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Schönegger D, Moubset O, Margaria P, Menzel W, Winter S, Roumagnac P, Marais A, Candresse T. Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community. J Virol 2023; 97:e0130023. [PMID: 37888981 PMCID: PMC10688312 DOI: 10.1128/jvi.01300-23] [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: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.
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Jailani AAK, Chattopadhyay A, Kumar P, Singh OW, Mukherjee SK, Roy A, Sanan-Mishra N, Mandal B. Accelerated Long-Fragment Circular PCR for Genetic Manipulation of Plant Viruses in Unveiling Functional Genomics. Viruses 2023; 15:2332. [PMID: 38140572 PMCID: PMC10747169 DOI: 10.3390/v15122332] [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: 09/29/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Molecular cloning, a crucial prerequisite for engineering plasmid constructs intended for functional genomic studies, relies on successful restriction and ligation processes. However, the lack of unique restriction sites often hinders construct preparation, necessitating multiple modifications. Moreover, achieving the successful ligation of large plasmid constructs is frequently challenging. To address these limitations, we present a novel PCR strategy in this study, termed 'long-fragment circular-efficient PCR' (LC-PCR). This technique involves one or two rounds of PCR with an additional third-long primer that complements both ends of the newly synthesized strand of a plasmid construct. This results in self-circularization with a nick-gap in each newly formed strand. The LC-PCR technique was successfully employed to insert a partial sequence (210 nucleotides) of the phytoene desaturase gene from Nicotiana benthamiana and a full capsid protein gene (770 nucleotides) of a begomovirus (tomato leaf curl New Delhi virus) into a 16.4 kb infectious construct of a tobamovirus, cucumber green mottle mosaic virus (CGMMV), cloned in pCambia. This was done to develop the virus-induced gene silencing vector (VIGS) and an expression vector for a foreign protein in plants, respectively. Furthermore, the LC-PCR could be applied for the deletion of a large region (replicase enzyme) and the substitution of a single amino acid in the CGMMV genome. Various in planta assays of these constructs validate their biological functionality, highlighting the utility of the LC-PCR technique in deciphering plant-virus functional genomics. The LC-PCR is not only suitable for modifying plant viral genomes but also applicable to a wide range of plant, animal, and human gene engineering under in-vitro conditions. Additionally, the LC-PCR technique provides an alternative to expensive kits, enabling quick introduction of modifications in any part of the nucleotide within a couple of days. Thus, the LC-PCR proves to be a suitable 'all in one' technique for modifying large plasmid constructs through site-directed gene insertion, deletion, and mutation, eliminating the need for restriction and ligation.
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Gong P, Shen Q, Zhang M, Qiao R, Jiang J, Su L, Zhao S, Fu S, Ma Y, Ge L, Wang Y, Lozano-Durán R, Wang A, Li F, Zhou X. Plant and animal positive-sense single-stranded RNA viruses encode small proteins important for viral infection in their negative-sense strand. MOLECULAR PLANT 2023; 16:1794-1810. [PMID: 37777826 DOI: 10.1016/j.molp.2023.09.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/03/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023]
Abstract
Positive-sense single-stranded RNA (+ssRNA) viruses, the most abundant viruses of eukaryotes in nature, require the synthesis of negative-sense RNA (-RNA) using their genomic (positive-sense) RNA (+RNA) as a template for replication. Based on current evidence, viral proteins are translated via viral +RNAs, whereas -RNA is considered to be a viral replication intermediate without coding capacity. Here, we report that plant and animal +ssRNA viruses contain small open reading frames (ORFs) in their -RNA (reverse ORFs [rORFs]). Using turnip mosaic virus (TuMV) as a model for plant +ssRNA viruses, we demonstrate that small proteins encoded by rORFs display specific subcellular localizations, and confirm the presence of rORF2 in infected cells through mass spectrometry analysis. The protein encoded by TuMV rORF2 forms punctuate granules that are localized in the perinuclear region and co-localized with viral replication complexes. The rORF2 protein can directly interact with the viral RNA-dependent RNA polymerase, and mutation of rORF2 completely abolishes virus infection, whereas ectopic expression of rORF2 rescues the mutant virus. Furthermore, we show that several rORFs in the -RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have the ability to suppress type I interferon production and facilitate the infection of vesicular stomatitis virus. In addition, we provide evidence that TuMV might utilize internal ribosome entry sites to translate these small rORFs. Taken together, these findings indicate that the -RNA of +ssRNA viruses can also have the coding capacity and that small proteins encoded therein play critical roles in viral infection, revealing a viral proteome larger than previously thought.
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Roslan ND, Sundram S, Hong LW, Ling KL, Vadamalai G. Analysis of Coconut cadang-cadang viroid variants on field samples exhibiting variation in orange spotting symptom expression and severity. Mol Biol Rep 2023; 50:9699-9705. [PMID: 37676433 DOI: 10.1007/s11033-023-08771-0] [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: 06/15/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND Sequence variation has been attributed to symptom variations but has not been investigated in Orange Spotting-Coconut cadang-cadang viroid (OS-CCCVd) infected palms. Likewise, the relationship between Coconut cadang-cadang viroid (CCCVd) variants, Orange Spotting (OS) severity and the accumulation of the viroid in the palms have not been elucidated. This paper describes the characterization of CCCVd variants by cloning and sequencing, followed by correlation with symptom expression. METHODS AND RESULTS Total nucleic acids were extracted from leaf samples harvested from frond 20 of seven Dura × Pisifera (D × P) African oil palm (Elaeis guineensis Jacq.) aged between 13 and 21 years old collected from local plantations. The nucleic acids were fractionated using 5% non-denaturing polyacrylamide gel electrophoresis (PAGE) before being subjected to detection by reverse transcribed polymerase chain reaction (RT-PCR). The PCR products were cloned into a plasmid vector and the sequence of the clones was analyzed. CCCVd variants were quantified using real-time qPCR assay with CCCVd specific primers. Sixteen randomly selected clones of (OP246) had an arbitrary 100% identity with CCCVdOP246 (GeneBank Accession No: HQ608513). Meanwhile, four clones had >93% similarity with several minor sequence variations forming variants of OP234, OP235, OP251 and OP279. CONCLUSION The OS symptoms observed in the field were characterized into three categories based on the size and morphology of the orange spots on the affected fronds. In addition, there was no direct correlation between disease severity and the accumulation of CCCVd variants in oil palm. This finding is the first report describing the sequence variation of the CCCVd RNA and symptom variation in OS oil palm field samples.
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Jailani AAK, Paret ML. Development of a multiplex RT-RPA assay for simultaneous detection of three viruses in cucurbits. MOLECULAR PLANT PATHOLOGY 2023; 24:1443-1450. [PMID: 37462133 PMCID: PMC10576173 DOI: 10.1111/mpp.13380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 10/15/2023]
Abstract
Begomoviruses and criniviruses, vectored by whiteflies (Bemisia tabaci), are important threats to crops worldwide. In recent years, the spread of cucurbit leaf crumple virus (CuLCrV), cucurbit yellow stunting disorder virus (CYSDV) and cucurbit chlorotic yellows virus (CCYV) on cucurbit crops has been reported to cause devastating crop losses in many regions of the world. In this study, a multiplex recombinase polymerase amplification (RPA) assay, an isothermal technique for rapid and simultaneous detection of DNA and RNA viruses CuLCrV, CYSDV and CCYV was developed. Highly specific and sensitive multiplex RPA primers for the coat protein region of these viruses were created and evaluated. The sensitivity of the multiplex RPA assay was examined using serially diluted plasmid containing the target regions. The results demonstrated that multiplex RPA primers have high sensitivity with a detection limit of a single copy of the viruses. The multiplex RPA primers were specific to the target as indicated by testing against other begomoviruses, potyviruses and an ilarvirus, and no nonspecific amplifications were noted. The primers simultaneously detected mixed infection of CCYV, CYSDV and CuLCrV in watermelon and squash crude extracts. This study is the first report of a multiplex RPA assay for simultaneous detection of mixed infection of DNA and RNA plant viruses.
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Scholthof HB, Scholthof KBG. Plant virology: an RNA treasure trove. TRENDS IN PLANT SCIENCE 2023; 28:1277-1289. [PMID: 37495453 DOI: 10.1016/j.tplants.2023.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/12/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023]
Abstract
Key principles pertaining to RNA biology not infrequently have their origins in plant virology. Examples have arisen from studies on viral RNA-intrinsic properties and the infection process from gene expression, replication, movement, and defense evasion to biotechnological applications. Since RNA is at the core of the central dogma in molecular biology, how plant virology assisted in the reinforcement or adaptations of this concept, while at other instances shook up elements of the doctrine, is discussed. Moreover, despite the negative effects of viral diseases in agriculture worldwide, plant viruses can be considered a scientific treasure trove. Today they remain tools of discovery for biotechnology, studying evolution, cell biology, and host-microbe interactions.
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Rozo-Lopez P, Brewer W, Käfer S, Martin MM, Parker BJ. Untangling an insect's virome from its endogenous viral elements. BMC Genomics 2023; 24:636. [PMID: 37875824 PMCID: PMC10594914 DOI: 10.1186/s12864-023-09737-z] [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: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Insects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have employed high-throughput RNA sequencing, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements (EVEs) with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery. METHODS In this study, we used a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphid Macrosiphum euphorbiae. We first used rRNA-depleted RNAseq to characterize the microbes found in individual insects. We then used PCR screening to measure the frequency of two heritable viruses in a local aphid population. Lastly, we generated a quality draft genome assembly for M. euphorbiae using Illumina-corrected Nanopore sequencing to identify transcriptionally active EVEs in the host genome. RESULTS We found reads from two insect-specific viruses (a Flavivirus and an Ambidensovirus) in our RNAseq data, as well as a parasitoid virus (Bracovirus), a plant pathogenic virus (Tombusvirus), and two phages (Acinetobacter and APSE). However, our genome assembly showed that part of the 'virome' of this insect can be attributed to EVEs in the host genome. CONCLUSION Our work shows that EVEs have led to the misidentification of aphid viruses from RNAseq data, and we argue that this is a widespread challenge for the study of viral diversity in insects.
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Jo Y, Choi H, Lee BC, Hong JS, Kim SM, Cho WK. Exploring Tomato Fruit Viromes through Transcriptome Data Analysis. Viruses 2023; 15:2139. [PMID: 38005817 PMCID: PMC10674750 DOI: 10.3390/v15112139] [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: 09/29/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
This study delves into the complex landscape of viral infections in tomatoes (Solanum lycopersicum) using available transcriptome data. We conducted a virome analysis, revealing 219 viral contigs linked to four distinct viruses: tomato chlorosis virus (ToCV), southern tomato virus (STV), tomato yellow leaf curl virus (TYLCV), and cucumber mosaic virus (CMV). Among these, ToCV predominated in contig count, followed by STV, TYLCV, and CMV. A notable finding was the prevalence of coinfections, emphasizing the concurrent presence of multiple viruses in tomato plants. Despite generally low viral levels in fruit transcriptomes, STV emerged as the primary virus based on viral read count. We delved deeper into viral abundance and the contributions of RNA segments to replication. While initially focused on studying the impact of sound treatment on tomato fruit transcriptomes, the unexpected viral presence underscores the importance of considering viruses in plant research. Geographical variations in virome communities hint at potential forensic applications. Phylogenetic analysis provided insights into viral origins and genetic diversity, enhancing our understanding of the Korean tomato virome. In conclusion, this study advances our knowledge of the tomato virome, stressing the need for robust pest control in greenhouse-grown tomatoes and offering insights into virus management and crop protection.
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Hua Y, Feng C, Gu T, Chen H, Liu D, Xu K, Zhang K. Development of Polyclonal Antibodies and a Serological-Based Reverse-Transcription Loop-Mediated Isothermal Amplification (S-RT-LAMP) Assay for Rice Black-Streaked Dwarf Virus Detection in Both Rice and Small Brown Planthopper. Viruses 2023; 15:2127. [PMID: 37896904 PMCID: PMC10612080 DOI: 10.3390/v15102127] [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: 09/19/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) infects rice and maize, and seriously affects rice yields in main rice-producing areas. It can be transmitted via small brown planthopper (SBPH: Laodelphax striatellus Fallén). To more rapidly, sensitively, and highly throughput diagnose RBSDV in the wild condition, we first purified the recombinant His-CPRBSDV protein, and prepared the polyclonal antibodies against the His-CPRBSDV protein (PAb-CPRBSDV). Based on the PAb-CPRBSDV, we developed a series of serological detections, such as Western blot, an enzyme-linked immunosorbent assay (ELISA), and a dot immunoblotting assay (DIBA). Furthermore, we developed a serological-based reverse-transcription loop-mediated isothermal amplification assay (S-RT-LAMP) that could accurately detect RBSDV in the wild. Briefly, the viral genomic dsRNA together with viral CP were precipitated by co-immunoprecipitation using the PAb-CPRBSDV, then the binding RNAs were crudely isolated and used for RT-LAMP diagnosis. Using the prepared PAb-CPRBSDV, four serology-based detection methods were established to specifically detect RBSDV-infected rice plants or SBPHs in the wild. The method of S-RT-LAMP has also been developed to specifically, high-throughput, and likely detect RBSDV in rice seedlings and SBPHs simultaneously. The antiserum prepared here laid the foundation for the rapid and efficient detection of RBSDV-infected field samples, which will benefit for determination of the virulence rate of the transmission vector SBPH and outbreak and epidemic prediction of RBSDV in a rice production area.
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Chaudhary S, Selvaraj V, Awasthi P, Bhuria S, Purohit R, Kumar S, Hallan V. Small Heat Shock Protein (sHsp22.98) from Trialeurodes vaporariorum Plays Important Role in Apple Scar Skin Viroid Transmission. Viruses 2023; 15:2069. [PMID: 37896846 PMCID: PMC10611230 DOI: 10.3390/v15102069] [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: 07/06/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 10/29/2023] Open
Abstract
Trialeurodes vaporariorum, commonly known as the greenhouse whitefly, severely infests important crops and serves as a vector for apple scar skin viroid (ASSVd). This vector-mediated transmission may cause the spread of infection to other herbaceous crops. For effective management of ASSVd, it is important to explore the whitefly's proteins, which interact with ASSVd RNA and are thereby involved in its transmission. In this study, it was found that a small heat shock protein (sHsp) from T. vaporariorum, which is expressed under stress, binds to ASSVd RNA. The sHsp gene is 606 bp in length and encodes for 202 amino acids, with a molecular weight of 22.98 kDa and an isoelectric point of 8.95. Intermolecular interaction was confirmed through in silico analysis, using electrophoretic mobility shift assays (EMSAs) and northwestern assays. The sHsp22.98 protein was found to exist in both monomeric and dimeric forms, and both forms showed strong binding to ASSVd RNA. To investigate the role of sHsp22.98 during ASSVd infection, transient silencing of sHsp22.98 was conducted, using a tobacco rattle virus (TRV)-based virus-induced gene silencing system. The sHsp22.98-silenced whiteflies showed an approximate 50% decrease in ASSVd transmission. These results suggest that sHsp22.98 from T. vaporariorum is associated with viroid RNA and plays a significant role in transmission.
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Li M, Zhang X, Huang K, Du Z. Identification of Host Factors Interacting with a γ-Shaped RNA Element from a Plant Virus-Associated Satellite RNA. Viruses 2023; 15:2039. [PMID: 37896816 PMCID: PMC10611174 DOI: 10.3390/v15102039] [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: 09/15/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Previously, we identified a highly conserved, γ-shaped RNA element (γRE) from satellite RNAs of cucumber mosaic virus (CMV), and we determined γRE to be structurally required for satRNA survival and the inhibition of CMV replication. It remains unknown how γRE biologically functions. In this work, pull-down assays were used to screen candidates of host factors from Nicotiana benthamiana plants using biotin-labeled γRE as bait. Nine host factors were found to interact specifically with γRE. Then, all of these host factors were down-regulated individually in N. benthamiana plants via tobacco rattle virus-induced gene silencing and tested with infection by GFP-expressing CMV (CMV-gfp) and the isolate T1 of satRNA (sat-T1). Out of nine candidates, three host factors, namely histone H3, GTPase Ran3, and eukaryotic translation initiation factor 4A, were extremely important for infection by CMV-gfp and sat-T1. Moreover, we found that cytosolic glyceraldehyde-3-phosphate dehydrogenase 2 contributed to the replication of CMV and sat-T1, but also negatively regulated CMV 2b activity. Collectively, our work provides essential clues for uncovering the mechanism by which satRNAs inhibit CMV replication.
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Xu Z, Zhou Z, Cheng Z, Zhou Y, Wang F, Li M, Li G, Li W, Du Q, Wang K, Lu X, Tai Y, Chen R, Hao Z, Han J, Chen Y, Meng Q, Kong X, Tie S, Mu C, Song W, Wang Z, Yong H, Zhang D, Wang H, Weng J, Li X. A transcription factor ZmGLK36 confers broad resistance to maize rough dwarf disease in cereal crops. NATURE PLANTS 2023; 9:1720-1733. [PMID: 37709955 DOI: 10.1038/s41477-023-01514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
Maize rough dwarf disease (MRDD), caused by maize rough dwarf virus (MRDV) or rice black-streaked dwarf virus (RBSDV), seriously threatens worldwide production of all major cereal crops, including maize, rice, wheat and barley. Here we report fine mapping and cloning of a previously reported major quantitative trait locus (QTL) (qMrdd2) for RBSDV resistance in maize. Subsequently, we show that qMrdd2 encodes a G2-like transcription factor named ZmGLK36 that promotes resistance to RBSDV by enhancing jasmonic acid (JA) biosynthesis and JA-mediated defence response. We identify a 26-bp indel located in the 5' UTR of ZmGLK36 that contributes to differential expression and resistance to RBSDV in maize inbred lines. Moreover, we show that ZmDBF2, an AP2/EREBP family transcription factor, directly binds to the 26-bp indel and represses ZmGLK36 expression. We further demonstrate that ZmGLK36 plays a conserved role in conferring resistance to RBSDV in rice and wheat using transgenic or marker-assisted breeding approaches. Our results provide insights into the molecular mechanisms of RBSDV resistance and effective strategies to breed RBSDV-resistant cereal crops.
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Spiegelman Z, Dinesh-Kumar SP. Breaking Boundaries: The Perpetual Interplay Between Tobamoviruses and Plant Immunity. Annu Rev Virol 2023; 10:455-476. [PMID: 37254097 DOI: 10.1146/annurev-virology-111821-122847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plant viruses of the genus Tobamovirus cause significant economic losses in various crops. The emergence of new tobamoviruses such as the tomato brown rugose fruit virus (ToBRFV) poses a major threat to global agriculture. Upon infection, plants mount a complex immune response to restrict virus replication and spread, involving a multilayered defense system that includes defense hormones, RNA silencing, and immune receptors. To counter these defenses, tobamoviruses have evolved various strategies to evade or suppress the different immune pathways. Understanding the interactions between tobamoviruses and the plant immune pathways is crucial for the development of effective control measures and genetic resistance to these viruses. In this review, we discuss past and current knowledge of the intricate relationship between tobamoviruses and host immunity. We use this knowledge to understand the emergence of ToBRFV and discuss potential approaches for the development of new resistance strategies to cope with emerging tobamoviruses.
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Atsumi G, Naramoto S, Nishihara M, Nakatsuka T, Tomita R, Matsushita Y, Hoshi N, Shirakawa A, Kobayashi K, Fukuda H, Sekine KT. Identification of a novel viral factor inducing tumorous symptoms by disturbing vascular development in planta. J Virol 2023; 97:e0046323. [PMID: 37668368 PMCID: PMC10537666 DOI: 10.1128/jvi.00463-23] [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: 03/28/2023] [Accepted: 06/14/2023] [Indexed: 09/06/2023] Open
Abstract
Plant viruses induce various disease symptoms that substantially impact agriculture, but the underlying mechanisms of viral disease in plants are poorly understood. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Here, we show that a gene fragment of gentian Kobu-sho-associated virus, which is designated as Kobu-sho-inducing factor (KOBU), induces gall formation accompanied by ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. Transgenic gentian expressing KOBU exhibited tumorous symptoms, confirming the gall-forming activity of KOBU. Surprisingly, KOBU expression can also induce differentiation of an additional leaf-like tissue on the abaxial side of veins in normal N. benthamiana and gentian leaves. Transcriptome analysis with Arabidopsis thaliana expressing KOBU revealed that KOBU activates signaling pathways that regulate xylem development. KOBU protein forms granules and plate-like structures and co-localizes with mRNA splicing factors within the nucleus. Our findings suggest that KOBU is a novel pleiotropic virulence factor that stimulates vascular and leaf development. IMPORTANCE While various mechanisms determine disease symptoms in plants depending on virus-host combinations, the details of how plant viruses induce symptoms remain largely unknown in most plant species. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Our findings demonstrate that a gene fragment of gentian Kobu-sho-associated virus (GKaV), which is designated as Kobu-sho-inducing factor, induces the gall formation accompanied by the ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. The molecular mechanism by which gentian Kobu-sho-associated virus induces the Kobu-sho symptoms will provide new insight into not only plant-virus interactions but also the regulatory mechanisms underlying vascular and leaf development.
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Dilweg IW, Peer J, Olsthoorn RCL. Xrn1-resistant RNA motifs are disseminated throughout the RNA virome and are able to block scanning ribosomes. Sci Rep 2023; 13:15987. [PMID: 37749116 PMCID: PMC10520033 DOI: 10.1038/s41598-023-43001-4] [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: 06/26/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
RNAs that are able to prevent degradation by the 5'-3' exoribonuclease Xrn1 have emerged as crucial structures during infection by an increasing number of RNA viruses. Several plant viruses employ the so-called coremin motif, an Xrn1-resistant RNA that is usually located in 3' untranslated regions. Investigation of its structural and sequence requirements has led to its identification in plant virus families beyond those in which the coremin motif was initially discovered. In this study, we identified coremin-like motifs that deviate from the original in the number of nucleotides present in the loop region of the 5' proximal hairpin. They are present in a number of viral families that previously did not have an Xrn1-resistant RNA identified yet, including the double-stranded RNA virus families Hypoviridae and Chrysoviridae. Through systematic mutational analysis, we demonstrated that a coremin motif carrying a 6-nucleotide loop in the 5' proximal hairpin generally requires a YGNNAD consensus for stalling Xrn1, similar to the previously determined YGAD consensus required for Xrn1 resistance of the original coremin motif. Furthermore, we determined the minimal requirements for the 3' proximal hairpin. Since some putative coremin motifs were found in intergenic regions or coding sequences, we demonstrated their capacity for inhibiting translation through an in vitro ribosomal scanning inhibition assay. Consequently, this study provides a further expansion on the number of viral families with known Xrn1-resistant elements, while adding a novel, potentially regulatory function for this structure.
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Lozano‐Durán R. More than annealing: RNAi is not alone in the fight against plant viruses. EMBO J 2023; 42:e115113. [PMID: 37592898 PMCID: PMC10505903 DOI: 10.15252/embj.2023115113] [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: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Cellular organisms have evolved different strategies to defend themselves against the invasion by viruses. In plants, RNA interference (RNAi) or RNA silencing, which is triggered by virus-derived double-stranded (ds)RNA, is considered the main antiviral defence mechanism. Martínez-Pérez et al have now uncovered an additional plant antiviral pathway, termed by the authors "m6 A-YTHDF axis," which relies on the modification and subsequent recognition of the viral RNA.
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Ramos-González PL, Dias Arena G, Tassi AD, Chabi-Jesus C, Watanabe Kitajima E, Freitas-Astúa J. Kitaviruses: A Window to Atypical Plant Viruses Causing Nonsystemic Diseases. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:97-118. [PMID: 37217202 DOI: 10.1146/annurev-phyto-021622-121351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Kitaviridae is a family of plant-infecting viruses that have multiple positive-sense, single-stranded RNA genomic segments. Kitaviruses are assigned into the genera Cilevirus, Higrevirus, and Blunervirus, mainly on the basis of the diversity of their genomic organization. Cell-to-cell movement of most kitaviruses is provided by the 30K family of proteins or the binary movement block, considered an alternative movement module among plant viruses. Kitaviruses stand out for producing conspicuously unusual locally restricted infections and showing deficient or nonsystemic movement likely resulting from incompatible or suboptimal interactions with their hosts. Transmission of kitaviruses is mediated by mites of many species of the genus Brevipalpus and at least one species of eriophyids. Kitavirus genomes encode numerous orphan open reading frames but RNA-dependent RNA polymerase and the transmembrane helix-containing protein, generically called SP24, typify a close phylogenetic link with arthropod viruses. Kitaviruses infect a large range of host plants and cause diseases of economic concern in crops such as citrus, tomato, passion fruit, tea, and blueberry.
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Sankari S, Lovelace AH. Unraveling the Molecular Arms Race: Grapevine Fanleaf Virus Proteins as Suppressors of Plant Antiviral Silencing Pathways. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:534-535. [PMID: 37843916 DOI: 10.1094/mpmi-08-23-0110-cm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
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Kasi Viswanath K, Hamid A, Ateka E, Pappu HR. CRISPR/Cas, Multiomics, and RNA Interference in Virus Disease Management. PHYTOPATHOLOGY 2023; 113:1661-1676. [PMID: 37486077 DOI: 10.1094/phyto-01-23-0002-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Plant viruses infect a wide range of commercially important crop plants and cause significant crop production losses worldwide. Numerous alterations in plant physiology related to the reprogramming of gene expression may result from viral infections. Although conventional integrated pest management-based strategies have been effective in reducing the impact of several viral diseases, continued emergence of new viruses and strains, expanding host ranges, and emergence of resistance-breaking strains necessitate a sustained effort toward the development and application of new approaches for virus management that would complement existing tactics. RNA interference-based techniques, and more recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing technologies have paved the way for precise targeting of viral transcripts and manipulation of viral genomes and host factors. In-depth knowledge of the molecular mechanisms underlying the development of disease would further expand the applicability of these recent methods. Advances in next-generation/high-throughput sequencing have made possible more intensive studies into host-virus interactions. Utilizing the omics data and its application has the potential to expedite fast-tracking traditional plant breeding methods, as well as applying modern molecular tools for trait enhancement, including virus resistance. Here, we summarize the recent developments in the CRISPR/Cas system, transcriptomics, endogenous RNA interference, and exogenous application of dsRNA in virus disease management.
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da Silva JPH, de Resende FMP, da Silva JCF, de Breuil S, Nome C, Bejerman N, Zerbini FM. Amesuviridae: a new family of plant-infecting viruses in the phylum Cressdnaviricota, realm Monodnaviria. Arch Virol 2023; 168:223. [PMID: 37561218 DOI: 10.1007/s00705-023-05852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
The phylum Cressdnaviricota comprises viruses with single-stranded, circular DNA genomes that encode an HUH-type endonuclease (known as Rep). The phylum includes two classes, eight orders, and 11 families. Here, we report the creation of a twelfth family in the order Mulpavirales, class Arfiviricetes of the phylum Cressdnaviricota. The family Amesuviridae comprises viruses that infect plants and is divided into two genera: Temfrudevirus, including the species Temfrudevirus temperatum (with temperate fruit decay-associated virus as a member), and Yermavirus, including the species Yermavirus ilicis (with yerba mate-associated circular DNA virus as a member). Both viruses encode Rep proteins with HUH endonuclease and SH3 superfamily helicase domains. Phylogenetic analysis indicates that the replicative module of amesuviruses constitutes a well-supported monophyletic clade related to Rep proteins from viruses in the order Mulpavirales. Furthermore, both viruses encode a single capsid protein (CP) related to geminivirus CPs. Phylogenetic incongruence between the replicative and structural modules of amesuviruses suggests a chimeric origin resulting from remote recombination events between ancestral mulpavirales and geminivirids. The creation of the family Amesuviridae has been ratified by the International Committee on Taxonomy of Viruses (ICTV).
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Pan D, Zhang S, Liu F, Tian Q, Yang X, Wang L, Yue Y. [Application of virus-induced gene silencing technology to investigate the phytochrome metabolism mechanism: a review]. SHENG WU GONG CHENG XUE BAO = CHINESE JOURNAL OF BIOTECHNOLOGY 2023; 39:2579-2599. [PMID: 37584116 DOI: 10.13345/j.cjb.230137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Color is an important indicator for evaluating the ornamental traits of horticultural plants, and plant pigments is a key factor affecting the color phenotype of plants. Plant pigments and their metabolites play important roles in color formation of ornamental organs, regulation of plant growth and development, and response to adversity stress. It has therefore became a hot topic in the field of plant research. Virus-induced gene silencing (VIGS) is a vital genomics tool that specifically reduces host endogenous gene expression utilizing plant homology-dependent defense mechanisms. In addition, VIGS enables characterization of gene function by rapidly inducing the gene-silencing phenotypes in plants. It provides an efficient and feasible alternative for verifying gene function in plant species lacking genetic transformation systems. This paper reviews the current status of the application of VIGS technology in the biosynthesis, degradation and regulatory mechanisms of plant pigments. Moreover, this review discusses the potential and future prospects of VIGS technology in exploring the regulatory mechanisms of plant pigments, with the aim to further our understandings of the metabolic processes and regulatory mechanisms of different plant pigments as well as improving plant color traits.
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Beernink BM, Whitham SA. Foxtail mosaic virus: A tool for gene function analysis in maize and other monocots. MOLECULAR PLANT PATHOLOGY 2023; 24:811-822. [PMID: 37036421 PMCID: PMC10257046 DOI: 10.1111/mpp.13330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/20/2023] [Accepted: 03/08/2023] [Indexed: 06/11/2023]
Abstract
Many plant viruses have been engineered into vectors for use in functional genomics studies, expression of heterologous proteins, and, most recently, gene editing applications. The use of viral vectors overcomes bottlenecks associated with mutagenesis and transgenesis approaches often implemented for analysis of gene function. There are several engineered viruses that are demonstrated or suggested to be useful in maize through proof-of-concept studies. However, foxtail mosaic virus (FoMV), which has a relatively broad host range, is emerging as a particularly useful virus for gene function studies in maize and other monocot crop or weed species. A few clones of FoMV have been independently engineered, and they have different features and capabilities for virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX) of proteins. In addition, FoMV can be used to deliver functional guide RNAs in maize and other plants expressing the Cas9 protein, demonstrating its potential utility in virus-induced gene editing applications. There is a growing number of studies in which FoMV vectors are being applied for VIGS or VOX in maize and the vast majority of these are related to maize-microbe interactions. In this review, we highlight the biology and engineering of FoMV as well as its applications in maize-microbe interactions and more broadly in the context of the monocot functional genomics toolbox.
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Jagram N, Dasgupta I. Principles and practice of virus induced gene silencing for functional genomics in plants. Virus Genes 2023; 59:173-187. [PMID: 36266497 DOI: 10.1007/s11262-022-01941-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/05/2022] [Indexed: 10/24/2022]
Abstract
Virus induced gene silencing (VIGS) has, of late, emerged as an important tool for transient silencing of genes in plants. This is now being increasingly used to determine functions of novel genes in a wide variety of plants, many of which are important crops yielding food and fiber or are sources of products having pharmaceutical uses. The technology for VIGS comprises the development of vectors derived from viruses, choosing the optimal orientation and size of the gene to be targeted and adopting the most suitable method of inoculation. This review gives a brief overview of the main aspects of VIGS technology as is being practiced. It also discusses the challenges the technology faces and the possible way ahead to improve its robustness, so that the technology finds wider applications.
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Rivarez MPS, Pecman A, Bačnik K, Maksimović O, Vučurović A, Seljak G, Mehle N, Gutiérrez-Aguirre I, Ravnikar M, Kutnjak D. In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem. MICROBIOME 2023; 11:60. [PMID: 36973750 PMCID: PMC10042675 DOI: 10.1186/s40168-023-01500-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/20/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data. RESULTS Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments. CONCLUSIONS We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies. Video Abstract.
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Debat H, Garcia ML, Bejerman N. Expanding the Repertoire of the Plant-Infecting Ophioviruses through Metatranscriptomics Data. Viruses 2023; 15:v15040840. [PMID: 37112821 PMCID: PMC10144540 DOI: 10.3390/v15040840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Ophioviruses (genus Ophiovirus, family Aspiviridae) are plant-infecting viruses with non-enveloped, filamentous, naked nucleocapsid virions. Members of the genus Ophiovirus have a segmented single-stranded negative-sense RNA genome (ca. 11.3–12.5 kb), encompassing three or four linear segments. In total, these segments encode four to seven proteins in the sense and antisense orientation, both in the viral and complementary strands. The genus Ophiovirus includes seven species with viruses infecting both monocots and dicots, mostly trees, shrubs and some ornamentals. From a genomic perspective, as of today, there are complete genomes available for only four species. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and molecular characterization of 33 novel viruses with genetic and evolutionary cues of ophioviruses. Genetic distance and evolutionary insights suggest that all the detected viruses could correspond to members of novel species, which expand the current diversity of ophioviruses ca. 4.5-fold. The detected viruses increase the tentative host range of ophioviruses for the first time to mosses, liverwort and ferns. In addition, the viruses were linked to several Asteraceae, Orchidaceae and Poaceae crops/ornamental plants. Phylogenetic analyses showed a novel clade of mosses, liverworts and fern ophioviruses, characterized by long branches, suggesting that there is still plenty of unsampled hidden diversity within the genus. This study represents a significant expansion of the genomics of ophioviruses, opening the door to future works on the molecular and evolutionary peculiarity of this virus genus.
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He R, Li Y, Bernards MA, Wang A. Manipulation of the Cellular Membrane-Cytoskeleton Network for RNA Virus Replication and Movement in Plants. Viruses 2023; 15:744. [PMID: 36992453 PMCID: PMC10056259 DOI: 10.3390/v15030744] [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: 02/01/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/15/2023] Open
Abstract
Viruses infect all cellular life forms and cause various diseases and significant economic losses worldwide. The majority of viruses are positive-sense RNA viruses. A common feature of infection by diverse RNA viruses is to induce the formation of altered membrane structures in infected host cells. Indeed, upon entry into host cells, plant-infecting RNA viruses target preferred organelles of the cellular endomembrane system and remodel organellar membranes to form organelle-like structures for virus genome replication, termed as the viral replication organelle (VRO) or the viral replication complex (VRC). Different viruses may recruit different host factors for membrane modifications. These membrane-enclosed virus-induced replication factories provide an optimum, protective microenvironment to concentrate viral and host components for robust viral replication. Although different viruses prefer specific organelles to build VROs, at least some of them have the ability to exploit alternative organellar membranes for replication. Besides being responsible for viral replication, VROs of some viruses can be mobile to reach plasmodesmata (PD) via the endomembrane system, as well as the cytoskeleton machinery. Viral movement protein (MP) and/or MP-associated viral movement complexes also exploit the endomembrane-cytoskeleton network for trafficking to PD where progeny viruses pass through the cell-wall barrier to enter neighboring cells.
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Feng C, Guo X, Gu T, Hua Y, Zhuang X, Zhang K. Generation of a Triple-Shuttling Vector and the Application in Plant Plus-Strand RNA Virus Infectious cDNA Clone Construction. Int J Mol Sci 2023; 24:ijms24065477. [PMID: 36982550 PMCID: PMC10056883 DOI: 10.3390/ijms24065477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Infectious cloning of plant viruses is a powerful tool for studying the reverse genetic manipulation of viral genes in virus–host plant interactions, contributing to a deeper understanding of the life history and pathogenesis of viruses. Yet, most of the infectious clones of RNA virus constructed in E. coli are unstable and toxic. Therefore, we modified the binary vector pCass4-Rz and constructed the ternary shuttle vector pCA4Y. The pCA4Y vector has a higher copy number in the E. coli than the conventional pCB301 vector, can obtain a high concentration of plasmid, and is economical and practical, so it is suitable for the construction of plant virus infectious clones in basic laboratories. The constructed vector can be directly extracted from yeast and transformed into Agrobacterium tumefaciens to avoid toxicity in E. coli. Taking advantage of the pCA4Y vector, we established a detailed large and multiple DNA HR-based cloning method in yeast using endogenous recombinase. We successfully constructed the Agrobacterium-based infectious cDNA clone of ReMV. This study provides a new choice for the construction of infectious viral clones.
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Shakir S, Zaidi SSEA, Hashemi FSG, Nyirakanani C, Vanderschuren H. Harnessing plant viruses in the metagenomics era: from the development of infectious clones to applications. TRENDS IN PLANT SCIENCE 2023; 28:297-311. [PMID: 36379846 DOI: 10.1016/j.tplants.2022.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Recent metagenomic studies which focused on virus characterization in the entire plant environment have revealed a remarkable viral diversity in plants. The exponential discovery of viruses also requires the concomitant implementation of high-throughput methods to perform their functional characterization. Despite several limitations, the development of viral infectious clones remains a method of choice to understand virus biology, their role in the phytobiome, and plant resilience. Here, we review the latest approaches for efficient characterization of plant viruses and technical advances built on high-throughput sequencing and synthetic biology to streamline assembly of viral infectious clones. We then discuss the applications of plant viral vectors in fundamental and applied plant research as well as their technical and regulatory limitations, and we propose strategies for their safer field applications.
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Mahmood MA, Naqvi RZ, Rahman SU, Amin I, Mansoor S. Plant Virus-Derived Vectors for Plant Genome Engineering. Viruses 2023; 15:v15020531. [PMID: 36851743 PMCID: PMC9958682 DOI: 10.3390/v15020531] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/25/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Advances in genome engineering (GE) tools based on sequence-specific programmable nucleases have revolutionized precise genome editing in plants. However, only the traditional approaches are used to deliver these GE reagents, which mostly rely on Agrobacterium-mediated transformation or particle bombardment. These techniques have been successfully used for the past decades for the genetic engineering of plants with some limitations relating to lengthy time-taking protocols and transgenes integration-related regulatory concerns. Nevertheless, in the era of climate change, we require certain faster protocols for developing climate-smart resilient crops through GE to deal with global food security. Therefore, some alternative approaches are needed to robustly deliver the GE reagents. In this case, the plant viral vectors could be an excellent option for the delivery of GE reagents because they are efficient, effective, and precise. Additionally, these are autonomously replicating and considered as natural specialists for transient delivery. In the present review, we have discussed the potential use of these plant viral vectors for the efficient delivery of GE reagents. We have further described the different plant viral vectors, such as DNA and RNA viruses, which have been used as efficient gene targeting systems in model plants, and in other important crops including potato, tomato, wheat, and rice. The achievements gained so far in the use of viral vectors as a carrier for GE reagent delivery are depicted along with the benefits and limitations of each viral vector. Moreover, recent advances have been explored in employing viral vectors for GE and adapting this technology for future research.
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Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
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Beris D, Tzima A, Gousi F, Rampou A, Psarra V, Theologidis I, Vassilakos N. Multiple integrations of a sense transgene, including a tandem inverted repeat confer stable RNA-silencing mediated virus resistance under different abiotic and biotic conditions. Transgenic Res 2023; 32:53-66. [PMID: 36633706 DOI: 10.1007/s11248-023-00333-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/30/2022] [Indexed: 01/13/2023]
Abstract
In a previous study, tobacco plants, transformed with a sense construct of the 57K domain of the replicase gene of tobacco rattle virus (TRV), provided resistance against genetically distant isolates of the virus. In this work, 57K-specific siRNAs were detected with RT-qPCR solely in the resistant line verifying the RNA-silencing base of the resistance. The integration sites of the transgene into the plant genome were identified with inverse-PCR. Moreover, the resistance against TRV was practically unaffected by low temperature conditions and the presence of heterologous viruses. The mechanism of the resistance was further examined by a gene expression analysis that showed increased transcript levels of genes with a key-role in the RNA silencing pathway and the basal antiviral defence. This work provides a comprehensive characterization of the robust virus resistance obtained by a sense transgene and underlines the usefulness of transgenic plants obtained by such a strategy.
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Su Y, Xu J, Jiang Q, Zhang Q, Wang C, Bin Y, Song Z. Construction of Full-Length Infectious cDNA Clones of Citrus Mosaic Virus RNA1 and RNA2 and Infection of Citrus Seedlings by Agrobacterium-Mediated Vacuum-Infiltration. PHYTOPATHOLOGY 2023; 113:6-10. [PMID: 35906769 DOI: 10.1094/phyto-05-22-0154-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of full-length infectious cDNA clones for plant RNA viruses is important for studying their molecular biological characteristics, functional genomics, pathogenesis, and vectorization applications. Citrus mosaic virus (CiMV), a member of the genus Sadwavirus, is of economic importance to the citrus industry and comprises a bipartite, positive-sense, single-stranded RNA genome encapsidated in icosahedral virions. In the present study, full-length cDNA clones of CiMV RNA1 and RNA2 were constructed based on a ternary yeast-Escherichia coli-Agrobacterium tumefaciens shuttle vector, pTY, using transformation-associated recombination (TAR) strategy. Infectivity of cDNA clones of CiMV RNA1 and RNA2 was examined in multiple citrus varieties via Agrobacterium-mediated vacuum-infiltration (AVI) through symptom observation, RT-PCR, and virion detection with an electron microscope. Furthermore, the genome-sized RT-PCR fragments of RNA1 and RNA2 were obtained from symptomatic Jinchengyou (Citrus grandis) plants infected by the cloned virus (CiMV211). In addition, CiMV211 produced typical symptoms of wild-type CiMV in cowpea (Vigna angularis) plants inoculated by Agrobacterium-mediated injection. This is the first report of infectious cDNA clones of CiMV, which may lay the foundation for research on the pathogenesis and vectorization of the virus.
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Marra M, D’Errico C, Montemurro C, Ratti C, Baldoni E, Matic S, Accotto GP. Fast and Sensitive Detection of Soil-Borne Cereal Mosaic Virus in Leaf Crude Extract of Durum Wheat. Viruses 2022; 15:140. [PMID: 36680180 PMCID: PMC9866084 DOI: 10.3390/v15010140] [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: 11/26/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Soil-borne cereal mosaic virus (SBCMV) is a furovirus with rigid rod-shaped particles containing an ssRNA genome, transmitted by Polymyxa graminis Led., a plasmodiophorid that can persist in soil for up to 20 years. SBCMV was reported on common and durum wheat and it can cause yield losses of up to 70%. Detection protocols currently available are costly and time-consuming (real-time PCR) or have limited sensitivity (ELISA). To facilitate an efficient investigation of the real dispersal of SBCMV, it is necessary to develop a new detection tool with the following characteristics: no extraction steps, very fast results, and high sensitivity to allow pooling of a large number of samples. In the present work, we have developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) protocol with such characteristics, and we have compared it with real-time PCR. Our results show that the sensitivity of LAMP and real-time PCR on cDNA and RT-LAMP on crude extracts are comparable, with the obvious advantage that RT-LAMP produces results in minutes rather than hours. This paves the way for extensive field surveys, leading to a better knowledge of the impact of this virus on wheat health and yield.
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Candresse T, Svanella-Dumas L, Marais A, Depasse F, Faure C, Lefebvre M. Identification of Seven Additional Genome Segments of Grapevine-Associated Jivivirus 1. Viruses 2022; 15:39. [PMID: 36680079 PMCID: PMC9862270 DOI: 10.3390/v15010039] [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: 11/09/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Jiviruses are a group of recently described viruses characterized with a tripartite genome and having affinities with Virgaviridae (RNA1 and 2) and Flaviviridae (RNA3). Using a combination of high-throughput sequencing, datamining and RT-PCR approaches, we demonstrate here that in grapevine samples infected by grapevine-associated jivivirus 1 (GaJV-1) up to 7 additional molecules can be consistently detected with conserved 5' and 3' non-coding regions in common with the three previously identified GaJV-1 genomic RNAs. RNA4, RNA5, RNA6, RNA7, RNA8 and RNA10, together with a recombinant RNArec7-8, are all members of a family sharing a previously non recognized conserved protein domain, while RNA9 is part of a distinct family characterized by another conserved motif. Datamining of pecan (Carya illinoinensis) public transcriptomic data allowed the identification of two further jiviviruses and the identification of supplementary genomic RNAs with homologies to those of GaJV-1. Taken together, these results reshape our vision of the divided genome of jiviviruses and raise novel questions about the function(s) of the proteins encoded by jiviviruses supplementary RNAs.
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Budzyńska D, Zwart MP, Hasiów-Jaroszewska B. Defective RNA Particles of Plant Viruses-Origin, Structure and Role in Pathogenesis. Viruses 2022; 14:v14122814. [PMID: 36560818 PMCID: PMC9786237 DOI: 10.3390/v14122814] [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: 11/28/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The genomes of RNA viruses may be monopartite or multipartite, and sub-genomic particles such as defective RNAs (D RNAs) or satellite RNAs (satRNAs) can be associated with some of them. D RNAs are small, deletion mutants of a virus that have lost essential functions for independent replication, encapsidation and/or movement. D RNAs are common elements associated with human and animal viruses, and they have been described for numerous plant viruses so far. Over 30 years of studies on D RNAs allow for some general conclusions to be drawn. First, the essential condition for D RNA formation is prolonged passaging of the virus at a high cellular multiplicity of infection (MOI) in one host. Second, recombination plays crucial roles in D RNA formation. Moreover, during virus propagation, D RNAs evolve, and the composition of the particle depends on, e.g., host plant, virus isolate or number of passages. Defective RNAs are often engaged in transient interactions with full-length viruses-they can modulate accumulation, infection dynamics and virulence, and are widely used, i.e., as a tool for research on cis-acting elements crucial for viral replication. Nevertheless, many questions regarding the generation and role of D RNAs in pathogenesis remain open. In this review, we summarise the knowledge about D RNAs of plant viruses obtained so far.
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86
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Atabekova AK, Lazareva EA, Lezzhov AA, Solovieva AD, Golyshev SA, Skulachev BI, Solovyev ID, Savitsky AP, Heinlein M, Morozov SY, Solovyev AG. Interaction between Movement Proteins of Hibiscus green spot virus. Viruses 2022; 14:v14122742. [PMID: 36560746 PMCID: PMC9780815 DOI: 10.3390/v14122742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Movement proteins (MPs) of plant viruses enable the translocation of viral genomes from infected to healthy cells through plasmodesmata (PD). The MPs functions involve the increase of the PD permeability and routing of viral genome both to the PD entrance and through the modified PD. Hibiscus green spot virus encodes two MPs, termed BMB1 and BMB2, which act in concert to accomplish virus cell-to-cell transport. BMB1, representing an NTPase/helicase domain-containing RNA-binding protein, localizes to the cytoplasm and the nucleoplasm. BMB2 is a small hydrophobic protein that interacts with the endoplasmic reticulum (ER) membranes and induces local constrictions of the ER tubules. In plant cells, BMB2 localizes to PD-associated membrane bodies (PAMBs) consisting of modified ER tubules and directs BMB1 to PAMBs. Here, we demonstrate that BMB1 and BMB2 interact in vitro and in vivo, and that their specific interaction is essential for BMB2-directed targeting of BMB1 to PAMBs. Using mutagenesis, we show that the interaction involves the C-terminal BMB1 region and the N-terminal region of BMB2.
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87
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Sett S, Prasad A, Prasad M. Resistance genes on the verge of plant-virus interaction. TRENDS IN PLANT SCIENCE 2022; 27:1242-1252. [PMID: 35902346 DOI: 10.1016/j.tplants.2022.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/06/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Viruses are acellular pathogens that cause severe infections in plants, resulting in worldwide crop losses every year. The lack of chemical agents to control viral diseases exacerbates the situation. Thus, to devise proper management strategies, it is important that the defense mechanisms of plants against viruses are understood. Resistance (R) genes regulate plant defense against invading pathogens by eliciting a hypersensitive response (HR). Compatible interaction between plant R gene and viral avirulence (Avr) protein activates the necrotic cell death response at the site of infection, resulting in the cessation of disease. Here, we review different aspects of R gene-mediated dominant resistance against plant viruses in dicotyledonous plants and possible ways for developing crops with better disease resistance.
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88
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Guo G, Li MJ, Lai JL, Du ZY, Liao QS. Development of tobacco rattle virus-based platform for dual heterologous gene expression and CRISPR/Cas reagent delivery. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111491. [PMID: 36216296 DOI: 10.1016/j.plantsci.2022.111491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/29/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
A large number of viral delivery systems have been developed for characterizing functional genes and producing heterologous recombinant proteins in plants, and but most of them are unable to co-express two fusion-free foreign proteins in the whole plant for extended periods of time. In this study, we modified tobacco rattle virus (TRV) as a TRVe dual delivery vector, using the strategy of gene substitution. The reconstructed TRVe had the capability to simultaneously produce two fusion-free foreign proteins at the whole level of Nicotiana benthamiana, and maintained the genetic stability for the insert of double foreign genes. Moreover, TRVe allowed systemic expression of two foreign proteins with the total lengths up to ∼900 aa residues. In addition, Cas12a protein and crRNA were delivered by the TRVe expression system for site-directed editing of genomic DNA in N. benthamiana 16c line constitutively expressing green fluorescent protein (GFP). Taker together, the TRV-based delivery system will be a simple and powerful means to rapidly co-express two non-fused foreign proteins at the whole level and facilitate functional genomics studies in plants.
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89
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Li X, Lin F, Li C, Du L, Liu Z, Shi W, Lv J, Cao X, Lan Y, Fan Y, Zhou Y, Zhou T. Golden 2-like transcription factor contributes to the major QTL against rice black-streaked dwarf virus disease. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4233-4243. [PMID: 36100693 DOI: 10.1007/s00122-022-04214-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
A major resistance QTL was identified on chromosome 6 in rice variety Wuke; both overexpression and knockdown experiments confirmed that OsGLK1 is the candidate gene for association with Rice black-streaked dwarf virus disease. Rice black-streaked dwarf virus disease is one of the most destructive rice viral diseases in China and East Asia. Progress has been limited in RBSDVD resistance breeding due to inadequate knowledge on the underlying functional genes. In this study, a major QTL for RBSDV (rice black-streaked dwarf virus) independent of SBPH (small brown planthopper) resistance was mapped in a 1.8 Mb interval on chromosome 6 by using an F2:3 population originated from resistant rice variety Wuke. Representative transcripts within this region were analysed and three genes showing amino acid sequence variation in functional domains were selected for transformation. Overexpression experiments showed that one gene exhibited significant enhanced resistance compared to control lines, encoding protein involving Myb domain and probable transcription factor Golden 2-like1 (GLK1). Furthermore, OsGLK1 knockdown rice lines were investigated and the resistance ability was significantly declined without this gene compared to the wild type. Taken together, both overexpression and knockdown experiments strongly suggested that OsGLK1 plays an important role for RBSDV resistance and contributes to the major QTL. The study paves the way for elucidating the molecular mechanism underlying RBSDVD resistance and the molecular markers associated with OsGLK1 may be used for marker-assisted selection.
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90
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Solovyev AG, Morozov SY. Uncovering Plant Virus Species Forming Novel Provisional Taxonomic Units Related to the Family Benyviridae. Viruses 2022; 14:v14122680. [PMID: 36560684 PMCID: PMC9781952 DOI: 10.3390/v14122680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022] Open
Abstract
Based on analyses of recent open-source data, this paper describes novel horizons in the diversity and taxonomy of beny-like viruses infecting hosts of the plant kingdom (Plantae or Archaeplastida). First, our data expand the known host range of the family Benyviridae to include red algae. Second, our phylogenetic analysis suggests that the evolution of this virus family may have involved cross-kingdom host change events and gene recombination/exchanges between distant taxa. Third, the identification of gene blocks encoding known movement proteins in beny-like RNA viruses infecting non-vascular plants confirms other evidence that plant virus genomic RNAs may have acquired movement proteins simultaneously or even prior to the evolutionary emergence of the plant vascular system. Fourth, novel data on plant virus diversity highlight that molecular evolution gave rise to numerous provisional species of land-plant-infecting viruses, which encode no known potential movement genetic systems.
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91
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Shvets D, Sandomirsky K, Porotikova E, Vinogradova S. Metagenomic Analysis of Ampelographic Collections of Dagestan Revealed the Presence of Two Novel Grapevine Viruses. Viruses 2022; 14:v14122623. [PMID: 36560627 PMCID: PMC9781968 DOI: 10.3390/v14122623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
In this study, we analyzed the virome of 73 grape samples from two Dagestan ampelographic collections in Russia using high-throughput sequencing of total RNAs. Fourteen viruses and four viroids were identified, with one to eleven of them detected in each plant. For the first time in Russia, we identified grapevine leafroll-associated virus 7 and grapevine Kizil Sapak virus. A total of 206 genomes of viruses and viroids were obtained, and their phylogenetic analysis was carried out. The de novo assembly and tblastx analysis allowed us to obtain contigs of a novel (+) ssRNA genome of a plant virus from the genus Umbravirus, which was tentatively named grapevine umbra-like virus (GULV), as well as contigs of a novel dsDNA pararetrovirus from the genus Caulimovirus, which was tentatively named grapevine pararetrovirus (GPRV). Complete genomes of these viruses were obtained and used for Sequence Demarcation Tool (SDT) analysis and phylogeny studies. GULV and GPRV were detected in 16 and 33 germplasm samples from the Dagestan collections, respectively.
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92
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Chao S, Wang H, Zhang S, Chen G, Mao C, Hu Y, Yu F, Wang S, Lv L, Chen L, Feng G. Novel RNA Viruses Discovered in Weeds in Rice Fields. Viruses 2022; 14:2489. [PMID: 36366587 PMCID: PMC9717734 DOI: 10.3390/v14112489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Weeds often grow alongside crop plants. In addition to competing with crops for nutrients, water and space, weeds host insect vectors or act as reservoirs for viral diversity. However, little is known about viruses infecting rice weeds. In this work, we used metatranscriptomic deep sequencing to identify RNA viruses from 29 weed samples representing 23 weed species. A total of 224 RNA viruses were identified: 39 newly identified viruses are sufficiently divergent to comprise new families and genera. The newly identified RNA viruses clustered within 18 viral families. Of the identified viruses, 196 are positive-sense single-stranded RNA viruses, 24 are negative-sense single-stranded RNA viruses and 4 are double-stranded RNA viruses. We found that some novel RNA viruses clustered within the families or genera of several plant virus species and have the potential to infect plants. Collectively, these results expand our understanding of viral diversity in rice weeds. Our work will contribute to developing effective strategies with which to manage the spread and epidemiology of plant viruses.
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93
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Boissinot S, Ducousso M, Brault V, Drucker M. Bioluminescence Production by Turnip Yellows Virus Infectious Clones: A New Way to Monitor Plant Virus Infection. Int J Mol Sci 2022; 23:ijms232213685. [PMID: 36430165 PMCID: PMC9692398 DOI: 10.3390/ijms232213685] [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: 09/27/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 11/10/2022] Open
Abstract
We used the NanoLuc luciferase bioluminescent reporter system to detect turnip yellows virus (TuYV) in infected plants. For this, TuYV was genetically tagged by replacing the C-terminal part of the RT protein with full-length NanoLuc (TuYV-NL) or with the N-terminal domain of split NanoLuc (TuYV-N65-NL). Wild-type and recombinant viruses were agro-infiltrated in Nicotiana benthamiana, Montia perfoliata, and Arabidopsis thaliana. ELISA confirmed systemic infection and similar accumulation of the recombinant viruses in N. benthamiana and M. perfoliata but reduced systemic infection and lower accumulation in A. thaliana. RT-PCR analysis indicated that the recombinant sequences were stable in N. benthamiana and M. perfoliata but not in A. thaliana. Bioluminescence imaging detected TuYV-NL in inoculated and systemically infected leaves. For the detection of split NanoLuc, we constructed transgenic N. benthamiana plants expressing the C-terminal domain of split NanoLuc. Bioluminescence imaging of these plants after agro-infiltration with TuYV-N65-NL allowed the detection of the virus in systemically infected leaves. Taken together, our results show that NanoLuc luciferase can be used to monitor infection with TuYV.
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94
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Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. PHYTOPATHOLOGY 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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95
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Robertson G, Burger J, Campa M. CRISPR/Cas-based tools for the targeted control of plant viruses. MOLECULAR PLANT PATHOLOGY 2022; 23:1701-1718. [PMID: 35920132 PMCID: PMC9562834 DOI: 10.1111/mpp.13252] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 05/15/2023]
Abstract
Plant viruses are known to infect most economically important crops and pose a major threat to global food security. Currently, few resistant host phenotypes have been delineated, and while chemicals are used for crop protection against insect pests and bacterial or fungal diseases, these are inefficient against viral diseases. Genetic engineering emerged as a way of modifying the plant genome by introducing functional genes in plants to improve crop productivity under adverse environmental conditions. Recently, new breeding technologies, and in particular the exciting CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) technology, was shown to be a powerful alternative to engineer resistance against plant viruses, thus has great potential for reducing crop losses and improving plant productivity to directly contribute to food security. Indeed, it could circumvent the "Genetic modification" issues because it allows for genome editing without the integration of foreign DNA or RNA into the genome of the host plant, and it is simpler and more versatile than other new breeding technologies. In this review, we describe the predominant features of the major CRISPR/Cas systems and outline strategies for the delivery of CRISPR/Cas reagents to plant cells. We also provide an overview of recent advances that have engineered CRISPR/Cas-based resistance against DNA and RNA viruses in plants through the targeted manipulation of either the viral genome or susceptibility factors of the host plant genome. Finally, we provide insight into the limitations and challenges that CRISPR/Cas technology currently faces and discuss a few alternative applications of the technology in virus research.
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Yue R, Sun Q, Ding J, Li W, Li W, Zhao M, Lu S, Zeng T, Zhang H, Zhao S, Tie S, Meng Z. Functional analysis revealed the involvement of ZmABCB15 in resistance to rice black-streaked dwarf virus infection. BMC PLANT BIOLOGY 2022; 22:484. [PMID: 36217105 PMCID: PMC9552357 DOI: 10.1186/s12870-022-03861-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Maize rough dwarf disease (MRDD), caused by rice black-streaked dwarf virus (RBSDV) belonging to the Fijivirus genus, seriously threatens maize production worldwide. Three susceptible varieties (Ye478, Zheng 58, and Zhengdan 958) and two resistant varieties (P138 and Chang7-2) were used in our study. RESULTS A set of ATP-binding cassette subfamily B (ABCB) transporter genes were screened to evaluate their possible involvements in RBSDV resistance. In the present study, ZmABCB15, an ABCB transporter family member, was cloned and functionally identified. Expression analysis showed that ZmABCB15 was significantly induced in the resistant varieties, not in the susceptible varieties, suggesting its involvement in resistance to the RBSDV infection. ZmABCB15 gene encodes a putative polar auxin transporter containing two trans-membrane domains and two P-loop nucleotide-binding domains. Transient expression analysis indicated that ZmABCB15 is a cell membrance localized protein. Over-expression of ZmABCB15 enhanced the resistance by repressing the RBSDV replication ratio. ZmABCB15 might participate in the RBSDV resistance by affecting the homeostasis of active and inactive auxins in RBSDV infected seedlings. CONCLUSIONS Polar auxin transport might participate in the RBSDV resistance by affecting the distribution of endogenous auxin among tissues. Our data showed the involvement of polar auxin transport in RBSDV resistance and provided novel mechanism underlying the auxin-mediated disease control technology.
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97
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Bhat AI, Aman R, Mahfouz M. Onsite detection of plant viruses using isothermal amplification assays. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1859-1873. [PMID: 35689490 PMCID: PMC9491455 DOI: 10.1111/pbi.13871] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/16/2022] [Accepted: 06/02/2022] [Indexed: 05/09/2023]
Abstract
Plant diseases caused by viruses limit crop production and quality, resulting in significant losses. However, options for managing viruses are limited; for example, as systemic obligate parasites, they cannot be killed by chemicals. Sensitive, robust, affordable diagnostic assays are needed to detect the presence of viruses in plant materials such as seeds, vegetative parts, insect vectors, or alternative hosts and then prevent or limit their introduction into the field by destroying infected plant materials or controlling insect hosts. Diagnostics based on biological and physical properties are not very sensitive and are time-consuming, but assays based on viral proteins and nucleic acids are more specific, sensitive, and rapid. However, most such assays require laboratories with sophisticated equipment and technical skills. By contrast, isothermal-based assays such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) are simple, easy to perform, reliable, specific, and rapid and do not require specialized equipment or skills. Isothermal amplification assays can be performed using lateral flow devices, making them suitable for onsite detection or testing in the field. To overcome non-specific amplification and cross-contamination issues, isothermal amplification assays can be coupled with CRISPR/Cas technology. Indeed, the collateral activity associated with some CRISPR/Cas systems has been successfully harnessed for visual detection of plant viruses. Here, we briefly describe traditional methods for detecting viruses and then examine the various isothermal assays that are being harnessed to detect viruses.
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98
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Yue J, Wei Y, Sun Z, Chen Y, Wei X, Wang H, Pasin F, Zhao M. AlkB RNA demethylase homologues and N 6 -methyladenosine are involved in Potyvirus infection. MOLECULAR PLANT PATHOLOGY 2022; 23:1555-1564. [PMID: 35700092 PMCID: PMC9452765 DOI: 10.1111/mpp.13239] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 05/28/2023]
Abstract
Proteins of the alkylation B (AlkB) superfamily show RNA demethylase activity removing methyl adducts from N6 -methyladenosine (m6 A). m6 A is a reversible epigenetic mark of RNA that regulates human virus replication but has unclear roles in plant virus infection. We focused on Potyvirus-the largest genus of plant RNA viruses-and report here the identification of AlkB domains within P1 of endive necrotic mosaic virus (ENMV) and an additional virus of a putative novel species within Potyvirus. We show that Nicotiana benthamiana m6 A levels are reduced by infection of plum pox virus (PPV) and potato virus Y (PVY). The two potyviruses lack AlkB and the results suggest a general involvement of RNA methylation in potyvirus infection and evolution. Methylated RNA immunoprecipitation sequencing of virus-infected samples showed that m6 A peaks are enriched in plant transcript 3' untranslated regions and in discrete internal and 3' terminal regions of PPV and PVY genomes. Down-regulation of N. benthamiana AlkB homologues of the plant-specific ALKBH9 clade caused a significant decrease in PPV and PVY accumulation. In summary, our study provides evolutionary and experimental evidence that supports the m6 A implication and the proviral roles of AlkB homologues in Potyvirus infection.
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Komatsu K, Hammond J. Plantago asiatica mosaic virus: An emerging plant virus causing necrosis in lilies and a new model RNA virus for molecular research. MOLECULAR PLANT PATHOLOGY 2022; 23:1401-1414. [PMID: 35856603 PMCID: PMC9452766 DOI: 10.1111/mpp.13243] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 06/01/2023]
Abstract
TAXONOMY Plantago asiatica mosaic virus belongs to the genus Potexvirus in the family Alphaflexiviridae of the order Tymovirales. VIRION AND GENOME PROPERTIES Plantago asiatica mosaic virus (PlAMV) has flexuous virions of approximately 490-530 nm in length and 10-15 nm in width. The genome of PlAMV consists of a single-stranded, positive-sense RNA of approximately 6.13 kb. It contains five open reading frames (ORFs 1-5), encoding a putative viral polymerase (RdRp), movement proteins (triple gene block proteins, TGBp1-3), and coat protein (CP), respectively. HOST RANGE PlAMV has an exceptionally wide host range and has been isolated from various wild plants, including Plantago asiatica, Nandina domestica, Rehmannia glutinosa, and other weed plants. Experimentally PlAMV can infect many plant species including Nicotiana benthamiana and Arabidopsis thaliana. It also infects ornamental lilies and frequently causes severe necrotic symptoms. However, host range varies depending on isolates, which show significant biological diversity within the species. GENOME DIVERSITY PlAMV can be separated into five clades based on phylogenetic analyses; nucleotide identities are significantly low between isolates in the different clades. TRANSMISSION PlAMV is not reported to be transmitted by biological vectors. Virions of PlAMV are quite stable and it can be transmitted efficiently by mechanical contact. DISEASE SYMPTOMS PlAMV causes red-rusted systemic necrosis in ornamental lilies, but it shows much weaker, if any, symptoms in wild plants such as P. asiatica. CONTROL Control of the disease caused by PlAMV is based mainly on rapid diagnosis and elimination of the infected bulbs or plants.
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Wang D, Chen S, Huang Z, Lin J. Identification and mapping of genetic locus conferring resistance to multiple plant viruses in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3293-3305. [PMID: 35932330 DOI: 10.1007/s00122-022-04187-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
A reliable locus confers broad-spectrum resistance to multiple plant viruses in soybean under field conditions. Soybean mosaic disease (SMD) can be caused by a variety of viruses, most of which have been largely overlooked in breeding programs. Effective mitigation of the adverse of SMD might result from breeding cultivars with broad-spectrum resistance. However, reports on broad-spectrum resistance to multiple virus have been limited. To catalog viral community members behind SMD, virus samples were collected from symptomatic field plots, and pathogenicity of component strains was assessed. Preliminary ELISA and PCR detection revealed that 39.58% and 66.67% of samples contained two or more virus strains, respectively. Only three soybean accessions were completely asymptomatic, while 42% exhibited moderate or severe susceptibility, indicating that co-infection of multiple virus remains a significant threat in current soybean production systems. Further, a RIL population consisting of 150 F7:9 strains derived from two soybean genotypes with contrasting reactions to virus infection was constructed and explored for significant markers and resistance genes. QTL analysis returned a reliable locus, named GmRmv, on chromosome 13. Significance of GmRmv in imparting resistance to SMD was further confirmed in NIL lines and delimited into a 157-kb interval that contains 17 annotated genes. Among these genes, three, Glyma.13G190000, Glyma.13G190300 and Glyma.13G190400, each contained LRR domains, as well as significant variation in coding sequences between resistant and susceptible parents. Hence, these three genes are considered strong candidate genes for explaining GmRmv significance. In summary, this research opens a new avenue for formulating strategies to breed soybean varieties with broad-spectrum resistance to multiple virus associated with SMD.
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