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Lal A, Shamim A, Kil EJ, Vo TTB, Qureshi MA, Bupi N, Tabassum M, Lee S. Insights into the Differential Composition of Stem-Loop Structures of Nanoviruses and Their Impacts. Microbiol Spectr 2023; 11:e0479822. [PMID: 37367433 PMCID: PMC10434203 DOI: 10.1128/spectrum.04798-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Multipartite viruses package their genomic segments independently and mainly infect plants; few of them target animals. Nanoviridae is a family of multipartite single-stranded DNA (ssDNA) plant viruses that individually encapsidate ssDNAs of ~1 kb and transmit them through aphids without replication in aphid vectors, thereby causing important diseases in host plants, mainly leguminous crops. All of these components constitute an open reading frame to perform a specific role in nanovirus infection. All segments contain conserved inverted repeat sequences, potentially forming a stem-loop structure and a conserved nonanucleotide, TAGTATTAC, within a common region. This study investigated the variations in the stem-loop structure of nanovirus segments and their impact using molecular dynamics (MD) simulations and wet lab approaches. Although the accuracy of MD simulations is limited by force field approximations and simulation time scale, explicit solvent MD simulations were successfully used to analyze the important aspects of the stem-loop structure. This study involves the mutants' design, based on the variations in the stem-loop region and construction of infectious clones, followed by their inoculation and expression analysis, based on nanosecond dynamics of the stem-loop structure. The original stem-loop structures showed more conformational stability than mutant stem-loop structures. The mutant structures were expected to alter the neck region of the stem-loop by adding and switching nucleotides. Changes in conformational stability are suggested expression variations of the stem-loop structures found in host plants with nanovirus infection. However, our results can be a starting point for further structural and functional analysis of nanovirus infection. IMPORTANCE Nanoviruses comprise multiple segments, each with a single open reading frame to perform a specific function and an intergenic region with a conserved stem-loop region. The genome expression of a nanovirus has been an intriguing area but is still poorly understood. We attempted to investigate the variations in the stem-loop structure of nanovirus segments and their impact on viral expression. Our results show that the stem-loop composition is essential in controlling the virus segments' expression level.
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Affiliation(s)
- Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, South Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong, South Korea
| | - Amen Shamim
- Department of Computer Science, University of Agriculture, Faisalabad, Pakistan
| | - Eui-Joon Kil
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, South Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong, South Korea
| | - Thuy T. B. Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Nattanong Bupi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Marjia Tabassum
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
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Vo TTB, Lal A, Nattanong B, Tabassum M, Qureshi MA, Troiano E, Parrella G, Kil EJ, Lee S. Coat protein is responsible for tomato leaf curl New Delhi virus pathogenicity in tomato. FRONTIERS IN PLANT SCIENCE 2023; 14:1206255. [PMID: 37492775 PMCID: PMC10364049 DOI: 10.3389/fpls.2023.1206255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/23/2023] [Indexed: 07/27/2023]
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV), a bipartite Begomovirus belonging to the family Geminiviridae, causes severe damage to many economically important crops worldwide. In the present study, pathogenicity of Asian (ToLCNDV-In from Pakistan) and Mediterranean isolates (ToLCNDV-ES from Italy) were examined using infectious clones in tomato plants. Only ToLCNDV-In could infect the three tomato cultivars, whereas ToLCNDV-ES could not. Genome-exchange of the two ToLCNDVs revealed the ToLCNDV DNA-A segment as the main factor for ToLCNDV infectivity in tomato. In addition, serial clones with chimeric ToLCNDV-In A and ToLCNDV-ES A genome segments were generated to identify the region determining viral infectivity in tomatoes. A chimeric clone carrying the ToLCNDV-In coat protein (CP) exhibited pathogenic adaptation in tomatoes, indicating that the CP of ToLCNDV is essential for its infectivity. Analyses of infectious clones carrying a single amino acid substitution revealed that amino acid at position 143 of the CP is critical for ToLCNDV infectivity in tomatoes. To better understand the molecular basis whereby CP function in pathogenicity, a yeast two-hybrid screen of a tomato cDNA library was performed using CPs as bait. The hybrid results showed different interactions between the two CPs and Ring finger protein 44-like in the tomato genome. The relative expression levels of upstream and downstream genes and Ring finger 44-like genes were measured using quantitative reverse transcription PCR (RT-qPCR) and compared to those of control plants. This is the first study to compare the biological features of the two ToLCNDV strains related to viral pathogenicity in the same host plant. Our results provide a foundation for elucidating the molecular mechanisms underlying ToLCNDV infection in tomatoes.
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Affiliation(s)
- Thuy T. B. Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Aamir Lal
- Agriculture Science and Technology Research Institute, Andong National University, Andong, Republic of Korea
| | - Bupi Nattanong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Marjia Tabassum
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Elisa Troiano
- Department of Biology, Agriculture and Food Sciences, Institute for Sustainable Plant Protection of the National Research Council (IPSP-CNR), Portici, Italy
| | - Giuseppe Parrella
- Department of Biology, Agriculture and Food Sciences, Institute for Sustainable Plant Protection of the National Research Council (IPSP-CNR), Portici, Italy
| | - Eui-Joon Kil
- Agriculture Science and Technology Research Institute, Andong National University, Andong, Republic of Korea
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
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Vo TTB, Cho WK, Jo Y, Lal A, Nattanong B, Qureshi MA, Tabssum M, Troiano E, Parrella G, Kil EJ, Lee TK, Lee S. Transcriptional Analysis of the Differences between ToLCNDV-India and ToLCNDV-ES Leading to Contrary Symptom Development in Cucumber. Int J Mol Sci 2023; 24:ijms24032181. [PMID: 36768502 PMCID: PMC9916722 DOI: 10.3390/ijms24032181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Tomato leaf curl New Delhi virus-ES (ToLCNDV-ES), a high threat to cucurbits in the Mediterranean Basin, is listed as a different strain from the Asian ToLCNDV isolates. In this study, the infectivity of two clones previously isolated from Italy and Pakistan were compared in cucumbers, which resulted in the opposite symptom appearance. The swapping subgenome was processed; however, the mechanisms related to the disease phenotype remain unclear. To identify the disease-associated genes that could contribute to symptom development under the two ToLCNDV infections, the transcriptomes of ToLCNDV-infected and mock-inoculated cucumber plants were compared 21 days postinoculation. The number of differentially expressed genes in ToLCNDV-India-infected plants was 10 times higher than in ToLCNDV-ES-infected samples. The gene ontology (GO) and pathway enrichment were analyzed using the Cucurbits Genomics Database. The flavonoid pathway-related genes were upregulated in ToLCNDV-ES, but some were downregulated in ToLCNDV-India infection, suggesting their role in resistance to the two ToLCNDV infections. The relative expression levels of the selected candidate genes were validated by qRT-PCR under two ToLCNDV-infected conditions. Our results reveal the different infectivity of the two ToLCNDVs in cucumber and also provide primary information based on RNA-seq for further analysis related to different ToLCNDV infections.
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Affiliation(s)
- Thuy T. B. Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yeonhwa Jo
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Bupi Nattanong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Marjia Tabssum
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Elisa Troiano
- Institute for Sustainable Plant Protection of the National Research Council (IPSP-CNR), 80055 Portici, Italy
| | - Giuseppe Parrella
- Institute for Sustainable Plant Protection of the National Research Council (IPSP-CNR), 80055 Portici, Italy
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong 36729, Republic of Korea
| | - Taek-Kyun Lee
- Risk Assessment Research Center, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
- Correspondence: (T.-K.L.); (S.L.)
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Correspondence: (T.-K.L.); (S.L.)
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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] [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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Vo TTB, Troiano E, Lal A, Hoang PT, Kil EJ, Lee S, Parrella G. ToLCNDV-ES infection in tomato is enhanced by TYLCV: Evidence from field survey and agroinoculation. Front Microbiol 2022; 13:954460. [PMID: 36425034 PMCID: PMC9679516 DOI: 10.3389/fmicb.2022.954460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Thuy Thi Bich Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Elisa Troiano
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Portici, Italy
| | - Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Phuong Thi Hoang
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Giuseppe Parrella
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Portici, Italy
- *Correspondence: Giuseppe Parrella,
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