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Chen Y, Guo S, Jiang L, Yan F, Hao K, Wang Z, An M, Xia Z, Li F, Zhou X, Wu Y. Molecular characterization and pathogenicity of a novel monopartite geminivirus infecting tobacco in China. Virology 2024; 594:110061. [PMID: 38518441 DOI: 10.1016/j.virol.2024.110061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/24/2024]
Abstract
The occurrence of geminiviruses causes significant economic losses in many economically important crops. In this study, a novel geminivirus isolated from tobacco in Sichuan province of China, named tomato leaf curl Chuxiong virus (TLCCxV), was characterized by small RNA-based deep sequencing. The full-length of TLCCxV genome was determined to be 2744 nucleotides (nt) encoding six open reading frames. Phylogenetic and genome-wide pairwise identity analysis revealed that TLCCxV shared less than 91% identities with reported geminiviruses. A TLCCxV infectious clone was constructed and successfully infected Nicotiana benthamiana, N. tabacum, N. glutinosa, Solanum lycopersicum and Petunia hybrida plants. Furthermore, expression of the V2, C1 and C4 proteins through a potato virus X vector caused severe chlorosis or necrosis symptom in N. benthamiana. Taken together, we identified a new geminivirus in tobacco plants, and found that V2, C1 and C4 contribute to symptom development.
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Affiliation(s)
- Yuan Chen
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Shiping Guo
- Sichuan Tobacco Company, Chengdu, Sichuan, 610000, China
| | - Lianqiang Jiang
- Liangshan Branch of Sichuan Tobacco Company, Xichang, Sichuan, 615000, China
| | - Fangfang Yan
- Panzhihua Branch of Sichuan Tobacco Company, Panzhihua, Sichuan, 617000, China
| | - Kaiqiang Hao
- 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
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xueping Zhou
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China.
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Zhao Y, Li Z, Wang Z, Huang L, Li G, Liu X, Yuan M, Huang W, Ling L, Yang C, He Z, Lai J. Improvement of plant resistance to geminiviruses via protein de-S-acylation. Stress Biol 2024; 4:23. [PMID: 38662136 DOI: 10.1007/s44154-024-00166-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/04/2024] [Indexed: 04/26/2024]
Abstract
Geminiviruses are an important group of viruses that infect a variety of plants and result in heavy agricultural losses worldwide. The homologs of C4 (or L4) in monopartite geminiviruses and AC4 (or AL4) in bipartite geminiviruses are critical viral proteins. The C4 proteins from several geminiviruses are the substrates of S-acylation, a dynamic post-translational modification, for the maintenance of their membrane localization and function in virus infection. Here we initiated a screening and identified a plant protein ABAPT3 (Alpha/Beta Hydrolase Domain-containing Protein 17-like Acyl Protein Thioesterase 3) as the de-S-acylation enzyme of C4 encoded by BSCTV (Beet severe curly top virus). Overexpression of ABAPT3 reduced the S-acylation of BSCTV C4, disrupted its plasma membrane localization, inhibited its function in pathogenesis, and suppressed BSCTV infection. Because the S-acylation motifs are conserved among C4 from different geminiviruses, we tested the effect of ABAPT3 on the C4 protein of ToLCGdV (Tomato leaf curl Guangdong virus) from another geminivirus genus. Consistently, ABAPT3 overexpression also disrupted the S-acylation, subcellular localization, and function of ToLCGdV C4, and inhibited ToLCGdV infection. In summary, we provided a new approach to globally improve the resistance to different types of geminiviruses in plants via de-S-acylation of the viral C4 proteins and it can be extendedly used for suppression of geminivirus infection in crops.
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Affiliation(s)
- Yawen Zhao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Zhenggang Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhiying Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Liting Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Gongda Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Xiaoshi Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Meiqi Yuan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Wei Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Lishan Ling
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
| | - Zifu He
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
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Melgarejo TA, Cespedes MK, Chen LF, Turini T, Lazicki PA, Vinchesi-Vahl A, Gilbertson RL. Unusual outbreaks of curly top disease in processing tomato fields in northern California in 2021 and 2022 were caused by a rare strain of beet curly top virus and facilitated by extreme weather events. Virology 2024; 591:109981. [PMID: 38211381 DOI: 10.1016/j.virol.2024.109981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/06/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
In the western United States, curly top disease (CTD) is caused by beet curly top virus (BCTV). In California, CTD causes economic loss to processing tomato production in central and southern areas but, historically, not in the north. Here, we document unusual CTD outbreaks in processing tomato fields in the northern production area in 2021 and 2022, and show that these were caused by the rare spinach curly top strain (BCTV-SpCT). These outbreaks were associated with proximity of fields to foothills and unusually hot, dry, and windy spring weather conditions, possibly by altering migrations of the beet leafhopper (BLH) vector from locations with BCTV-SpCT reservoirs. Support for this hypothesis came from the failure to observe CTD outbreaks and BLH migrations in 2023, when spring weather conditions were cool and wet. Our results show the climate-induced emergence of a rare plant virus strain to cause an economically important disease in a new crop and location.
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Affiliation(s)
- Tomas A Melgarejo
- Department of Plant Pathology, University of California, Davis, One Shield Avenue, Hutchison Hall 273-274, Davis, CA, 95616, United States.
| | - Margaret K Cespedes
- Department of Plant Pathology, University of California, Davis, One Shield Avenue, Hutchison Hall 273-274, Davis, CA, 95616, United States
| | - Li-Fang Chen
- Bayer Crop Science, 37437 CA-16, Woodland, CA, 95695, United States
| | - Thomas Turini
- University of California - Agriculture and Natural Resources, Cooperative Extension Fresno County, 550 E. Shaw Avenue, Suite 210-B, Fresno, CA, 93710, United States
| | - Patricia A Lazicki
- University of California - Agriculture and Natural Resources, Vegetable Crops Advisor, Woodland Administrative Office, 70 Cottonwood Street, Woodland, CA, 95695, United States
| | - Amber Vinchesi-Vahl
- University of New Hampshire, UNH Cooperative Extension Food and Agriculture, 129 Main St., Durham, NH, 03824, United States
| | - Robert L Gilbertson
- Department of Plant Pathology, University of California, Davis, One Shield Avenue, Hutchison Hall 273-274, Davis, CA, 95616, United States
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Ye X, Ding D, Chen Y, Liu C, Li Z, Lou B, Zhou Y. Identification of RNA silencing suppressor encoded by citrus chlorotic dwarf-associated virus. Front Microbiol 2024; 15:1328289. [PMID: 38333582 PMCID: PMC10850569 DOI: 10.3389/fmicb.2024.1328289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024] Open
Abstract
Introduction Citrus chlorotic dwarf-associated virus (CCDaV) is an economically important citrus virus associated with leaf curling, deformation, and chlorosis found in China. Plants have evolved RNA silencing to defend against viral infections; however, the mechanism by which CCDaV suppresses RNA silencing in citrus remains unknown. Methods Six proteins encoded by CCDaV were ectopically expressed in Nicotiana benthamiana 16c using the pCHF3 vector to identify RNA-silencing suppression activities. Results V2 protein encoded by CCDaV suppressed local RNA silencing and systemic RNA silencing triggered by GFP RNA, but did not impede short-distance movement of the RNA silencing signal in N. benthamiana 16c. GFP fluorescence observations showed that the ability of V2 protein to suppress RNA silencing was weaker than tomato bushy stunt virus P19. Deletion analysis showed that the putative nuclear localization signal (NLS, 25-54 aa) was involved in the RNA silencing suppression activity of V2 protein. Furthermore, V2 protein cannot block dsRNA-triggered RNA silencing. The subcellular localization assay suggested that V2 protein was localized to nucleus of N. benthamiana. Conclusion Overall, the results of this study demonstrate that CCDaV-V2 acts as an activity of silencing suppression. This is the first reported RNA-silencing suppressor encoded by Citlodavirus and will be valuable in revealing the molecular mechanism of CCDaV infection.
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Affiliation(s)
- Xiao Ye
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/Citrus Research Institute, Southwest University, Chongqing, China
| | - Dongdong Ding
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/Citrus Research Institute, Southwest University, Chongqing, China
| | - Yuan Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/Citrus Research Institute, Southwest University, Chongqing, China
| | - Chuang Liu
- Lemon Industry Development Center, Anyue, Sichuan, China
| | - Zhongan Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/Citrus Research Institute, Southwest University, Chongqing, China
| | - Binghai Lou
- Guangxi Citrus Breeding and Cultivation Research Center of Engineering Technology/Guangxi Academy of Specialty Crops, Guilin, Guangxi, China
| | - Yan Zhou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/Citrus Research Institute, Southwest University, Chongqing, China
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Morais IJ, Ferreira YFM, Nakasu EYT, Nagata T, Inoue-Nagata AK. Agroinoculation of Geminiviral Infectious Clones into Plants. Methods Mol Biol 2024; 2724:65-70. [PMID: 37987898 DOI: 10.1007/978-1-0716-3485-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Most geminiviruses are not transmitted by mechanical inoculation. Therefore, pathogenicity and plant-pathogen interaction studies rely on agroinoculation using infectious clones, which involves cloning the geminiviral genome in a binary vector (see previous chapter for details). A suspension containing the infectious clone inserted into Agrobacterium tumefaciens cells is then inoculated into plants, i.e., agroinoculated. Below is a simple protocol for agroinoculation of an infectious geminivirus clone into plants.
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Affiliation(s)
- Ivair J Morais
- Department of Phytopathology, University of Brasília, Brasília, DF, Brazil
| | - Yanca F M Ferreira
- Laboratory of Virology and Molecular Biology, Embrapa Vegetables, Brasília, DF, Brazil
| | - Erich Y T Nakasu
- Laboratory of Virology and Molecular Biology, Embrapa Vegetables, Brasília, DF, Brazil
| | - Tatsuya Nagata
- Department of Molecular Biology, University of Brasília, Brasília, DF, Brazil
| | - Alice K Inoue-Nagata
- Laboratory of Virology and Molecular Biology, Embrapa Vegetables, Brasília, DF, Brazil.
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Morais IJ, Inoue-Nagata AK, Nakasu EYT. Construction of Geminivirus Infectious Clones for Agroinoculation into Plants. Methods Mol Biol 2024; 2724:47-64. [PMID: 37987897 DOI: 10.1007/978-1-0716-3485-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The production of geminiviral infectious clones provides a standardized inoculum for use in several host-virus studies. Geminiviruses present either one (monopartite) or two (bipartite) circular single-stranded DNA components, which commonly range from 2.6 to 2.8 kb. Cloning of a monomeric genome is useful for obtaining its precise sequence. For infectious clones, however, it is essential that more than one copy of the genome, more specifically of the origin of replication, is present in order to guarantee the production of full-length progeny DNA. Here, the complete process of preparing infectious geminiviral clones is described starting from the DNA extraction and selection of restriction endonucleases followed by two protocols for constructing dimeric clones: restriction endonuclease digestion and ligation (1) and Gibson Assembly (2).
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Affiliation(s)
- Ivair J Morais
- Department of Phytopathology, University of Brasília, Brasília, DF, Brazil
| | - Alice K Inoue-Nagata
- Laboratory of Virology and Molecular Biology, Embrapa Vegetables, Brasília, DF, Brazil.
| | - Erich Y T Nakasu
- Laboratory of Virology and Molecular Biology, Embrapa Vegetables, Brasília, DF, Brazil.
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Ascencio-Ibáñez JT, Dallas MM, Hanley-Bowdoin L. Begomovirus Inoculation in Arabidopsis and Cassava. Methods Mol Biol 2024; 2724:71-79. [PMID: 37987899 DOI: 10.1007/978-1-0716-3485-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The use of infectious clones to inoculate plant viruses allows for controlled studies that lead to a better understanding of plant-virus interactions. The main methods used for laboratory inoculation of geminiviruses are agroinoculation and biolistics. We describe how to successfully inoculate geminiviruses, focusing on Arabidopsis as a model plant and cassava as a crop.
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Affiliation(s)
- José T Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA.
| | - Mary M Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
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Romero-Rodríguez B, Petek M, Jiao C, Križnik M, Zagorščak M, Fei Z, Bejarano ER, Gruden K, Castillo AG. Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomato. BMC Plant Biol 2023; 23:651. [PMID: 38110861 PMCID: PMC10726652 DOI: 10.1186/s12870-023-04534-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/17/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies allow the simultaneous analysis of multiple aspects of viral infection at a large scale, generating new insights into the molecular mechanisms underlying plant-virus interactions. However, an integrative study of the changes in the host transcriptome, small RNA profile and methylome during a geminivirus infection has not been performed yet. Using a time-scale approach, we aim to decipher the gene regulation in tomato in response to the infection with the geminivirus, tomato yellow leaf curl virus (TYLCV). RESULTS We showed that tomato undergoes substantial transcriptional and post-transcriptional changes upon TYLCV infection and identified the main altered regulatory pathways. Interestingly, although the principal plant defense-related processes, gene silencing and the immune response were induced, this cannot prevent the establishment of the infection. Moreover, we identified extra- and intracellular immune receptors as targets for the deregulated microRNAs (miRNAs) and established a network for those that also produced phased secondary small interfering RNAs (phasiRNAs). On the other hand, there were no significant genome-wide changes in tomato methylome at 14 days post infection, the time point at which the symptoms were general, and the amount of viral DNA had reached its maximum level, but we were able to identify differentially methylated regions that could be involved in the transcriptional regulation of some of the differentially expressed genes. CONCLUSION We have conducted a comprehensive and reliable study on the changes at transcriptional, post-transcriptional and epigenetic levels in tomato throughout TYLCV infection. The generated genomic information is substantial for understanding the genetic, molecular and physiological changes caused by TYLCV infection in tomato.
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Affiliation(s)
- Beatriz Romero-Rodríguez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- The Key Lab of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Araceli G Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Científicas (UMA-CSIC), Boulevard Louis Pasteur, 49, Málaga, 29010, Spain.
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Prasad A, Sharma S, Prasad M. Post translational modifications at the verge of plant- geminivirus interaction. Biochim Biophys Acta Gene Regul Mech 2023; 1866:194983. [PMID: 37717937 DOI: 10.1016/j.bbagrm.2023.194983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
Plant-virus interaction is a complex phenomenon and involves the communication between plant and viral factors. Viruses have very limited coding ability yet, they are able to cause infection which results in huge agro-economic losses throughout the globe each year. Post-translational modifications (PTMs) are covalent modifications of proteins that have a drastic effect on their conformation, stability and function. Like the host proteins, geminiviral proteins are also subject to PTMs and these modifications greatly expand the diversity of their functions. Additionally, these viral proteins can also interact with the components of PTM pathways and modulate them. Several studies have highlighted the importance of PTMs such as phosphorylation, ubiquitination, SUMOylation, myristoylation, S-acylation, acetylation and methylation in plant-geminivirus interaction. PTMs also regulate epigenetic modifications during geminivirus infection which determines viral gene expression. In this review, we have summarized the role of PTMs in regulating geminiviral protein function, influence of PTMs on viral gene expression and how geminiviral proteins interact with the components of PTM pathways to modulate their function.
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Affiliation(s)
- 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.
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Kumar M, Ghosh A, Jadon KS, Kaur B, Kakani RK, Solanki RK. Association of a novel begomovirus species with fenugreek yellow vein disease in India. Mol Biol Rep 2023; 50:9203-9211. [PMID: 37776416 DOI: 10.1007/s11033-023-08806-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 09/07/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Fenugreek (Trigonella foenum-graecum L.) is an annual medicinal and spice crop belonging to the family Fabaceae. The occurrence of a yellow vein disease was recorded in fenugreek in Jodhpur (India) in 2022. The infection of begomoviruses in legume crops results in significant yield loss and major economic loss. The current study reports an association of a novel begomovirus species associated with yellow vein disease in Fenugreek. METHODS AND RESULTS In symptomatic fenugreek plants, geminivirus-like particles were visible under a transmission electron microscope. Further, nucleotide sequence analysis of the rolling circle amplified product revealed 2743 nucleotide DNA-A genome with close relatedness to French bean leaf curl virus (88.21%) and Senna leaf curl virus (87.63%). It was proposed as a new begomovirus species, Fenugreek yellow vein Rajasthan virus. The genome organization suggested the presence of a typical nonanucleotide sequence along with 7 ORFs in DNA-A. A possible recombination event took place in the coat protein (V1) region with Pedilanthus leaf curl virus and Chilli leaf curl virus as major and minor parents. The recombinant virus poses possible threats to several other legume crops. To the best of our knowledge, this is the first report of the association of FeYVRaV with fenugreek yellow vein disease from northwestern India. CONCLUSIONS In conclusion, the presence of a novel begomovirus species associated with yellow vein disease in fenugreek is alarming and needs further studies on its infectivity to prevent its spread to legume crops.
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Affiliation(s)
- Manish Kumar
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Department of Plant Pathology, College of Agricultural & Environmental Sciences, University of Georgia, Tifton, GA, 31793, USA
| | - Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Kuldeep Singh Jadon
- ICAR-Central Arid Zone Research Institute, Jodhpur, Rajasthan, 342003, India.
| | - Baljeet Kaur
- Division of Plant Pathology, TEM Facility, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rajesh K Kakani
- ICAR-Central Arid Zone Research Institute, Jodhpur, Rajasthan, 342003, India
| | - Ramesh K Solanki
- ICAR-Central Arid Zone Research Institute, Jodhpur, Rajasthan, 342003, India
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11
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Lin W, Qiu P, Xu Y, Chen L, Wu Z, Zhang J, Du Z. Transcription start site mapping of geminiviruses using the in vitro cap-snatching of a tenuivirus. J Virol Methods 2023; 319:114757. [PMID: 37257758 DOI: 10.1016/j.jviromet.2023.114757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
Geminiviruses are a family of single-stranded DNA viruses that cause significant yield losses in crop production worldwide. Transcription start site (TSS) mapping is crucial in understanding the gene expression mechanisms of geminiviruses. However, this often requires costly and laborious experiments. Rice stripe virus (RSV) has a mechanism called cap-snatching, whereby it cleaves cellular mRNAs and uses the 5' cleavage product, a capped-RNA leader (CRL), as primers for transcription. Our previous work demonstrated that RSV snatches CRLs from geminiviral mRNAs in co-infected plants, providing a convenient and powerful approach to map the TSSs of geminiviruses. However, co-infections are not always feasible for all geminiviruses. In this study, we evaluated the use of in vitro cap-snatching of RSV for the same purpose, using tomato yellow leaf curl virus (TYLCV) as an example. We incubated RNA extracted from TYLCV-infected plants with purified RSV ribonucleoproteins in a reaction mixture that supports in vitro cap-snatching of RSV. The RSV mRNAs produced in the reaction were deep sequenced. The CRLs snatched by RSV allowed us to locate 28 TSSs in TYLCV. These results provide support for using RSV's in vitro cap-snatching to map geminiviral TSSs.
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Affiliation(s)
- Wenzhong Lin
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Ping Qiu
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Yixing Xu
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Lihong Chen
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Zujian Wu
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jie Zhang
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Zhenguo Du
- Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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12
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Namgial T, Singh AK, Singh NP, Francis A, Chattopadhyay D, Voloudakis A, Chakraborty S. Differential expression of genes during recovery of Nicotiana tabacum from tomato leaf curl Gujarat virus infection. Planta 2023; 258:37. [PMID: 37405593 PMCID: PMC10322791 DOI: 10.1007/s00425-023-04182-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/10/2023] [Indexed: 07/06/2023]
Abstract
MAIN CONCLUSION Nicotiana tabacum exhibits recovery response towards tomato leaf curl Gujarat virus. Transcriptome analysis revealed the differential expression of defense-related genes. Genes encoding for cysteine protease inhibitor, hormonal- and stress-related to DNA repair mechanism are found to be involved in the recovery process. Elucidating the role of host factors in response to viral infection is crucial in understanding the plant host-virus interaction. Begomovirus, a genus in the family Geminiviridae, is reported throughout the globe and is known to cause serious crop diseases. Tomato leaf curl Gujarat virus (ToLCGV) infection in Nicotiana tabacum resulted in initial symptom expression followed by a quick recovery in the systemic leaves. Transcriptome analysis using next-generation sequencing (NGS) revealed a large number of differentially expressed genes both in symptomatic as well as recovered leaves when compared to mock-inoculated plants. The virus infected N. tabacum results in alteration of various metabolic pathways, phytohormone signaling pathway, defense related protein, protease inhibitor, and DNA repair pathway. RT-qPCR results indicated that Germin-like protein subfamily T member 2 (NtGLPST), Cysteine protease inhibitor 1-like (NtCPI), Thaumatin-like protein (NtTLP), Kirola-like (NtKL), and Ethylene-responsive transcription factor ERF109-like (NtERTFL) were down-regulated in symptomatic leaves when compared to recovered leaves of ToLCGV-infected plants. In contrast, the Auxin-responsive protein SAUR71-like (NtARPSL) was found to be differentially down-regulated in recovered leaves when compared to symptomatic leaves and the mock-inoculated plants. Lastly, Histone 2X protein like (NtHH2L) gene was found to be down-regulated, whereas Uncharacterized (NtUNCD) was up-regulated in both symptomatic as well as recovered leaves compared to the mock-inoculated plants. Taken together, the present study suggests potential roles of the differentially expressed genes that might govern tobacco's susceptibility and/or recovery response towards ToLCGV infection.
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Affiliation(s)
- T Namgial
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - A K Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - N P Singh
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Francis
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - D Chattopadhyay
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Voloudakis
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece.
| | - S Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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13
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Kumar S, Gupta N, Chakraborty S. Geminiviral betasatellites: critical viral ammunition to conquer plant immunity. Arch Virol 2023; 168:196. [PMID: 37386317 DOI: 10.1007/s00705-023-05776-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/30/2023] [Indexed: 07/01/2023]
Abstract
Geminiviruses have mastered plant cell modulation and immune invasion to ensue prolific infection. Encoding a relatively small number of multifunctional proteins, geminiviruses rely on satellites to efficiently re-wire plant immunity, thereby fostering virulence. Among the known satellites, betasatellites have been the most extensively investigated. They contribute significantly to virulence, enhance virus accumulation, and induce disease symptoms. To date, only two betasatellite proteins, βC1, and βV1, have been shown to play a crucial role in virus infection. In this review, we offer an overview of plant responses to betasatellites and counter-defense strategies deployed by betasatellites to overcome those responses.
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Affiliation(s)
- Sunil Kumar
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Neha Gupta
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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14
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Sangeeta, Kumar RV, Yadav BK, Bhatt BS, Krishna R, Krishnan N, Karkute SG, Kumar S, Singh B, Singh AK. Diverse begomovirus-betasatellite complexes cause tomato leaf curl disease in the western India. Virus Res 2023; 328:199079. [PMID: 36813240 DOI: 10.1016/j.virusres.2023.199079] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
In the Indian sub-continent, tomato leaf curl disease (ToLCD) of tomato caused by begomoviruses has emerged as a major limiting factor for tomato cultivation. Despite the spread of this disease in the western India, a systematic study on the characterization of virus complexes with ToLCD is lacking. Here, we report the identification of a complex of begomoviruses including 19 DNA-A and 4 DNA-B as well as 15 betasatellites with ToLCD in the western part of the country. Additionally, a novel betasatellite and an alphasatellite were also identified. The recombination breakpoints were detected in the cloned begomoviruses and betasatellites. The cloned infectious DNA constructs cause disease on the tomato (a moderately virus-resistant cultivar) plants, thus fulfilling Koch's postulates for these virus complexes. Further, the role of non-cognate DNA B/betasatellite with ToLCD-associated begomoviruses on disease development was demonstrated. It also emphasizes the evolutionary potential of these virus complexes in breaking disease resistance and plausible expansion of its host range. This necessitates to investigate the mechanism of the interaction between resistance breaking virus complexes and the infected host.
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Affiliation(s)
- Sangeeta
- School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat 382 030, India; Present address-Department of Science & Technology, Gujarat Council of Science & Technology, Gandhinagar, Gujarat 382 011, India
| | - R Vinoth Kumar
- Department of Biotechnology, College of Science & Humanities, SRM Institute of Science & Technology, Ramapuram, Chennai, Tamil Nadu 600 089, India
| | - Brijesh K Yadav
- School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat 382 030, India; Faculty of Education and Methodology, Jayoti Vidyapeeth Women's University, Jaipur, Rajasthan 303 122, India
| | - Bhavin S Bhatt
- School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat 382 030, India; Faculty of Science, Sarvajanik University, Surat, Gujarat 395 001, India
| | - Ram Krishna
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Nagendran Krishnan
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Suhas G Karkute
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Sudhir Kumar
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Bijendra Singh
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India
| | - Achuit K Singh
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221 305, India.
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15
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Quadros AFF, Ferro CG, de Rezende RR, Godinho MT, Xavier CAD, Nogueira AM, Alfenas-Zerbini P, Zerbini FM. Begomovirus populations in single plants are complex and may include both well-adapted and poorly-adapted viruses. Virus Res 2023; 323:198969. [PMID: 36257487 PMCID: PMC10194161 DOI: 10.1016/j.virusres.2022.198969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
Abstract
Begomoviruses (single-stranded DNA plant viruses transmitted by whiteflies) are economically important pathogens causing epidemics worldwide. Tomato-infecting begomoviruses emerged in Brazil in the 1990's following the introduction of Bemisia tabaci Middle East-Asia Minor 1. It is believed that these viruses evolved from indigenous viruses infecting non-cultivated hosts. However, tomato-infecting viruses are rarely found in non-cultivated hosts, and vice-versa. It is possible that viral populations in a given host are composed primarily of viruses which are well adapted to this host, but also include a small proportion of poorly adapted viruses. Following transfer to a new host, the composition of the viral population would shift rapidly, with the viruses which are better adapted to the new host becoming predominant. To test this hypothesis, we collected tomato and Sida plants growing next to each other at two locations in 2014 and 2018. Total DNA was extracted from tomato and Sida samples from each location and year and used as a template for high-throughput sequencing. Reads were mapped following a highly stringent set of criteria. For the 2014 samples, >98% of the Sida reads mapped to Sida micrantha mosaic virus (SiMMV), but 0.1% of the reads mapped to tomato severe rugose virus (ToSRV). Conversely, >99% of the tomato reads mapped to ToSRV, with 0.18% mapping to SiMMV. For the 2018 samples, 41% of the Sida reads mapped to three Sida-adapted viruses and 0.1% of the reads mapped to ToSRV, while 99.9% of the tomato reads mapped to ToSRV. These results are consistent with the hypothesis that viral populations in a single plant are composed primarily of the virus that is better adapted to the host but also include a small proportion of viruses that are poorly adapted.
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Affiliation(s)
- Ayane F F Quadros
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Camila G Ferro
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Rafael R de Rezende
- Dep. de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Márcio T Godinho
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - César A D Xavier
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Angélica M Nogueira
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - P Alfenas-Zerbini
- Dep. de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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16
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García-Rodríguez DA, Partida-Palacios BL, Regla-Márquez CF, Centeno-Leija S, Serrano-Posada H, Bañuelos-Hernández B, Cárdenas-Conejo Y. Sida chlorotic leaf virus: a new recombinant begomovirus found in non-cultivated plants and Cucumis sativus L. PeerJ 2023; 11:e15047. [PMID: 36974135 PMCID: PMC10039651 DOI: 10.7717/peerj.15047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Background Begomoviruses are circular single-stranded DNA plant viruses that cause economic losses worldwide. Weeds have been pointed out as reservoirs for many begomoviruses species, especially from members of the Sida and Malvastrum genera. These weeds have the ability to host multiple begomoviruses species simultaneously, which can lead to the emergence of new viral species that can spread to commercial crops. Additionally, begomoviruses have a natural tendency to recombine, resulting in the emergence of new variants and species. Methods To explore the begomoviruses biodiversity in weeds from genera Sida and Malvastrum in Colima, México, we collected symptomatic plants from these genera throughout the state. To identify BGVs infecting weeds, we performed circular DNA genomics (circomics) using the Illumina platform. Contig annotation was conducted with the BLASTn tool using the GenBank nucleotide "nr" database. We corroborated by PCR the presence of begomoviruses in weeds samples and isolated and sequenced the complete genome of a probable new species of begomovirus using the Sanger method. The demarcation process for new species determination followed the International Committee on Taxonomy of Viruses criteria. Phylogenetic and recombination analyses were implemented to infer the evolutionary relationship of the new virus. Results We identified a new begomovirus species from sida and malvastrum plants that has the ability to infect Cucumis sativus L. According to our findings, the novel species Sida chlorotic leaf virus is the result of a recombination event between one member of the group known as the Squash leaf curl virus (SLCV) clade and another from the Abutilon mosaic virus (AbMV) clade. Additionally, we isolated three previously identified begomoviruses species, two of which infected commercial crops: okra (Okra yellow mosaic Mexico virus) and cucumber (Cucumber chlorotic leaf virus). Conclusion These findings support the idea that weeds act as begomovirus reservoirs and play essential roles in begomovirus biodiversity. Therefore, controlling their populations near commercial crops must be considered in order to avoid the harmful effects of these phytopathogens and thus increase agricultural efficiency, ensuring food and nutritional security.
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Affiliation(s)
| | | | | | - Sara Centeno-Leija
- Universidad de Colima, Consejo Nacional de Ciencia y Tecnología-Laboratorio de Biología Sintética, Estructural y Molecular, Colima, México
| | - Hugo Serrano-Posada
- Universidad de Colima, Consejo Nacional de Ciencia y Tecnología-Laboratorio de Biología Sintética, Estructural y Molecular, Colima, México
| | | | - Yair Cárdenas-Conejo
- Universidad de Colima, Consejo Nacional de Ciencia y Tecnología-Laboratorio de Biología Sintética, Estructural y Molecular, Colima, México
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17
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Rauniyar N, Singhal P, Diksha D, Srivastava D, Baranwal VK. Characterization of a recombinant tomato leaf curl New Delhi Virus (ToLCNDV) in a perennial medicinal climber host ( Ipomoea cairica (L.) Sweet). 3 Biotech 2023; 13:3. [PMID: 36514482 PMCID: PMC9741688 DOI: 10.1007/s13205-022-03418-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/26/2022] [Indexed: 12/14/2022] Open
Abstract
During the year 2020-2021, a disease syndrome very commonly observed in railway creepers (Ipomoea cairica (L.) Sweet) was taken into consideration from Gorakhpur Province (UP East region). Whitefly, a common vector for plant-related viral diseases was observed for wide transmission of disease. DNA from 17 infected leaf samples was isolated and analyzed through PCR using specific primers designed for the detection of Begomoviruses. Further amplification of isolated DNA fragments supporting a begomovirus infection with an estimated size of (2.7 kb). RCA of the isolated DNA sample was carried out using ϕ29 DNA polymerase by digesting it through a set of restriction endonucleases (such as BamHI, Kpn1, HindIII, EcoRI) obtaining the best result through KpnI. The amplified segment was cloned into pUC 18vectors. The obtained sequences were matched using the NCBI BLAST database showing the highest sequence similarity of 98.7% with ToLCNDV of snake gourd (Accession no. KY780199), isolates of CP genes sequence in Varanasi. ToLCNDV, a begomovirus of bipartite nature was first reported to be from Tomato (Solanaceae), later affecting certain members of the Cucurbitaceae family in India and adjacent countries. The obtained DNA sequence was submitted at NCBI with the name ToLCNDV-IP (GenBank Accession no. OM777194). The phylogenetic analysis clubbed the current isolate ToLCNDV-IP with Asian isolates. All European isolates were clubbed in separate clades indicating two distinct groups of ToLCNDV isolates. ToLCNDV-IP isolate was found to be an intralineage recombinant between two Asian isolates viz ToLCNDV isolate from Papaya (India) and ToLCNDV isolate from Tomato (Pakistan). This study shows the association of recombinant ToLCNDV infection in a new host Ipomoea cairica for the first time in India.
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Affiliation(s)
- Neha Rauniyar
- Department of Botany, Deen Dayal, Upadhyay Gorakhpur University, Gorakhpur, India
| | - Pankhuri Singhal
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Damini Diksha
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Deepa Srivastava
- Department of Botany, Deen Dayal, Upadhyay Gorakhpur University, Gorakhpur, India
| | - V. K. Baranwal
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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18
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Jammes M, Urbino C, Diouf MB, Peterschmitt M. Refining the emergence scenario of the invasive recombinant Tomato yellow leaf curl virus -IS76. Virology 2023; 578:71-80. [PMID: 36473279 DOI: 10.1016/j.virol.2022.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/02/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
TYLCV-IS76, a unique recombinant between tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV), has replaced its parental viruses in southern Morocco. To refine its emergence scenario, its fitness was monitored experimentally in conditions aiming at reproducing natural situations, i.e. superinfection of plants already infected with parental viruses and competition with other TYLCV/TYLCSV recombinants (LSRec) automatically generated in plants coinfected with TYLCV and TYLCSV. TYLCV-IS76 accumulated significantly more than parental viruses regardless of plant age and superinfection delay. Although TYLCV-IS76 and LSRec both accumulated more than parental viruses in laboratory conditions, LSRec were displaced by TYLCV-IS76 in nature like parental viruses were. TYLCV-IS76 did not exhibit any vector transmission advantage over LSRec and TYLCV the most competitive parental virus. Thus, it is apparently only in the plant compartment that the recombination event that generated TYLCV-IS76, induced the competitiveness advantage by which the last became first.
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Affiliation(s)
- Margaux Jammes
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Cica Urbino
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Mame Boucar Diouf
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Michel Peterschmitt
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
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19
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Rizvi I, Hisamuddin M, Malik A, Khan RH. Identification of mungbean yellow mosaic India virus (MYMIV) Rep interacting partners using phage display and influence of Arabidopsis thaliana MCM3 on geminivirus DNA replication. J Biomol Struct Dyn 2022; 40:10507-10517. [PMID: 34121621 DOI: 10.1080/07391102.2021.1935319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Geminiviruses consist of a single-stranded DNA genome that replicates by a rolling circle (RCR) and recombination-dependent (RDR) modes of replication. The AC1 or Rep is the indispensable viral protein required for the RCR mode of replication. Since these viruses encode only a few proteins, they depend on several host factors for replication, transcription, and other physiological processes. To get insights into the repertoire of host factors influencing the replication of geminiviruses, we performed phage display experiments which led to the identification of putative mungbean yellow mosaic India virus (MYMIV) Rep interacting host proteins. These proteins might directly or indirectly participate in geminivirus biology. MCM3 was one of the Rep-interacting partners obtained in the phage display results. Using bimolecular fluorescence complementation (BiFC), the interaction of the MYMIV Rep with Arabidopsis thaliana MCM3 (AtMCM3) was confirmed. We report the involvement of AtMCM3 in the replication of MYMIV DNA through an ex vivo system. The physiological relevance of the interaction between AtMCM3 and MYMIV Rep is reflected by yeast replication assay.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Irum Rizvi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.,International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Malik Hisamuddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Ajamaluddin Malik
- Department of Biochemistry, King Saud University, Riyadh, Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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20
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More P, Agarwal P, Agarwal PK. The Jatropha leaf curl Gujarat virus on infection in Jatropha regulates the sugar and tricarboxylic acid cycle metabolic pathways. 3 Biotech 2022; 12:275. [PMID: 36110567 PMCID: PMC9468196 DOI: 10.1007/s13205-022-03306-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/10/2022] [Indexed: 11/25/2022] Open
Abstract
Jatropha, a popular biodiesel crop, suffers severe losses due to Jatropha leaf curl Gujarat virus (JLCuGV) infection in Gujarat (India). Metabolite profiling can help to understand the plant's innate immune response to geminivirus infection. Our study aims to compare metabolic profiles of an infected and healthy plant to unravel the changes in biochemical pathways on geminivirus infection in Jatropha. Gas chromatography-mass spectrometry (GC-MS) analysis was performed in healthy and infected tissue of Jatropha field plants which were identified to be infected with geminivirus. GC-MS analysis revealed that the metabolites like sugars, polyols, carboxylic acids, fatty acids, polyphenols, and amino acids were regulated on JLCuGV infection. The sugars (glucose, sucrose, and fructose) increased, while carboxylic acids (malic acid, citric acid and quinic acid) and polyols (galactinol, butanetriol, triethylene glycol, myo-inositol, erythritol) decreased remarkably in infected Jatropha tissue. All these metabolic variations indicated that sugar metabolism and tricarboxylic acid (TCA) cycle pathways are regulated as a defense response and a disease development response to geminivirus infection in Jatropha.
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Affiliation(s)
- Prashant More
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific & Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, Gujarat 364 002 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Parinita Agarwal
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific & Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, Gujarat 364 002 India
| | - Pradeep K. Agarwal
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific & Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, Gujarat 364 002 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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21
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Ebrahimi S, Eini O, Koolivand D, Varrelmann M. The Rep and C1 of Beet curly top Iran virus represent pathogenicity factors and induce hypersensitive response in Nicotiana benthamiana plants. Virus Genes 2022. [PMID: 35960462 DOI: 10.1007/s11262-022-01927-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/26/2022] [Indexed: 10/15/2022]
Abstract
Beet curly top Iran virus (BCTIV) is a member of the genus Becurtovirus (Family Geminiviridae) with a circular single-strand DNA genome. BCTIV causes leaf curling and vein swelling symptoms in plants. However, the potential pathogenicity factor/s in BCTIV is/are not known. This study presents characterization of complementary-sense transcripts of BCTIV and the viral factors in directing the pathogenicity and hypersensitive response (HR) in Nicotiana benthamiana plants. In both local and systemic infection, splicing of the complementary transcripts of BCTIV was observed. Notably, a small number (8.3%) of transcripts were spliced to produce Rep (C1:C2) transcripts after deletion of 155 nt (position 1892-2046 from BCTIV). Expression of BCTIV genes in N. benthamiana using tobacco rattle virus (TRV)-based vector showed that Rep together with C1 are the main pathogenicity factors which cause typical viral leaf curling symptoms. In addition, the V2 caused a mild leaf curling, thickening, and asymmetric leaves, while the V1, V3, and C2 had no clear effect on the plant phenotype. Transient expression of individual viral genes showed that both the C1 and Rep trigger a HR response in N. benthamiana. The higher expression of HR marker genes, harpin-induced 1 (Hin1) and hypersensitivity-related (Hsr203JI), supported the role of C1 and Rep in HR response in plants. It is concluded that Rep and C1 are the main pathogenicity factors that also trigger HR response in plants.
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22
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Patil BL, Dasgupta I. Characterization of the functional domains of nuclear shuttle protein (NSP) of Indian cassava mosaic virus using green fluorescent protein as reporter. Virus Genes 2022; 58:308-318. [PMID: 35567667 DOI: 10.1007/s11262-022-01909-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/27/2022] [Indexed: 11/30/2022]
Abstract
Indian cassava mosaic virus (ICMV), responsible for the cassava mosaic disease in India, harbours two circular genomic components, DNA-A and DNA-B; the former being responsible for the encapsidation and replication and the latter for intra- and inter-cellular movement of the viral DNA. Two proteins, encoded by DNA-B, the movement protein (MP) and the nuclear shuttle protein (NSP), act in concert on the newly replicated viral DNA to move it from the nucleus to the cell periphery. To map the functional domains of NSP, the intra-cellular localization of its full-length protein and deletion derivatives was studied in the epidermal cells of detached leaves of the laboratory host plant, Nicotiana benthamiana, where the target proteins were transiently expressed as GFP fusions. This analysis revealed domains for nuclear localization at the N-terminus, as well as for localization towards the cell periphery both at the C-terminus and center of the NSP.
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Affiliation(s)
- Basavaprabhu L Patil
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
- ICAR-Indian Institute of Horticultural Research, Bengaluru, 560089, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Huang W, Zhao Y, Liu X, Ling L, Han D, Huang L, Gao C, Yang C, Lai J. ABA INSENSITIVE 5 confers geminivirus resistance via suppression of the viral promoter activity in plants. J Plant Physiol 2022; 275:153742. [PMID: 35696829 DOI: 10.1016/j.jplph.2022.153742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/21/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Geminiviruses are a large group of plant viruses that have been a serious threat to worldwide agriculture. Transcription of the virus-encoded genes is necessary for geminiviruses to complete their life cycle, but the host proteins which directly target geminivirus promoters for suppression of viral gene transcription remain to be identified. Using Beet severe curly top virus (BSCTV) which causes severe plant symptoms as a system, we performed a yeast one-hybrid screening and identified ABA INSENSITIVE 5 (ABI5), a critical transcription factor in Abscisic acid (ABA) signaling transduction, as an interactor with the viral promoter. Further data showed that an ABA-responsive element in the viral promoter is necessary for its interaction with ABI5 and symptom development. Overexpression of ABI5 suppresses the transcription activity of the viral promoter and BSCTV infection in Nicotiana benthamiana and Arabidopsis; whilst depletion of ABI5 enhances the infection of BSCTV in Arabidopsis. Taken together, our study uncovered the function of ABI5 in the plant-virus interaction and will provide us with a new strategy to protect crops from geminivirus infection.
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Affiliation(s)
- Wei Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Yawen Zhao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Xiaoshi Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Lishan Ling
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Liting Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China.
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, 510631, Guangzhou, China.
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24
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Wang C, Fan S, Xu N, Li Z, Zhang S, Zhu S. Structural basis of DNA recognition of tomato yellow leaf curl virus replication-associated protein. Int J Biol Macromol 2022; 205:316-328. [PMID: 35192905 DOI: 10.1016/j.ijbiomac.2022.02.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/05/2022]
Abstract
Conserved and multifunctional Geminivirus Replication-associated Protein (Rep) specifically recognizes the replication origin and initiates viral DNA replication. We report the X-ray crystallography-based structures of two complexes containing the N-terminal domain (5-117aa) of Tomato yellow leaf curl virus (TYLCV) Rep: the catalytically-dead Rep in complex with nonanucleotide ssDNA (Rep5-117 Y101F-ssDNA) as well as the catalytically-active phosphotyrosine covalent adduct (Rep5-117-ssDNA). These structures provide functional insight into the role of Rep in viral replication. Metal ions stabilize the DNA conformation by interacting with the phosphate group of adenine and thus promote formation of the catalytic center. Furthermore, we identified a compound that inhibits the binding of Rep to ssDNA and dsDNA and found that the addition of metal ions compromises the inhibitory effectiveness of this compound. This study demonstrates the mechanism of DNA recognition and cleavage process of viral Rep, emphasizing the role of metal ions.
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Affiliation(s)
- Chaonan Wang
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shilong Fan
- The Technology Center for Protein Sciences, Tsinghua University, Beijing 100084, China
| | - Ning Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhihong Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Senyan Zhang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
| | - Shuifang Zhu
- College of Plant Protection, China Agricultural University, Beijing 100193, China; Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
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25
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Gupta K, Rishishwar R, Dasgupta I. The interplay of plant hormonal pathways and geminiviral proteins: partners in disease development. Virus Genes 2022; 58:1-14. [PMID: 35034268 DOI: 10.1007/s11262-021-01881-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/28/2021] [Indexed: 10/19/2022]
Abstract
Viruses belonging to the family Geminiviridae infect plants and are responsible for a number of diseases of crops in the tropical and sub-tropical regions of the World. The innate immune response of the plant assists in its defense against such viral pathogens by the recognition of pathogen/microbe-associated molecular patterns through pattern-recognition receptors. Phytohormone signalling pathways play a vital role in plant defense responses against these devastating viruses. Geminiviruses, however, have developed counter-defense strategies that prevail over the above defense pathways. The proteins encoded by geminiviruses act as suppressors of plant immunity by interacting with the signalling components of several hormones. In this review we focus on the molecular interplay of phytohormone pathways and geminiviral infection and try to find interesting parallels with similar mechanisms known in other plant-infecting viruses and strengthen the argument that this interplay is necessary for disease development.
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Affiliation(s)
- Kanika Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, -110021, India
| | - Rashmi Rishishwar
- Department of Botany, Bhagat Singh Government P.G. College, Jaora, Ratlam, Madhya Pradesh, 457226, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, -110021, India.
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26
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Srivastava A, Gupta T, Srivastava S, Dhir S, Kumar P, Singhal T, Rani A, Rishi N. Development of a new Collateral Cleavage-independent CRISPR/Cas12a based easy detection system for plant viruses. J Virol Methods 2021; 300:114432. [PMID: 34919973 DOI: 10.1016/j.jviromet.2021.114432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022]
Abstract
Plant virus spread through various means, from mechanically to the insect vectors and act as obligate parasite, therefore, are extremely challenging to eradicate. Geminiviruses are an important class of viruses which have reported extensively in last two decades on several new hosts. They infect wide range of annual crops and perineal shrubs, therefore, essentially required to detect them on field and dispose to check their vector transmission to healthy crops. In this study, we have chosen two important begomovirus viz. Mungbean yellow mosaic India virus which infect wide range of leguminous crops while Ageratum enation virus is reported to infect a wide range of crops from weed to opium poppy. Here, we have utilized the binding and cleaving ability of LbaCas12a protein with target to detect the virus infection on field. We proposed here a new Collateral Cleavage Independent CRISPR/Cas12a based detection system (CCI-CRISPR) for plant viruses.
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Affiliation(s)
- Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India.
| | - Taruna Gupta
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Sonal Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Sunny Dhir
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Tripti Singhal
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Asha Rani
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Narayan Rishi
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313, India
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27
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Abstract
BACKGROUND Alphasatellites are small coding DNA satellites frequently associated with a begomovirus/betasatellite complex, where they are known to modulate virulence and symptom development. Two distinct alphasatellites, namely, Cotton leaf curl Multan alphasatellite (CLCuMuA), and Gossypium darwinii symptomless alphasatellite (GDarSLA) associated with Cotton leaf curl Multan virus-India (CLCuMuV-IN) and Ludwigia leaf distortion betasatellite (LuLDB) were found to be associated with yellow mosaic disease of hollyhock (Alcea rosea) plants. In this study, we show that alphasatellites CLCuMuA and GDarSLA attenuate and delay symptom development in Nicotiana benthamiana. The presence of either alphasatellites reduce the accumulation of the helper virus CLCuMuV-IN. However, the levels of the associated betasatellite, LuLDB, remains unchanged. These results suggest that the alphasatellites could contribute to the host defence and understanding their role in disease development is important for developing resistance strategies. METHODS Tandem repeat constructs of two distinct alphasatellites, namely, CLCuMuA and GDarSLA associated with CLCuMuV-IN and LuLDB were generated. N. benthamiana plants were co-agroinoculated with CLCuMuV and its associated alphasatellites and betasatellite molecules and samples were collected at 7, 14 and 21 days post inoculation (dpi). The viral DNA molecules were quantified in N. benthamiana plants by qPCR. The sequences were analysed using the MEGA-X tool, and a phylogenetic tree was generated. Genetic diversity among the CLCuMuA and GDarSLA was analysed using the DnaSP tool. RESULTS We observed a reduction in symptom severity and accumulation of helper virus in the presence of two alphasatellites isolated from naturally infected hollyhock plants. However, no reduction in the accumulation of betasatellite was observed. The phylogenetic and genetic variability study revealed the evolutionary dynamics of these distinct alphasatellites , which could explain the role of hollyhock-associated alphasatellites in plants. CONCLUSIONS This study provides evidence that alphasatellites have a role in symptom modulation and suppress helper virus replication without any discernible effect on the replication of the associated betasatellite.
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Affiliation(s)
- Manish Kumar
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067 India
| | - Fauzia Zarreen
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067 India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067 India
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28
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Eini O, Schumann N, Niessen M, Varrelmann M. Targeted mutagenesis in plants using Beet curly top virus for efficient delivery of CRISPR/Cas12a components. N Biotechnol 2021; 67:1-11. [PMID: 34896246 DOI: 10.1016/j.nbt.2021.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 10/19/2022]
Abstract
Genome editing using CRISPR/Cas is rapidly being developed for gene targeting in eukaryotes including plants. However, gene targeting by homology-directed DNA recombination (HDR) is an infrequent event compared to the dominant DNA repair by non-homologous end-joining. Another bottleneck is the ineffective delivery of CRISPR/Cas components into plant cells. To overcome these constraints, here a geminiviral replicon from Beet curly top virus (BCTV) has been produced with a wide host range and high DNA accumulation capacity for efficient delivery of CRISPR/Cas12a components into plant cells. Initially, a BCTV replicon was prepared after removing the virion sense genes from an infectious full-length clone for agrobacterium mediated infection. This replicon expressed a green fluorescent protein (GFP) marker gene at a high level compared to T-DNA binary vector. In transient assay, the BCTV replicon produced a higher rate of mutagenesis and HDR in the GFP transgene in Nicotiana benthamiana through efficient delivery of CRISPR/Cas12a components compared to the cognate T-DNA control. This was through a range of complete or partial HDR for conversion of GFP into YFP after exchange of a single amino acid (Thr224Tyr) in the target gene. In addition, induced mutagenesis and HDR in the target gene were heritable. Thus, the BCTV replicon provides a new tool for efficient delivery of CRISPR/Cas12a components that could be used in a wide range of dicotyledonous plants. The established GFP to YFP system and the GFP mutant line produced also enable further optimization and understanding of HDR in plants via CRISPR/Cas12a system using geminiviral replicons.
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Affiliation(s)
- Omid Eini
- Department of Plant Protection, University of Zanjan, 313, Zanjan, Iran; Department of Phytopathology, Institute for Sugar Beet Research, 37079, Göttingen, Germany.
| | | | | | - Mark Varrelmann
- Department of Phytopathology, Institute for Sugar Beet Research, 37079, Göttingen, Germany
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29
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Zakeel MCM, Geering ADW, Thomas JE, Akinsanmi OA. Characterisation of novel endogenous geminiviral elements in macadamia. BMC Genomics 2021; 22:858. [PMID: 34837949 PMCID: PMC8626973 DOI: 10.1186/s12864-021-08174-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/11/2021] [Indexed: 11/11/2022] Open
Abstract
Background The presence of geminivirus sequences in a preliminary analysis of sRNA sequences from the leaves of macadamia trees with abnormal vertical growth (AVG) syndrome was investigated. Results A locus of endogenous geminiviral elements (EGE) in the macadamia genome was analysed, and the sequences revealed a high level of deletions and/or partial integrations, thus rendering the EGE transcriptionally inactive. The replication defective EGE in the macadamia genome indicates its inability to be the source of new viral infections and thus cause AVG or any other disease in macadamia. The EGE sequences were detected in two edible Macadamia species that constitute commercial cultivars and the wild germplasm of edible and inedible species of Macadamia. This strongly suggests that the integration preceded speciation of the genus Macadamia. A draft genome of a locus of EGE in Macadamia was developed. The findings of this study provide evidence to suggest the endogenization of the geminiviral sequences in the macadamia genome and the ancestral relationship of EGE with Macadamia in the Proteaceae family. Random mutations accumulating in the EGE inform that the sequence is evolving. Conclusions The EGE in Macadamia is inactive and thus not a direct cause of any diseases or syndromes including AVG in macadamia. The insertion of the EGE in the macadamia genome preceded speciation of the genus Macadamia. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08174-0.
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Affiliation(s)
- Mohamed C M Zakeel
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, GPO Box 267, Brisbane, QLD, 4001, Australia.
| | - Andrew D W Geering
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - John E Thomas
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - Olufemi A Akinsanmi
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, GPO Box 267, Brisbane, QLD, 4001, Australia.
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Watanabe K, Ugaki M. Mastrevirus Rep and RepA Proteins Suppress de novo Transcriptional Gene Silencing. Int J Mol Sci 2021; 22:11462. [PMID: 34768892 DOI: 10.3390/ijms222111462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 01/13/2023] Open
Abstract
Transcriptional gene silencing (TGS) in plants is a defense mechanism against DNA virus infection. The genomes of viruses in the Geminiviridae family encode several TGS suppressors. In this study, we induced de novo TGS against the transgenic GFP gene encoding green fluorescent protein by expressing a hairpin-shaped self-complementary RNA corresponding to the enhancer region of the 35S promoter (hpE35S). In addition, we examined the TGS suppression activity of proteins encoded in the genome of Tobacco yellow dwarf virus (TYDV, genus Mastrevirus). The results show that the replication-associated protein (Rep) and RepA encoded by TYDV have TGS suppressor activity and lead to decreased accumulation of 24-nt siRNAs. These results suggest that Rep and RepA can block the steps before the loading of siRNAs into Argonaute (AGO) proteins. This is the first report of TGS suppressors in the genus Mastrevirus.
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Happle A, Jeske H, Kleinow T. Dynamic subcellular distribution of begomoviral nuclear shuttle and movement proteins. Virology 2021; 562:158-175. [PMID: 34339930 DOI: 10.1016/j.virol.2021.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/20/2021] [Accepted: 07/25/2021] [Indexed: 11/30/2022]
Abstract
The Abutilon mosaic virus (AbMV) encodes a nuclear shuttle protein (NSP), and a movement protein (MP) which cooperatively accomplish viral DNA transport through the plant. Subcellular distribution patterns of fluorescent protein-tagged NSP and MP were tracked in Nicotiana benthamiana leaves in presence or absence of an AbMV infection using light microscopy. NSP was located within the nucleus and associated with early endosomes in the presence of MP. MP appeared at the plasma membrane, plasmodesmata and in motile vesicles, trafficking along the endoplasmic reticulum in an actin-dependent manner. MP and NSP did not co-localize and employed separate cellular pathways. Correspondingly, Förster resonance energy transfer analysis did not support physical interaction between NSP and MP. Time lapse movies illustrate the cellular dynamics of both proteins on their way around the nucleus and to the cell periphery and provide a first hint for the nuclear egress of NSP complexes.
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Affiliation(s)
- Andrea Happle
- Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Holger Jeske
- Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Tatjana Kleinow
- Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany.
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Xavier CAD, Nogueira AM, Bello VH, Watanabe LFM, Barbosa TMC, Alves Júnior M, Barbosa L, Beserra-Júnior JEA, Boari A, Calegario R, Gorayeb ES, Honorato Júnior J, Koch G, Lima GSDA, Lopes C, de Mello RN, Pantoja K, Silva FN, Ramos Sobrinho R, Santana EN, da Silva JWP, Krause-Sakate R, Zerbini FM. Assessing the diversity of whiteflies infesting cassava in Brazil. PeerJ 2021; 9:e11741. [PMID: 34316398 PMCID: PMC8286705 DOI: 10.7717/peerj.11741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background The necessity of a competent vector for transmission is a primary ecological factor driving the host range expansion of plant arthropod-borne viruses, with vectors playing an essential role in disease emergence. Cassava begomoviruses severely constrain cassava production in Africa. Curiously, begomoviruses have never been reported in cassava in South America, the center of origin for this crop. It has been hypothesized that the absence of a competent vector in cassava is the reason why begomoviruses have not emerged in South America. Methods We performed a country-wide whitefly diversity study in cassava in Brazil. Adults and/or nymphs of whiteflies were collected from sixty-six cassava fields in the main agroecological zones of the country. A total of 1,385 individuals were genotyped based on mitochondrial cytochrome oxidase I sequences. Results A high species richness was observed, with five previously described species and two putative new ones. The prevalent species were Tetraleurodes acaciae and Bemisia tuberculata, representing over 75% of the analyzed individuals. Although we detected, for the first time, the presence of Bemisia tabaci Middle East-Asia Minor 1 (BtMEAM1) colonizing cassava in Brazil, it was not prevalent. The species composition varied across regions, with fields in the Northeast region showing a higher diversity. These results expand our knowledge of whitefly diversity in cassava and support the hypothesis that begomovirus epidemics have not occurred in cassava in Brazil due to the absence of competent vector populations. However, they indicate an ongoing adaptation process of BtMEAM1 to cassava, increasing the likelihood of begomovirus emergence in this crop.
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Affiliation(s)
- Cesar A D Xavier
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | | | | | | - Miguel Alves Júnior
- Faculdade de Engenharia Agronômica, Universidade Federal do Pará, Altamira, PA, Brazil
| | - Leonardo Barbosa
- Instituto Federal do Sudeste de Minas Gerais, Rio Pomba, MG, Brazil
| | | | | | - Renata Calegario
- Dep. de Fitotecnia e Fitossanidade, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Silva Gorayeb
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Jaime Honorato Júnior
- Centro Multidisciplinar do Campus de Barra, Universidade Federal do Oeste da Bahia, Barra, BA, Brazil
| | - Gabriel Koch
- Dep. de Fitotecnia e Fitossanidade, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Cristian Lopes
- Instituto Federal do Sudeste de Minas Gerais, Rio Pomba, MG, Brazil
| | | | | | - Fábio Nascimento Silva
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Roberto Ramos Sobrinho
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, AL, Brazil
| | | | | | | | - Francisco M Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Abstract
BACKGROUND Geminiviruses are circular, single-stranded viruses responsible for enormous crop loss worldwide. Rapid expansion of geminivirus diversity outweighs the continuous effort to control its spread. Geminiviruses channelize the host cell machinery in their favour by manipulating the gene expression, cell signalling, protein turnover, and metabolic reprogramming of plants. As a response to viral infection, plants have evolved to deploy various strategies to subvert the virus invasion and reinstate cellular homeostasis. MAIN BODY Numerous reports exploring various aspects of plant-geminivirus interaction portray the subtlety and flexibility of the host-pathogen dynamics. To leverage this pool of knowledge towards raising antiviral resistance in host plants, a comprehensive account of plant's defence response against geminiviruses is required. This review discusses the current knowledge of plant's antiviral responses exerted to geminivirus in the light of resistance mechanisms and the innate genetic factors contributing to the defence. We have revisited the defence pathways involving transcriptional and post-transcriptional gene silencing, ubiquitin-proteasomal degradation pathway, protein kinase signalling cascades, autophagy, and hypersensitive responses. In addition, geminivirus-induced phytohormonal fluctuations, the subsequent alterations in primary and secondary metabolites, and their impact on pathogenesis along with the recent advancements of CRISPR-Cas9 technique in generating the geminivirus resistance in plants have been discussed. CONCLUSIONS Considering the rapid development in the field of plant-virus interaction, this review provides a timely and comprehensive account of molecular nuances that define the course of geminivirus infection and can be exploited in generating virus-resistant plants to control global agricultural damage.
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Affiliation(s)
- Neha Gupta
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Kishorekumar Reddy
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Dhriti Bhattacharyya
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Supriya Chakraborty✉
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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34
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Liu X, Huang W, Zhai Z, Ye T, Yang C, Lai J. Protein modification: A critical modulator in the interaction between geminiviruses and host plants. Plant Cell Environ 2021; 44:1707-1715. [PMID: 33506956 DOI: 10.1111/pce.14008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/06/2021] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Geminiviruses are a large group of single-stranded DNA viruses that infect plants and cause severe agricultural losses worldwide. Given geminiviruses only have small genomes that encode a few proteins, viral factors have to interact with host components to establish an environment suitable for virus infection, whilst the host immunity system recognizes and targets these viral components during infection. Post-translational protein modifications, such as phosphorylation, lipidation, ubiquitination, SUMOylation, acetylation and methylation, have been reported to be critical during the interplay between host plants and geminiviruses. Here we summarize the research progress, including phosphorylation and lipidation which usually control the activity and localization of viral factors; as well as ubiquitination and histone modification which are predominantly interfered with by viral components. We also discuss the dynamic competition on protein modifications between host defence and geminivirus efficient infection, as well as potential applications of protein modifications in geminivirus resistance. The summary and perspective of this topic will improve our understanding on the mechanism of geminivirus-plant interaction and contribute to further protection of plants from virus infection.
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Affiliation(s)
- Xiaoshi Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Wei Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Zhenqian Zhai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Tushu Ye
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
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Ban F, Zhong Y, Pan L, Mao L, Wang X, Liu Y. Coinfection by Two Begomoviruses Aggravates Plant Symptoms But Does Not Influence the Performance and Preference of Insect Vector Bemisia tabaci (Hemiptera: Aleyrodidae). J Econ Entomol 2021; 114:547-554. [PMID: 33503240 DOI: 10.1093/jee/toaa326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Indexed: 06/12/2023]
Abstract
In nature, a plant can be infected by multiple viruses simultaneously. However, the effects of coinfection on plant-vector interactions are less well studied. Two begomoviruses of the family Geminiviridae, Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl China virus (TYLCCNV), occur sympatrically in China. Each of them is reported to increase the performance of whitefly vector via manipulation of plant traits. In this study, we examined the effects of coinfection by the two viruses TYLCV and TYLCCNV on plant-whitefly interactions, compared to that infected by a single virus. We found that plants infected by two viruses showed aggravated symptoms but the performance and preference of whiteflies were not altered significantly compared to singly-infected plants. Coinfection suppressed the transcription of genes involved in jasmonic acid (JA) signaling pathway in plants, but showed no significant difference to single-virus infected plants. These findings suggest that although TYLCV and TYLCCNV may synergistically induce plant symptoms, they did not manipulate synergistically plant-mediated responses to the insect vector.
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Affiliation(s)
- Feixue Ban
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogen and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yuwei Zhong
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogen and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Lilong Pan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogen and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Lijuan Mao
- Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences (ACAES), Zhejiang University, Hangzhou, China
| | - Xiaowei Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogen and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yinquan Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogen and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Sangeeta, Ranjan P, Kumar RV, Bhatt BS, Chahwala FD, Yadav BK, Patel S, Singh B, Singh AK. Two distinct monopartite begomovirus-betasatellite complexes in western India cause tomato leaf curl disease. Virus Res 2021; 295:198319. [PMID: 33508355 DOI: 10.1016/j.virusres.2021.198319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/06/2021] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
In India, begomovirus infection causing tomato leaf curl disease (ToLCD) is a major constraint for tomato productivity. Here, we have identified two distinct monopartite begomovirus and betasatellite complexes causing ToLCD in the western part of India. A new monopartite begomovirus (Tomato leaf curl Mumbai virus, ToLCMumV) and betasatellite (Tomato leaf curl Mumbai betasatellite, ToLCMumB) were isolated from the Mumbai sample. A distinct Tomato leaf curl Gandhinagar virus (ToLCGanV) and Tomato leaf curl Gandhinagar betasatellite (ToLCGanB) were identified from the Gandhinagar sample. Both of the cloned begomoviruses were recombinants. The demonstration of systemic infection caused by begomovirus (ToLCGanV or ToLCMumV) alone in N. benthamiana and tomato (a virus resistant variety) emphasizes that they were monopartite begomoviruses. Co-inoculation of cognate begomovirus and betasatellite reduces the incubation period and increases symptom severity. Thus, Koch's postulates were satisfied for these virus complexes. Further, an enhanced accumulation of ToLCGanV was detected in the presence of cognate ToLCGanB, however ToLCMumB did not influence the level of ToLCMumV in the agro-inoculated tomato plants. Our results indicate that the cloned viruses form potential virus resistance breaking disease complexes in India. This necessitates to investigate the spread of these disease complexes to major tomato growing regions in the country.
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Affiliation(s)
- Sangeeta
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Punam Ranjan
- Department of Botany, Patna Science College, Patna University, Patna, 800 005, Bihar, India
| | - R Vinoth Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India
| | - Bhavin S Bhatt
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Fenisha D Chahwala
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Brijesh K Yadav
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Sunita Patel
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382 030, Gujarat, India
| | - Bijendra Singh
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, 221 305, Uttar Pradesh, India
| | - Achuit K Singh
- Crop Improvement Division, ICAR-Indian Institute of Vegetable Research, Varanasi, 221 305, Uttar Pradesh, India.
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Sun K, Liang Y, Zhong X, Hu X, Zhang P, Yu X. Nightshade Curly Top Virus: A Possible New Virus of the Genus Topocuvirus Infecting Solanum nigrum in China. Plant Dis 2021; 105:1006-1012. [PMID: 33026306 DOI: 10.1094/pdis-03-20-0572-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Virus-like symptoms, including leaf deformation and curling, were observed on nightshade (Solanum nigrum) in Zhejiang Province, China. To identify possible pathogenic viruses or viroids, a symptomatic sample was subjected to deep sequencing of small interfering RNAs. Assembly of the resulting sequences led to identification of a novel geminivirus, provisionally designated nightshade curly top virus (NCTV). The complete genomic DNA sequence is 2,867 nucleotides and encodes seven open reading frames. NCTV shares 77.1% overall nucleotide sequence identity, 86.3% coat protein amino acid identity, and 78.9% replication-associated protein amino acid sequence identity with Tomato pseudo-curly top virus, a member of the genus Topocuvirus. PCR screening of nightshade field isolates indicated that NCTV is widely distributed in Zhejiang. Agrobacterium-mediated inoculation revealed that NCTV is highly infectious to Nicotiana benthamiana, S. nigrum, S. lycopersicum, and S. tuberosum. Based on pairwise comparisons and phylogenetic analyses, NCTV is proposed as a provisional member of the genus Topocuvirus.
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Affiliation(s)
- Kai Sun
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang Province, People's Republic of China
| | - Yan Liang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang Province, People's Republic of China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, People's Republic of China
| | - Xuenan Hu
- Guangzhou Customs Technology Center, Guangzhou 510623, People's Republic of China
| | - Pengjun Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang Province, People's Republic of China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang Province, People's Republic of China
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Yogindran S, Kumar M, Sahoo L, Sanatombi K, Chakraborty S. Occurrence of Cotton leaf curl Multan virus and associated betasatellites with leaf curl disease of Bhut-Jolokia chillies (Capsicum chinense Jacq.) in India. Mol Biol Rep 2021; 48:2143-2152. [PMID: 33635470 PMCID: PMC7908524 DOI: 10.1007/s11033-021-06223-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022]
Abstract
Geminiviridae comprises the largest family of plant viruses which causes severe crop losses in India. The highest pungency chilli Bhut-Jolokia or ghost pepper (Capsicum chinense Jaqc.) hails from North-East region of India and is used in many dishes to add flavors and also for its medicinal value. However, this chilli variety is also affected by viruses leading to crop and economic losses. The present study reports the identification of begomoviruses in the infected chilli Bhut-Jolokia leaf samples collected from eight different places of North-East region (Manipur) of India. The infected leaf samples were screened for the presence of viral genome by rolling circle amplification (RCA) followed by PCR using degenerate primer pairs. The subsequent analyses using restriction fragment length polymorphism and sequencing revealed the presence of Cotton leaf curl Multan virus (CLCuMuV), and Tomato leaf curl Patna betasatellite (ToLCPaB). The findings focus on the phylogenetic relatedness, probable recombinational hot-spots and evolutionary divergence of the viral DNA sequences with the current reported begomoviral genome. To the best of our knowledge, this is the first report showing the presence of CLCuMuV, and associated non-cognate ToLCPaB with leaf curl disease of Bhut-Jolokia chillies. The study reveals potential recombination sites on both viral genome and betsatellite which, during the course of evolution, may have aided the virus to progress and successfully establish infection in chilli plants. Taken together, our results suggest a possible spread of CLCuMuV to the hitherto non-host crop in the North-East region of India.
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Affiliation(s)
- Sneha Yogindran
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manish Kumar
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Lingaraj Sahoo
- Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | | | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Chatukuta P, Rey MEC. A cassava protoplast system for screening genes associated with the response to South African cassava mosaic virus. Virol J 2020; 17:184. [PMID: 33228712 PMCID: PMC7685591 DOI: 10.1186/s12985-020-01453-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
Background The study of transient gene expression in cassava plants during virus infection using existing protocols is laborious and may take approximately fifteen weeks due to cassava’s recalcitrance to transformation. The combination of a protoplast system with CRISPR-mediated gene editing promises to shorten the turnaround time from plant tissue culture to high-throughput gene expression screening for candidate genes. Here, we detail a protocol for screening genes associated with the response to South African cassava mosaic virus (SACMV) in cassava protoplasts, with reference to the ubiquitin E3 ligase gene, MeE3L.
Methods Cassava protoplasts of model, and SACMV-susceptible and -tolerant genotypes, were transformed with SACMV infectious clones and/or a CRISPR-editing construct targeting the MeE3L using PEG4000-mediated transfection. DNA and RNA were extracted from transformed protoplasts at 24 h post-transfection. Relative SACMV DNA accumulation was determined via qPCR using DpnI-digested total DNA, MeE3L relative expression was determined via reverse transcriptase qPCR, and results were analysed using one-way ANOVA, Tukey’s HSD test and the 2−ΔΔCTstatistical method. The MeE3L exonic region was sequenced on the ABI 3500XL Genetic Analyzer platform; and sequences were analysed for mutations using MAFTT and MEGA-X software. Construction of a phylogenetic tree was done using the Maximum Likelihood method and Jones-Taylor-Thornton (JTT) matrix-based model. Results The differential expression of unedited and mutant MeE3L during SACMV infection of model, susceptible and tolerant cassava protoplasts was determined within 7 weeks after commencement of tissue culture. The study also revealed that SACMV DNA accumulation in cassava protoplasts is genotype-dependent and induces multiple mutations in the tolerant landrace MeE3L homolog. Notably, the susceptible cassava landrace encodes a RINGless MeE3Lwhich is silenced by SACMV-induced mutations. SACMV also induces mutations which silence the MeE3L RING domain in protoplasts from and tolerant cassava landraces. Conclusions This protocol presented here halves the turnaround time for high-throughput screening of genes associated with the host response to SACMV. It provides evidence that a cassava E3 ligase is associated with the response to SACMV and forms a basis for validation of these findings by in planta functional and interaction studies.
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Affiliation(s)
- Patience Chatukuta
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Marie Emma Christine Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
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Pinto VB, Quadros AFF, Godinho MT, Silva JC, Alfenas-Zerbini P, Zerbini FM. Intra-host evolution of the ssDNA virus tomato severe rugose virus (ToSRV). Virus Res 2020; 292:198234. [PMID: 33232784 DOI: 10.1016/j.virusres.2020.198234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 01/17/2023]
Abstract
To evaluate and quantify the evolutionary dynamics of the bipartite begomovirus tomato severe rugose virus (ToSRV) in a cultivated and a non-cultivated host, plants of tomato and Nicandra physaloides were biolistically inoculated with an infectious clone and systemically infected leaves were sampled at 30, 75 and 120 days after inoculation. Total DNA was extracted and sequenced in the Illumina HiSeq 2000 platform. The datasets were trimmed with the quality score limit set to 0.01, and the assembly was performed using the infectious clone sequence as reference. SNPs were filtered using a minimum p-value of 0.001 and the sum frequencies were used to calculate the deviation from the original clone sequence. Nucleotide substitution rates were calculated for the two DNA components in both hosts: 1.73 × 10-3 and 3.07 × 10-4 sub/site/year for the DNA-A and DNA-B, respectively, in N. physaloides, and 8.05 × 10-4 and 7.02 × 10-5 sub/site/year the for DNA-A and DNA-B, respectively, in tomato. These values are in the same range of those estimated for viruses with single-stranded RNA genomes and for other begomoviruses. Strikingly, the number of substitutions decreased over time, suggesting the presence of bottlenecks during systemic infection. Determination of Shannon's entropy indicated different patterns of variation in the DNA-A and the DNA-B, suggesting distinct evolutionary forces acting upon each component.
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Affiliation(s)
- Vitor Batista Pinto
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Ayane Fernanda Ferreira Quadros
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Márcio Tadeu Godinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - José Cleydson Silva
- National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Poliane Alfenas-Zerbini
- National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; Dep. de Microbiologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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Ogden AJ, Boukari W, Nava A, Lucinda N, Sunter G, Curtis WR, Adkins JN, Polston JE. Characterization of Local and Systemic Impact of Whitefly ( Bemisia tabaci) Feeding and Whitefly-Transmitted Tomato Mottle Virus Infection on Tomato Leaves by Comprehensive Proteomics. Int J Mol Sci 2020; 21:E7241. [PMID: 33008056 DOI: 10.3390/ijms21197241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/21/2020] [Accepted: 09/26/2020] [Indexed: 11/23/2022] Open
Abstract
Tomato mottle virus (ToMoV) is a single-stranded DNA (ssDNA) begomovirus transmitted to solanaceous crops by the whitefly species complex (Bemisia tabaci), causing stunted growth, leaf mottling, and reduced yield. Using a genetic repertoire of seven genes, ToMoV pathogenesis includes the manipulation of multiple plant biological processes to circumvent antiviral defenses. To further understand the effects of whitefly feeding and whitefly-transmitted ToMoV infection on tomato plants (Solanum lycopersicum ‘Florida Lanai’), we generated comprehensive protein profiles of leaves subjected to feeding by either viruliferous whiteflies harboring ToMoV, or non-viruliferous whiteflies, or a no-feeding control. The effects of whitefly feeding and ToMoV infection were measured both locally and systemically by sampling either a mature leaf directly from the site of clip-cage confined whitefly feeding, or from a newly formed leaf 10 days post feeding (dpf). At 3 dpf, tomato’s response to ToMoV included proteins associated with translation initiation and elongation as well as plasmodesmata dynamics. In contrast, systemic impacts of ToMoV on younger leaves 10 dpf were more pronounced and included a virus-specific change in plant proteins associated with mRNA maturation and export, RNA-dependent DNA methylation, and other antiviral plant processes. Our analysis supports previous findings and provides novel insight into tomato’s local and systemic response to whitefly feeding and ToMoV infection.
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Sanchez-Chavez S, Regla-Marquez CF, Cardenas-Conejo ZE, Garcia-Rodriguez DA, Centeno-Leija S, Serrano-Posada H, Liñan-Rico A, Partida-Palacios BL, Cardenas-Conejo Y. First report of begomoviruses infecting Cucumis sativus L. in North America and identification of a proposed new begomovirus species. PeerJ 2020; 8:e9245. [PMID: 32728488 PMCID: PMC7357562 DOI: 10.7717/peerj.9245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/06/2020] [Indexed: 12/02/2022] Open
Abstract
Background Members of the Begomovirus genus are phytopathogens that infect dicotyledonous plants, producing economic losses in tropical and subtropical regions. To date, only seven species of begomoviruses (BGVs) infecting cucumber have been described. Most cucumber infections were reported in South Asia. In the Americas, begomoviral infections affecting cucumber are scarce; just one report of begomovirus has been described in South America. The presence of whitefly and typical symptoms of viral infections observed in a cucumber field in Colima, Mexico, suggested that plants in this field were affected by BGVs. Methods To identify the BGVs infecting cucumber, we performed a high-throughput sequencing and compared the assembled contigs against the GenBank nucleic acid sequence database. To confirm the presence of viruses in cucumber samples, we performed a PCR detection using specific oligonucleotides. We cloned and sequenced by Sanger method the complete genome of a potential new begomovirus. Begomovirus species demarcation was performed according to the International Committee on Taxonomy of Viruses. The evolutionary relationship of the new virus was inferred using phylogenetic and recombination analyses. Results We identified five species of begomovirus infecting plants in a field. None of these have been previously reported infecting cucumber. One of the five species of viruses here reported is a new begomovirus species. Cucumber chlorotic leaf virus, the new species, is a bipartite begomovirus that has distinctive features of viruses belonging to the squash leaf curl virus clade. Conclusions The findings here described represent the first report of begomoviral infection affecting cucumber plants in North America. Previous to this report, only seven begomovirus species have been reported in the world, here we found five species infecting cucumber plants in a small sample suggesting that cucumber is vulnerable to BGVs. One of these viruses is a new species of begomovirus which is the first begomovirus originally isolated from the cucumber. The findings of this report could help to develop strategies to fight the begomoviral infections that affect cucumber crops.
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Affiliation(s)
| | | | | | | | - Sara Centeno-Leija
- Laboratorio de Agrobiotecnologia, Consejo Nacional de Ciencia y Tecnologia-Universidad de Colima, Colima, Mexico
| | - Hugo Serrano-Posada
- Laboratorio de Agrobiotecnologia, Consejo Nacional de Ciencia y Tecnologia-Universidad de Colima, Colima, Mexico
| | - Andromeda Liñan-Rico
- Centro Universitario de Investigaciones Biomedicas, Consejo Nacional de Ciencia y Tecnologia-Universidad de Colima, Colima, Mexico
| | | | - Yair Cardenas-Conejo
- Laboratorio de Agrobiotecnologia, Consejo Nacional de Ciencia y Tecnologia-Universidad de Colima, Colima, Mexico
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Prakash V, Singh A, Singh AK, Dalmay T, Chakraborty S. Tobacco RNA-dependent RNA polymerase 1 affects the expression of defence-related genes in Nicotiana benthamiana upon Tomato leaf curl Gujarat virus infection. Planta 2020; 252:11. [PMID: 32613448 DOI: 10.1007/s00425-020-03417-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/26/2020] [Indexed: 05/25/2023]
Abstract
MAIN CONCLUSION RNA-dependent RNA polymerase 1 of Nicotiana tabacum modulates ToLCGV pathogenesis by influencing a number of defence-related genes in N. benthamiana plants. Key means of plants protecting themselves from the invading viruses is through RNA silencing. RNA-dependent RNA polymerase-1 (RDR1) is one of the crucial proteins of the RNA silencing pathway, which is induced after infection by viruses. RDR1 functions in the generation of small interfering RNAs (siRNAs) against the viral genome, thus it is antiviral in nature. Here, we used the transgenic Nicotiana benthamiana plant expressing N. tabacum NtRDR1 and observed reduced susceptibility towards Tomato leaf curl Gujarat virus (ToLCGV) infection compared to the wild-type N. benthamiana plants. To understand the reason for such reduced susceptibility, we prepared high-definition small RNA (sRNA) cDNA libraries from ToLCGV-infected wild-type N. benthamiana and NtRDR1 expressing N. benthamiana lines and carried out next-generation sequencing (NGS). We found that upon ToLCGV infection the majority of siRNAs generated from the host genome were of the 24 nucleotide (nt) class, while viral siRNAs (vsiRNAs) were of the 21-22-nt class, indicating that transcriptional gene silencing (TGS) is the major pathway for silencing of host genes while viral genes are silenced, predominantly, by post transcriptional gene silencing (PTGS) pathways. We estimated the changes in the expression of various defence-related genes, such as Constitutively Photomorphogenic-9 (COP9) signalosome (CSN) complex subunit-7, Pentatricopeptide repeat containing protein (PPRP), Laccase-3, Glutathione peroxidase-1 (GPX-1), Universal stress protein (USP) A-like protein, Heat shock transcription factor B4 (HSTF-B4), Auxin response factor-18 (ARF18), WRKY-6 and Short chain dehydrogenase reductase-3a. The differential expression of these genes might be linked with the enhanced tolerance of NtRDR1 N. benthamiana transgenic plants to ToLCGV. Our study suggests that reduced expression of subunit-7 of CSN complex and WRKY6, and increased expression of USPA-like protein might be linked with the reduced susceptibility of NtRDR1-transgenic N. benthamiana plants to ToLCGV.
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Affiliation(s)
- Ved Prakash
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Archana Singh
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ashish Kumar Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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Fadhila C, Lal A, Vo TTB, Ho PT, Hidayat SH, Lee J, Kil EJ, Lee S. The threat of seed-transmissible pepper yellow leaf curl Indonesia virus in chili pepper. Microb Pathog 2020; 143:104132. [PMID: 32169496 DOI: 10.1016/j.micpath.2020.104132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 11/23/2022]
Abstract
Recently, chili pepper (Capsicum annuum) plants in Indonesia have been devastated by a notorious bipartite begomovirus infection named Pepper yellow leaf curl Indonesia virus (PepYLCIV), which causes a distinct decrease in chili pepper production. Pepper yellow diseases have been known since early 2000; however, the spread of this virus thus far is distressing. These diseases can reduce chili yields by 20-100% in Indonesia. As previously known, begomovirus can be transmitted through whitefly to several host plants from the families Solanaceae, Compositae, and Leguminosae. In the field, a single plant was observed with severe symptoms of pepper yellow leaf curl disease, while other plants in the same field were asymptomatic and healthy. The observation leads to the possibility that the virus can be transmitted from previously infected chili pepper plants through seeds, as begomovirus transmission through seeds has been reported before. This study was conducted using seeds from chili peppers infected with viruses from different places in Indonesia. Whole seeds, embryos, and seedlings from PepYLCIV infected seeds were investigated in this study by performing viral genome DNA extraction, uracil DNA glycosylase-PCR, and sequencing analysis. Results revealed that both DNA-A and DNA-B of PepYLCIV in seeds and embryos of infected chili pepper plants were detected. The results also showed that 25-67% of PepYLCIV DNA-A and 50-100% of DNA-B were detected from seedlings grown from infected chili pepper seed collected from different location, thus confirming PepYLCIV as a seed-transmissible virus in chili pepper plants.
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Urbino C, Regragui ZF, Granier M, Peterschmitt M. Fitness advantage of inter-species TYLCV recombinants induced by beneficial intra-genomic interactions rather than by specific mutations. Virology 2020; 542:20-27. [PMID: 31957662 DOI: 10.1016/j.virol.2020.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/09/2019] [Accepted: 01/02/2020] [Indexed: 11/19/2022]
Abstract
Tomato yellow leaf curl virus (TYLCV) and its related viruses are prone to recombination. It was reported that random homologous recombination between 20% diverging TYLCV related species is rarely deleterious and may be associated with a fitness advantage. Indeed, TYLCV-IS76, a recombinant between the 20% divergent TYLCV and tomato yellow leaf curl Sardinia virus (TYLCSV), exhibited a higher fitness than that of parental viruses. As this typical fitness advantage was observed with TYLCV-IS76 representatives of different pedigrees, it was thought that it is induced by beneficial intra-genomic interactions rather than by specific mutations. This hypothesis was further supported with TYLCV-IS141, a TYLCV recombinant with a short TYLCSV inherited fragment of around 141 nts, slightly longer than that of TYLCV-IS76. Indeed, the typical fitness advantage was detected irrespective of the position of the recombination breakpoint (loci 76 or 141) and the sequences of the TYLCV and TYLCSV inherited fragments.
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Affiliation(s)
- Cica Urbino
- CIRAD, UMR BGPI, Montpellier, France; BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Zohra Fatima Regragui
- CIRAD, UMR BGPI, Montpellier, France; BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Martine Granier
- CIRAD, UMR BGPI, Montpellier, France; BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Michel Peterschmitt
- CIRAD, UMR BGPI, Montpellier, France; BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
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Abstract
The geminivirus capsid architecture is unique and built from twinned pseudo T=1 icosahedrons with 110 copies of the coat protein (CP). The CP is multifunctional. It performs various functions during the infection of a wide range of agriculturally important plant hosts. The CP multimerizes via pentameric intermediates during assembly and encapsulates the ssDNA genome to generate the unique capsid morphology. The virus capsid protects and transports the genome in the insect vector and plant host enroute to the plant nucleus for replication and the production of progeny. This review further explores CP:CP and CP:DNA interactions, and the environmental conditions that govern the assembly of the geminivirus capsid. This analysis was facilitated by new data available for the family, including three-dimensional structures and molecular biology data for several members. In addition, current and promising new control strategies of plant crop infection, which can lead to starvation for subsistence farmers, are discussed.
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Affiliation(s)
- Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States.
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Pouramini N, Heydarnejad J, Massumi H, Varsani A. Identification of the wild and cultivated hosts of wheat dwarf virus and oat dwarf virus in Iran. Virusdisease 2019; 30:545-550. [PMID: 31897417 PMCID: PMC6917689 DOI: 10.1007/s13337-019-00557-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 11/15/2019] [Indexed: 11/29/2022] Open
Abstract
In the last decade two mastreviruses, Wheat dwarf virus (WDV) and Oat dwarf virus (ODV) have been reported from cereal farms in Iran. In a survey, wild and cultivated hosts of these mastreviruses were studied during 2015 to 2017. Symptomatic small grain cereal samples and weed species were collected and assayed for WDV and/or ODV infection by PCR. While WDV which was detected in 139/284 (49%) of total symptomatic samples, low incidence (2%) was recorded for ODV which was detected only in slender wild oat (Avena barbata Pott ex Link) and red brome (Bromus rubens L.). In agroinfection studies, the clone of ODV infected common oat (A. sativa) and slender wild oat (A. barbata) with the low efficiency and did not infect wheat or barley. ODV was transmitted by the leafhopper Psammotettix alienus, from agroinfected common oat to healthy seedlings. The results show that, in contrast to WDV, ODV has a low incidence and a narrow host range in gramineous plants.
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Affiliation(s)
- Najmeh Pouramini
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111 Iran
| | - Jahangir Heydarnejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111 Iran
| | - Hossain Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111 Iran
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001 USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
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Shahid MS, Shafiq M, Raza A, Al-Sadi AM, Briddon RW. Molecular and biological characterization of Chilli leaf curl virus and associated Tomato leaf curl betasatellite infecting tobacco in Oman. Virol J 2019; 16:131. [PMID: 31706358 PMCID: PMC6842478 DOI: 10.1186/s12985-019-1235-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/03/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Oman tobacco (Nicotiana tabacum; family Solanaceae) is a minor crop, which is produced only for local consumption. In 2015, tobacco plants exhibiting severe downward leaf curling, leaf thickening, vein swelling, yellowing and stunting were identified in fields of tobacco in Suhar Al-Batina region, Oman. These symptoms are suggestive of begomovirus (genus Begomovirus, family Geminiviridae) infection. METHODS Circular DNA molecules were amplified from total DNA extracted from tobacco plants by rolling circle amplification (RCA). Viral genomes were cloned from RCA products by restriction digestion and betasatellites were cloned by PCR amplification from RCA product, using universal primers. The sequences of full-length clones were obtained by Sanger sequencing and primer walking. Constructs for the infectivity of virus and betasatellite were produced and introduced into plants by Agrobacterium-mediated inoculation. RESULTS The full-length sequences of 3 begomovirus and 3 betasatellite clones, isolated from 3 plants, were obtained. Analysis of the full-length sequences determined showed the virus to be a variant of Chilli leaf curl virus (ChiLCV) and the betasatellite to be a variant of Tomato leaf curl betasatellite (ToLCB). Both the virus and the betasatellite isolated from tobacco show the greatest levels of sequence identity to isolates of ChiLCV and ToLCB identified in other hosts in Oman. Additionally clones of ChiLCV and ToLCB were shown, by Agrobacterium-mediated inoculation, to be infectious to 3 Nicotiana species, including N. tabacum. In N. benthamiana the betasatellite was shown to change the upward leaf rolling symptoms to a severe downward leaf curl, as is typical for many monopartite begomoviruses with betasatellites. CONCLUSIONS The leaf curl disease of tobacco in Oman was shown to be caused by ChiLCV and ToLCB. This is the first identification of ChiLCV with ToLCB infecting tobacco. The study shows that, despite the low diversity of begomoviruses and betasatellites in Oman, the extant viruses/betasatellites are able to fill the niches that present themselves.
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Affiliation(s)
- Muhammad Shafiq Shahid
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, 123, Muscat, Oman.
| | - Muhammad Shafiq
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, 123, Muscat, Oman
| | - Amir Raza
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, 123, Muscat, Oman
| | - Abdullah M Al-Sadi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, 123, Muscat, Oman
| | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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Singh A, Mohorianu I, Green D, Dalmay T, Dasgupta I, Mukherjee SK. Artificially induced phased siRNAs promote virus resistance in transgenic plants. Virology 2019; 537:208-215. [PMID: 31513956 DOI: 10.1016/j.virol.2019.08.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/27/2019] [Accepted: 08/30/2019] [Indexed: 11/29/2022]
Abstract
We previously developed transgenic tobacco plants that were resistant to two geminiviruses. We generated resistance using RNAi constructs that produced trans-acting siRNA (tasiRNA) like secondary siRNAs known as phased siRNA (phasiRNA) that targeted several regions of Tomato Leaf Curl New Delhi Virus (ToLCNDV) and Tomato Leaf Curl Gujarat Virus (ToLCGV) transcripts encoding the RNA silencing suppressor proteins AC2 and AC4. Here, we performed degradome analysis to determine the precise cleavage sites of RNA-RNA interaction between phasiRNA and viral transcripts. We then applied our RNAi technology in tomato, which is the natural host for ToLCNDV and ToLCGV. The relative ease of developing and using phasiRNA constructs represents a significant technical advance in imparting virus resistance in crops and/or important model systems.
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Affiliation(s)
- Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Darrell Green
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| | - Sunil Kumar Mukherjee
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India
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Kushwaha NK, Sahu PP, Prasad M, Chakrabroty S. Chilli leaf curl virus infection downregulates the expression of the genes encoding chloroplast proteins and stress-related proteins. Physiol Mol Biol Plants 2019; 25:1185-1196. [PMID: 31564781 PMCID: PMC6745583 DOI: 10.1007/s12298-019-00693-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/25/2019] [Accepted: 07/16/2019] [Indexed: 05/05/2023]
Abstract
Virus infection alters the expression of several host genes involved in various cellular and biological processes in plants. Most of the studies performed till now have mainly focused on genes which are up-regulated and later projected them as probable stress tolerant/susceptible genes. Nevertheless, genes which are down-regulated during plant-virus interaction could also play a critical role on disease development as well as in combating the virus infection. Hence, to identify such down-regulated genes and pathway, we performed reverse suppression subtractive hybridization in Capsicum annuum var. Punjab Lal following Chilli leaf curl virus (ChiLCV) infection. The screening and further processing suggested that majority of the genes (approximately 35% ESTs) showed homology with the genes encoding chloroplast proteins and 16% genes involved in the biotic and abiotic stress response. Additionally, we identified several genes, functionally known to be involved in metabolic processes, protein synthesis and degradation, ribosomal proteins, energy production, DNA replication and transcription, and transporters. We also found 3% transcripts which did not show homology with any known genes. The redundancy analysis revealed the maximum percentage of chlorophyll a-b binding protein (15/96) and auxin-binding proteins (13/96). We developed a protein interactome network to characterise the relationships between proteins and pathway involved during the ChiLCV infection. We identified that the most of the interaction occurs either among the chloroplast proteins (Arabidopsis proteins interactive map) or biotic and abiotic stress responsive proteins (Solanum lycopersicum interactome). Taken together, our study provides the first transcriptome and protein interactome of the down-regulated genes during C. annuum-ChiLCV interaction. These resources could be exploited in deciphering the steps involved in the process of virus infection.
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Affiliation(s)
- Nirbhay Kumar Kushwaha
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Pranav Pankaj Sahu
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Supriya Chakrabroty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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