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Varma A, Singh MK. The Role of Satellites in the Evolution of Begomoviruses. Viruses 2024; 16:970. [PMID: 38932261 PMCID: PMC11209209 DOI: 10.3390/v16060970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Begomoviruses have emerged as destructive pathogens of crops, particularly in the tropics and subtropics, causing enormous economic losses and threatening food security. Epidemics caused by begomoviruses have even spread in regions and crops that were previously free from these viruses. The most seriously affected crops include cassava; cotton; grain legumes; and cucurbitaceous, malvaceous, and solanaceous vegetables. Alphasatellites, betasatellites, and deltasatellites are associated with the diseases caused by begomoviruses, but begomovirus-betasatellite complexes have played significant roles in the evolution of begomoviruses, causing widespread epidemics in many economically important crops throughout the world. This article provides an overview of the evolution, distribution, and approaches used by betasatellites in the suppression of host plant defense responses and increasing disease severity.
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Affiliation(s)
- Anupam Varma
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India;
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2
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Torralba B, Blanc S, Michalakis Y. Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations. Virus Evol 2024; 10:veae010. [PMID: 38384786 PMCID: PMC10880892 DOI: 10.1093/ve/veae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/23/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae, and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately transmitted by insect vectors from host to host. These capacities potentially allow such viruses to reassort at a much larger spatial scale, since reassortants could arise from parental genotypes that do not co-infect the same cell or even the same host. To assess the limitations affecting reassortment and their implications in genome integrity maintenance, the objective of this review is to identify putative molecular constraints influencing reassorted segments throughout the infection cycle and to confront expectations based on these constraints with empirical observations. Trans-replication of the reassorted segments emerges as the major constraint, while encapsidation, viral movement, and transmission compatibilities appear more permissive. Confronting the available molecular data and the resulting predictions on reassortments to field population surveys reveals notable discrepancies, particularly a surprising rarity of interspecific natural reassortments within the Nanoviridae family. These apparent discrepancies unveil important knowledge gaps in the biology of ssDNA multipartite viruses and call for further investigation on the role of reassortment in their biology.
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Affiliation(s)
- Babil Torralba
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Stéphane Blanc
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Yannis Michalakis
- MIVEGEC, Université Montpellier, CNRS, IRD, 911, Avenue Agropolis, Montpellier 34394, France
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Guyot V, Rajeswaran R, Chu HC, Karthikeyan C, Laboureau N, Galzi S, Mukwa LFT, Krupovic M, Kumar PL, Iskra-Caruana ML, Pooggin MM. A newly emerging alphasatellite affects banana bunchy top virus replication, transcription, siRNA production and transmission by aphids. PLoS Pathog 2022; 18:e1010448. [PMID: 35413079 PMCID: PMC9049520 DOI: 10.1371/journal.ppat.1010448] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/28/2022] [Accepted: 03/16/2022] [Indexed: 12/22/2022] Open
Abstract
Banana bunchy top virus (BBTV) is a six-component ssDNA virus (genus Babuvirus, family Nanoviridae) transmitted by aphids, infecting monocots (mainly species in the family Musaceae) and likely originating from South-East Asia where it is frequently associated with self-replicating alphasatellites. Illumina sequencing analysis of banana aphids and leaf samples from Africa revealed an alphasatellite that should be classified in a new genus, phylogenetically related to alphasatellites of nanoviruses infecting dicots. Alphasatellite DNA was encapsidated by BBTV coat protein and accumulated at high levels in plants and aphids, thereby reducing helper virus loads, altering relative abundance (formula) of viral genome components and interfering with virus transmission by aphids. BBTV and alphasatellite clones infected dicot Nicotiana benthamiana, followed by recovery and symptomless persistence of alphasatellite, and BBTV replication protein (Rep), but not alphasatellite Rep, induced leaf chlorosis. Transcriptome sequencing revealed 21, 22 and 24 nucleotide small interfering (si)RNAs covering both strands of the entire viral genome, monodirectional Pol II transcription units of viral mRNAs and pervasive transcription of each component and alphasatellite in both directions, likely generating double-stranded precursors of viral siRNAs. Consistent with the latter hypothesis, viral DNA formulas with and without alphasatellite resembled viral siRNA formulas but not mRNA formulas. Alphasatellite decreased transcription efficiency of DNA-N encoding a putative aphid transmission factor and increased relative siRNA production rates from Rep- and movement protein-encoding components. Alphasatellite itself spawned the most abundant siRNAs and had the lowest mRNA transcription rate. Collectively, following African invasion, BBTV got associated with an alphasatellite likely originating from a dicot plant and interfering with BBTV replication and transmission. Molecular analysis of virus-infected banana plants revealed new features of viral DNA transcription and siRNA biogenesis, both affected by alphasatellite. Costs and benefits of alphasatellite association with helper viruses are discussed. Self-replicating alphasatellites are frequently associated with plant ssDNA viruses. Their origin and costs versus benefits for helper virus replication, antiviral defense evasion and transmission by insect vectors are poorly understood. Here we describe identification in Africa and in depth molecular and biological characterization of a newly emerging alphasatellite of BBTV, a multicomponent ssDNA babuvirus causing one of the most economically-important diseases of monocotyledonous bananas and plantains. Phylogenetically, this alphasatellite represents a novel genus and is more related to alphasatellites of nanoviruses infecting dicot hosts than to other BBTV alphasatellites previously identified only in Asia. Consistent with its hypothetical dicot origin, cloned alphasatellite and BBTV can establish systemic infection in a model dicot plant, followed by recovery and symptomless alphasatellite persistence. In banana plants, alphasatellite competes for the host replication and transcription machinery and accumulates at high levels, thereby reducing loads of the helper virus, modifying relative abundance of its components and interfering with its acquisition and transmission by aphids. On the other hand, plant antiviral defenses silence alphasatellite gene expression at both transcriptional and posttranscriptional levels, generating highly-abundant 21, 22 and 24 nucleotide small interfering RNAs, suggesting that alphasatellite may serve as a decoy protecting its helper virus from gene silencing.
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Affiliation(s)
- Valentin Guyot
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
| | - Rajendran Rajeswaran
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
| | - Huong Cam Chu
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
| | - Chockalingam Karthikeyan
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
| | - Nathalie Laboureau
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
| | - Serge Galzi
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
| | - Lyna F. T. Mukwa
- Faculté des Sciences Agronomiques, Université Pédagogique Nationale, Kinshasa, Democratic Republic of the Congo
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - P. Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Marie-Line Iskra-Caruana
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
- CIRAD, DGD-RS, Montpellier, France
| | - Mikhail M. Pooggin
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, IRD, Institute Agro, Montpellier, France
- * E-mail:
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Hasanvand V, Heydanejad J, Massumi H, Kleinow T, Jeske H, Fontenele RS, Kraberger S, Varsani A. Genome characterization of parsley severe stunt-associated virus in Iran. Virus Genes 2021; 57:293-301. [PMID: 33881682 DOI: 10.1007/s11262-021-01835-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
Parsley severe stunt-associated virus (PSSaV) is a recently identified nanovirus first reported in Germany. During a survey for identification of nanoviruses infecting apiaceous plants in south-eastern Iran, PSSaV was identified and characterized using a combination of rolling circle amplification (RCA) and high-throughput sequencing. Parsley plant samples were collected from vegetable production farms in Kerman province. From two symptomatic samples (39Ba and 40Ba), seven PSSaV components (DNA-C, -S, -M, -R, -N, -U1 and -U2) with two phylogenetically distinct variants of DNA-R (R1 and R2) were identified. In common with the German isolate of PSSaV, no DNA-U4 component was identified. In addition, associated alphasatellite molecules were identified in samples 39Ba [n = 6] and 40Ba [n = 5]. Sequence analyses showed that concatenated component sequences of the two Iranian PSSaVs share 97.2% nucleotide identity with each other and 82% to the German isolate. The coat proteins (CPs) of the PSSaV Iranian sequences share 97.2% amino acid identity and ~ 84% identity with that of the German isolate. Sequence and phylogenetic analyses of a total of 11 recovered alphasatellites from the two samples can be classified into the genera Fabenesatellite [n = 2], Milvetsatellite [n = 1], Mivedwarsatellite [n = 2], Subclovsatellite [n = 2], Sophoyesatellite [n = 4] in the family Alphasatellitidae. Identification of PSSaV and other nanoviruses in wild and cultivated plants in Iran reveals that nanoviruses could be causing yield reduction in crops plants in this country.
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Affiliation(s)
- Vahid Hasanvand
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran
| | - Jahangir Heydanejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran. .,Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran.
| | - Hossain Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran
| | - Tatjana Kleinow
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Holger Jeske
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Rafaela S Fontenele
- 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
| | - Simona Kraberger
- 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
| | - 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 Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
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Lal A, Vo TTB, Sanjaya IGNPW, Ho PT, Kim JK, Kil EJ, Lee S. Nanovirus Disease Complexes: An Emerging Threat in the Modern Era. FRONTIERS IN PLANT SCIENCE 2020; 11:558403. [PMID: 33329624 PMCID: PMC7710663 DOI: 10.3389/fpls.2020.558403] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/28/2020] [Indexed: 06/12/2023]
Abstract
Multipartite viruses package their genomic segments independently and mainly infect plants; few target animals. Nanoviridae is a family of multipartite single-stranded DNA plant viruses that individually encapsidate single-stranded DNAs of approximately 1 kb and transmit them through aphids without replication in the aphid vectors, thereby causing important diseases of leguminous crops and banana. Significant findings regarding nanoviruses have recently been made on important features, such as their multicellular way of life, the transmission of distinct encapsidated genome segments through the vector body, evolutionary ambiguities, mode of infection, host range and geographical distribution. This review deals with all the above-mentioned features in view of recent advances with special emphasis on the emergence of new species and recognition of new host range of nanoviruses and aims to shed light on the evolutionary linkages, the potentially devastating impact on the world economy, and the future challenges imposed by nanoviruses.
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Affiliation(s)
- Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Thuy Thi Bich Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | | | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Ji-Kwang Kim
- Research and Development Bureau, Chungcheongnam-do Agricultural Research and Extension Services, Yesan, South Korea
| | - Eui-Joon Kil
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
- Department of Plant Medicals, Andong National University, Andong, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
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Liu Q, Wang H, Ling Y, Yang SX, Wang XC, Zhou R, Xiao YQ, Chen X, Yang J, Fu WG, Zhang W, Qi GL. Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer. Virol J 2020; 17:61. [PMID: 32334626 PMCID: PMC7183601 DOI: 10.1186/s12985-020-01332-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/16/2020] [Indexed: 01/08/2023] Open
Abstract
Background Musk deer can produce musk which has high medicinal value and is closely related to human health. Viruses in forest musk deer both threaten the health of forest musk deer and human beings. Methods Using viral metagenomics we investigated the virome in 85 faeces samples collected from forest musk deer. Results In this article, eight novel CRESS-DNA viruses were characterized, whole genomes were 2148 nt–3852 nt in length. Phylogenetic analysis indicated that some viral genomes were part of four different groups of CRESS-DNA virus belonging in the unclassified CRESS-DNA virus, Smacoviridae, pCPa-like virus and pPAPh2-like virus. UJSL001 (MN621482), UJSL003 (MN621469) and UJSL017 (MN621476) fall into the branch of unclassified CRESS-DNA virus (CRESSV1–2), UJSL002 (MN621468), UJSL004 (MN621481) and UJSL007 (MN621470) belong to the cluster of Smacoviridae, UJSL005 (MN604398) showing close relationship with pCPa-like (pCRESS4–8) clusters and UJSL006 (MN621480) clustered into the branch of pPAPh2-like (pCRESS9) virus, respectively. Conclusion The virome in faeces samples of forest musk deer from Chengdu, Sichuan province, China was revealed, which further characterized the diversity of viruses in forest musk deer intestinal tract.
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Affiliation(s)
- Qi Liu
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China.,Agricultural Engineering Research Institute, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Hao Wang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Yu Ling
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Shi-Xing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Xiao-Chun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Rui Zhou
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Yu-Qing Xiao
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Xu Chen
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Jie Yang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China
| | - Wei-Guo Fu
- Agricultural Engineering Research Institute, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, China.
| | - Gui-Lan Qi
- Institute of Animal Husbandry, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, Sichuan 611130, China.
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