1
|
Zhao X, Li F, Ali M, Li X, Fu X, Zhang X. Emerging roles and mechanisms of lncRNAs in fruit and vegetables. HORTICULTURE RESEARCH 2024; 11:uhae046. [PMID: 38706580 PMCID: PMC11069430 DOI: 10.1093/hr/uhae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 05/07/2024]
Abstract
With the development of genome sequencing technologies, many long non-coding RNAs (lncRNAs) have been identified in fruit and vegetables. lncRNAs are primarily transcribed and spliced by RNA polymerase II (Pol II) or plant-specific Pol IV/V, and exhibit limited evolutionary conservation. lncRNAs intricately regulate various aspects of fruit and vegetables, including pigment accumulation, reproductive tissue development, fruit ripening, and responses to biotic and abiotic stresses, through diverse mechanisms such as gene expression modulation, interaction with hormones and transcription factors, microRNA regulation, and involvement in alternative splicing. This review presents a comprehensive overview of lncRNA classification, basic characteristics, and, most importantly, recent advances in understanding their functions and regulatory mechanisms.
Collapse
Affiliation(s)
- Xiuming Zhao
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Fujun Li
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Maratab Ali
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Xiaoan Li
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Xiaodong Fu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Xinhua Zhang
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| |
Collapse
|
2
|
Yadhav Y, Selvaraj K, Ramasamy S, Venkataraman S. Computational studies on rep and capsid proteins of CRESS DNA viruses. Virusdisease 2024; 35:17-26. [PMID: 38817400 PMCID: PMC11133267 DOI: 10.1007/s13337-024-00858-x] [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: 11/20/2023] [Accepted: 01/29/2024] [Indexed: 06/01/2024] Open
Abstract
The circular rep-encoding single-stranded DNA viruses (CRESS DNA viruses) are among the smallest, with 2-6 kb ssDNA genomes that encode for a coat protein (C) and a replication protein (R). To comprehend the complexity and divergence of the C and R proteins, we have created predictive structural models of representative viruses infecting unique hosts from each family using the neural network-based method AlphaFold2 and carried out molecular dynamic simulations to assess their stability. The structural characteristics indicate that differences in loops and amino-terminus may play a significant role in facilitating adaptations to multiple hosts and vectors. In comparison to the C, the Rs show a high degree of conservation and structural mimicry of the nuclease-helicase domains of plasmids. A phylogenetic analysis based on the structures and sequences of the C and R proteins reveals evolutionary variances. Our study also highlights the conservation of structural components involved in the interaction of R with the conserved intergenic region of the genome. Further, we envisage that the adaptability of R's central linker may be crucial for establishing interactions with multiple protein partners, including C. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00858-x.
Collapse
Affiliation(s)
- Yagavi Yadhav
- Department of Biotechnology, Anna University, Guindy, Chennai, 600025 India
| | - Karthiga Selvaraj
- Department of Biotechnology, Anna University, Guindy, Chennai, 600025 India
| | | | | |
Collapse
|
3
|
Gao X, Hao K, Du Z, Zhang S, Guo J, Li J, Wang Z, An M, Xia Z, Wu Y. Whole-transcriptome characterization and functional analysis of lncRNA-miRNA-mRNA regulatory networks responsive to sugarcane mosaic virus in maize resistant and susceptible inbred lines. Int J Biol Macromol 2024; 257:128685. [PMID: 38096927 DOI: 10.1016/j.ijbiomac.2023.128685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/18/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
Sugarcane mosaic virus (SCMV) is one of the most important pathogens causing maize dwarf mosaic disease, which seriously affects the yield and quality of maize. Currently, the molecular mechanism of non-coding RNAs (ncRNAs) responding to SCMV infection in maize is still uncovered. In this study, a total of 112 differentially expressed (DE)-long non-coding RNAs (lncRNAs), 24 DE-microRNAs (miRNAs), and 1822 DE-messenger RNAs (mRNAs), and 363 DE-lncRNAs, 230 DE-miRNAs, and 4376 DE-mRNAs were identified in maize resistant (Chang7-2) and susceptible (Mo17) inbred lines in response to SCMV infection through whole-transcriptome RNA sequencing, respectively. Moreover, 4874 mRNAs potentially targeted by 635 miRNAs were obtained by degradome sequencing. Subsequently, several crucial SCMV-responsive lncRNA-miRNA-mRNA networks were established, of which the expression levels of lncRNA10865-miR166j-3p-HDZ25/69 (class III homeodomain-leucine zipper 25/69) module, and lncRNA14234-miR394a-5p-SPL11 (squamosal promoter-binding protein-like 11) module were further verified. Additionally, silencing lncRNA10865 increased the accumulations of SCMV and miR166j-3p, while silencing lncRNA14234 decreased the accumulations of SCMV and SPL11 targeted by miR394a-5p. This study revealed the interactions of lncRNAs, miRNAs and mRNAs in maize resistant and susceptible materials, providing novel clues to reveal the mechanism of maize in resistance to SCMV from the perspective of competing endogenous RNA (ceRNA) regulatory networks.
Collapse
Affiliation(s)
- Xinran Gao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Kaiqiang Hao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Zhichao Du
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Sijia Zhang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Jinxiu Guo
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Jian Li
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Zhiping Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Mengnan An
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Zihao Xia
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
| |
Collapse
|
4
|
Liu Q, Xue J, Zhang L, Jiang L, Li C. Unveiling the Roles of LncRNA MOIRAs in Rice Blast Disease Resistance. Genes (Basel) 2024; 15:82. [PMID: 38254971 PMCID: PMC10815219 DOI: 10.3390/genes15010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Rice blast disease, caused by the fungal pathogen Magnaporthe oryzae, is a major threat to rice production worldwide. This study investigates the role of long non-coding RNAs (lncRNAs) in rice's response to this destructive disease, with a focus on their impacts on disease resistance and yield traits. Three specific lncRNAs coded by M. oryzae infection-responsive lncRNAs (MOIRAs), MOIRA1, MOIRA2, and MOIRA3, were identified as key regulators of rice's response to M. oryzae infection. Strikingly, when MOIRA1 and MOIRA2 were overexpressed, they exhibited a dual function: they increased rice's susceptibility to blast fungus, indicating a negative role in disease resistance, while simultaneously enhancing tiller numbers and single-plant yield, with no adverse effects on other yield-related traits. This unexpected improvement in productivity suggests the possibility of overcoming the traditional trade-off between disease resistance and crop yield. These findings provide a novel perspective on crop enhancement, offering a promising solution to global food security challenges by developing rice varieties that effectively balance disease resistance and increased productivity.
Collapse
Affiliation(s)
- Qing Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (L.J.); (C.L.)
| | - Jiao Xue
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Lanlan Zhang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (L.J.); (C.L.)
| | - Liqun Jiang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (L.J.); (C.L.)
| | - Chen Li
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (L.J.); (C.L.)
| |
Collapse
|
5
|
Zhang L, Lin T, Zhu G, Wu B, Zhang C, Zhu H. LncRNAs exert indispensable roles in orchestrating the interaction among diverse noncoding RNAs and enrich the regulatory network of plant growth and its adaptive environmental stress response. HORTICULTURE RESEARCH 2023; 10:uhad234. [PMID: 38156284 PMCID: PMC10753412 DOI: 10.1093/hr/uhad234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/01/2023] [Indexed: 12/30/2023]
Abstract
With the advent of advanced sequencing technologies, non-coding RNAs (ncRNAs) are increasingly pivotal and play highly regulated roles in the modulation of diverse aspects of plant growth and stress response. This includes a spectrum of ncRNA classes, ranging from small RNAs to long non-coding RNAs (lncRNAs). Notably, among these, lncRNAs emerge as significant and intricate components within the broader ncRNA regulatory networks. Here, we categorize ncRNAs based on their length and structure into small RNAs, medium-sized ncRNAs, lncRNAs, and circle RNAs. Furthermore, the review delves into the detailed biosynthesis and origin of these ncRNAs. Subsequently, we emphasize the diverse regulatory mechanisms employed by lncRNAs that are located at various gene regions of coding genes, embodying promoters, 5'UTRs, introns, exons, and 3'UTR regions. Furthermore, we elucidate these regulatory modes through one or two concrete examples. Besides, lncRNAs have emerged as novel central components that participate in phase separation processes. Moreover, we illustrate the coordinated regulatory mechanisms among lncRNAs, miRNAs, and siRNAs with a particular emphasis on the central role of lncRNAs in serving as sponges, precursors, spliceosome, stabilization, scaffolds, or interaction factors to bridge interactions with other ncRNAs. The review also sheds light on the intriguing possibility that some ncRNAs may encode functional micropeptides. Therefore, the review underscores the emergent roles of ncRNAs as potent regulatory factors that significantly enrich the regulatory network governing plant growth, development, and responses to environmental stimuli. There are yet-to-be-discovered roles of ncRNAs waiting for us to explore.
Collapse
Affiliation(s)
- Lingling Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Tao Lin
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Guoning Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Bin Wu
- Institute of Agro-products Storage and Processing, Xinjiang Academy of Agricultural Science, Urumqi, Xinjiang 830091, China
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| |
Collapse
|
6
|
Riyazuddin R, Singh K, Iqbal N, Labhane N, Ramteke P, Singh VP, Gupta R. Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107978. [PMID: 37660607 DOI: 10.1016/j.plaphy.2023.107978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.
Collapse
Affiliation(s)
- Riyazuddin Riyazuddin
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary.
| | - Kalpita Singh
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary; Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, H-2462, Martonvásár, Hungary.
| | - Nadeem Iqbal
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, 6726, Szeged, Hungary; Doctoral School of Environmental Sciences, University of Szeged, Szeged, Hungary.
| | - Nitin Labhane
- Department of Botany, Bhavan's College Andheri West, Mumbai, 400058, India.
| | - Pramod Ramteke
- Department of Biotechnology, Dr. Ambedkar College, Nagpur, India.
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Ravi Gupta
- College of General Education, Kookmin University, 02707, Seoul, Republic of Korea.
| |
Collapse
|
7
|
Sharma S, Sett S, Das T, Prasad A, Prasad M. Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107852. [PMID: 37356385 DOI: 10.1016/j.plaphy.2023.107852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/06/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.
Collapse
Affiliation(s)
| | - Susmita Sett
- National Institute of Plant Genome Research, New Delhi, India.
| | - Tuhin Das
- National Institute of Plant Genome Research, New Delhi, India.
| | - Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
| |
Collapse
|
8
|
Li W, Zhao P, Sun J, Yu X, Zou L, Li S, Di R, Ruan M, Peng M. Biological function research of Fusarium oxysporum f. sp. cubense inducible banana long noncoding RNA Malnc2310 in Arabidopsis. PLANT MOLECULAR BIOLOGY 2023:10.1007/s11103-023-01360-6. [PMID: 37507516 DOI: 10.1007/s11103-023-01360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/20/2023] [Indexed: 07/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) participate in plant biological processes under biotic and abiotic stresses. However, little is known about the function and regulation mechanism of lncRNAs related to the pathogen at a molecular level. A banana lncRNA, Malnc2310, is a Fusarium oxysporum f. sp. cubense inducible lncRNA in roots. In this study, we demonstrate the nuclear localization of Malnc2310 by fluorescence in situ hybridization and it can bind to several proteins that are related to flavonoid pathway, pathogen response and programmed cell death. Overexpression of Malnc2310 increases susceptibility to Fusarium crude extract (Fu), salinity, and cold in transgenic Arabidopsis. In addition, Malnc2310 transgenic Arabidopsis accumulated more anthocyanins under Fusarium crude extract and cold treatments that are related to upregulation of these genes involved in anthocyanin biosynthesis. Based on our findings, we propose that Malnc2310 may participate in flavonoid metabolism in plants under stress. Furthermore, phenylalanine ammonia lyase (PAL) protein expression was enhanced in Malnc2310 overexpressed transgenic Arabidopsis, and Malnc2310 may participate in PAL regulation by binding to it. This study provides new insights into the role of Malnc2310 in mediating plant stress adaptation.
Collapse
Affiliation(s)
- Wenbin Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Pingjuan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianbo Sun
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaoling Yu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Liangping Zou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shuxia Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Rong Di
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, USA
| | - Mengbin Ruan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Hainan Key Laboratory of Conservation and Utilization of Tropical Agricultural Biological Resources, Hainan Institute for Tropical Agricultural Resources, Haikou, China.
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China.
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, P.R.China / Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China.
| |
Collapse
|
9
|
Li C, Lai X, Yu X, Xiong Z, Chen J, Lang X, Feng H, Wan X, Liu K. Plant long noncoding RNAs: Recent progress in understanding their roles in growth, development, and stress responses. Biochem Biophys Res Commun 2023; 671:270-277. [PMID: 37311264 DOI: 10.1016/j.bbrc.2023.05.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/15/2023]
Abstract
Long noncoding RNA (lncRNA) transcripts are longer than 200 nt and are not translated into proteins. LncRNAs function in a wide variety of processes in plants and animals, but, perhaps because of their lower expression and conservation levels, plant lncRNAs had attracted less attention than protein-coding mRNAs. Now, recent studies have made remarkable progress in identifying lncRNAs and understanding their functions. In this review, we discuss a number of lncRNAs that have important functions in growth, development, reproduction, responses to abiotic stresses, and regulation of disease and insect resistance in plants. Additionally, we describe the known mechanisms of action of plant lncRNAs according to their origins within the genome. This review thus provides a guide for identifying and functionally characterizing new lncRNAs in plants.
Collapse
Affiliation(s)
- Chunmei Li
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaofeng Lai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xuanyue Yu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Zhiwen Xiong
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jie Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xingxuan Lang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Haotian Feng
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaorong Wan
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Kai Liu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| |
Collapse
|
10
|
Zwolinski AM, Brigden A, Rey MEC. Differences in the 3' intergenic region and the V2 protein of two sequence variants of tomato curly stunt virus play an important role in disease pathology in Nicotiana benthamiana. PLoS One 2023; 18:e0286149. [PMID: 37220127 DOI: 10.1371/journal.pone.0286149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023] Open
Abstract
Tomato production in South Africa is threatened by the emergence of tomato curly stunt virus (ToCSV), a monopartite Begomovirus transmitted by the whitefly vector Bemisia tabaci (Genn.). We investigated the role of sequence differences present in the 3' intergenic region (IR) and the V2 coding region on the differing infectivity of ToCSV sequence variant isolates V30 and V22 in the model host Nicotiana benthamiana. Using virus mutant chimeras, we determined that the development of the upward leaf roll symptom phenotype is mediated by sequence differences present in the 3' IR containing the TATA-associated composite element. Sequence differences present in the V2 coding region are responsible for modulating disease severity and symptom recovery in V22-infected plants. Serine substitution of V22 V2 Val27 resulted in a significant increase in disease severity with reduced recovery, the first study to demonstrate the importance of this V2 residue in disease development. Two putative ORFs, C5 and C6, were identified using in silico analysis and detection of an RNA transcript spanning their coding region suggests that these ORFs may be transcribed during infection. Additional virus-derived RNA transcripts spanning multiple ORFs and crossing the boundaries of recognised polycistronic transcripts, as well as the origin of replication within the IR, were detected in ToCSV-infected plants providing evidence of bidirectional readthrough transcription. From our results, we conclude that the diverse responses of the model host to ToCSV infection is influenced by select sequence differences and our findings provide several avenues for further investigation into the mechanisms behind these responses to infection.
Collapse
Affiliation(s)
- Alexander M Zwolinski
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Alison Brigden
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Marie E C Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
11
|
Wu R, Wu G, Huang Y, Zhang H, Tang J, Li M, Qing L. vsiRNA18 derived from tobacco curly shoot virus can regulate virus infection in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2023; 24:466-473. [PMID: 36797647 PMCID: PMC10098052 DOI: 10.1111/mpp.13310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 05/03/2023]
Abstract
Virus-derived small interfering RNAs (vsiRNAs) play important roles in regulating host endogenous gene expression to promote virus infection and induce RNA silencing to suppress virus infection. However, to date, how vsiRNAs affect geminivirus infection in host plants has been less studied. In this study, we found that tobacco curly shoot virus (TbCSV)-derived vsiRNA18 (TvsiRNA18) can regulate TbCSV infection in Nicotiana benthamiana plants. The virus-mediated small RNA expression system and stable transformation technique were used to clarify the molecular role of TvsiRNA18 in TbCSV infection. The results indicate that TvsiRNA18 can aggravate disease symptoms in these plants and enhance viral DNA accumulation. ATP-dependent RNA helicase (ATP-dRH) was proven to be a target of TvsiRNA18, and down-regulation of ATP-dRH in plants was shown to induce virus-like leaf curling symptoms and increase TbCSV infection. These results suggest that TvsiRNA18 is an important regulator of TbCSV infection by suppressing ATP-dRH expression. This is the first report to demonstrate that TbCSV-derived vsiRNA can target host endogenous genes to affect symptom development, which helps to reveal the molecular mechanism of symptom occurrence after the virus infects the host.
Collapse
Affiliation(s)
- Rui Wu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant ProtectionSouthwest UniversityChongqingChina
| | - Gentu Wu
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant ProtectionSouthwest UniversityChongqingChina
| | - Yongjie Huang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant ProtectionSouthwest UniversityChongqingChina
| | - Haolan Zhang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant ProtectionSouthwest UniversityChongqingChina
| | - Jiaxin Tang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant ProtectionSouthwest UniversityChongqingChina
| | - Mingjun Li
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant ProtectionSouthwest UniversityChongqingChina
| | - Ling Qing
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant ProtectionSouthwest UniversityChongqingChina
- National Citrus Engineering Research CenterSouthwest UniversityChongqingChina
| |
Collapse
|
12
|
Abstract
Robust plant immune systems are fine-tuned by both protein-coding genes and non-coding RNAs. Long non-coding RNAs (lncRNAs) refer to RNAs with a length of more than 200 nt and usually do not have protein-coding function and do not belong to any other well-known non-coding RNA types. The non-protein-coding, low expression, and non-conservative characteristics of lncRNAs restrict their recognition. Although studies of lncRNAs in plants are in the early stage, emerging studies have shown that plants employ lncRNAs to regulate plant immunity. Moreover, in response to stresses, numerous lncRNAs are differentially expressed, which manifests the actions of low-expressed lncRNAs and makes plant-microbe/insect interactions a convenient system to study the functions of lncRNAs. Here, we summarize the current advances in plant lncRNAs, discuss their regulatory effects in different stages of plant immunity, and highlight their roles in diverse plant-microbe/insect interactions. These insights will not only strengthen our understanding of the roles and actions of lncRNAs in plant-microbe/insect interactions but also provide novel insight into plant immune responses and a basis for further research in this field.
Collapse
Affiliation(s)
- Juan Huang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Wenling Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- HainanYazhou Bay Seed Lab, Sanya, China
| | - Yi Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| |
Collapse
|
13
|
Matsumura EE, Kormelink R. Small Talk: On the Possible Role of Trans-Kingdom Small RNAs during Plant-Virus-Vector Tritrophic Communication. PLANTS (BASEL, SWITZERLAND) 2023; 12:1411. [PMID: 36987098 PMCID: PMC10059270 DOI: 10.3390/plants12061411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Small RNAs (sRNAs) are the hallmark and main effectors of RNA silencing and therefore are involved in major biological processes in plants, such as regulation of gene expression, antiviral defense, and plant genome integrity. The mechanisms of sRNA amplification as well as their mobile nature and rapid generation suggest sRNAs as potential key modulators of intercellular and interspecies communication in plant-pathogen-pest interactions. Plant endogenous sRNAs can act in cis to regulate plant innate immunity against pathogens, or in trans to silence pathogens' messenger RNAs (mRNAs) and impair virulence. Likewise, pathogen-derived sRNAs can act in cis to regulate expression of their own genes and increase virulence towards a plant host, or in trans to silence plant mRNAs and interfere with host defense. In plant viral diseases, virus infection alters the composition and abundance of sRNAs in plant cells, not only by triggering and interfering with the plant RNA silencing antiviral response, which accumulates virus-derived small interfering RNAs (vsiRNAs), but also by modulating plant endogenous sRNAs. Here, we review the current knowledge on the nature and activity of virus-responsive sRNAs during virus-plant interactions and discuss their role in trans-kingdom modulation of virus vectors for the benefit of virus dissemination.
Collapse
|
14
|
Zhong X, Li J, Yang L, Wu X, Xu H, Hu T, Wang Y, Wang Y, Wang Z. Genome-wide identification and expression analysis of wall-associated kinase (WAK) and WAK-like kinase gene family in response to tomato yellow leaf curl virus infection in Nicotiana benthamiana. BMC PLANT BIOLOGY 2023; 23:146. [PMID: 36927306 PMCID: PMC10021985 DOI: 10.1186/s12870-023-04112-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Tomato yellow leaf curl virus (TYLCV) is a major monopartite virus in the family Geminiviridae and has caused severe yield losses in tomato and tobacco planting areas worldwide. Wall-associated kinases (WAKs) and WAK-like kinases (WAKLs) are a subfamily of the receptor-like kinase family implicated in cell wall signaling and transmitting extracellular signals to the cytoplasm, thereby regulating plant growth and development and resistance to abiotic and biotic stresses. Recently, many studies on WAK/WAKL family genes have been performed in various plants under different stresses; however, identification and functional survey of the WAK/WAKL gene family of Nicotiana benthamiana have not yet been performed, even though its genome has been sequenced for several years. Therefore, in this study, we aimed to identify the WAK/WAKL gene family in N. benthamiana and explore their possible functions in response to TYLCV infection. RESULTS Thirty-eight putative WAK/WAKL genes were identified and named according to their locations in N. benthamiana. Phylogenetic analysis showed that NbWAK/WAKLs are clustered into five groups. The protein motifs and gene structure compositions of NbWAK/WAKLs appear to be highly conserved among the phylogenetic groups. Numerous cis-acting elements involved in phytohormone and/or stress responses were detected in the promoter regions of NbWAK/WAKLs. Moreover, gene expression analysis revealed that most of the NbWAK/WAKLs are expressed in at least one of the examined tissues, suggesting their possible roles in regulating the growth and development of plants. Virus-induced gene silencing and quantitative PCR analyses demonstrated that NbWAK/WAKLs are implicated in regulating the response of N. benthamiana to TYLCV, ten of which were dramatically upregulated in locally or systemically infected leaves of N. benthamiana following TYLCV infection. CONCLUSIONS Our study lays an essential base for the further exploration of the potential functions of NbWAK/WAKLs in plant growth and development and response to viral infections in N. benthamiana.
Collapse
Affiliation(s)
- Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Lianlian Yang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Xiaoyin Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Hong Xu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Yajun Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| |
Collapse
|
15
|
Zhuo X, Yu Q, Russo R, Zhang Y, Wei X, Wang YZ, Holden PM, Gmitter FG. Role of long non-coding RNA in regulatory network response to Candidatus Liberibacter asiaticus in citrus. FRONTIERS IN PLANT SCIENCE 2023; 14:1090711. [PMID: 36890903 PMCID: PMC9986497 DOI: 10.3389/fpls.2023.1090711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) serve as crucial regulators in plant response to various diseases, while none have been systematically identified and characterized in response to citrus Huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus (CLas) bacteria. Here, we comprehensively investigated the transcriptional and regulatory dynamics of the lncRNAs in response to CLas. Samples were collected from leaf midribs of CLas- and mock-inoculated HLB-tolerant rough lemon (Citrus jambhiri) and HLB-sensitive sweet orange (C. sinensis) at week 0, 7, 17, and 34 following inoculation using CLas+ budwood of three biological replicates in the greenhouse. A total of 8,742 lncRNAs, including 2,529 novel lncRNAs, were identified from RNA-seq data with rRNA-removed from strand-specific libraries. Genomic variation analyses of conserved lncRNAs from 38 citrus accessions showed that 26 single nucleotide polymorphisms (SNPs) were significantly correlated with HLB. In addition, lncRNA-mRNA weighted gene co-expression network analysis (WGCNA) showed a significant module correlated with CLas-inoculation in rough lemon. Notably, the most significant LNC_28805 and multiple co-expressed genes related to plant defense in the module were targeted by miRNA5021, suggesting that LNC28805 might compete with endogenous miR5021 to maintain the homeostasis of immune gene expression levels. Candidate WRKY33 and SYP121 genes targeted by miRNA5021 were identified as two key hub genes interacting with bacteria pathogen response genes based on the prediction of protein-protein interaction (PPI) network. These two genes were also found within HLB-associated QTL in linkage group 6. Overall, our findings provide a reference for a better understanding of the role of lncRNAs involved in citrus HLB regulation.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Fred G. Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| |
Collapse
|
16
|
Ai G, Li T, Zhu H, Dong X, Fu X, Xia C, Pan W, Jing M, Shen D, Xia A, Tyler BM, Dou D. BPL3 binds the long non-coding RNA nalncFL7 to suppress FORKED-LIKE7 and modulate HAI1-mediated MPK3/6 dephosphorylation in plant immunity. THE PLANT CELL 2023; 35:598-616. [PMID: 36269178 PMCID: PMC9806616 DOI: 10.1093/plcell/koac311] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
RNA-binding proteins (RBPs) participate in a diverse set of biological processes in plants, but their functions and underlying mechanisms in plant-pathogen interactions are largely unknown. We previously showed that Arabidopsis thaliana BPA1-LIKE PROTEIN3 (BPL3) belongs to a conserved plant RBP family and negatively regulates reactive oxygen species (ROS) accumulation and cell death under biotic stress. In this study, we demonstrate that BPL3 suppresses FORKED-LIKE7 (FL7) transcript accumulation and raises levels of the cis-natural antisense long non-coding RNA (lncRNA) of FL7 (nalncFL7). FL7 positively regulated plant immunity to Phytophthora capsici while nalncFL7 negatively regulated resistance. We also showed that BPL3 directly binds to and stabilizes nalncFL7. Moreover, nalncFL7 suppressed accumulation of FL7 transcripts. Furthermore, FL7 interacted with HIGHLY ABA-INDUCED PP2C1 (HAI1), a type 2C protein phosphatase, and inhibited HAI1 phosphatase activity. By suppressing HAI1 activity, FL7 increased the phosphorylation levels of MITOGEN-ACTIVATED PROTEIN KINASE 3 (MPK3) and MPK6, thus enhancing immunity responses. BPL3 and FL7 are conserved in all plant species tested, but the BPL3-nalncFL7-FL7 cascade was specific to the Brassicaceae. Thus, we identified a conserved BPL3-nalncFL7-FL7 cascade that coordinates plant immunity.
Collapse
Affiliation(s)
- Gan Ai
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai Zhu
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohua Dong
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowei Fu
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuyan Xia
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiye Pan
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Maofeng Jing
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai Xia
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Brett M Tyler
- Center for Quantitative Life Sciences and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Daolong Dou
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
17
|
H. El-Sappah A, Qi S, A. Soaud S, Huang Q, M. Saleh A, A. S. Abourehab M, Wan L, Cheng GT, Liu J, Ihtisham M, Noor Z, Rouf Mir R, Zhao X, Yan K, Abbas M, Li J. Natural resistance of tomato plants to Tomato yellow leaf curl virus. FRONTIERS IN PLANT SCIENCE 2022; 13:1081549. [PMID: 36600922 PMCID: PMC9807178 DOI: 10.3389/fpls.2022.1081549] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) is one of the most harmful afflictions in the world that affects tomato growth and production. Six regular antagonistic genes (Ty-1, Ty-2, Ty-3, Ty-4, ty-5, and Ty-6) have been transferred from wild germplasms to commercial cultivars as TYLCV protections. With Ty-1 serving as an appropriate source of TYLCV resistance, only Ty-1, Ty-2, and Ty-3 displayed substantial levels of opposition in a few strains. It has been possible to clone three TYLCV opposition genes (Ty-1/Ty-3, Ty-2, and ty-5) that target three antiviral safety mechanisms. However, it significantly impacts obtaining permanent resistance to TYLCV, trying to maintain opposition whenever possible, and spreading opposition globally. Utilizing novel methods, such as using resistance genes and identifying new resistance resources, protects against TYLCV in tomato production. To facilitate the breeders make an informed decision and testing methods for TYLCV blockage, this study highlights the portrayal of typical obstruction genes, common opposition sources, and subatomic indicators. The main goal is to provide a fictitious starting point for the identification and application of resistance genes as well as the maturation of tomato varieties that are TYLCV-resistant.
Collapse
Affiliation(s)
- Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Shiming Qi
- College of Agriculture and Ecological Engineering, Hexi University, Zhangye, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Alaa M. Saleh
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Lingyun Wan
- Key Laboratory of Guangxi for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guo-ting Cheng
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan’an University, Yan’an, China
| | - Jingyi Liu
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Muhammad Ihtisham
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Zarqa Noor
- School of Chemical Engineering Beijing Institute of Technology, Beijing, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST–Kashmir, Sopore, India
| | - Xin Zhao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Kuan Yan
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| |
Collapse
|
18
|
Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
Collapse
Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
19
|
Kong X, Yang M, Le BH, He W, Hou Y. The master role of siRNAs in plant immunity. MOLECULAR PLANT PATHOLOGY 2022; 23:1565-1574. [PMID: 35869407 PMCID: PMC9452763 DOI: 10.1111/mpp.13250] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 06/01/2023]
Abstract
Gene silencing mediated by small noncoding RNAs (sRNAs) is a fundamental gene regulation mechanism in eukaryotes that broadly governs cellular processes. It has been established that sRNAs are critical regulators of plant growth, development, and antiviral defence, while accumulating studies support positive roles of sRNAs in plant defence against bacteria and eukaryotic pathogens such as fungi and oomycetes. Emerging evidence suggests that plant sRNAs move between species and function as antimicrobial agents against nonviral parasites. Multiple plant pathosystems have been shown to involve a similar exchange of small RNAs between species. Recent analysis about extracellular sRNAs shed light on the understanding of the selection and transportation of sRNAs moving from plant to parasites. In this review, we summarize current advances regarding the function and regulatory mechanism of plant endogenous small interfering RNAs (siRNAs) in mediating plant defence against pathogen intruders including viruses, bacteria, fungi, oomycetes, and parasitic plants. Beyond that, we propose potential mechanisms behind the sorting of sRNAs moving between species and the idea that engineering siRNA-producing loci could be a useful strategy to improve disease resistance of crops.
Collapse
Affiliation(s)
- Xiuzhen Kong
- Shanghai Collaborative Innovation Center of Agri‐Seeds/School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Meng Yang
- Shanghai Collaborative Innovation Center of Agri‐Seeds/School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Brandon H. Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome BiologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Wenrong He
- Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCaliforniaUSA
| | - Yingnan Hou
- Shanghai Collaborative Innovation Center of Agri‐Seeds/School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| |
Collapse
|
20
|
Abstract
Adaptive antiviral immunity in plants is an RNA-based mechanism in which small RNAs derived from both strands of the viral RNA are guides for an Argonaute (AGO) nuclease. The primed AGO specifically targets and silences the viral RNA. In plants this system has diversified to involve mobile small interfering RNAs (siRNAs), an amplification system involving secondary siRNAs and targeting mechanisms involving DNA methylation. Most, if not all, plant viruses encode multifunctional proteins that are suppressors of RNA silencing that may also influence the innate immune system and fine-tune the virus-host interaction. Animal viruses similarly trigger RNA silencing, although it may be masked in differentiated cells by the interferon system and by the action of the virus-encoded suppressor proteins. There is huge potential for RNA silencing to combat viral disease in crops, farm animals, and people, although there are complications associated with the various strategies for siRNA delivery including transgenesis. Alternative approaches could include using breeding or small molecule treatment to enhance the inherent antiviral capacity of infected cells.
Collapse
Affiliation(s)
- David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom;
| |
Collapse
|
21
|
Samarfard S, Ghorbani A, Karbanowicz TP, Lim ZX, Saedi M, Fariborzi N, McTaggart AR, Izadpanah K. Regulatory non-coding RNA: The core defense mechanism against plant pathogens. J Biotechnol 2022; 359:82-94. [PMID: 36174794 DOI: 10.1016/j.jbiotec.2022.09.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022]
Abstract
Plant pathogens damage crops and threaten global food security. Plants have evolved complex defense networks against pathogens, using crosstalk among various signaling pathways. Key regulators conferring plant immunity through signaling pathways include protein-coding genes and non-coding RNAs (ncRNAs). The discovery of ncRNAs in plant transcriptomes was first considered "transcriptional noise". Recent reviews have highlighted the importance of non-coding RNAs. However, understanding interactions among different types of noncoding RNAs requires additional research. This review attempts to consider how long-ncRNAs, small-ncRNAs and circular RNAs interact in response to pathogenic diseases within different plant species. Developments within genomics and bioinformatics could lead to the further discovery of plant ncRNAs, knowledge of their biological roles, as well as an understanding of their importance in exploiting the recent molecular-based technologies for crop protection.
Collapse
Affiliation(s)
- Samira Samarfard
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, the Islamic Republic of Iran.
| | | | - Zhi Xian Lim
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Mahshid Saedi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, the Islamic Republic of Iran
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, the Islamic Republic of Iran
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Keramatollah Izadpanah
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, the Islamic Republic of Iran
| |
Collapse
|
22
|
Zhao Z, Zang S, Zou W, Pan YB, Yao W, You C, Que Y. Long Non-Coding RNAs: New Players in Plants. Int J Mol Sci 2022; 23:ijms23169301. [PMID: 36012566 PMCID: PMC9409372 DOI: 10.3390/ijms23169301] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
During the process of growth and development, plants are prone to various biotic and abiotic stresses. They have evolved a variety of strategies to resist the adverse effects of these stresses. lncRNAs (long non-coding RNAs) are a type of less conserved RNA molecules of more than 200 nt (nucleotides) in length. lncRNAs do not code for any protein, but interact with DNA, RNA, and protein to affect transcriptional, posttranscriptional, and epigenetic modulation events. As a new regulatory element, lncRNAs play a critical role in coping with environmental pressure during plant growth and development. This article presents a comprehensive review on the types of plant lncRNAs, the role and mechanism of lncRNAs at different molecular levels, the coordination between lncRNA and miRNA (microRNA) in plant immune responses, the latest research progress of lncRNAs in plant growth and development, and their response to biotic and abiotic stresses. We conclude with a discussion on future direction for the elaboration of the function and mechanism of lncRNAs.
Collapse
Affiliation(s)
- Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Bao Pan
- Sugarcane Research Unit, USDA-ARS, Houma, LA 70360, USA
| | - Wei Yao
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China
| | - Cuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
| |
Collapse
|
23
|
Wang L, Gao J, Wang C, Xu Y, Li X, Yang J, Chen K, Kang Y, Wang Y, Cao P, Xie X. Comprehensive Analysis of Long Non-coding RNA Modulates Axillary Bud Development in Tobacco ( Nicotiana tabacum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:809435. [PMID: 35237286 PMCID: PMC8884251 DOI: 10.3389/fpls.2022.809435] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression and are crucial for plant growth and development. However, the mechanisms underlying the effects of activated lncRNAs on axillary bud development remain largely unknown. By lncRNA transcriptomes of axillary buds in topped and untopped tobacco plants, we identified a total of 13,694 lncRNAs. LncRNA analysis indicated that the promoted growth of axillary bud by topping might be partially ascribed to the genes related to hormone signal transduction and glycometabolism, trans-regulated by differentially expressed lncRNAs, such as MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1. Metabolite profiling indicated that auxin, abscisic acid and gibberellin were decreased in axillary buds of topped tobacco lines, while cytokinin was increased, consistent with the expression levels of related lncRNAs. MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1 were shown to be influenced by hormones and sucrose treatments, and were associated with changes of axillary bud growth in the overexpression of NtCCD8 plants (with reduced axillary buds) and RNA interference of NtTB1 plants (with increased axillary buds). Moreover, MSTRG.28151.1 was identified as the antisense lncRNA of NtTB1. Silencing of MSTRG.28151.1 in tobacco significantly attenuated the expression of NtTB1 and resulted in larger axillary buds, suggesting the vital function of MSTRG.28151.1 axillary bud developmen by NtTB1. Our findings shed light on lncRNA-mRNA interactions and their functional roles in axillary bud growth, which would improve our understanding of lncRNAs as important regulators of axillary bud development and plant architecture.
Collapse
Affiliation(s)
- Lin Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Junping Gao
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Chen Wang
- 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
| | - Xiaoxu Li
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Kai Chen
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Yile Kang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Yaofu Wang
- 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
| | - Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| |
Collapse
|
24
|
Wang C, Jiang F, Zhu S. Complex Small RNA-mediated Regulatory Networks between Viruses/Viroids/Satellites and Host Plants. Virus Res 2022; 311:198704. [DOI: 10.1016/j.virusres.2022.198704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/16/2022] [Accepted: 01/29/2022] [Indexed: 12/26/2022]
|
25
|
Sharma Y, Sharma A, Madhu, Shumayla, Singh K, Upadhyay SK. Long Non-Coding RNAs as Emerging Regulators of Pathogen Response in Plants. Noncoding RNA 2022; 8:4. [PMID: 35076574 PMCID: PMC8788567 DOI: 10.3390/ncrna8010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts without protein-coding potential that contain more than 200 nucleotides that play important roles in plant survival in response to different stresses. They interact with molecules such as DNA, RNA, and protein, and play roles in the regulation of chromatin remodeling, RNA metabolism, and protein modification activities. These lncRNAs regulate the expression of their downstream targets through epigenetic changes, at the level of transcription and post-transcription. Emerging information from computational biology and functional characterization of some of them has revealed their diverse mechanisms of action and possible roles in biological processes such as flowering time, reproductive organ development, as well as biotic and abiotic stress responses. In this review, we have mainly focused on the role of lncRNAs in biotic stress response due to the limited availability of knowledge in this domain. We have discussed the available molecular mechanisms of certain known lncRNAs against specific pathogens. Further, considering that fungal, viral, and bacterial diseases are major factors in the global food crisis, we have highlighted the importance of lncRNAs against pathogen responses and the progress in plant research to develop a better understanding of their functions and molecular mechanisms.
Collapse
Affiliation(s)
- Yashraaj Sharma
- Department of Botany, Panjab University, Chandigarh 160014, India; (Y.S.); (A.S.); (M.); (S.)
- Department of Biotechnology, Panjab University, Chandigarh 160014, India;
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh 160014, India; (Y.S.); (A.S.); (M.); (S.)
| | - Madhu
- Department of Botany, Panjab University, Chandigarh 160014, India; (Y.S.); (A.S.); (M.); (S.)
| | - Shumayla
- Department of Botany, Panjab University, Chandigarh 160014, India; (Y.S.); (A.S.); (M.); (S.)
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh 160014, India;
| | - Santosh Kumar Upadhyay
- Department of Botany, Panjab University, Chandigarh 160014, India; (Y.S.); (A.S.); (M.); (S.)
| |
Collapse
|
26
|
Jiao Y, Zhao X, Hao K, Gao X, Xing D, Wang Z, An M, Xia Z, Wu Y. Characterization of small interfering RNAs derived from pepper mild mottle virus in infected pepper plants by high-throughput sequencing. Virus Res 2022; 307:198607. [PMID: 34688783 DOI: 10.1016/j.virusres.2021.198607] [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: 07/12/2021] [Revised: 10/12/2021] [Accepted: 10/17/2021] [Indexed: 11/25/2022]
Abstract
Pepper mild mottle virus (PMMoV) infects pepper plants and induces severe yield losses in China. However, the molecular interaction between PMMoV and pepper plants is largely unknown. RNA silencing is a eukaryotically conserved mechanism against viruses mediated by virus-derived small interfering RNAs (vsiRNAs) in plants. In this study, the profiles of vsiRNAs from PMMoV in infected pepper plants were obtained by high-throughput sequencing. The results showed that vsiRNAs were predominantly 21 and 22 nucleotides (nts) in length, and had a U bias at the 5'-terminal. The single-nucleotide resolution maps revealed that vsiRNAs were heterogeneously distributed throughout PMMoV genomic RNAs and hotspots of sense and antisense strands were mainly located in the RdRp and CP coding regions. The host transcripts targeted by vsiRNAs were predicted and they are mainly involved in physiological pathways related to stress response, cell regulation, and metabolism process. In addition, PMMoV infection induced significant up-regulation of CaAGO1a/1b/2, CaDCL2 and CaRDR1 gene transcripts in pepper plants, which are important components involved in antiviral RNA silencing pathway. Taken together, our results suggest the possible roles of vsiRNAs in PMMoV-pepper interactions.
Collapse
Affiliation(s)
- Yubing Jiao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Xiuxiang Zhao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Kaiqiang Hao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinran Gao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Dan Xing
- Institute of Pepper, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Zhiping Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Mengnan An
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zihao Xia
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
| |
Collapse
|
27
|
Kumar KK, Varanavasiappan S, Arul L, Kokiladevi E, Sudhakar D. Strategies for Efficient RNAi-Based Gene Silencing of Viral Genes for Disease Resistance in Plants. Methods Mol Biol 2022; 2408:23-35. [PMID: 35325414 DOI: 10.1007/978-1-0716-1875-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RNA interference (RNAi) is an evolutionarily conserved gene silencing mechanism in eukaryotes including fungi, plants, and animals. In plants, gene silencing regulates gene expression, provides genome stability, and protect against invading viruses. During plant virus interaction, viral genome derived siRNAs (vsiRNA) are produced to mediate gene silencing of viral genes to prevent virus multiplication. After the discovery of RNAi phenomenon in eukaryotes, it is used as a powerful tool to engineer plant viral disease resistance against both RNA and DNA viruses. Despite several successful reports on employing RNA silencing methods to engineer plant for viral disease resistance, only a few of them have reached the commercial stage owing to lack of complete protection against the intended virus. Based on the knowledge accumulated over the years on genetic engineering for viral disease resistance, there is scope for effective viral disease control through careful design of RNAi gene construct. The selection of target viral gene(s) for developing the hairpin RNAi (hp-RNAi) construct is very critical for effective protection against the viral disease. Different approaches and bioinformatics tools which can be employed for effective target selection are discussed. The selection of suitable target regions for RNAi vector construction can help to achieve a high level of transgenic virus resistance.
Collapse
Affiliation(s)
- Krish K Kumar
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
| | - Shanmugam Varanavasiappan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
| | - Loganathan Arul
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Easwaran Kokiladevi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Duraialagaraja Sudhakar
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| |
Collapse
|
28
|
Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits.
Collapse
|
29
|
Javaran VJ, Moffett P, Lemoyne P, Xu D, Adkar-Purushothama CR, Fall ML. Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112355. [PMID: 34834718 PMCID: PMC8623739 DOI: 10.3390/plants10112355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 05/30/2023]
Abstract
Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for the direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses, the principle of third-generation sequencing platforms, and the application of nanopore sequencing technology in grapevine virus detection, virus-plant interactions, as well as the characterization of viral RNA modifications.
Collapse
Affiliation(s)
- Vahid Jalali Javaran
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - Peter Moffett
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - Pierre Lemoyne
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
| | - Dong Xu
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
| | - Charith Raj Adkar-Purushothama
- Département de Biochimie, Faculté de Médecine des Sciences de la Santé, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada;
| | - Mamadou Lamine Fall
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
| |
Collapse
|
30
|
Martin IR, Vigne E, Velt A, Hily JM, Garcia S, Baltenweck R, Komar V, Rustenholz C, Hugueney P, Lemaire O, Schmitt-Keichinger C. Severe Stunting Symptoms upon Nepovirus Infection Are Reminiscent of a Chronic Hypersensitive-like Response in a Perennial Woody Fruit Crop. Viruses 2021; 13:2138. [PMID: 34834945 PMCID: PMC8625034 DOI: 10.3390/v13112138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 12/02/2022] Open
Abstract
Virus infection of plants can result in various degrees of detrimental impacts and disparate symptom types and severities. Although great strides have been made in our understanding of the virus-host interactions in herbaceous model plants, the mechanisms underlying symptom development are poorly understood in perennial fruit crops. Grapevine fanleaf virus (GFLV) causes variable symptoms in most vineyards worldwide. To better understand GFLV-grapevine interactions in relation to symptom development, field and greenhouse trials were conducted with a grapevine genotype that exhibits distinct symptoms in response to a severe and a mild strain of GFLV. After validation of the infection status of the experimental vines by high-throughput sequencing, the transcriptomic and metabolomic profiles in plants infected with the two viral strains were tested and compared by RNA-Seq and LC-MS, respectively, in the differentiating grapevine genotype. In vines infected with the severe GFLV strain, 1023 genes, among which some are implicated in the regulation of the hypersensitive-type response, were specifically deregulated, and a higher accumulation of resveratrol and phytohormones was observed. Interestingly, some experimental vines restricted the virus to the rootstock and remained symptomless. Our results suggest that GFLV induces a strain- and cultivar-specific defense reaction similar to a hypersensitive reaction. This type of defense leads to a severe stunting phenotype in some grapevines, whereas others are resistant. This work is the first evidence of a hypersensitive-like reaction in grapevine during virus infection.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Corinne Schmitt-Keichinger
- Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, 68000 Colmar, France; (E.V.); (A.V.); (J.-M.H.); (S.G.); (R.B.); (V.K.); (C.R.); (P.H.); (O.L.)
| |
Collapse
|
31
|
Zhang YY, Hong YH, Liu YR, Cui J, Luan YS. Function identification of miR394 in tomato resistance to Phytophthora infestans. PLANT CELL REPORTS 2021; 40:1831-1844. [PMID: 34230985 DOI: 10.1007/s00299-021-02746-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
MiR394 plays a negative role in tomato resistance to late blight. The lncRNA40787 severing as an eTM for miR394 to regulate LCR and exerting functions in tomato resistance. Tomato (Solanum lycopersicum), which was used as model species for studying the mechanism of plant disease defense, is susceptible to multiple pathogens. Non-coding RNA (ncRNA) has a pivotal role in plants response to biological stresses. It has previously been observed that the expression level of miR394 changed significantly after the infection of various pathogens. However, there has been no detailed investigation of the accumulated or suppressed mechanism of miR394. Our previous study predicted three lncRNAs (lncRNA40787, lncRNA27177, and lncRNA42566) that contain miR394 endogenous target mimics (eTM), which may exist as the competitive endogenous RNAs (ceRNAs) of miR394. In our study, the transcription levels of these three lncRNAs were strongly up-regulated in tomato upon infection with P. infestans. In contrast with the three lncRNAs, the accumulation of miR394 was significantly suppressed. Based on the expression pattern, and value of minimum free energy (mfes) that represents the binding ability between lncRNA and miRNA, lncRNA40787 was chosen for further investigation. Results showed that overexpression of lncRNA40787 reduced the expression of miR394 along with decreased lesion area and enhanced disease resistance. Overexpression of miR394, however, decreased the expression of its target gene Leaf Curling Responsiveness (LCR), and suppressed the synthesis components genes of jasmonic acid (JA), depressing the resistance of tomato to P. infestans infection. Taken together, our findings indicated that miR394 can be decoyed by lncRNA40787, and negatively regulated the expression of LCR to enhance tomato susceptibility under P. infestans infection. Our study provided detailed information on the lncRNA40787-miR394-LCR regulatory network and serves as a reference for future research.
Collapse
Affiliation(s)
- Yuan-Yuan Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yu-Hui Hong
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Ya-Rong Liu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yu-Shi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
| |
Collapse
|
32
|
Cheng C, Liu F, Tian N, Mensah RA, Sun X, Liu J, Wu J, Wang B, Li D, Lai Z. Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing. Sci Rep 2021; 11:16363. [PMID: 34381122 PMCID: PMC8358008 DOI: 10.1038/s41598-021-95832-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/29/2021] [Indexed: 12/03/2022] Open
Abstract
Fusarium wilt disease, caused by Fusarium oxysporum f.sp. cubense (Foc), has been recognized as the most devastating disease to banana. The regulatory role of long non-coding RNAs (lncRNAs) in plant defense has been verified in many plant species. However, the understanding of their role during early FocTR4 (Foc tropical race 4) infection stage is very limited. In this study, lncRNA sequencing was used to reveal banana root transcriptome profile changes during early FocTR4 infection stages. Quantitative real time PCR (qRT-PCR) was performed to confirm the expression of eight differentially expressed (DE) lncRNAs (DELs) and their predicted target genes (DETs), and three DE genes (DEGs). Totally, 12,109 lncRNAs, 36,519 mRNAs and 2642 novel genes were obtained, of which 1398 (including 78 DELs, 1220 DE known genes and 100 DE novel genes) were identified as FocTR4 responsive DE transcripts. Gene function analysis revealed that most DEGs were involved in biosynthesis of secondary metabolites, plant–pathogen interaction, plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis, alpha-linolenic acid metabolism and so on. Coincidently, many DETs have been identified as DEGs in previous transcriptome studies. Moreover, many DETs were found to be involved in ribosome, oxidative phosphorylation, lipoic acid metabolism, ubiquitin mediated proteolysis, N-glycan biosynthesis, protein processing in endoplasmic reticulum and DNA damage response pathways. QRT-PCR result showed the expression patterns of the selected transcripts were mostly consistent with our lncRNA sequencing data. Our present study showed the regulatory role of lncRNAs on known biotic and abiotic stress responsive genes and some new-found FocTR4 responsive genes, which can provide new insights into FocTR4-induced changes in the banana root transcriptome during the early pathogen infection stage.
Collapse
Affiliation(s)
- Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China.
| | - Fan Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Na Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Raphael Anue Mensah
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueli Sun
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiapeng Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Junwei Wu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bin Wang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
33
|
Xiao Y, Li Q, Wang W, Fu Y, Cui F. Regulation of RNA Interference Pathways in the Insect Vector Laodelphax striatellus by Viral Proteins of Rice Stripe Virus. Viruses 2021; 13:1591. [PMID: 34452456 PMCID: PMC8402809 DOI: 10.3390/v13081591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/29/2022] Open
Abstract
RNA interference (RNAi), especially the small interfering RNA (siRNA) and microRNA (miRNA) pathways, plays an important role in defending against viruses in plants and insects. However, how insect-transmitted phytoviruses regulate the RNAi-mediated antiviral response in vector insects has barely been uncovered. In this study, we explored the interaction between rice stripe virus (RSV) and the miRNA and siRNA pathways of the small brown planthopper, which is a vector insect. The transcript and protein levels of key genes in the two RNAi pathways did not change during the RSV infection process. When the expression of insect Ago1, Ago2, or Translin was silenced by the injection of double-stranded RNAs targeting these genes, viral replication was promoted with Ago2 silencing but inhibited with Translin silencing. Protein-protein binding assays showed that viral NS2 and RNA-dependent RNA polymerase interacted with insect Ago2 and Translin, respectively. When NS2 was knocked down, the transcript level of Ago2 increased and viral replication was inhibited. Therefore, viral NS2 behaved like an siRNA suppressor in vector insects. This protein-binding regulation of insect RNAi systems reflects a complicated and diverse coevolution of viruses with their vector insects.
Collapse
Affiliation(s)
- Yan Xiao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.X.); (Q.L.); (W.W.)
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Qiong Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.X.); (Q.L.); (W.W.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.X.); (Q.L.); (W.W.)
| | - Yumei Fu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China;
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (Y.X.); (Q.L.); (W.W.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
34
|
Tao X, Li M, Zhao T, Feng S, Zhang H, Wang L, Han J, Gao M, Lu K, Chen Q, Zhou B, Guan X. Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation. PLANT PHYSIOLOGY 2021; 186:2152-2168. [PMID: 33871645 PMCID: PMC8331171 DOI: 10.1093/plphys/kiab179] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/31/2021] [Indexed: 05/26/2023]
Abstract
The genomic shock of whole-genome duplication (WGD) and hybridization introduces great variation into transcriptomes, for both coding and noncoding genes. An altered transcriptome provides a molecular basis for improving adaptation during the evolution of new species. The allotetraploid cotton, together with the putative diploid ancestor species compose a fine model for study the rapid gene neofunctionalization over the genome shock. Here we report on Drought-Associated Non-coding gene 1 (DAN1), a long intergenic noncoding RNA (lincRNA) that arose from the cotton progenitor A-diploid genome after hybridization and WGD events during cotton evolution. DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm. Chromatin isolation by RNA purification profiling and electrophoretic mobility shift assay analysis demonstrated that GhDAN1 RNA can bind with DNA fragments containing AAAG motifs, similar to DNA binding with one zinc finger transcription factor binding sequences. The suppression of GhDAN1 mainly regulates genes with AAAG motifs in auxin-response pathways, which are associated with drought stress regulation. As a result, GhDAN1-silenced plants exhibit improved tolerance to drought stress. This phenotype resembles the drought-tolerant phenotype of the A-diploid cotton ancestor species, which has an undetectable expression of DAN1. The role of DAN1 in cotton evolution and drought tolerance regulation suggests that the genomic shock of interspecific hybridization and WGD stimulated neofunctionalization of non-coding genes during the natural evolutionary process.
Collapse
Affiliation(s)
- Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Menglin Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shouli Feng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hailin Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Luyao Wang
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Center of Ministry of Cotton Education, Urumqi 830052, China
| | - Jin Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengtao Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kening Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Center of Ministry of Cotton Education, Urumqi 830052, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
35
|
Cui W, Wang S, Han K, Zheng E, Ji M, Chen B, Wang X, Chen J, Yan F. Ferredoxin 1 is downregulated by the accumulation of abscisic acid in an ABI5-dependent manner to facilitate rice stripe virus infection in Nicotiana benthamiana and rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1183-1197. [PMID: 34153146 DOI: 10.1111/tpj.15377] [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: 11/29/2021] [Accepted: 06/14/2021] [Indexed: 05/07/2023]
Abstract
Ferredoxin 1 (FD1) accepts and distributes electrons in the electron transfer chain of plants. Its expression is universally downregulated by viruses and its roles in plant immunity have been brought into focus over the past decade. However, the mechanism by which viruses regulate FD1 remains to be defined. In a previous report, we found that the expression of Nicotiana benthamiana FD1 (NbFD1) was downregulated following infection with potato virus X (PVX) and that NbFD1 regulates callose deposition at plasmodesmata to play a role in defense against PVX infection. We now report that NbFD1 is downregulated by rice stripe virus (RSV) infection and that silencing of NbFD1 also facilitates RSV infection, while viral infection was inhibited in a transgenic line overexpressing NbFD1, indicating that NbFD1 also functions in defense against RSV infection. Next, a RSV-derived small interfering RNA was identified that contributes to the downregulation of FD1 transcripts. Further analysis showed that the abscisic acid (ABA) which accumulates in RSV-infected plants also represses NbFD1 transcription. It does this by stimulating expression of ABA insensitive 5 (ABI5), which binds the ABA response element motifs in the NbFD1 promoter, resulting in negative regulation. Regulation of FD1 by ABA was also confirmed in RSV-infected plants of the natural host rice. The results therefore suggest a mechanism by which virus regulates chloroplast-related genes to suppress their defense roles.
Collapse
Affiliation(s)
- Weijun Cui
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Shu Wang
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Nebraska, NE 68583, USA
| | - Kelei Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Ersong Zheng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Mengfei Ji
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Binghua Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Xuming Wang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jianping Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| |
Collapse
|
36
|
Song L, Fang Y, Chen L, Wang J, Chen X. Role of non-coding RNAs in plant immunity. PLANT COMMUNICATIONS 2021; 2:100180. [PMID: 34027394 PMCID: PMC8132121 DOI: 10.1016/j.xplc.2021.100180] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/01/2021] [Accepted: 03/17/2021] [Indexed: 05/06/2023]
Abstract
Crops are exposed to attacks by various pathogens that cause substantial yield losses and severely threaten food security. To cope with pathogenic infection, crops have elaborated strategies to enhance resistance against pathogens. In addition to the role of protein-coding genes as key regulators in plant immunity, accumulating evidence has demonstrated the importance of non-coding RNAs (ncRNAs) in the plant immune response. Here, we summarize the roles and molecular mechanisms of endogenous ncRNAs, especially microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), in plant immunity. We discuss the coordination between miRNAs and small interfering RNAs (siRNAs), between lncRNAs and miRNAs or siRNAs, and between circRNAs and miRNAs in the regulation of plant immune responses. We also address the role of cross-kingdom mobile small RNAs in plant-pathogen interactions. These insights improve our understanding of the mechanisms by which ncRNAs regulate plant immunity and can promote the development of better approaches for breeding disease-resistant crops.
Collapse
Affiliation(s)
- Li Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Yu Fang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Lin Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
- Corresponding author
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
- Corresponding author
| |
Collapse
|
37
|
Meng X, Li A, Yu B, Li S. Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation. Comput Struct Biotechnol J 2021; 19:2567-2574. [PMID: 34025943 PMCID: PMC8114054 DOI: 10.1016/j.csbj.2021.04.062] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/24/2021] [Accepted: 04/24/2021] [Indexed: 11/28/2022] Open
Abstract
Plants employ sophisticated mechanisms to control developmental processes and to cope with environmental changes at transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs), two classes of endogenous noncoding RNAs, are key regulators of gene expression in plants. Recent studies have identified the interplay between miRNAs and lncRNAs as a novel regulatory layer of gene expression in plants. On one hand, miRNAs target lncRNAs for the production of phased small interfering RNAs (phasiRNAs). On the other hand, lncRNAs serve as origin of miRNAs or regulate the accumulation or activity of miRNAs at transcription and post-transcriptional levels. Theses lncRNA-miRNA interplays are crucial for plant development, physiology and responses to biotic and abiotic stresses. In this review, we summarize recent advances in the biological roles, interaction mechanisms and computational predication methods of the interplay between miRNAs and lncRNAs in plants.
Collapse
Affiliation(s)
- Xiangxiang Meng
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Aixia Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bin Yu
- School of Biological Sciences & Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| |
Collapse
|
38
|
Elvira González L, Peiró R, Rubio L, Galipienso L. Persistent Southern Tomato Virus (STV) Interacts with Cucumber Mosaic and/or Pepino Mosaic Virus in Mixed- Infections Modifying Plant Symptoms, Viral Titer and Small RNA Accumulation. Microorganisms 2021; 9:689. [PMID: 33810543 PMCID: PMC8066132 DOI: 10.3390/microorganisms9040689] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/27/2022] Open
Abstract
Southern tomato virus (STV) is a persistent virus that was, at the beginning, associated with some tomato fruit disorders. Subsequent studies showed that the virus did not induce apparent symptoms in single infections. Accordingly, the reported symptoms could be induced by the interaction of STV with other viruses, which frequently infect tomato. Here, we studied the effect of STV in co- and triple-infections with Cucumber mosaic virus (CMV) and Pepino mosaic virus (PepMV). Our results showed complex interactions among these viruses. Co-infections leaded to a synergism between STV and CMV or PepMV: STV increased CMV titer and plant symptoms at early infection stages, whereas PepMV only exacerbated the plant symptoms. CMV and PepMV co-infection showed an antagonistic interaction with a strong decrease of CMV titer and a modification of the plant symptoms with respect to the single infections. However, the presence of STV in a triple-infection abolished this antagonism, restoring the CMV titer and plant symptoms. The siRNAs analysis showed a total of 78 miRNAs, with 47 corresponding to novel miRNAs in tomato, which were expressed differentially in the plants that were infected with these viruses with respect to the control mock-inoculated plants. These miRNAs were involved in the regulation of important functions and their number and expression level varied, depending on the virus combination. The number of vsiRNAs in STV single-infected tomato plants was very small, but STV vsiRNAs increased with the presence of CMV and PepMV. Additionally, the rates of CMV and PepMV vsiRNAs varied depending on the virus combination. The frequencies of vsiRNAs in the viral genomes were not uniform, but they were not influenced by other viruses.
Collapse
Affiliation(s)
- Laura Elvira González
- Biotechnology and Plant Protection Center, Valencian Institute of Agricultural Research (IVIA), 46113 Valencia, Spain; (L.E.G.); (L.R.)
- Biotechnology Department, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Rosa Peiró
- Biotechnology Department, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Luis Rubio
- Biotechnology and Plant Protection Center, Valencian Institute of Agricultural Research (IVIA), 46113 Valencia, Spain; (L.E.G.); (L.R.)
| | - Luis Galipienso
- Biotechnology and Plant Protection Center, Valencian Institute of Agricultural Research (IVIA), 46113 Valencia, Spain; (L.E.G.); (L.R.)
| |
Collapse
|
39
|
Host-virus interactions mediated by long non-coding RNAs. Virus Res 2021; 298:198402. [PMID: 33771610 DOI: 10.1016/j.virusres.2021.198402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/21/2022]
Abstract
Viruses are obligate pathogens that cause a wide range of diseases across all kingdoms of life. They have a colossal impact on the economy and healthcare infrastructure world-wide. Plants and animals have developed sophisticated molecular mechanisms to defend themselves against viruses and viruses in turn hijack host mechanisms to ensure their survival inside their hosts. Long non-coding (lnc) RNAs have emerged as important macromolecules that regulate plant-virus and animal-virus interactions. Both pro-viral and anti-viral lncRNAs have been reported and they show immense potential to be used as markers and in therapeutics. The current review is focussed on the recent developments that have been made in viral interactions of animals and plants.
Collapse
|
40
|
Zheng W, Hu H, Lu Q, Jin P, Cai L, Hu C, Yang J, Dai L, Chen J. Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana. BIOLOGY 2021; 10:biology10030232. [PMID: 33802832 PMCID: PMC8002735 DOI: 10.3390/biology10030232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/23/2021] [Accepted: 03/11/2021] [Indexed: 12/30/2022]
Abstract
Simple Summary Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. However, the roles of long non-coding RNAs (lncRNAs) in the interaction between plants and viruses is unclear, particularly for the Chinese wheat mosaic virus (CWMV) interaction. In this study, we used a deep RNA sequencing strategy to profile lncRNAs involved in the response to CWMV infection in Nicotiana benthamiana and analyzed differentially expressed lncRNAs that responded to CWMV infection, using a bioinformatics method. We identified 1175 new lncRNAs in N. benthamiana infected with CWMV, with 65 lncRNAs showing differential expression. These lncRNAs were mainly enriched in plant hormone signal transduction and other pathways according to GO and KEGG pathway enrichment analyses. In addition, differential expression of XLOC_006393 after CWMV infection may be the precursor of NbmiR168c, which can respond to CWMV infection by modulating the expression of its target gene NbAGO1. We believe that our study makes a significant contribution to the literature because these results provide a valuable resource for studying lncRNAs involved in CWMV infection and improving the understanding of the molecular mechanism of CWMV infection. Abstract Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.
Collapse
Affiliation(s)
- Weiran Zheng
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
| | - Haichao Hu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Qisen Lu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Peng Jin
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Linna Cai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Cailin Hu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- Correspondence: (L.D.); (J.C.)
| | - Jianping Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
- Correspondence: (L.D.); (J.C.)
| |
Collapse
|
41
|
Flores R, Navarro B, Delgado S, Serra P, Di Serio F. Viroid pathogenesis: a critical appraisal of the role of RNA silencing in triggering the initial molecular lesion. FEMS Microbiol Rev 2021; 44:386-398. [PMID: 32379313 DOI: 10.1093/femsre/fuaa011] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
The initial molecular lesions through which viroids, satellite RNAs and viruses trigger signal cascades resulting in plant diseases are hotly debated. Since viroids are circular non-protein-coding RNAs of ∼250-430 nucleotides, they appear very convenient to address this issue. Viroids are targeted by their host RNA silencing defense, generating viroid-derived small RNAs (vd-sRNAs) that are presumed to direct Argonaute (AGO) proteins to inactivate messenger RNAs, thus initiating disease. Here, we review the existing evidence. Viroid-induced symptoms reveal a distinction. Those attributed to vd-sRNAs from potato spindle tuber viroid and members of the family Pospiviroidae (replicating in the nucleus) are late, non-specific and systemic. In contrast, those attributed to vd-sRNAs from peach latent mosaic viroid (PLMVd) and other members of the family Avsunviroidae (replicating in plastids) are early, specific and local. Remarkably, leaf sectors expressing different PLMVd-induced chloroses accumulate viroid variants with specific pathogenic determinants. Some vd-sRNAs containing such determinant guide AGO1-mediated cleavage of mRNAs that code for proteins regulating chloroplast biogenesis/development. Therefore, the initial lesions and the expected phenotypes are connected by short signal cascades, hence supporting a cause-effect relationship. Intriguingly, one virus satellite RNA initiates disease through a similar mechanism, whereas in the Pospiviroidae and in plant viruses the situation remains uncertain.
Collapse
Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n 46010, Valencia, Spain
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Via Amendola 122/D, 70126 Bari, Italy
| | - Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n 46010, Valencia, Spain
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n 46010, Valencia, Spain
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Via Amendola 122/D, 70126 Bari, Italy
| |
Collapse
|
42
|
Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants. Int J Mol Sci 2020; 22:ijms22010086. [PMID: 33374835 PMCID: PMC7795044 DOI: 10.3390/ijms22010086] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.
Collapse
|
43
|
Zhou X, Cui J, Meng J, Luan Y. Interactions and links among the noncoding RNAs in plants under stresses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3235-3248. [PMID: 33025081 DOI: 10.1007/s00122-020-03690-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/16/2020] [Indexed: 05/11/2023]
Abstract
The complex interplay among sRNAs, lncRNAs and circRNAs has been implicated in plants under biotic and abiotic stresses. Here, we review current advances in our understanding of ncRNA interactions and links, which have considerable potential for improving the agronomic traits and the environmental adaptability of plants. Plants can respond to biotic or abiotic stresses. To cope with various conditions, numerous intricate molecular regulatory mechanisms have evolved in plants. Noncoding RNAs (ncRNAs) can be divided into small noncoding RNAs (sRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). Emerging evidence has demonstrated that interplay among the ncRNAs acts as a novel layer in the regulatory mechanisms, which has attracted substantial interest. Links between sRNAs can affect plant immune responses and development in synergistic or antagonistic manners. Additionally, multiple interactions between lncRNAs and sRNAs are involved in crop breeding, disease resistance and high tolerance to environmental stresses. Here, we summarize current knowledge of the interactions and links among the ncRNAs in plant responses to stresses and the methods for identifying ncRNA interactions. Furthermore, challenges and prospects for further progress in elucidating ncRNA interactions and links are highlighted.
Collapse
Affiliation(s)
- Xiaoxu Zhou
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
| |
Collapse
|
44
|
Prasad A, Sharma N, Hari-Gowthem G, Muthamilarasan M, Prasad M. Tomato Yellow Leaf Curl Virus: Impact, Challenges, and Management. TRENDS IN PLANT SCIENCE 2020; 25:897-911. [PMID: 32371058 DOI: 10.1016/j.tplants.2020.03.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 05/26/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) is one of the most studied plant viral pathogens because it is the most damaging virus for global tomato production. In order to combat this global threat, it is important that we understand the biology of TYLCV and devise management approaches. The prime objective of this review is to highlight management strategies for efficiently tackling TYLCV epidemics and global spread. For that purpose, we focus on the impact TYLCV has on worldwide agriculture and the role of recent advances for our understanding of TYLCV interaction with its host and vector. Another important focus is the role of recombination and mutations in shaping the evolution of TYLCV genome and geographical distribution.
Collapse
Affiliation(s)
- Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | | | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| |
Collapse
|
45
|
Zhang T, Liang Q, Li C, Fu S, Kundu JK, Zhou X, Wu J. Transcriptome Analysis of Rice Reveals the lncRNA-mRNA Regulatory Network in Response to Rice Black-Streaked Dwarf Virus Infection. Viruses 2020; 12:v12090951. [PMID: 32867233 PMCID: PMC7552052 DOI: 10.3390/v12090951] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 01/05/2023] Open
Abstract
The plant genome can produce long non-coding RNAs (lncRNAs), some of which have been identified as important regulators of gene expression. To better understand the response mechanism of rice plants to Rice black-streaked dwarf virus (RBSDV) infection, we performed a comparative transcriptome analysis between the RBSDV-infected and non-infected rice plants. A total of 1342 mRNAs and 22 lncRNAs were identified to be differentially expressed after RBSDV infection. Most differentially expressed transcripts involved in the plant–pathogen interaction pathway were upregulated after RBSDV infection, indicating the activation of rice defense response by RBSDV. A network of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) was then constructed. In this network, there are 56 plant–pathogen interaction-related DEmRNAs co-expressing with 20 DElncRNAs, suggesting these DElncRNAs and DEmRNAs may play essential roles in rice innate immunity against RBSDV. Moreover, some of the lncRNA–mRNA regulatory relationships were experimentally verified in rice calli by a quick and effective method established in this study. Three DElncRNAs were selected to be tested, and the results indicated that five mRNAs were found to be regulated by them. Together, we give a whole landscape of rice mRNAs and lncRNAs in response to RBSDV infection, and a feasible method to rapidly verify the lncRNA–mRNA regulatory relationship in rice.
Collapse
Affiliation(s)
- Tianze Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | - Qian Liang
- Key Laboratory of microorganism technology and bioinformatics research of Zhejiang Province, NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang TianKe High-Technology Development Co. Ltd., Hangzhou 310023, China;
| | - Chenyang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | | | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
| |
Collapse
|
46
|
Jiang N, Cui J, Hou X, Yang G, Xiao Y, Han L, Meng J, Luan Y. Sl-lncRNA15492 interacts with Sl-miR482a and affects Solanum lycopersicum immunity against Phytophthora infestans. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1561-1574. [PMID: 32432801 DOI: 10.1111/tpj.14847] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 05/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are involved in the resistance of plants to infection by pathogens via interactions with microRNAs (miRNAs). Long non-coding RNAs are cleaved by miRNAs to produce phased small interfering RNAs (phasiRNAs), which, as competing endogenous RNAs (ceRNAs), function as decoys for mature miRNAs, thus inhibiting their expression, and contain pre-miRNA sequences to produce mature miRNAs. However, whether lncRNAs and miRNAs mediate other molecular mechanisms during plant resistance to pathogens is unknown. In this study, as a positive regulator, Sl-lncRNA15492 from tomato (Solanum lycopersicum Zaofen No. 2) plants affected tomato resistance to Phytophthora infestans. Gain- and loss-of-function experiments and RNA ligase-mediated 5'-amplification of cDNA ends (RLM-5' RACE) also revealed that Sl-miR482a was negatively involved in tomato resistance by targeting Sl-NBS-LRR genes and that silencing of Sl-NBS-LRR1 decreased tomato resistance. Sl-lncRNA15492 inhibited the expression of mature Sl-miR482a, whose precursor was located within the antisense sequence of Sl-lncRNA15492. Further degradome analysis and additional RLM-5' RACE experiments verified that mature Sl-miR482a could also cleave Sl-lncRNA15492. These results provide a mechanism by which lncRNAs might inhibit precursor miRNA expression through antisense strands of lncRNAs, and demonstrate that Sl-lncRNA15492 and Sl-miR482a mutually inhibit the maintenance of Sl-NBS-LRR1 homeostasis during tomato resistance to P. infestans.
Collapse
Affiliation(s)
- Ning Jiang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Xinxin Hou
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Guanglei Yang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yu Xiao
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Lu Han
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| |
Collapse
|
47
|
Aguilar E, Garnelo Gomez B, Lozano-Duran R. Recent advances on the plant manipulation by geminiviruses. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:56-64. [PMID: 32464465 DOI: 10.1016/j.pbi.2020.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/06/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
As intracellular parasites, viruses co-opt the molecular machinery of the cells they infect in order to multiply and spread, and the extensiveness and effectiveness of this manipulation ultimately determine the outcome of the interaction between virus and host. Members of the Geminiviridae family, causal agents of devastating diseases in crops, encode only a handful of multifunctional, fast-evolving proteins, which efficiently target host proteins to re-wire plant development and physiology and enable replication and spread of the viral genome. In this review, we offer an overview of the different steps in the geminiviral invasion of the host plant, and explore the knowns and unknowns in geminivirus biology.
Collapse
Affiliation(s)
- Emmanuel Aguilar
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Borja Garnelo Gomez
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
| |
Collapse
|
48
|
Tian H, Guo F, Zhang Z, Ding H, Meng J, Li X, Peng Z, Wan S. Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L. BMC PLANT BIOLOGY 2020; 20:308. [PMID: 32615935 PMCID: PMC7330965 DOI: 10.1186/s12870-020-02510-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/22/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs), which are typically > 200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. RESULTS A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. Approximately 44.17% of the lncRNAs with an exon/intron structure were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. CONCLUSIONS This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.
Collapse
Affiliation(s)
- Haiying Tian
- College of Life Science, Shandong University, Jinan, 250014 China
| | - Feng Guo
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Zhimeng Zhang
- Peanut Research Institute of Shandong, Qingdao, 266100 China
| | - Hong Ding
- Peanut Research Institute of Shandong, Qingdao, 266100 China
| | - Jingjing Meng
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Xinguo Li
- College of Life Science, Shandong University, Jinan, 250014 China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Zhenying Peng
- College of Life Science, Shandong University, Jinan, 250014 China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Shubo Wan
- College of Life Science, Shandong University, Jinan, 250014 China
- Shandong Academy of Agricultural Science, Jinan, 250014 China
| |
Collapse
|
49
|
Leonetti P, Miesen P, van Rij RP, Pantaleo V. Viral and subviral derived small RNAs as pathogenic determinants in plants and insects. Adv Virus Res 2020; 107:1-36. [PMID: 32711727 DOI: 10.1016/bs.aivir.2020.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The phenotypic manifestations of disease induced by viruses and subviral infectious entities are the result of complex molecular interactions between host and viral factors. The viral determinants of the diseased phenotype have traditionally been sought at the level of structural or non-structural proteins. However, the discovery of RNA silencing mechanisms has led to speculations that determinants of the diseased phenotype are caused by viral nucleic acid sequences in addition to proteins. RNA silencing is a gene regulation mechanism conserved within eukaryotic kingdoms (with the exception of some yeast species), and in plants and insects it also functions as an antiviral mechanism. Non-coding RNAs of viral origin, ranging in size from 21 to 24 nucleotides (viral small interfering RNAs, vsiRNAs) accumulate in virus-infected tissues and organs, in some cases to comparable levels as the entire complement of host-encoded small interfering RNAs. Upon incorporation into RNA-induced silencing complexes, vsiRNAs can mediate cleavage or induce translational inhibition of nucleic acid targets in a sequence-specific manner. This review focuses on recent findings that suggest an increased complexity of small RNA-based interactions between virus and host. We mainly address plant viruses, but where applicable discuss insect viruses as well. Prominence is given to studies that have indisputably demonstrated that vsiRNAs determine diseased phenotype by either carrying sequence determinants or, indirectly, by altering host-gene regulatory pathways. Results from these studies suggest biotechnological applications, which are also discussed.
Collapse
Affiliation(s)
- Paola Leonetti
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, CNR, Bari, Italy
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Vitantonio Pantaleo
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, CNR, Bari, Italy..
| |
Collapse
|
50
|
The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress. Int J Mol Sci 2020; 21:ijms21082659. [PMID: 32290420 PMCID: PMC7215362 DOI: 10.3390/ijms21082659] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/31/2022] Open
Abstract
Growing interest and recent evidence have identified long non-coding RNA (lncRNA) as the potential regulatory elements for eukaryotes. LncRNAs can activate various transcriptional and post-transcriptional events that impact cellular functions though multiple regulatory functions. Recently, a large number of lncRNAs have also been identified in higher plants, and an understanding of their functional role in plant resistance to infection is just emerging. Here, we focus on their identification in crop plant, and discuss their potential regulatory functions and lncRNA-miRNA-mRNA network in plant pathogen stress responses, referring to possible examples in a model plant. The knowledge gained from a deeper understanding of this colossal special group of plant lncRNAs will help in the biotechnological improvement of crops.
Collapse
|