNA families that repress large numbers of plant immunity genes, either directly, or through triggering the biogenesis of secondary siRNAs. However, understanding of their role in defense and of their manipulation to enhance pathogen resistance are still lacking. Secondly, highly conserved miRNAs that indirectly impact disease resistance through their targets that are primarily regulating development or hormone signaling. Any alteration of these miRNAs usually results in pleiotropic impacts, which may alter disease resistance in some plant species, and against some pathogens. Thirdly, are the comparatively diverse and evolutionary dynamic set of non-conserved miRNAs, some of which contribute to pathogen resistance, but whose narrow evolutionary presence will likely restrict their utility. Therefore, reflecting the diverse and evolving nature of plant-pathogen interactions, a complex interplay of plant miRNAs with pathogen responses exists. Any miRNA-based solution for pathogen resistance will likely be highly specific, rather than a general panacea.
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Affiliation(s)
- Mohsen Asadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran; Department of Agricultural Science, Technical and Vocational University (TVU), Tehran, Iran
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australia; ARC Training Centre for Accelerated Future Crop development, ANU, Canberra, Australia.
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5
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Bashyal S, Gautam CK, Müller LM. CLAVATA signaling in plant-environment interactions. PLANT PHYSIOLOGY 2024; 194:1336-1357. [PMID: 37930810 PMCID: PMC10904329 DOI: 10.1093/plphys/kiad591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Plants must rapidly and dynamically adapt to changes in their environment. Upon sensing environmental signals, plants convert them into cellular signals, which elicit physiological or developmental changes that allow them to respond to various abiotic and biotic cues. Because plants can be simultaneously exposed to multiple environmental cues, signal integration between plant cells, tissues, and organs is necessary to induce specific responses. Recently, CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides and their cognate CLAVATA-type receptors received increased attention for their roles in plant-environment interactions. CLE peptides are mobile signaling molecules, many of which are induced by a variety of biotic and abiotic stimuli. Secreted CLE peptides are perceived by receptor complexes on the surface of their target cells, which often include the leucine-rich repeat receptor-like kinase CLAVATA1. Receptor activation then results in cell-type and/or environment-specific responses. This review summarizes our current understanding of the diverse roles of environment-regulated CLE peptides in modulating plant responses to environmental cues. We highlight how CLE signals regulate plant physiology by fine-tuning plant-microbe interactions, nutrient homeostasis, and carbon allocation. Finally, we describe the role of CLAVATA receptors in the perception of environment-induced CLE signals and discuss how diverse CLE-CLAVATA signaling modules may integrate environmental signals with plant physiology and development.
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Affiliation(s)
- Sagar Bashyal
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | | | - Lena Maria Müller
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
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6
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Si X, Liu H, Cheng X, Xu C, Han Z, Dai Z, Wang R, Pan C, Lu G. Integrative transcriptomic analysis unveils lncRNA-miRNA-mRNA interplay in tomato plants responding to Ralstonia solanacearum. Int J Biol Macromol 2023; 253:126891. [PMID: 37709224 DOI: 10.1016/j.ijbiomac.2023.126891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/26/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Ralstonia solanacearum, a bacterial plant pathogen, poses a significant threat to tomato (Solanum lycopersicum) production through destructive wilt disease. While noncoding RNA has emerged as a crucial regulator in plant disease, its specific involvement in tomato bacterial wilt remains limited. Here, we conducted a comprehensive analysis of the transcriptional landscape, encompassing both mRNAs and noncoding RNAs, in a tomato resistant line ('ZRS_7') and a susceptible line ('HTY_9') upon R. solanacearum inoculation using high-throughput RNA sequencing. Differential expression (DE) analysis revealed significant alterations in 7506 mRNAs, 997 lncRNAs, and 69 miRNAs between 'ZRS_7' and 'HTY_9' after pathogen exposure. Notably, 4548 mRNAs, 367 lncRNAs, and 26 miRNAs exhibited genotype-specific responses to R. solanacearum inoculation. GO and KEGG pathway analyses unveiled the potential involvement of noncoding RNAs in the response to bacterial wilt disease, targeting receptor-like kinases, cell wall-related genes, glutamate decarboxylases, and other key pathways. Furthermore, we constructed a comprehensive competing endogenous RNA (ceRNA) network incorporating 13 DE-miRNAs, 30 DE-lncRNAs, and 127 DEGs, providing insights into their potential contributions to the response against bacterial inoculation. Importantly, the characterization of possible endogenous target mimics (eTMs) of Sly-miR482e-3p via VIGS technology demonstrated the significant impact of eTM482e-3p-1 silencing on tomato's sensitivity to R. solanacearum. These findings support the existence of an eTM482e-3p-1-Sly-miR482e-3p-NBS-LRRs network in regulating tomato's response to the pathogen. Collectively, our findings shed light on the intricate interactions among lncRNAs, miRNAs, and mRNAs as underlying factors in conferring resistance to R. solanacearum in tomato.
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Affiliation(s)
- Xiuyang Si
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongyan Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xi Cheng
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chengcui Xu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanghui Han
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhongren Dai
- Branch Academy of Horticultural Research, Harbin Academy of Agricultural Sciences, Harbin 150029, China
| | - Rongqing Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China
| | - Changtian Pan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China
| | - Gang Lu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China.
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7
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Vailleau F, Genin S. Ralstonia solanacearum: An Arsenal of Virulence Strategies and Prospects for Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:25-47. [PMID: 37506349 DOI: 10.1146/annurev-phyto-021622-104551] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The group of strains constituting the Ralstonia solanacearum species complex (RSSC) is a prominent model for the study of plant-pathogenic bacteria because of its impact on agriculture, owing to its wide host range, worldwide distribution, and long persistence in the environment. RSSC strains have led to numerous studies aimed at deciphering the molecular bases of virulence, and many biological functions and mechanisms have been described to contribute to host infection and pathogenesis. In this review, we put into perspective recent advances in our understanding of virulence in RSSC strains, both in terms of the inventory of functions that participate in this process and their evolutionary dynamics. We also present the different strategies that have been developed to combat these pathogenic strains through biological control, antimicrobial agents, plant genetics, or microbiota engineering.
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Affiliation(s)
- Fabienne Vailleau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France; ,
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France; ,
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8
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Nie Z, Li W, Deng L, Gao K, Liu Q, Zhou Z. Comprehensive analysis of LRR-RLKs and key gene identification in Pinus massoniana resistant to pine wood nematode. FRONTIERS IN PLANT SCIENCE 2022; 13:1043261. [PMID: 36589100 PMCID: PMC9795191 DOI: 10.3389/fpls.2022.1043261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Pinus massoniana is a pioneer tree widely planted for afforestation on barren hills in southern China where the total planted area is 8.04 million ha. The invasive pine wood nematode (Bursaphelenchus xylophilus) poses a serious threat to the survival of P. massoniana. Plant resistance genes encoded by leucine-rich repeat-containing transmembrane-receptor proteins play important roles in plant defense. Leucine-rich repeat receptor-like kinases (LRR-RLKs), the largest subfamily of the RLK protein family, play an important role in sensing stress signals in plants. However, the LRR-RLKs of P. massoniana have not been characterized previously, and their role in resistance to B. xylophilus is unknown. In this study, 185 members of the LRR-RLK subfamily were identified in P. massoniana and were categorized into 14 subgroups. Transcriptomic and quantitative real-time RT-PCR analyses showed that PmRLKs32 was highly expressed in the stem tissue after inoculation with B. xylophilus. The gene exhibited high homology with AtFLS2 of Arabidopsis thaliana. PmRLKs32 was localized to the plasma membrane and was significantly upregulated in nematode-resistant and nematode-susceptible individuals. The transient expression of PmRLKs32 resulted in a burst of reactive oxygen species production in P. massoniana and Nicotiana benthamiana seedlings. These results lay a foundation for further exploration of the regulatory mechanism of LRR-RLKs in response to biotic stress in P. massoniana.
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Affiliation(s)
- Ziyan Nie
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Engineering Research Center of Masson Pine of State Forestry and Grassland Administration, Key Laboratory of Tree Breeding of Zhejiang Province, Hangzhou, Zhejiang, China
- Nanjing Forestry University, Nanjing, China
| | - Wenhua Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Engineering Research Center of Masson Pine of State Forestry and Grassland Administration, Key Laboratory of Tree Breeding of Zhejiang Province, Hangzhou, Zhejiang, China
- Nanjing Forestry University, Nanjing, China
| | - Lili Deng
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Engineering Research Center of Masson Pine of State Forestry and Grassland Administration, Key Laboratory of Tree Breeding of Zhejiang Province, Hangzhou, Zhejiang, China
- Nanjing Forestry University, Nanjing, China
| | - Kai Gao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Engineering Research Center of Masson Pine of State Forestry and Grassland Administration, Key Laboratory of Tree Breeding of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Qinghua Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Engineering Research Center of Masson Pine of State Forestry and Grassland Administration, Key Laboratory of Tree Breeding of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Zhichun Zhou
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Engineering Research Center of Masson Pine of State Forestry and Grassland Administration, Key Laboratory of Tree Breeding of Zhejiang Province, Hangzhou, Zhejiang, China
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9
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Wang L, Xie X, Xu Y, Li Z, Xu G, Cheng L, Yang J, Li L, Pu W, Cao P. Comprehensive analysis of the carboxylesterase gene reveals that NtCXE22 regulates axillary bud growth through strigolactone metabolism in tobacco. FRONTIERS IN PLANT SCIENCE 2022; 13:1019538. [PMID: 36600915 PMCID: PMC9806860 DOI: 10.3389/fpls.2022.1019538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Carboxylesterases (CXE) are a class of hydrolytic enzymes with α/β-folding domains that play a vital role in plant growth, development, stress response, and activation of herbicide-active substances. In this study, 49 Nicotiana tabacum L. CXE genes (NtCXEs) were identified using a sequence homology search. The basic characteristics, phylogenetic evolution, gene structure, subcellular location, promoter cis-elements, and gene expression patterns of the CXE family were systematically analyzed. RNA-seq data and quantitative real-time PCR showed that the expression level of CXEs was associated with various stressors and hormones; gene expression levels were significantly different among the eight tissues examined and at different developmental periods. As a new class of hormones, strigolactones (SLs) are released from the roots of plants and can control the germination of axillary buds.NtCXE7, NtCXE9, NtCXE22, and NtCXE24 were homologous to Arabidopsis SLs hydrolase AtCXE15, and changes in their expression levels were induced by topping and by GR24 (a synthetic analogue of strigolactone). Further examination revealed that NtCXE22-mutant (ntcxe22) plants generated by CRISPR-Cas9 technology had shorter bud outgrowth with lower SLs content. Validation of NtCXE22 was also performed in NtCCD8-OE plants (with fewer axillary buds) and in ntccd8 mutant plants (with more axillary buds). The results suggest that NtCXE22 may act as an efficient SLs hydrolase and affects axillary bud development, thereby providing a feasible method for manipulating endogenous SLs in crops and ornamental plants.
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Affiliation(s)
- Lin Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Guoyun Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Lingtong Cheng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Wenxuan Pu
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
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10
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Rao S, Gupta A, Bansal C, Sorin C, Crespi M, Mathur S. A conserved HSF:miR169:NF-YA loop involved in tomato and Arabidopsis heat stress tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:7-26. [PMID: 36050841 DOI: 10.1111/tpj.15963] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/15/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Heat stress transcription factors (HSFs) and microRNAs (miRNAs) regulate different stress and developmental networks in plants. Regulatory feedback mechanisms are at the basis of these networks. Here, we report that plants improve their heat stress tolerance through HSF-mediated transcriptional regulation of MIR169 and post-transcriptional regulation of Nuclear Factor-YA (NF-YA) transcription factors. We show that HSFs recognize tomato (Solanum lycopersicum) and Arabidopsis MIR169 promoters using yeast one-hybrid/chromatin immunoprecipitation-quantitative PCR. Silencing tomato HSFs using virus-induced gene silencing (VIGS) reduced Sly-MIR169 levels and enhanced Sly-NF-YA9/A10 target expression. Further, Sly-NF-YA9/A10 VIGS knockdown tomato plants and Arabidopsis plants overexpressing At-MIR169d or At-nf-ya2 mutants showed a link with increased heat tolerance. In contrast, Arabidopsis plants overexpressing At-NF-YA2 and those expressing a non-cleavable At-NF-YA2 form (miR169d-resistant At-NF-YA2) as well as plants in which At-miR169d regulation is inhibited (miR169d mimic plants) were more sensitive to heat stress, highlighting NF-YA as a negative regulator of heat tolerance. Furthermore, post-transcriptional cleavage of NF-YA by elevated miR169 levels resulted in alleviation of the repression of the heat stress effector HSFA7 in tomato and Arabidopsis, revealing a retroactive control of HSFs by the miR169:NF-YA node. Hence, a regulatory feedback loop involving HSFs, miR169s and NF-YAs plays a critical role in the regulation of the heat stress response in tomato and Arabidopsis plants.
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Affiliation(s)
- Sombir Rao
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
| | - Apoorva Gupta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
| | - Chandni Bansal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
| | - Celine Sorin
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Univ Evry, 91405, Orsay, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405, Orsay, France
| | - Martin Crespi
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Univ Evry, 91405, Orsay, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405, Orsay, France
| | - Saloni Mathur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110 067, India
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11
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Kashyap A, Jiménez-Jiménez ÁL, Zhang W, Capellades M, Srinivasan S, Laromaine A, Serra O, Figueras M, Rencoret J, Gutiérrez A, Valls M, Coll NS. Induced ligno-suberin vascular coating and tyramine-derived hydroxycinnamic acid amides restrict Ralstonia solanacearum colonization in resistant tomato. THE NEW PHYTOLOGIST 2022; 234:1411-1429. [PMID: 35152435 DOI: 10.1111/nph.17982] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Tomato varieties resistant to the bacterial wilt pathogen Ralstonia solanacearum have the ability to restrict bacterial movement in the plant. Inducible vascular cell wall reinforcements seem to play a key role in confining R. solanacearum into the xylem vasculature of resistant tomato. However, the type of compounds involved in such vascular physico-chemical barriers remain understudied, while being a key component of resistance. Here we use a combination of histological and live-imaging techniques, together with spectroscopy and gene expression analysis to understand the nature of R. solanacearum-induced formation of vascular coatings in resistant tomato. We describe that resistant tomato specifically responds to infection by assembling a vascular structural barrier formed by a ligno-suberin coating and tyramine-derived hydroxycinnamic acid amides. Further, we show that overexpressing genes of the ligno-suberin pathway in a commercial susceptible variety of tomato restricts R. solanacearum movement inside the plant and slows disease progression, enhancing resistance to the pathogen. We propose that the induced barrier in resistant plants does not only restrict the movement of the pathogen, but may also prevent cell wall degradation by the pathogen and confer anti-microbial properties, effectively contributing to resistance.
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Affiliation(s)
- Anurag Kashyap
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain
| | | | - Weiqi Zhang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain
| | - Montserrat Capellades
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), 08001, Barcelona, Spain
| | - Sumithra Srinivasan
- Institute of Material Science of Barcelona (ICMAB), CSIC, Campus UAB, 08193, Bellaterra, Spain
| | - Anna Laromaine
- Institute of Material Science of Barcelona (ICMAB), CSIC, Campus UAB, 08193, Bellaterra, Spain
| | - Olga Serra
- Laboratori del Suro, Biology Department, University of Girona, Campus Montilivi, 17003, Girona, Spain
| | - Mercè Figueras
- Laboratori del Suro, Biology Department, University of Girona, Campus Montilivi, 17003, Girona, Spain
| | - Jorge Rencoret
- Institute of Natural Resources and Agrobiology of Seville (IRNAS), CSIC, 41012, Seville, Spain
| | - Ana Gutiérrez
- Institute of Natural Resources and Agrobiology of Seville (IRNAS), CSIC, 41012, Seville, Spain
| | - Marc Valls
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain
- Department of Genetics, University of Barcelona, 08028, Barcelona, Spain
| | - Nuria S Coll
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), 08001, Barcelona, Spain
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12
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Ma D, Endo S, Betsuyaku E, Fujiwara T, Betsuyaku S, Fukuda H. Root-specific CLE3 expression is required for WRKY33 activation in Arabidopsis shoots. PLANT MOLECULAR BIOLOGY 2022; 108:225-239. [PMID: 35038066 DOI: 10.1007/s11103-021-01234-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
This study focused on the role of CLE1-7 peptides as defense mediators, and showed that root-expressed CLE3 functions as a systemic signal to regulate defense-related gene expression in shoots. In the natural environment, plants employ diverse signaling molecules including peptides to defend themselves against various pathogen attacks. In this study, we investigated whether CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) genes (CLE1-7) respond to biotic stimuli. CLE3 showed significant up-regulation upon treatment with flg22, Pep2, and salicylic acid (SA). Quantitative real-time PCR (qRT-PCR) analysis revealed that CLE3 expression is regulated by the NON-EXPRESSOR OF PR GENES1 (NPR1)-dependent SA signaling and flg22-FLAGELLIN-SENSITIVE 2 (FLS2) signaling pathways. We demonstrated that SA-induced up-regulation of CLE3 in roots was required for activation of WRKY33, a gene involved in the regulation of systemic acquired resistance (SAR), in shoots, suggesting that CLE3 functions as a root-derived signal that regulates the expression of defense-related genes in shoots. Microarray analysis of transgenic Arabidopsis lines overexpressing CLE3 under the control of a β-estradiol-inducible promoter revealed that root-confined CLE3 overexpression affected gene expression in both roots and shoots. Comparison of CLE2- and CLE3-induced genes indicated that CLE2 and CLE3 peptides target a few common but largely distinct downstream genes. These results suggest that root-derived CLE3 is involved in the regulation of systemic rather than local immune responses. Our study also sheds light on the potential role of CLE peptides in long-distance regulation of plant immunity.
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Affiliation(s)
- Dichao Ma
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Satoshi Endo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute of Interdisciplinary Research, Kyoto University of Advanced Science, 1-1 Nanjo-Ohtani, Sogabe-cho, Kameoka-city, Kyoto, 621-8555, Japan
| | - Eriko Betsuyaku
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shigeyuki Betsuyaku
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan.
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Sciences, Kyoto University of Advanced Science, 1-1 Nanjo-Ohtani, Sogabe-cho, Kameoka-city, Kyoto, 621-8555, Japan.
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13
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Xing L, Zhu M, Luan M, Zhang M, Jin L, Liu Y, Zou J, Wang L, Xu M. miR169q and NUCLEAR FACTOR YA8 enhance salt tolerance by activating PEROXIDASE1 expression in response to ROS. PLANT PHYSIOLOGY 2022; 188:608-623. [PMID: 34718783 PMCID: PMC8774724 DOI: 10.1093/plphys/kiab498] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/28/2021] [Indexed: 05/10/2023]
Abstract
Salt stress significantly reduces the productivity of crop plants including maize (Zea mays). miRNAs are major regulators of plant growth and stress responses, but few studies have examined the potential impacts of miRNAs on salt stress responses in maize. Here, we show that ZmmiR169q is responsive to stress-induced ROS signals. After detecting that salt stress and exogenous H2O2 treatment reduced the accumulation of ZmmiR169q, stress assays with transgenic materials showed that depleting ZmmiR169q increased seedling salt tolerance whereas overexpressing ZmmiR169q decreased salt tolerance. Helping explain these observations, we found that ZmmiR169q repressed the transcript abundance of its target NUCLEAR FACTOR YA8 (ZmNF-YA8), and overexpression of ZmNF-YA8 in maize improved salt tolerance, specifically by transcriptionally activating the expression of the efficient antioxidant enzyme PEROXIDASE1. Our study reveals a direct functional link between salt stress and a miR169q-NF-YA8 regulatory module that plants use to manage ROS stress and strongly suggests that ZmNF-YA8 can be harnessed as a resource for developing salt-tolerant crop varieties.
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Affiliation(s)
- Lijuan Xing
- CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, Biotechnology Research Institute, 100081 Beijing, China
| | - Ming Zhu
- CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, Biotechnology Research Institute, 100081 Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, 100081 Beijing, China
| | - Mingda Luan
- CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, Biotechnology Research Institute, 100081 Beijing, China
| | - Min Zhang
- CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, Biotechnology Research Institute, 100081 Beijing, China
| | - Lian Jin
- CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, Biotechnology Research Institute, 100081 Beijing, China
| | - Yueping Liu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, 102206 Beijing, China
| | - Junjie Zou
- CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, Biotechnology Research Institute, 100081 Beijing, China
| | - Lei Wang
- CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, Biotechnology Research Institute, 100081 Beijing, China
| | - Miaoyun Xu
- CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, Biotechnology Research Institute, 100081 Beijing, China
- Author for communication:
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14
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Xu C, Zhong L, Huang Z, Li C, Lian J, Zheng X, Liang Y. Real-time monitoring of Ralstonia solanacearum infection progress in tomato and Arabidopsis using bioluminescence imaging technology. PLANT METHODS 2022; 18:7. [PMID: 35033123 PMCID: PMC8761306 DOI: 10.1186/s13007-022-00841-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/06/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Ralstonia solanacearum, one of the most devastating bacterial plant pathogens, is the causal agent of bacterial wilt. Recently, several studies on resistance to bacterial wilt have been conducted using the Arabidopsis-R. solanacearum system. However, the progress of R. solanacearum infection in Arabidopsis is still unclear. RESULTS We generated a bioluminescent R. solanacearum by expressing plasmid-based luxCDABE. Expression of luxCDABE did not alter the bacterial growth and pathogenicity. The light intensity of bioluminescent R. solanacearum was linearly related to bacterial concentrations from 104 to 108 CFU·mL-1. After root inoculation with bioluminescent R. solanacearum strain, light signals in tomato and Arabidopsis were found to be transported from roots to stems via the vasculature. Quantification of light intensity from the bioluminescent strain accurately reported the difference in disease resistance between Arabidopsis wild type and resistant mutants. CONCLUSIONS Bioluminescent R. solanacearum strain spatially and quantitatively measured bacterial growth in tomato and Arabidopsis, and offered a tool for the high-throughput study of R. solanacearum-Arabidopsis interaction in the future.
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Affiliation(s)
- Cuihong Xu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Lingkun Zhong
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zeming Huang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Chenying Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xuefang Zheng
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, No. 247 Wusi Road, Fuzhou, 350003, China
| | - Yan Liang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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15
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Jaiswal N, Liao CJ, Mengesha B, Han H, Lee S, Sharon A, Zhou Y, Mengiste T. Regulation of plant immunity and growth by tomato receptor-like cytoplasmic kinase TRK1. THE NEW PHYTOLOGIST 2022; 233:458-478. [PMID: 34655240 DOI: 10.1111/nph.17801] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/11/2021] [Indexed: 05/27/2023]
Abstract
The molecular mechanisms of quantitative resistance (QR) to fungal pathogens and their relationships with growth pathways are poorly understood. We identified tomato TRK1 (TPK1b Related Kinase1) and determined its functions in tomato QR and plant growth. TRK1 is a receptor-like cytoplasmic kinase that complexes with tomato LysM Receptor Kinase (SlLYK1). SlLYK1 and TRK1 are required for chitin-induced fungal resistance, accumulation of reactive oxygen species, and expression of immune response genes. Notably, TRK1 and SlLYK1 regulate SlMYC2, a major transcriptional regulator of jasmonic acid (JA) responses and fungal resistance, at transcriptional and post-transcriptional levels. Further, TRK1 is also required for maintenance of proper meristem growth, as revealed by the ectopic meristematic activity, enhanced branching, and altered floral structures in TRK1 RNAi plants. Consistently, TRK1 interacts with SlCLV1 and SlWUS, and TRK1 RNAi plants show increased expression of SlCLV3 and SlWUS in shoot apices. Interestingly, TRK1 suppresses chitin-induced gene expression in meristems but promotes expression of the same genes in leaves. SlCLV1 and TRK1 perform contrasting functions in defense but similar functions in plant growth. Overall, through molecular and biochemical interactions with critical regulators, TRK1 links upstream defense and growth signals to downstream factor in fungal resistance and growth homeostasis response regulators.
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Affiliation(s)
- Namrata Jaiswal
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Chao-Jan Liao
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Bemnet Mengesha
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Han Han
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Sanghun Lee
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
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16
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Zhang Q, Wu L, Yin H, Xu Z, Zhao Y, Gao M, Wu H, Chen Y, Wang Y. D6 protein kinase in root xylem benefiting resistance to Fusarium reveals infection and defense mechanisms in tung trees. HORTICULTURE RESEARCH 2021; 8:240. [PMID: 34719680 PMCID: PMC8558330 DOI: 10.1038/s41438-021-00656-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/04/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Fusarium oxysporum, a global soil-borne pathogen, causes severe disease in various cultivated plants. The mechanism underlying infection and resistance remains largely elusive. Vernicia fordii, known as the tung tree, suffers from disease caused by F. oxysporum f. sp. fordiis (Fof-1), while its sister species V. montana displays high resistance to Fof-1. To investigate the process of infection and resistance ability, we demonstrated that Fof-1 can penetrate the epidermis of root hairs and then centripetally invade the cortex and phloem in both species. Furthermore, Fof-1 spread upwards through the root xylem in susceptible V. fordii trees, whereas it failed to infect the root xylem in resistant V. montana trees. We found that D6 PROTEIN KINASE LIKE 2 (VmD6PKL2) was specifically expressed in the lateral root xylem and was induced after Fof-1 infection in resistant trees. Transgenic analysis in Arabidopsis and tomato revealed that VmD6PKL2 significantly enhanced resistance in both species, whereas the d6pkl2 mutant displayed reduced resistance against Fof-1. Additionally, VmD6PKL2 was identified to interact directly with synaptotagmin (VmSYT3), which is specifically expressed in the root xylem and mediates the negative regulation responding to Fof-1. Our data suggested that VmD6PKL2 could act as a resistance gene against Fof-1 through suppression of VmSYT3-mediated negative regulation in the lateral root xylem of the resistant species. These findings provide novel insight into Fusarium wilt resistance in plants.
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Affiliation(s)
- Qiyan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang Province, China
| | - Liwen Wu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang Province, China
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang Province, China
| | - Zilong Xu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang Province, China
| | - Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang Province, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang Province, China
| | - Hong Wu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang Province, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang Province, China.
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang Province, China.
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17
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The Same against Many: AtCML8, a Ca 2+ Sensor Acting as a Positive Regulator of Defense Responses against Several Plant Pathogens. Int J Mol Sci 2021; 22:ijms221910469. [PMID: 34638807 PMCID: PMC8508799 DOI: 10.3390/ijms221910469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 01/11/2023] Open
Abstract
Calcium signals are crucial for the activation and coordination of signaling cascades leading to the establishment of plant defense mechanisms. Here, we studied the contribution of CML8, an Arabidopsis calmodulin-like protein in response to Ralstonia solanacearum and to pathogens with different lifestyles, such as Xanthomonas campestris pv. campestris and Phytophtora capsici. We used pathogenic infection assays, gene expression, RNA-seq approaches, and comparative analysis of public data on CML8 knockdown and overexpressing Arabidopsis lines to demonstrate that CML8 contributes to defense mechanisms against pathogenic bacteria and oomycetes. CML8 gene expression is finely regulated at the root level and manipulated during infection with Ralstonia, and CML8 overexpression confers better plant tolerance. To understand the processes controlled by CML8, genes differentially expressed at the root level in the first hours of infection have been identified. Overexpression of CML8 also confers better tolerance against Xanthomonas and Phytophtora, and most of the genes differentially expressed in response to Ralstonia are differentially expressed in these different pathosystems. Collectively, CML8 acts as a positive regulator against Ralstonia solanaceraum and against other vascular or root pathogens, suggesting that CML8 is a multifunctional protein that regulates common downstream processes involved in the defense response of plants to several pathogens.
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18
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Blümke P, Schlegel J, Gonzalez-Ferrer C, Becher S, Pinto KG, Monaghan J, Simon R. Receptor-like cytoplasmic kinase MAZZA mediates developmental processes with CLAVATA1 family receptors in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4853-4870. [PMID: 33909893 DOI: 10.1093/jxb/erab183] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
The receptor-like kinases (RLKs) CLAVATA1 (CLV1) and BARELY ANY MERISTEMs (BAM1-BAM3) form the CLV1 family (CLV1f), which perceives peptides of the CLV3/EMBRYO SURROUNDING REGION (ESR)-related (CLE) family within various signaling pathways of Arabidopsis thaliana. CLE peptide signaling, which is required for meristem size control, vascular development, and pathogen responses, involves the formation of receptor complexes at the plasma membrane. These complexes comprise RLKs and co-receptors in varying compositions depending on the signaling context, and regulate expression of target genes, such as WUSCHEL (WUS). How the CLE signal is transmitted intracellularly after perception at the plasma membrane is not known in detail. Here, we found that the membrane-associated receptor-like cytoplasmic kinase (RLCK) MAZZA (MAZ) and additional members of the Pti1-like protein family interact in vivo with CLV1f receptors. MAZ, which is widely expressed throughout the plant, localizes to the plasma membrane via post-translational palmitoylation, potentially enabling stimulus-triggered protein re-localization. We identified a role for a CLV1-MAZ signaling module during stomatal and root development, and redundancy could potentially mask other phenotypes of maz mutants. We propose that MAZ, and related RLCKs, mediate CLV1f signaling in a variety of developmental contexts, paving the way towards understanding the intracellular processes after CLE peptide perception.
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Affiliation(s)
- Patrick Blümke
- Institute for Developmental Genetics, Heinrich Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Jenia Schlegel
- Institute for Developmental Genetics, Heinrich Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Carmen Gonzalez-Ferrer
- Department of Biology, Queen's University, 116 Barrie Street, Kingston ON K7L 3N6,Canada
| | - Sabine Becher
- Institute for Developmental Genetics, Heinrich Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Karine Gustavo Pinto
- Institute for Developmental Genetics, Heinrich Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Jacqueline Monaghan
- Department of Biology, Queen's University, 116 Barrie Street, Kingston ON K7L 3N6,Canada
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany
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19
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Yu RM, Suo YY, Yang R, Chang YN, Tian T, Song YJ, Wang HJ, Wang C, Yang RJ, Liu HL, Gao G. StMBF1c positively regulates disease resistance to Ralstonia solanacearum via it's primary and secondary upregulation combining expression of StTPS5 and resistance marker genes in potato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 307:110877. [PMID: 33902863 DOI: 10.1016/j.plantsci.2021.110877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Multiprotein bridging factor 1 (MBF1) is a transcription coactivator that has a general defense response to pathogens. However, the regulatory mechanisms of MBF1 resistance bacterial wilt remain largely unknown. Here, the role of StMBF1c in potato resistance to Ralstonia solanacearum infection was characterized. qRT-PCR assays indicated that StMBF1c could was elicited by SA, MJ and ABA and the time-course expression pattern of the StMBF1c gene induced by R. solanacearum was found to be twice significant upregulated expression during the early and middle stages of bacterial wilt. Combined with the co-expression analysis of disease-resistant marker genes, gain-of-function and loss-of-function assays demonstrated that StMBF1c was associated with defence priming. Overexpression or silencing the MBF1c could enhance plants resistance or sensitivity to R. solanacearum through inducing or reducing NPR and PR genes related to SA signal pathway. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) experiment results confirmed the interaction of StMBF1c with StTPS5 which played a key role in ABA signal pathway in potato. It is speculated that by combining StTPS5 and resistance marker genes, StMBF1c is activated twice to participate in potato bacterial wilt resistance, in which EPI, PTI involved.
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Affiliation(s)
- Rui-Min Yu
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Yan-Yun Suo
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Rui Yang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Yan-Nan Chang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Tian Tian
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Yan-Jie Song
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Huan-Jun Wang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Cong Wang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Ru-Jie Yang
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Hong-Liang Liu
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
| | - Gang Gao
- Genetic Engineering Laboratory, College of Life Science, Shanxi Normal University, Linfen, China.
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20
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Zhang C, Fu F, Lin C, Ding X, Zhang J, Yan H, Wang P, Zhang W, Peng B, Zhao L. MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean. Front Genet 2021; 12:654146. [PMID: 34054917 PMCID: PMC8153375 DOI: 10.3389/fgene.2021.654146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is an important plant characteristic for exploiting heterosis to enhance crop traits during breeding. However, the CMS regulatory network remains unclear in plants, even though researchers have attempted to isolate genes associated with CMS. In this study, we performed high-throughput sequencing and degradome analyses to identify microRNAs (miRNAs) and their targets in a soybean CMS line (JLCMS9A) and its maintainer line (JLCMS9B). Additionally, the differentially expressed genes during reproductive development were identified using RNA-seq data. A total of 280 miRNAs matched soybean miRNA sequences in miRBase, including mature miRNAs and pre-miRNAs. Of the 280 miRNAs, 30, 23, and 21 belonged to the miR166, miR156, and miR171 families, respectively. Moreover, 410 novel low-abundant miRNAs were identified in the JLCMS9A and JLCMS9B flower buds. Furthermore, 303 and 462 target genes unique to JLCMS9A and JLCMS9B, respectively, as well as 782 common targets were predicted based on the degradome analysis. Target genes differentially expressed between the CMS line and the maintainer line were revealed by an RNA-seq analysis. Moreover, all target genes were annotated with diverse functions related to biological processes, cellular components, and molecular functions, including transcriptional regulation, the nucleus, meristem maintenance, meristem initiation, cell differentiation, auxin-activated signaling, plant ovule development, and anther development. Finally, a network was built based on the interactions. Analyses of the miRNA, degradome, and transcriptome datasets generated in this study provided a comprehensive overview of the reproductive development of a CMS soybean line. The data presented herein represent useful information for soybean hybrid breeding. Furthermore, the study results indicate that miRNAs might contribute to the soybean CMS regulatory network by modulating the expression of CMS-related genes. These findings lay the foundation for future studies on the molecular mechanisms underlying soybean CMS.
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Affiliation(s)
- Chunbao Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Fuyou Fu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Chunjing Lin
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiaoyang Ding
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jingyong Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Hao Yan
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Pengnian Wang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wei Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Bao Peng
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Limei Zhao
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
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21
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Alonso-Díaz A, Satbhai SB, de Pedro-Jové R, Berry HM, Göschl C, Argueso CT, Novak O, Busch W, Valls M, Coll NS. A genome-wide association study reveals cytokinin as a major component in the root defense responses against Ralstonia solanacearum. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2727-2740. [PMID: 33475698 PMCID: PMC8006551 DOI: 10.1093/jxb/eraa610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/19/2021] [Indexed: 05/30/2023]
Abstract
Bacterial wilt caused by the soil-borne pathogen Ralstonia solancearum is economically devastating, with no effective methods to fight the disease. This pathogen invades plants through their roots and colonizes their xylem, clogging the vasculature and causing rapid wilting. Key to preventing colonization are the early defense responses triggered in the host's root upon infection, which remain mostly unknown. Here, we have taken advantage of a high-throughput in vitro infection system to screen natural variability associated with the root growth inhibition phenotype caused by R. solanacearum in Arabidopsis during the first hours of infection. To analyze the genetic determinants of this trait, we have performed a genome-wide association study, identifying allelic variation at several loci related to cytokinin metabolism, including genes responsible for biosynthesis and degradation of cytokinin. Further, our data clearly demonstrate that cytokinin signaling is induced early during the infection process and cytokinin contributes to immunity against R. solanacearum. This study highlights a new role for cytokinin in root immunity, paving the way for future research that will help in understanding the mechanisms underpinning root defenses.
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Affiliation(s)
- Alejandro Alonso-Díaz
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Santosh B Satbhai
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, Vienna 1030, Austria
- Salk Institute For Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Roger de Pedro-Jové
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Hannah M Berry
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Christian Göschl
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, Vienna 1030, Austria
| | - Cristiana T Argueso
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Ondrej Novak
- Laboratory of Growth Regulators, Olomouc, The Czech Republic
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, Vienna 1030, Austria
- Salk Institute For Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Marc Valls
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
- Genetics Department, University of Barcelona, Barcelona, Spain
| | - Núria S Coll
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
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22
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Sun Y, Xiong X, Wang Q, Zhu L, Wang L, He Y, Zeng H. Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the MiR156, MiR5488 and MiR399 are Involved in the Regulation of Male Sterility in PTGMS Rice. Int J Mol Sci 2021; 22:ijms22052260. [PMID: 33668376 PMCID: PMC7956645 DOI: 10.3390/ijms22052260] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 02/07/2023] Open
Abstract
A photoperiod- and thermo-sensitive genic male sterile (PTGMS) line is the basic material for two-hybrid rice and is an important genetic breeding resource. Peiai64S (PA64S) is an important germplasm resource of PTGMS rice, and it has been applied to two-line hybrid rice systems in China. Pollen fertility in PA64S is regulated by the temperature and photoperiod, but the mechanism of the fertility transition is unclear. In this study, we obtained the male fertile plant PA64S(F) and the male sterile plant PA64S(S) by controlling different temperatures under long light conditions and used the male fertile and sterile plants to investigate the role of microRNAs (miRNAs) in regulating male fertility in rice. We performed the small RNA library sequencing of anthers from PA64S(S) and PA64S(F). A total of 196 miRNAs were identified-166 known miRNAs among 27 miRNA families and 30 novel miRNAs. In the transcriptome analysis, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes revealed significant enrichment in the synthesis and metabolism of fatty acids and some secondary metabolism pathways such as fatty acid metabolism and phenylalanine metabolism. With a comprehensive analysis of miRNA, transcriptome, and degradome sequencing, we identified that 13 pairs of miRNA/target genes regulated male fertility in rice by responding to temperature change, among which the miR156, miR5488, and miR399 affect the male fertility of PA64S by influencing SPLs, the lignin synthesis of anther walls, and the flavonoid metabolism pathway. The results provide a new understanding of PTGMS rice, which will help us better understand the potential regulatory mechanisms of male sterility in the future.
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Affiliation(s)
| | | | | | | | | | - Ying He
- Correspondence: (Y.H.); (H.Z.)
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23
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Fu F, Girma G, Mengiste T. Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum. BMC Genomics 2020; 21:760. [PMID: 33143636 PMCID: PMC7641857 DOI: 10.1186/s12864-020-07138-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/11/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Anthracnose is a damaging disease of sorghum caused by the fungal pathogen Colletotrichum sublineolum. Genome-wide mRNA and microRNA (miRNA) profiles of resistant and susceptible sorghum genotypes were studied to understand components of immune responses, and fungal induced miRNA and target gene networks. RESULTS A total of 18 mRNA and 12 miRNA libraries from resistant and susceptible sorghum lines were sequenced prior to and after inoculation with C. sublineolum. Significant differences in transcriptomes of the susceptible and resistant genotypes were observed with dispersion distance and hierarchical cluster tree analyses. Of the total 33,032 genes predicted in the sorghum genome, 19,593 were induced by C. sublineolum, and 15,512 were differentially expressed (DEGs) between the two genotypes. The resistant line was marked by significant reprogramming of the transcriptome at 24 h post inoculation (hpi), and a decrease at 48 hpi, whereas the susceptible line displayed continued changes in gene expression concordant with elevated fungal growth in the susceptible genotype. DEGs encode proteins implicated in diverse functions including photosynthesis, synthesis of tetrapyrrole, carbohydrate and secondary metabolism, immune signaling, and chitin binding. Genes encoding immune receptors, MAPKs, pentatricopeptide repeat proteins, and WRKY transcription factors were induced in the resistant genotype. In a parallel miRNA profiling, the susceptible line displayed greater number of differentially expressed miRNAs than the resistant line indicative of a widespread suppression of gene expression. Interestingly, we found 75 miRNAs, including 36 novel miRNAs, which were differentially expressed in response to fungal inoculation. The expression of 50 miRNAs was significantly different between resistant and susceptible lines. Subsequently, for 35 differentially expressed miRNAs, the corresponding 149 target genes were identified. Expression of 56 target genes were significantly altered after inoculation, showing inverse expression with the corresponding miRNAs. CONCLUSIONS We provide insights into genome wide dynamics of mRNA and miRNA profiles, biological and cellular processes underlying host responses to fungal infection in sorghum. Resistance is correlated with early transcriptional reprogramming of genes in various pathways. Fungal induced genes, miRNAs and their targets with a potential function in host responses to anthracnose were identified, opening avenues for genetic dissection of resistance mechanisms.
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Affiliation(s)
- Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- Present address: Agriculture and Agri-Food Canada, Plant Gene Resources of Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
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24
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Hidden in plain sight: Systematic investigation of Leucine-rich repeat containing genes unveil the their regulatory network in response to Fusarium wilt in tung tree. Int J Biol Macromol 2020; 163:1759-1767. [DOI: 10.1016/j.ijbiomac.2020.09.106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022]
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25
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Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both. Int J Mol Sci 2020; 21:ijms21207552. [PMID: 33066159 PMCID: PMC7589798 DOI: 10.3390/ijms21207552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022] Open
Abstract
Organisms alter development in response to environmental cues. Recent studies demonstrate that they can transmit this plasticity to progeny. While the phenotypic and transcriptomic evidence for this “transgenerational plasticity” has accumulated, genetic and developmental mechanisms remain unclear. Plant defenses, gene expression and DNA methylation are modified as an outcome of parental wounding in Mimulus guttatus. Here, we sequenced M. guttatus small RNAs (sRNA) to test their possible role in mediating transgenerational plasticity. We sequenced sRNA populations of leaf-wounded and control plants at 1 h and 72 h after damage and from progeny of wounded and control parents. This allowed us to test three components of an a priori model of sRNA mediated transgenerational plasticity—(1) A subset of sRNAs will be differentially expressed in response to wounding, (2) these will be associated with previously identified differentially expressed genes and differentially methylated regions and (3) changes in sRNA abundance in wounded plants will be predictive of sRNA abundance, DNA methylation, and/or gene expression shifts in the following generation. Supporting (1) and (2), we found significantly different sRNA abundances in wounded leaves; the majority were associated with tRNA fragments (tRFs) rather than small-interfering RNAs (siRNA). However, siRNAs responding to leaf wounding point to Jasmonic Acid mediated responses in this system. We found that different sRNA classes were associated with regions of the genome previously found to be differentially expressed or methylated in progeny of wounded plants. Evidence for (3) was mixed. We found that non-dicer sRNAs with increased abundance in response to wounding tended to be nearby genes with decreased expression in the next generation. Counter to expectations, we did not find that siRNA responses to wounding were associated with gene expression or methylation changes in the next generation and within plant and transgenerational sRNA plasticity were negatively correlated.
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26
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Jung J, Kim SK, Jung SH, Jeong MJ, Ryu CM. Sound Vibration-Triggered Epigenetic Modulation Induces Plant Root Immunity Against Ralstonia solanacearum. Front Microbiol 2020; 11:1978. [PMID: 32973716 PMCID: PMC7472266 DOI: 10.3389/fmicb.2020.01978] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 07/27/2020] [Indexed: 12/21/2022] Open
Abstract
Sound vibration (SV) is one of the several environmental stimuli that induce physiological changes in plants including changes in plant immunity. Immune activation is a complicated process involving epigenetic modifications, however, SV-induced epigenetic modifications remain unexplored. Here, we performed an integrative analysis comprising chromatin immunoprecipitation (ChIP) and microRNA sequencing (miRNA-seq) to understand the role of SV-mediated epigenetic modifications in immune activation in Arabidopsis thaliana against the root pathogen Ralstonia solanacearum. Plants exposed to SV (10 kHz) showed abundant H3K27me3 modification in the promoter regions of aliphatic glucosinolate biosynthesis and cytokinin signaling genes, leading to transcriptional changes that promote immunity. Additionally, 10 kHz SV down-regulated miR397b expression, thus activating three target LACCASE transcripts that mediate cell wall reinforcement via lignin accumulation. Taken together, SV triggers epigenetic modification of genes involved in secondary metabolite biosynthesis, defense hormone signaling, and pre-formed defense in A. thaliana, leading to the activation of plant immunity against R. solanacearum.
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Affiliation(s)
- Jihye Jung
- Molecular Phytobacteriology Laboratory, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Seon-Kyu Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Sung-Hee Jung
- Molecular Phytobacteriology Laboratory, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, South Korea
| | - Mi-Jeong Jeong
- National Institute of Agricultural Science, Rural Development Administration, Wanju, South Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, South Korea
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27
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Bacete L, Mélida H, López G, Dabos P, Tremousaygue D, Denancé N, Miedes E, Bulone V, Goffner D, Molina A. Arabidopsis Response Regulator 6 (ARR6) Modulates Plant Cell-Wall Composition and Disease Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:767-780. [PMID: 32023150 DOI: 10.1094/mpmi-12-19-0341-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The cytokinin signaling pathway, which is mediated by Arabidopsis response regulator (ARR) proteins, has been involved in the modulation of some disease-resistance responses. Here, we describe novel functions of ARR6 in the control of plant disease-resistance and cell-wall composition. Plants impaired in ARR6 function (arr6) were more resistant and susceptible, respectively, to the necrotrophic fungus Plectosphaerella cucumerina and to the vascular bacterium Ralstonia solanacearum, whereas Arabidopsis plants that overexpress ARR6 showed the opposite phenotypes, which further support a role of ARR6 in the modulation of disease-resistance responses against these pathogens. Transcriptomics and metabolomics analyses revealed that, in arr6 plants, canonical disease-resistance pathways, like those activated by defensive phytohormones, were not altered, whereas immune responses triggered by microbe-associated molecular patterns were slightly enhanced. Cell-wall composition of arr6 plants was found to be severely altered compared with that of wild-type plants. Remarkably, pectin-enriched cell-wall fractions extracted from arr6 walls triggered more intense immune responses than those activated by similar wall fractions from wild-type plants, suggesting that arr6 pectin fraction is enriched in wall-related damage-associated molecular patterns, which trigger immune responses. This work supports a novel function of ARR6 in the control of cell-wall composition and disease resistance and reinforces the role of the plant cell wall in the modulation of specific immune responses.
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Affiliation(s)
- Laura Bacete
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Hugo Mélida
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Patrick Dabos
- LIPM, Université de Toulouse, INRA, CNRS, UPS, Castanet-Tolosan Cedex, France
| | | | - Nicolas Denancé
- LIPM, Université de Toulouse, INRA, CNRS, UPS, Castanet-Tolosan Cedex, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, Université Paul Sabatier, UMR 5546, Chemin de Borde Rouge, F-31326 Castanet-Tolosan, France
| | - Eva Miedes
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Vincent Bulone
- Royal Institute of Technology (KTH), School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Glycoscience, AlbaNova University Center, SE-106 91 Stockholm, Sweden
- ARC Centre of Excellence in Plant Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Deborah Goffner
- Laboratoire de Recherche en Sciences Végétales, CNRS, Université Paul Sabatier, UMR 5546, Chemin de Borde Rouge, F-31326 Castanet-Tolosan, France
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
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28
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Wen T, Zhao M, Liu T, Huang Q, Yuan J, Shen Q. High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome. BMC PLANT BIOLOGY 2020; 20:166. [PMID: 32293273 PMCID: PMC7160980 DOI: 10.1186/s12870-020-02365-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/26/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Rhizosphere microbiome is dynamic and influenced by environment factors surrounded including pathogen invasion. We studied the effects of Ralstonia solanacearum pathogen abundance on rhizosphere microbiome and metabolome by using high throughput sequencing and GC-MS technology. RESULTS There is significant difference between two rhizosphere bacterial communities of higher or lower pathogen abundance, and this difference of microbiomes was significant even ignoring the existence of pathogen. Higher pathogen abundance decreased the alpha diversity of rhizosphere bacterial community as well as connections in co-occurrence networks. Several bacterial groups such as Bacillus and Chitinophaga were negatively related to the pathogen abundance. The GC-MS analysis revealed significantly different metabolomes in two groups of rhizosphere soils, i.e., the rhizosphere soil of lower harbored more sugars such as fructose, sucrose and melibiose than that in high pathogen abundance. CONCLUSIONS The dissimilar metabolomes in two rhizosphere soils likely explained the difference of bacterial communities with Mantel test. Bacillus and Chitinophaga as well as sugar compounds negatively correlated with high abundance of pathogen indicated their potential biocontrol ability.
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Affiliation(s)
- Tao Wen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengli Zhao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Yuan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
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29
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Habe I, Miyatake K, Nunome T, Yamasaki M, Hayashi T. QTL analysis of resistance to bacterial wilt caused by Ralstonia solanacearum in potato. BREEDING SCIENCE 2019; 69:592-600. [PMID: 31988623 PMCID: PMC6977455 DOI: 10.1270/jsbbs.19059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
Ralstonia solanacearum causes bacterial wilt, a soil-borne disease and one of the most important maladies of potato and other Solanaceae crops. We analyzed the resistance of a potato clone to bacterial wilt by quantitative trait locus (QTL) analysis. A resistant diploid potato clone 10-03-30 was crossed with a susceptible diploid clone F1-1 to generate a diploid, two-way pseudo-testcross F1 population comprised of 94 genotypes. Dense linkage maps, containing 4,139 single nucleotide polymorphism markers with an average distance of 0.6 and 0.3 cM between markers, were constructed for both parents. The resistance level was evaluated by in vitro inoculation test with R. solanacearum (phylotype I/biovar 4/race 1). Five QTLs (qBWR-1 to -5) were identified on potato chromosomes 1, 3, 7, 10, and 11, and they explained 9.3-18.4% of the phenotypic variance. The resistant parent had resistant alleles in qBWR-2, qBWR-3, and qBWR-4 and susceptible alleles in qBWR-1 and qBWR-5. Accumulation of the resistant alleles in all five QTLs increased the level of resistance compared with that of the resistant parent. This is the first study to identify novel QTLs for bacterial wilt resistance in potato by using genome-wide markers.
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Affiliation(s)
- Ippei Habe
- Nagasaki Agricultural and Forestry Technical Development Center,
3118 Kaizu-cho, Isahaya, Nagasaki 854-0063,
Japan
| | - Koji Miyatake
- Institute of Vegetable and Floriculture Science, NARO,
Kusawa 360, Tsu, Mie 514-2392,
Japan
| | - Tsukasa Nunome
- Institute of Vegetable and Floriculture Science, NARO,
Kusawa 360, Tsu, Mie 514-2392,
Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University,
1348 Uzurano, Kasai, Hyogo 675-2103,
Japan
| | - Takeshi Hayashi
- Institute of Crop Science, NARO,
Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602,
Japan
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30
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Zhang C, Chen H, Zhuang RR, Chen YT, Deng Y, Cai TC, Wang SY, Liu QZ, Tang RH, Shan SH, Pan RL, Chen LS, Zhuang WJ. Overexpression of the peanut CLAVATA1-like leucine-rich repeat receptor-like kinase AhRLK1 confers increased resistance to bacterial wilt in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5407-5421. [PMID: 31173088 PMCID: PMC6793444 DOI: 10.1093/jxb/erz274] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 05/31/2019] [Indexed: 06/04/2023]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a devastating disease affecting hundreds of plant species, yet the host factors remain poorly characterized. The leucine-rich repeat receptor-like kinase gene AhRLK1, characterized as CLAVATA1, was found to be up-regulated in peanut upon inoculation with R. solanacearum. The AhRLK1 protein was localized in the plasma membrane and cell wall. qPCR results showed AhRLK1 was induced in a susceptible variety but little changed in a resistant cultivar after inoculated with R. solanacearum. Hormones such as salicylic acid, abscisic acid, methyl jasmonate, and ethephon induced AhRLK1 expression. In contrast, AhRLK1 expression was down-regulated under cold and drought treatments. Transient overexpression of AhRLK1 led to a hypersensitive response (HR) in Nicotiana benthamiana. Furthermore, AhRLK1 overexpression in tobacco significantly increased the resistance to R. solanacearum. Besides, the transcripts of most representative defense responsive genes in HR and hormone signal pathways were significantly increased in the transgenic lines. EDS1 and PAD4 in the R gene signaling pathway were also up-regulated, but NDR1 was down-regulated. Accordingly, AhRLK1 may increase the defense response to R. solanacearum via HR and hormone defense signaling, in particular through the EDS1 pathway of R gene signaling. These results provide a new understanding of the CLAVATA1 function and will contribute to genetic enhancement of peanut.
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Affiliation(s)
- Chong Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hua Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rui-Rong Zhuang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Ting Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tie-Cheng Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuai-Yin Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qin-Zheng Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rong-Hua Tang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Shi-Hua Shan
- Shandong Peanut Research Institute, Qingdao, China
| | - Rong-Long Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, Taiwan
| | - Li-Song Chen
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Jian Zhuang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
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31
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Identification of miRNAs Involved in Bacillus velezensis FZB42-Activated Induced Systemic Resistance in Maize. Int J Mol Sci 2019; 20:ijms20205057. [PMID: 31614702 PMCID: PMC6829523 DOI: 10.3390/ijms20205057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 12/18/2022] Open
Abstract
Bacillus velezensis FZB42 is able to activate induced systemic resistance (ISR) to enhance plant defense response against pathogen infections. Though the roles of microRNAs (miRNAs) in Bacillus-triggered ISR have been reported in Arabidopsis, the maize miRNAs responsible for the Bacillus-activated ISR process have not been discovered. To explore the maize miRNAs involved in ISR, maize miRNAs in response to FZB42 (ISR activating), FZB42△sfp△alss (deficient in triggering ISR), and a control for 12 h were sequenced. A total of 146 known miRNAs belonging to 30 miRNA families and 217 novel miRNAs were identified. Four miRNAs specifically repressed in FZB42-treatment were selected as candidate ISR-associated miRNAs. All of them contained at least one defense response-related cis-element, suggesting their potential roles in activating the ISR process. Interestingly, three of the four candidate ISR-associated miRNAs belong to the conserved miR169 family, which has previously been confirmed to play roles in abiotic stress response. Moreover, 52 mRNAs were predicted as potential targets of these candidate ISR-associated miRNAs through TargetFinder software and degradome sequencing. Gene Ontology (GO) and network analyses of target genes showed that these differentially expressed miRNA might participate in the ISR process by regulating nuclear factor Y transcription factor. This study is helpful in better understanding the regulatory roles of maize miRNAs in the Bacillus-activated ISR process.
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32
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Loh SC, Othman AS, Veera Singham G. Identification and characterization of jasmonic acid- and linolenic acid-mediated transcriptional regulation of secondary laticifer differentiation in Hevea brasiliensis. Sci Rep 2019; 9:14296. [PMID: 31586098 PMCID: PMC6778104 DOI: 10.1038/s41598-019-50800-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 09/17/2019] [Indexed: 11/30/2022] Open
Abstract
Hevea brasiliensis remains the primary crop commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. Here, we described the transcriptional events related to jasmonic acid (JA)- and linolenic acid (LA)-induced secondary laticifer differentiation (SLD) in H. brasiliensis clone RRIM 600 based on RNA-seq approach. Histochemical approach proved that JA- and LA-treated samples resulted in SLD in H. brasiliensis when compared to ethephon and untreated control. RNA-seq data resulted in 86,614 unigenes, of which 2,664 genes were differentially expressed in JA and LA-induced secondary laticifer harvested from H. brasiliensis bark samples. Among these, 450 genes were unique to JA and LA as they were not differentially expressed in ethephon-treated samples compared with the untreated samples. Most transcription factors from the JA- and LA-specific dataset were classified under MYB, APETALA2/ethylene response factor (AP2/ERF), and basic-helix-loop-helix (bHLH) gene families that were involved in tissue developmental pathways, and we proposed that Bel5-GA2 oxidase 1-KNOTTED-like homeobox complex are likely involved in JA- and LA-induced SLD in H. brasiliensis. We also discovered alternative spliced transcripts, putative novel transcripts, and cis-natural antisense transcript pairs related to SLD event. This study has advanced understanding on the transcriptional regulatory network of SLD in H. brasiliensis.
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Affiliation(s)
- Swee Cheng Loh
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Ahmad Sofiman Othman
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - G Veera Singham
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
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33
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An M, Zhou T, Guo Y, Zhao X, Wu Y. Molecular Regulation of Host Defense Responses Mediated by Biological Anti-TMV Agent Ningnanmycin. Viruses 2019; 11:E815. [PMID: 31484426 PMCID: PMC6784071 DOI: 10.3390/v11090815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 12/28/2022] Open
Abstract
Ningnanmycin (NNM) belongs to microbial pesticides that display comprehensive antiviral activity against plant viruses. NNM treatment has been shown to efficiently delay or suppress the disease symptoms caused by tobacco mosaic virus (TMV) infection in local-inoculated or systemic-uninoculated tobacco leaves, respectively. However, the underlying molecular mechanism of NNM-mediated antiviral activity remains to be further elucidated. In this study, 414 differentially expressed genes (DEGs), including 383 which were up-regulated and 31 down-regulated, caused by NNM treatment in TMV-infected BY-2 protoplasts, were discovered by RNA-seq. In addition, KEGG analysis indicated significant enrichment of DEGs in the plant-pathogen interaction and MAPK signaling pathway. The up-regulated expression of crucial DEGs, including defense-responsive genes, such as the receptor-like kinase FLS2, RLK1, and the mitogen-activated protein kinase kinase kinase MAPKKK, calcium signaling genes, such as the calcium-binding protein CML19, as well as phytohormone responsive genes, such as the WRKY transcription factors WRKY40 and WRKY70, were confirmed by RT-qPCR. These findings provided valuable insights into the antiviral mechanisms of NNM, which indicated that the agent induces tobacco systemic resistance against TMV via activating multiple plant defense signaling pathways.
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Affiliation(s)
- Mengnan An
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Tao Zhou
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Yi Guo
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Xiuxiang Zhao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
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34
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Yao S, Yang Z, Yang R, Huang Y, Guo G, Kong X, Lan Y, Zhou T, Wang H, Wang W, Cao X, Wu J, Li Y. Transcriptional Regulation of miR528 by OsSPL9 Orchestrates Antiviral Response in Rice. MOLECULAR PLANT 2019; 12:1114-1122. [PMID: 31059826 DOI: 10.1016/j.molp.2019.04.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/15/2019] [Accepted: 04/25/2019] [Indexed: 05/04/2023]
Abstract
Many microRNAs (miRNAs) are critical regulators of plant antiviral defense. However, little is known about how these miRNAs respond to virus invasion at the transcriptional level. We previously show that defense against Rice stripe virus (RSV) invasion entailed a reduction of miR528 accumulation in rice, alleviating miR528-mediated degradation of L-Ascorbate Oxidase (AO) mRNA and bolstering the antiviral activity of AO. Here we show that the miR528-AO defense module is regulated by the transcription factor SPL9. SPL9 displayed high-affinity binding to specific motifs within the promoter region of miR528 and activated the expression of miR528 gene in vivo. Loss-of-function mutations in SPL9 caused a significant reduction in miR528 accumulation but a substantial increase of AO mRNA, resulting in enhanced plant resistance to RSV. Conversely, transgenic overexpression of SPL9 stimulated the expression of miR528 gene, hence lowering the level of AO mRNA and compromising rice defense against RSV. Importantly, gain in RSV susceptibility did not occur when SPL9 was overexpressed in mir528 loss-of-function mutants, or in transgenic rice expressing a miR528-resistant AO. Taken together, the finding of SPL9-mediated transcriptional activation of miR528 expression adds a new regulatory layer to the miR528-AO antiviral defense pathway.
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Affiliation(s)
- Shengze Yao
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhirui Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Rongxin Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Huang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ge Guo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiangyue Kong
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - He Wang
- Rice Research Institute and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenming Wang
- Rice Research Institute and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
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35
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Yu Y, Ni Z, Wang Y, Wan H, Hu Z, Jiang Q, Sun X, Zhang H. Overexpression of soybean miR169c confers increased drought stress sensitivity in transgenic Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:68-78. [PMID: 31203895 DOI: 10.1016/j.plantsci.2019.05.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 05/03/2023]
Abstract
The miR169 family, a large-scale microRNA gene family conserved in plants, is involved in stress responses, although how soybean miR169 functions in response to drought stress remains unclear. We show that gma-miR169c exerts a negative regulatory role in the response to drought stress by inhibiting the expression of its target gene, nuclear factor Y-A (NF-YA). A real-time RT-PCR analysis indicated that gma-miR169c is widely expressed in soybean tissues and induced by polyethylene glycol (PEG), high salt, cold stress and abscisic acid (ABA). Histochemical ß-glucuronidase (GUS) staining showed that the gma-miR169c promoter drives GUS reporter gene expression in various transgenic Arabidopsis tissues, and the stress-induced pattern was confirmed in transgenic Arabidopsis and transgenic soybean hairy roots. Arabidopsis overexpressing gma-miR169c is more sensitive to drought stress, with reduced survival, accelerated leaf water loss, and shorter root length than wild-type plants. We identified a precise cleavage site for 10 gma-miR169c targets and found reduced transcript levels of the AtNFYA1 and AtNFYA5 transcription factors in gma-miR169c-overexpressing Arabidopsis and reduced expression of the stress response genes AtRD29A, AtRD22, AtGSTU25 and AtCOR15A. These results indicate that gma-miR169c plays a negative regulatory role in drought stress and is a candidate miRNA for improving plant drought adaptation.
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Affiliation(s)
- Yuehua Yu
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, PR China
| | - Zhiyong Ni
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, PR China.
| | - Yi Wang
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, PR China
| | - Huina Wan
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, PR China
| | - Zheng Hu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Qiyan Jiang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Xianjun Sun
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Hui Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
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36
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Zhou D, Li G, Sun H, Liu F, Chen L, Xiong S, Yin Y. In silico studies reveal RSc1154 and RhlE as temperature-related pathogenic proteins of Ralstonia solanacearum. FEMS Microbiol Lett 2019; 366:5556940. [PMID: 31504466 DOI: 10.1093/femsle/fnz183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/29/2019] [Indexed: 11/13/2022] Open
Abstract
This study aimed to explore the temperature-related pathogenic mechanism of Ralstonia solanacearum infection in tomato (Lycopersicon esculentum Mill.). Based on bioinformatics analysis of microarray dataset (GSE33657), the co-differentially expressed genes (co-DEGs) ribonucleic acids were identified in R. solanacearum GMI1000-infected L. esculentum Mill., which was cultured at 20°C and 28°C, in rich medium containing casamino acids, peptone, and glucose (CPG) and planta. In total, 63 upregulated co-DEGs and 57 downregulated co-DEGs were identified between 20°C and 28°C in the CPG and planta groups. Protein-protein interaction network revealed 70 protein interaction pairs and 59 nodes. Notably, iolG, iolE, ioll and RSc1248 played critical roles in the network. The subcellular localization and functional annotation showed that the increased expressed proteins were mainly localized in the inner cell membrane, while those with decreased expression were localized in the cytoplasm. Furthermore, these proteins were mainly enriched in regulation of DNA-templated transcription. RSc1154 and RhlE were predicted to be temperature-related pathogenic genes for R. solanacearum in tomato. Furthermore, phosphorelay signal transduction system function might play an important role in R. solanacearum infection. The candidate genes were verified by quantitative real-time PCR, and the results were consistent with gene expression profile.
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Affiliation(s)
- Daxiang Zhou
- College of Life Science, Chongqing University, Chongqing 400044, China.,Chongqing Engineering Laboratory of Green Planting and Deep Processing of famous-region drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404120, China
| | - Guoli Li
- Department of Basic Medicine, Chongqing Three Gorges Medical College, Chongqing 404120, China
| | - Houliang Sun
- Department of Basic Medicine, Chongqing Three Gorges Medical College, Chongqing 404120, China
| | - Feng Liu
- Department of Basic Medicine, Chongqing Three Gorges Medical College, Chongqing 404120, China
| | - Lin Chen
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of famous-region drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404120, China
| | - Shu Xiong
- Department of Basic Medicine, Chongqing Three Gorges Medical College, Chongqing 404120, China
| | - Youping Yin
- College of Life Science, Chongqing University, Chongqing 400044, China
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37
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Zhang X, Xie S, Han J, Zhou Y, Liu C, Zhou Z, Wang F, Cheng Z, Zhang J, Hu Y, Hao Z, Li M, Zhang D, Yong H, Huang Y, Weng J, Li X. Integrated transcriptome, small RNA, and degradome analysis reveals the complex network regulating starch biosynthesis in maize. BMC Genomics 2019; 20:574. [PMID: 31296166 PMCID: PMC6625009 DOI: 10.1186/s12864-019-5945-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background Starch biosynthesis in endosperm is a key process influencing grain yield and quality in maize. Although a number of starch biosynthetic genes have been well characterized, the mechanisms by which the expression of these genes is regulated, especially in regard to microRNAs (miRNAs), remain largely unclear. Results Sequence data for small RNAs, degradome, and transcriptome of maize endosperm at 15 and 25 d after pollination (DAP) from inbred lines Mo17 and Ji419, which exhibit distinct starch content and starch granule structure, revealed the mediation of starch biosynthetic pathways by miRNAs. Transcriptome analysis of these two lines indicated that 33 of 40 starch biosynthetic genes were differentially expressed, of which 12 were up-regulated in Ji419 at 15 DAP, one was up-regulated in Ji419 at 25 DAP, 14 were up-regulated in Ji419 at both 15 and 25 DAP, one was down-regulated in Ji419 at 15 DAP, two were down-regulated in Ji419 at 25 DAP, and three were up-regulated in Ji419 at 15 DAP and down-regulated in Ji419 at 25 DAP, compared with Mo17. Through combined analyses of small RNA and degradome sequences, 22 differentially expressed miRNAs were identified, including 14 known and eight previously unknown miRNAs that could target 35 genes. Furthermore, a complex co-expression regulatory network was constructed, in which 19 miRNAs could modulate starch biosynthesis in endosperm by tuning the expression of 19 target genes. Moreover, the potential operation of four miRNA-mediated pathways involving transcription factors, miR169a-NF-YA1-GBSSI/SSIIIa and miR169o-GATA9-SSIIIa/SBEIIb, was validated via analyses of expression pattern, transient transformation assays, and transactivation assays. Conclusion Our results suggest that miRNAs play a critical role in starch biosynthesis in endosperm, and that miRNA-mediated networks could modulate starch biosynthesis in this tissue. These results have provided important insights into the molecular mechanism of starch biosynthesis in developing maize endosperm. Electronic supplementary material The online version of this article (10.1186/s12864-019-5945-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaocong Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sidi Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jienan Han
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Chang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feifei Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zixiang Cheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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38
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Zhao C, Wang H, Lu Y, Hu J, Qu L, Li Z, Wang D, He Y, Valls M, Coll NS, Chen Q, Lu H. Deep Sequencing Reveals Early Reprogramming of Arabidopsis Root Transcriptomes Upon Ralstonia solanacearum Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:813-827. [PMID: 31140930 DOI: 10.1094/mpmi-10-18-0268-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Bacterial wilt caused by the bacterial pathogen Ralstonia solanacearum is one of the most devastating crop diseases worldwide. The molecular mechanisms controlling the early stage of R. solanacearum colonization in the root remain unknown. Aiming to better understand the mechanism of the establishment of R. solanacearum infection in root, we established four stages in the early interaction of the pathogen with Arabidopsis roots and determined the transcriptional profiles of these stages of infection. A total 2,698 genes were identified as differentially expressed genes during the initial 96 h after infection, with the majority of changes in gene expression occurring after pathogen-triggered root-hair development observed. Further analysis of differentially expressed genes indicated sequential activation of multiple hormone signaling cascades, including abscisic acid (ABA), auxin, jasmonic acid, and ethylene. Simultaneous impairment of ABA receptor genes promoted plant wilting symptoms after R. solanacearum infection but did not affect primary root growth inhibition or root-hair and lateral root formation caused by R. solanacearum. This indicated that ABA signaling positively regulates root defense to R. solanacearum. Moreover, transcriptional changes of genes involved in primary root, lateral root, and root-hair formation exhibited high temporal dynamics upon infection. Taken together, our results suggest that successful infection of R. solanacearum on roots is a highly programmed process involving in hormone crosstalk.
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Affiliation(s)
- Cuizhu Zhao
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huijuan Wang
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yao Lu
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinxue Hu
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ling Qu
- 2 National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia 750002, China
| | - Zheqing Li
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dongdong Wang
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yizhe He
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Marc Valls
- 3 Genetics section, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
- 4 Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Catalonia, Spain
| | - Núria S Coll
- 4 Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Catalonia, Spain
| | - Qin Chen
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haibin Lu
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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39
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Lineage-Specific Evolved MicroRNAs Regulating NB-LRR Defense Genes in Triticeae. Int J Mol Sci 2019; 20:ijms20133128. [PMID: 31248042 PMCID: PMC6651130 DOI: 10.3390/ijms20133128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/04/2023] Open
Abstract
Disease resistance genes encoding proteins with nucleotide binding sites and Leucine-Rich Repeat (NB-LRR) domains include many members involved in the effector-triggered immunity pathway in plants. The transcript levels of these defense genes are negatively regulated by diverse microRNAs (miRNAs) in angiosperms and gymnosperms. In wheat, using small RNA expression datasets and degradome datasets, we identified five miRNA families targeting NB-LRR defense genes in monocots, some of which arose in the Triticeae species era. These miRNAs regulate different types of NB-LRR genes, most of them with coil-coiled domains, and trigger the generation of secondary small interfering RNAs (siRNA) as a phased pattern in the target site regions. In addition to acting in response to biotic stresses, they are also responsive to abiotic stresses such as heat, drought, salt, and light stress. Their copy number and expression variation in Triticeae suggest a rapid birth and death frequency. Altogether, non-conserved miRNAs as conserved transcriptional regulators in gymnosperms and angiosperms regulating the disease resistance genes displayed quick plasticity including the variations of sequences, gene copy number, functions, and expression level, which accompanied with NB-LRR genes may be tune-regulated to plants in natural environments with various biotic and abiotic stresses.
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40
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Chen H, Yang Q, Chen K, Zhao S, Zhang C, Pan R, Cai T, Deng Y, Wang X, Chen Y, Chu W, Xie W, Zhuang W. Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.). BMC Genomics 2019; 20:392. [PMID: 31113378 PMCID: PMC6528327 DOI: 10.1186/s12864-019-5770-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
Background Peanut embryo development is a complex process involving a series of gene regulatory pathways and is easily affected by various elements in the soil. Calcium deficiency in the soil induces early embryo abortion in peanut, which provides an opportunity to determine the mechanism underlying this important event. MicroRNA (miRNA)-guided target gene regulation is vital to a wide variety of biological processes. However, whether miRNAs participate in peanut embryo abortion under calcium deficiency has yet to be explored. Results In this study, with the assistance of a recently established platform for genome sequences of wild peanut species, we analyzed small RNAs (sRNAs) in early peanut embryos. A total of 29 known and 132 potential novel miRNAs were discovered in 12 peanut-specific miRNA families. Among the identified miRNAs, 87 were differentially expressed during early embryo development under calcium deficiency and sufficiency conditions, and 117 target genes of the differentially expressed miRNAs were identified. Integrated analysis of miRNAs and transcriptome expression revealed 52 differentially expressed target genes of 20 miRNAs. The expression profiles for some differentially expressed targets by gene chip analysis were consistent with the transcriptome sequencing results. Together, our results demonstrate that seed/embryo development-related genes such as TCP3, AP2, EMB2750, and GRFs; cell division and proliferation-related genes such as HsfB4 and DIVARICATA; plant hormone signaling pathway-related genes such as CYP707A1 and CYP707A3, with which abscisic acid (ABA) is involved; and BR1, with which brassinosteroids (BRs) are involved, were actively modulated by miRNAs during early embryo development. Conclusions Both a number of miRNAs and corresponding target genes likely playing key roles in the regulation of peanut embryo abortion under calcium deficiency were identified. These findings provide for the first time new insights into miRNA-mediated regulatory pathways involved in peanut embryo abortion under calcium deficiency. Electronic supplementary material The online version of this article (10.1186/s12864-019-5770-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hua Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Qiang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Kun Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Shanshan Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Chong Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Ronglong Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, 30013, Taiwan
| | - Tiecheng Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Ye Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Yuting Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Wenting Chu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Wenping Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Weijian Zhuang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China. .,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China. .,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.
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41
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Song X, Li Y, Cao X, Qi Y. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:489-525. [PMID: 30848930 DOI: 10.1146/annurev-arplant-050718-100334] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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42
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Xing Q, Zhang W, Liu M, Li L, Li X, Yan J. Genome-Wide Identification of Long Non-coding RNAs Responsive to Lasiodiplodia theobromae Infection in Grapevine. Evol Bioinform Online 2019; 15:1176934319841362. [PMID: 30992656 PMCID: PMC6449811 DOI: 10.1177/1176934319841362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) refer to a class of RNA molecules that are longer
than 200 nucleotides and do not encode proteins. Numerous lncRNAs have recently
emerged as important regulators of many biological processes in animals and
plants, including responses to environmental stress and pathogens.
Botryosphaeria dieback is one of the more severe grapevine
trunk diseases worldwide. However, how lncRNAs function during
Botryosphaeriaceae infection is largely unknown. We performed high-throughput
RNA-sequencing (RNA-seq) of susceptible and more tolerant grapevine cultivars
infected with Lasiodiplodia theobromae. Overall, we predicted
1826 novel candidate lncRNAs, including long intergenic non-coding RNAs
(lincRNAs) and natural antisense transcripts (lncNATs). The data reveal the
functions of a set of lncRNAs that were differentially expressed between the
resistant cultivar Merlot and the susceptible cultivar Cabernet Franc. Several
lncRNAs were predicted to be precursors for grape microRNAs involved in the
L theobromae infection. These results provide new insight
into the lncRNAs of grapevine that are involved in the response to L
theobromae infection.
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Affiliation(s)
- Qikai Xing
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Beijing, China
| | - Wei Zhang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Beijing, China
| | - Mei Liu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Lingxian Li
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xinghong Li
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Beijing, China
| | - Jiye Yan
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Beijing, China
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43
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Sun J, Cao L, Li H, Wang G, Wang S, Li F, Zou X, Wang J. Early responses given distinct tactics to infection of Peronophythora litchii in susceptible and resistant litchi cultivar. Sci Rep 2019; 9:2810. [PMID: 30808947 PMCID: PMC6391439 DOI: 10.1038/s41598-019-39100-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 01/11/2019] [Indexed: 12/20/2022] Open
Abstract
Litchi downy blight, a destructive litchi disease caused by Peronophythora litchii, is controlled by intensive fungicide applying. Sources of resistance are used in conventional breeding approaches, but the mechanism is not well understood. Follow-up six years investigation, 'Guiwei' and 'Heiye' displayed stable susceptible and resistant against to P. litchii, respectively. After 72 hour inoculation, 'Heiye' showed few disease spots, while 'Guiwei' appeared brown and covered with white sporangia. Germination of sporangia and growth of mycelium in 'Guiwei' is more quickly than in 'Heiye'. Transcript levels were measured at 6, 24, and 48 hour post-inoculation. 'Oxidation-reduction process' was dramatically enhanced in 'Heiye', which could promote its resistance to pathogen infection. A small ratio (3.78%) of common DEGs indicates that resistant and susceptible cultivars take different strategies to defense against P. litchii. At early infection stage, 'Heiye' induced a larger number of genes, including seven receptor-like kinases, which quickly recognized attack of pathogen and led to a rapidly resistance by regulation of degradation of proteasome, transcription factors, and cell wall remodeling. The early DGEs were exiguous in 'Guiwei', suggesting a weak response. Once the infection was successful, the resistance was repressed by down-regulated genes involved in phenylpropanoid metabolism, ET biosynthesis and signaling conduction in 'Guiwei'. In conclusion, quickly recognition and early responses to pathogen, as well as minimal pathogen development and basal expression of resistance-related genes, were correlated with a high level of resistance in 'Heiye', while susceptible 'Guiwei' suffered massive infection due to lagging response and repressed signal transduction.
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Affiliation(s)
- Jinhua Sun
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Lulu Cao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Huanling Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Guo Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Shujun Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Fang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Xiaoxiao Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Jiabao Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.
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44
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Evolution of Disease Defense Genes and Their Regulators in Plants. Int J Mol Sci 2019; 20:ijms20020335. [PMID: 30650550 PMCID: PMC6358896 DOI: 10.3390/ijms20020335] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Biotic stresses do damage to the growth and development of plants, and yield losses for some crops. Confronted with microbial infections, plants have evolved multiple defense mechanisms, which play important roles in the never-ending molecular arms race of plant–pathogen interactions. The complicated defense systems include pathogen-associated molecular patterns (PAMP) triggered immunity (PTI), effector triggered immunity (ETI), and the exosome-mediated cross-kingdom RNA interference (CKRI) system. Furthermore, plants have evolved a classical regulation system mediated by miRNAs to regulate these defense genes. Most of the genes/small RNAs or their regulators that involve in the defense pathways can have very rapid evolutionary rates in the longitudinal and horizontal co-evolution with pathogens. According to these internal defense mechanisms, some strategies such as molecular switch for the disease resistance genes, host-induced gene silencing (HIGS), and the new generation of RNA-based fungicides, have been developed to control multiple plant diseases. These broadly applicable new strategies by transgene or spraying ds/sRNA may lead to reduced application of pesticides and improved crop yield.
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45
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Identification of browning-related microRNAs and their targets reveals complex miRNA-mediated browning regulatory networks in Luffa cylindrica. Sci Rep 2018; 8:16242. [PMID: 30389964 PMCID: PMC6214963 DOI: 10.1038/s41598-018-33896-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/07/2018] [Indexed: 11/09/2022] Open
Abstract
As a non-coding and endogenous small RNA, MicroRNA (miRNA) takes a vital regulatory role in plant growth and development. Long-term storage and processing of many fruits and vegetables, including Luffa, are subject to influences from browning, a common post-harvest problem that adversely affects flavor, aroma, and nutritional value. The browning regulatory networks mediated by miRNA, however, remain largely unexplored. For a systematic identification of browning-responsive miRNAs and the targets, we built two RNA libraries from Luffa pulps of near-isogenic line, with resistant and sensitive browning characteristics respectively, and then sequenced them using Solexa high-throughput technology. We consequently identified 179 known miRNAs that represent 17 non-conserved miRNA families and 24 conserved families, as well as 84 potential novel miRNAs, among which 16 miRNAs (eight known and eight novel miRNAs) were found to exhibit significant differential expressions and were thus identified as browning-related miRNAs. We then studied those browning-responsive miRNAs and the corresponding targets with RT-qPCR and finally validated their expression patterns. The results revealed that the expression patterns are specific to plant development stages and the miRNAs are identified with 39 target transcripts, which involve in plant development, defense response, transcriptional regulation, and signal transduction. After characterizing these miRNAs and their targets, we propose a browning regulatory network model of miRNA-mediatation in this paper. The findings of the work are helpful for the understanding of miRNA-mediated regulatory mechanisms of browning in Luffa, and will facilitate genetic improvement of pulp characteristics in Luffa.
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46
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Danilevicz MF, Moharana KC, Venancio TM, Franco LO, Cardoso SRS, Cardoso M, Thiebaut F, Hemerly AS, Prosdocimi F, Ferreira PCG. Copaifera langsdorffii Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes. Noncoding RNA 2018; 4:ncrna4040027. [PMID: 30297664 PMCID: PMC6316758 DOI: 10.3390/ncrna4040027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in multiple regulatory pathways and its versatile form of action has disclosed a new layer in gene regulation. LncRNAs have their expression levels modulated during plant development, and in response to stresses with tissue-specific functions. In this study, we analyzed lncRNA from leaf samples collected from the legume Copaifera langsdorffii Desf. (copaíba) present in two divergent ecosystems: Cerrado (CER; Ecological Station of Botanical Garden in Brasília, Brazil) and Atlantic Rain Forest (ARF; Rio de Janeiro, Brazil). We identified 8020 novel lncRNAs, and they were compared to seven Fabaceae genomes and transcriptomes, to which 1747 and 2194 copaíba lncRNAs were mapped, respectively, to at least one species. The secondary structures of the lncRNAs that were conserved and differentially expressed between the populations were predicted using in silico methods. A few selected lncRNA were confirmed by RT-qPCR in the samples from both biomes; Additionally, the analysis of the lncRNA sequences predicted that some might act as microRNA (miRNA) targets or decoys. The emerging studies involving lncRNAs function and conservation have shown their involvement in several types of biotic and abiotic stresses. Thus, the conservation of lncRNAs among Fabaceae species considering their rapid turnover, suggests they are likely to have been under functional conservation pressure. Our results indicate the potential involvement of lncRNAs in the adaptation of C. langsdorffii in two different biomes.
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Affiliation(s)
- Monica F Danilevicz
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil.
| | - Luciana O Franco
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Sérgio R S Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Mônica Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Adriana S Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Paulo C G Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
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47
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Chaudhary V, Jangra S, Yadav NR. Nanotechnology based approaches for detection and delivery of microRNA in healthcare and crop protection. J Nanobiotechnology 2018; 16:40. [PMID: 29653577 PMCID: PMC5897953 DOI: 10.1186/s12951-018-0368-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/07/2018] [Indexed: 12/31/2022] Open
Abstract
Nanobiotechnology has the potential to revolutionize diverse sectors including medicine, agriculture, food, textile and pharmaceuticals. Disease diagnostics, therapeutics and crop protection strategies are fast emerging using nanomaterials preferably nanobiomaterials. It has potential for development of novel nanobiomolecules which offer several advantages over conventional treatment methods. RNA nanoparticles with many unique features are promising candidates in disease treatment. The miRNAs are involved in many biochemical and developmental pathways and their regulation in plants and animals. These appear to be a powerful tool for controlling various pathological diseases in human, plants and animals, however there are challenges associated with miRNA based nanotechnology. Several advancements made in the field of miRNA therapeutics make it an attractive approach, but a lot more has to be explored in nanotechnology assisted miRNA therapy. The miRNA based technologies can be employed for detection and combating crop diseases as well. Despite these potential advantages, nanobiotechnology applications in the agricultural sector are still in its infancy and have not yet made its mark in comparison with healthcare sector. The review provides a platform to discuss nature, role and use of miRNAs in nanobiotechnology applications.
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Affiliation(s)
- Vrantika Chaudhary
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Sumit Jangra
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Neelam R. Yadav
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
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48
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Je BI, Xu F, Wu Q, Liu L, Meeley R, Gallagher JP, Corcilius L, Payne RJ, Bartlett ME, Jackson D. The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors. eLife 2018; 7:35673. [PMID: 29543153 DOI: 10.7554/elife.35673.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 02/21/2018] [Indexed: 05/29/2023] Open
Abstract
Meristems contain groups of indeterminate stem cells, which are maintained by a feedback loop between CLAVATA (CLV) and WUSCHEL (WUS) signaling. CLV signaling involves the secretion of the CLV3 peptide and its perception by a number of Leucine-Rich-Repeat (LRR) receptors, including the receptor-like kinase CLV1 and the receptor-like protein CLV2 coupled with the CORYNE (CRN) pseudokinase. CLV2, and its maize ortholog FASCIATED EAR2 (FEA2) appear to function in signaling by CLV3 and several related CLV3/EMBRYO-SURROUNDING REGION (CLE) peptide ligands. Nevertheless, how signaling specificity is achieved remains unknown. Here we show that FEA2 transmits signaling from two distinct CLE peptides, the maize CLV3 ortholog ZmCLE7 and ZmFON2-LIKE CLE PROTEIN1 (ZmFCP1) through two different candidate downstream effectors, the alpha subunit of the maize heterotrimeric G protein COMPACT PLANT2 (CT2), and ZmCRN. Our data provide a novel framework to understand how diverse signaling peptides can activate different downstream pathways through common receptor proteins.
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Affiliation(s)
- Byoung Il Je
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
- Department of Horticultural Bioscience, College of Natural Resource and Life Science, Pusan National University, Miryang, Republic of Korea
| | - Fang Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Qingyu Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Lei Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Robert Meeley
- DuPont Pioneer, Agricultural Biotechnology, Johnston, United States
| | | | | | | | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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49
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Je BI, Xu F, Wu Q, Liu L, Meeley R, Gallagher JP, Corcilius L, Payne RJ, Bartlett ME, Jackson D. The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors. eLife 2018. [PMID: 29543153 PMCID: PMC5854466 DOI: 10.7554/elife.35673] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Meristems contain groups of indeterminate stem cells, which are maintained by a feedback loop between CLAVATA (CLV) and WUSCHEL (WUS) signaling. CLV signaling involves the secretion of the CLV3 peptide and its perception by a number of Leucine-Rich-Repeat (LRR) receptors, including the receptor-like kinase CLV1 and the receptor-like protein CLV2 coupled with the CORYNE (CRN) pseudokinase. CLV2, and its maize ortholog FASCIATED EAR2 (FEA2) appear to function in signaling by CLV3 and several related CLV3/EMBRYO-SURROUNDING REGION (CLE) peptide ligands. Nevertheless, how signaling specificity is achieved remains unknown. Here we show that FEA2 transmits signaling from two distinct CLE peptides, the maize CLV3 ortholog ZmCLE7 and ZmFON2-LIKE CLE PROTEIN1 (ZmFCP1) through two different candidate downstream effectors, the alpha subunit of the maize heterotrimeric G protein COMPACT PLANT2 (CT2), and ZmCRN. Our data provide a novel framework to understand how diverse signaling peptides can activate different downstream pathways through common receptor proteins.
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Affiliation(s)
- Byoung Il Je
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Department of Horticultural Bioscience, College of Natural Resource and Life Science, Pusan National University, Miryang, Republic of Korea
| | - Fang Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Qingyu Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Lei Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Robert Meeley
- DuPont Pioneer, Agricultural Biotechnology, Johnston, United States
| | | | | | | | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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50
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Abstract
Plant peptides secreted as signal molecular to trigger cell-to-cell signaling are indispensable for plant growth and defense processes. Preciously, it is regraded some plant peptides function in plant growth and development, whereas others regulate defense response in plant-microbe interactions. However, this prejudice is got rid due to more and more evidence showed growth-related plant peptides also exhibit bifunctional roles in plant defense response against different microbial pathogens. Here we provide a mini-review of reported types of plant peptides, including their basic information, reported receptor ligands, and especially direct or indirect roles in plant immune responses.
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Affiliation(s)
- Z. Hu
- Department of Horticulture, Zhejiang University, Hangzhou, P.R. China
| | - H. Zhang
- Department of Horticulture, Zhejiang University, Hangzhou, P.R. China
| | - K. Shi
- Department of Horticulture, Zhejiang University, Hangzhou, P.R. China
- CONTACT Kai Shi Department of Horticulture, Zhejiang University, Hangzhou, P.R. China
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