Journal articles: 'RNA viruses Plant viruses'

1

Roossinck, Marilyn J. "Lifestyles of plant viruses." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1548 (June 27, 2010): 1899–905. http://dx.doi.org/10.1098/rstb.2010.0057.

Full text

Abstract:

The vast majority of well-characterized eukaryotic viruses are those that cause acute or chronic infections in humans and domestic plants and animals. However, asymptomatic persistent viruses have been described in animals, and are thought to be sources for emerging acute viruses. Although not previously described in these terms, there are also many viruses of plants that maintain a persistent lifestyle. They have been largely ignored because they do not generally cause disease. The persistent viruses in plants belong to the family Partitiviridae or the genus Endornavirus . These groups also have members that infect fungi. Phylogenetic analysis of the partitivirus RNA-dependent RNA polymerase genes suggests that these viruses have been transmitted between plants and fungi. Additional families of viruses traditionally thought to be fungal viruses are also found frequently in plants, and may represent a similar scenario of persistent lifestyles, and some acute or chronic viruses of crop plants may maintain a persistent lifestyle in wild plants. Persistent, chronic and acute lifestyles of plant viruses are contrasted from both a functional and evolutionary perspective, and the potential role of these lifestyles in host evolution is discussed.

APA, Harvard, Vancouver, ISO, and other styles

2

Elena, S. F., P. Agudelo-Romero, P. Carrasco, F. M. Codoñer, S. Martín, C. Torres-Barceló, and R. Sanjuán. "Experimental evolution of plant RNA viruses." Heredity 100, no. 5 (February 6, 2008): 478–83. http://dx.doi.org/10.1038/sj.hdy.6801088.

Full text

APA, Harvard, Vancouver, ISO, and other styles

3

Goldbach, R. W. "Molecular Evolution of Plant RNA Viruses." Annual Review of Phytopathology 24, no. 1 (September 1986): 289–310. http://dx.doi.org/10.1146/annurev.py.24.090186.001445.

Full text

APA, Harvard, Vancouver, ISO, and other styles

4

ISHIKAWA, Masayuki. "Special issue: Plant viruses. Studies on the replication mechanisms of plant RNA viruses." Uirusu 44, no. 1 (1994): 3–10. http://dx.doi.org/10.2222/jsv.44.3.

Full text

APA, Harvard, Vancouver, ISO, and other styles

5

Wang, Ming-Bo, Chikara Masuta, Neil A. Smith, and Hanako Shimura. "RNA Silencing and Plant Viral Diseases." Molecular Plant-Microbe Interactions® 25, no. 10 (October 2012): 1275–85. http://dx.doi.org/10.1094/mpmi-04-12-0093-cr.

Full text

Abstract:

RNA silencing plays a critical role in plant resistance against viruses, with multiple silencing factors participating in antiviral defense. Both RNA and DNA viruses are targeted by the small RNA-directed RNA degradation pathway, with DNA viruses being also targeted by RNA-directed DNA methylation. To evade RNA silencing, plant viruses have evolved a variety of counter-defense mechanisms such as expressing RNA-silencing suppressors or adopting silencing-resistant RNA structures. This constant defense–counter defense arms race is likely to have played a major role in defining viral host specificity and in shaping viral and possibly host genomes. Recent studies have provided evidence that RNA silencing also plays a direct role in viral disease induction in plants, with viral RNA-silencing suppressors and viral siRNAs as potentially the dominant players in viral pathogenicity. However, questions remain as to whether RNA silencing is the principal mediator of viral pathogenicity or if other RNA-silencing-independent mechanisms also account for viral disease induction. RNA silencing has been exploited as a powerful tool for engineering virus resistance in plants as well as in animals. Further understanding of the role of RNA silencing in plant–virus interactions and viral symptom induction is likely to result in novel anti-viral strategies in both plants and animals.

APA, Harvard, Vancouver, ISO, and other styles

6

Rao, A. L. N. "Genome Packaging by Spherical Plant RNA Viruses." Annual Review of Phytopathology 44, no. 1 (September 2006): 61–87. http://dx.doi.org/10.1146/annurev.phyto.44.070505.143334.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

Lai, M. M. "RNA recombination in animal and plant viruses." Microbiological Reviews 56, no. 1 (1992): 61–79. http://dx.doi.org/10.1128/mmbr.56.1.61-79.1992.

Full text

APA, Harvard, Vancouver, ISO, and other styles

8

Lai, M. M. "RNA recombination in animal and plant viruses." Microbiological Reviews 56, no. 1 (1992): 61–79. http://dx.doi.org/10.1128/mr.56.1.61-79.1992.

Full text

APA, Harvard, Vancouver, ISO, and other styles

9

Chare, Elizabeth R., and Edward C. Holmes. "Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission." Journal of General Virology 85, no. 10 (October 1, 2004): 3149–57. http://dx.doi.org/10.1099/vir.0.80134-0.

Full text

Abstract:

To determine the selection pressures faced by RNA viruses of plants, patterns of nonsynonymous (d N) and synonymous (d S) substitution in the capsid genes of 36 viruses with differing modes of transmission were analysed. This analysis provided strong evidence that the capsid proteins of vector-borne plant viruses are subject to greater purifying selection on amino acid change than those viruses transmitted by other routes and that virus–vector interactions impose greater selective constraints than those between virus and plant host. This could be explained by specific interactions between capsid proteins and cellular receptors in the insect vectors that are necessary for successful transmission. However, contrary to initial expectations based on phylogenetic relatedness, vector-borne plant viruses are subject to weaker selective constraints than vector-borne animal viruses. The results suggest that the greater complexity involved in the transmission of circulative animal viruses compared with non-circulative plant viruses results in more intense purifying selection.

APA, Harvard, Vancouver, ISO, and other styles

10

Garcia-Ruiz, Hernan. "Susceptibility Genes to Plant Viruses." Viruses 10, no. 9 (September 10, 2018): 484. http://dx.doi.org/10.3390/v10090484.

Full text

Abstract:

Plant viruses use cellular factors and resources to replicate and move. Plants respond to viral infection by several mechanisms, including innate immunity, autophagy, and gene silencing, that viruses must evade or suppress. Thus, the establishment of infection is genetically determined by the availability of host factors necessary for virus replication and movement and by the balance between plant defense and viral suppression of defense responses. Host factors may have antiviral or proviral activities. Proviral factors condition susceptibility to viruses by participating in processes essential to the virus. Here, we review current advances in the identification and characterization of host factors that condition susceptibility to plant viruses. Host factors with proviral activity have been identified for all parts of the virus infection cycle: viral RNA translation, viral replication complex formation, accumulation or activity of virus replication proteins, virus movement, and virion assembly. These factors could be targets of gene editing to engineer resistance to plant viruses.

APA, Harvard, Vancouver, ISO, and other styles

11

Thekke-Veetil, Thanuja, Doris Lagos-Kutz, Nancy K. McCoppin, Glen L. Hartman, Hye-Kyoung Ju, Hyoun-Sub Lim, and Leslie L. Domier. "Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses." Viruses 12, no. 12 (December 1, 2020): 1376. http://dx.doi.org/10.3390/v12121376.

Full text

Abstract:

Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. The novel viruses were predicted to have positive-sense RNA, negative-stranded RNA, double-stranded RNA, and single-stranded DNA genomes. The assembled sequences included 100 contigs that represented at least 95% coverage of a virus genome or genome segment. Sequences represented 12 previously described arthropod viruses including eight viruses reported from Hubei Province in China, and 12 plant virus sequences of which six have been previously described. The presence of diverse populations of plant viruses within soybean thrips suggests they feed on and acquire viruses from multiple host plant species that could be transmitted to soybean. Assessment of the virome of soybean thrips provides, for the first time, information on the diversity of viruses present in thrips.

APA, Harvard, Vancouver, ISO, and other styles

12

Bian, Ruiling, Ida Bagus Andika, Tianxing Pang, Ziqian Lian, Shuang Wei, Erbo Niu, Yunfeng Wu, Hideki Kondo, Xili Liu, and Liying Sun. "Facilitative and synergistic interactions between fungal and plant viruses." Proceedings of the National Academy of Sciences 117, no. 7 (February 3, 2020): 3779–88. http://dx.doi.org/10.1073/pnas.1915996117.

Full text

Abstract:

Plants and fungi are closely associated through parasitic or symbiotic relationships in which bidirectional exchanges of cellular contents occur. Recently, a plant virus was shown to be transmitted from a plant to a fungus, but it is unknown whether fungal viruses can also cross host barriers and spread to plants. In this study, we investigated the infectivity of Cryphonectria hypovirus 1 (CHV1, family Hypoviridae), a capsidless, positive-sense (+), single-stranded RNA (ssRNA) fungal virus in a model plant, Nicotiana tabacum. CHV1 replicated in mechanically inoculated leaves but did not spread systemically, but coinoculation with an unrelated plant (+)ssRNA virus, tobacco mosaic virus (TMV, family Virgaviridae), or other plant RNA viruses, enabled CHV1 to systemically infect the plant. Likewise, CHV1 systemically infected transgenic plants expressing the TMV movement protein, and coinfection with TMV further enhanced CHV1 accumulation in these plants. Conversely, CHV1 infection increased TMV accumulation when TMV was introduced into a plant pathogenic fungus, Fusarium graminearum. In the in planta F. graminearum inoculation experiment, we demonstrated that TMV infection of either the plant or the fungus enabled the horizontal transfer of CHV1 from the fungus to the plant, whereas CHV1 infection enhanced fungal acquisition of TMV. Our results demonstrate two-way facilitative interactions between the plant and fungal viruses that promote cross-kingdom virus infections and suggest the presence of plant–fungal-mediated routes for dissemination of fungal and plant viruses in nature.

APA, Harvard, Vancouver, ISO, and other styles

13

Sanfaçon, Hélène. "Replication of positive-strand RNA viruses in plants: contact points between plant and virus components." Canadian Journal of Botany 83, no. 12 (December 2005): 1529–49. http://dx.doi.org/10.1139/b05-121.

Full text

Abstract:

Positive-strand RNA viruses constitute the largest group of plant viruses and have an important impact on world agriculture. These viruses have small genomes that encode a limited number of proteins and depend on their hosts to complete the various steps of their replication cycle. In this review, the contact points between positive-strand RNA plant viruses and their hosts, which are necessary for the translation and replication of the viral genomes, are discussed. Special emphasis is placed on the description of viral replication complexes that are associated with specific membranous compartments derived from plant intracellular membranes and contain viral RNAs and proteins as well as a variety of host proteins. These complexes are assembled via an intricate network of protein–protein, protein–membrane, and protein–RNA interactions. The role of host factors in regulating the assembly, stability, and activity of viral replication complexes are also discussed.

APA, Harvard, Vancouver, ISO, and other styles

14

Taliansky, Michael, Viktoria Samarskaya, Sergey K. Zavriev, Igor Fesenko, Natalia O. Kalinina, and Andrew J. Love. "RNA-Based Technologies for Engineering Plant Virus Resistance." Plants 10, no. 1 (January 2, 2021): 82. http://dx.doi.org/10.3390/plants10010082.

Full text

Abstract:

In recent years, non-coding RNAs (ncRNAs) have gained unprecedented attention as new and crucial players in the regulation of numerous cellular processes and disease responses. In this review, we describe how diverse ncRNAs, including both small RNAs and long ncRNAs, may be used to engineer resistance against plant viruses. We discuss how double-stranded RNAs and small RNAs, such as artificial microRNAs and trans-acting small interfering RNAs, either produced in transgenic plants or delivered exogenously to non-transgenic plants, may constitute powerful RNA interference (RNAi)-based technology that can be exploited to control plant viruses. Additionally, we describe how RNA guided CRISPR-CAS gene-editing systems have been deployed to inhibit plant virus infections, and we provide a comparative analysis of RNAi approaches and CRISPR-Cas technology. The two main strategies for engineering virus resistance are also discussed, including direct targeting of viral DNA or RNA, or inactivation of plant host susceptibility genes. We also elaborate on the challenges that need to be overcome before such technologies can be broadly exploited for crop protection against viruses.

APA, Harvard, Vancouver, ISO, and other styles

15

Elena, Santiago F., Stéphanie Bedhomme, Purificación Carrasco, José M. Cuevas, Francisca de la Iglesia, Guillaume Lafforgue, Jasna Lalić, Àngels Pròsper, Nicolas Tromas, and Mark P. Zwart. "The Evolutionary Genetics of Emerging Plant RNA Viruses." Molecular Plant-Microbe Interactions® 24, no. 3 (March 2011): 287–93. http://dx.doi.org/10.1094/mpmi-09-10-0214.

Full text

Abstract:

Over the years, agriculture across the world has been compromised by a succession of devastating epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that acquired new virulence factors or changed their epidemiological patterns. Viral emergence is usually associated with ecological change or with agronomical practices bringing together reservoirs and crop species. The complete picture is, however, much more complex, and results from an evolutionary process in which the main players are ecological factors, viruses' genetic plasticity, and host factors required for virus replication, all mixed with a good measure of stochasticity. The present review puts emergence of plant RNA viruses into the framework of evolutionary genetics, stressing that viral emergence begins with a stochastic process that involves the transmission of a preexisting viral strain into a new host species, followed by adaptation to the new host.

APA, Harvard, Vancouver, ISO, and other styles

16

Kanakala, Surapathrudu, and Murad Ghanim. "RNA Interference in Insect Vectors for Plant Viruses." Viruses 8, no. 12 (December 12, 2016): 329. http://dx.doi.org/10.3390/v8120329.

Full text

APA, Harvard, Vancouver, ISO, and other styles

17

Dreher, Theo W., and W. Allen Miller. "Translational control in positive strand RNA plant viruses." Virology 344, no. 1 (January 2006): 185–97. http://dx.doi.org/10.1016/j.virol.2005.09.031.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

Kormelink, Richard, Maria Laura Garcia, Michael Goodin, Takahide Sasaya, and Anne-Lise Haenni. "Negative-strand RNA viruses: The plant-infecting counterparts." Virus Research 162, no. 1-2 (December 2011): 184–202. http://dx.doi.org/10.1016/j.virusres.2011.09.028.

Full text

APA, Harvard, Vancouver, ISO, and other styles

19

Ruark, Casey L., Michael Gardner, Melissa G. Mitchum, Eric L. Davis, and Tim L. Sit. "Novel RNA viruses within plant parasitic cyst nematodes." PLOS ONE 13, no. 3 (March 6, 2018): e0193881. http://dx.doi.org/10.1371/journal.pone.0193881.

Full text

APA, Harvard, Vancouver, ISO, and other styles

20

Mann, Krin, and Hélène Sanfaçon. "Expanding Repertoire of Plant Positive-Strand RNA Virus Proteases." Viruses 11, no. 1 (January 15, 2019): 66. http://dx.doi.org/10.3390/v11010066.

Full text

Abstract:

Many plant viruses express their proteins through a polyprotein strategy, requiring the acquisition of protease domains to regulate the release of functional mature proteins and/or intermediate polyproteins. Positive-strand RNA viruses constitute the vast majority of plant viruses and they are diverse in their genomic organization and protein expression strategies. Until recently, proteases encoded by positive-strand RNA viruses were described as belonging to two categories: (1) chymotrypsin-like cysteine and serine proteases and (2) papain-like cysteine protease. However, the functional characterization of plant virus cysteine and serine proteases has highlighted their diversity in terms of biological activities, cleavage site specificities, regulatory mechanisms, and three-dimensional structures. The recent discovery of a plant picorna-like virus glutamic protease with possible structural similarities with fungal and bacterial glutamic proteases also revealed new unexpected sources of protease domains. We discuss the variety of plant positive-strand RNA virus protease domains. We also highlight possible evolution scenarios of these viral proteases, including evidence for the exchange of protease domains amongst unrelated viruses.

APA, Harvard, Vancouver, ISO, and other styles

21

Charon, Justine, Vanessa Rossetto Marcelino, Richard Wetherbee, Heroen Verbruggen, and Edward C. Holmes. "Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures." Viruses 12, no. 10 (October 19, 2020): 1180. http://dx.doi.org/10.3390/v12101180.

Full text

Abstract:

Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.

APA, Harvard, Vancouver, ISO, and other styles

22

Sanjuán, Rafael, Patricia Agudelo-Romero, and Santiago F. Elena. "Upper-limit mutation rate estimation for a plant RNA virus." Biology Letters 5, no. 3 (February 25, 2009): 394–96. http://dx.doi.org/10.1098/rsbl.2008.0762.

Full text

Abstract:

It is generally accepted that mutation rates of RNA viruses are inherently high due to the lack of proofreading mechanisms. However, direct estimates of mutation rate are surprisingly scarce, in particular for plant viruses. Here, based on the analysis of in vivo mutation frequencies in tobacco etch virus , we calculate an upper-bound mutation rate estimation of 3×10 −5 per site and per round of replication; a value which turns out to be undistinguishable from the methodological error. Nonetheless, the value is barely on the lower side of the range accepted for RNA viruses, although in good agreement with the only direct estimate obtained for other plant viruses. These observations suggest that, perhaps, differences in the selective pressures operating during plant virus evolution may have driven their mutation rates towards values lower than those characteristic of other RNA viruses infecting bacteria or animals.

APA, Harvard, Vancouver, ISO, and other styles

23

V, Maksimov I., Sorokan A. V, Burkhanova G. F, Veselova S. V, Alekseev V. Yu, Shein M. Yu, Avalbaev A. M, et al. "Mechanisms of Plant Tolerance to RNA Viruses Induced by Plant-Growth-Promoting Microorganisms." Plants 8, no. 12 (December 5, 2019): 575. http://dx.doi.org/10.3390/plants8120575.

Full text

Abstract:

Plant viruses are globally responsible for the significant crop losses of economically important plants. All common approaches are not able to eradicate viral infection. Many non-conventional strategies are currently used to control viral infection, but unfortunately, they are not always effective. Therefore, it is necessary to search for efficient and eco-friendly measures to prevent viral diseases. Since the genomic material of 90% higher plant viruses consists of single-stranded RNA, the best way to target the viral genome is to use ribonucleases (RNase), which can be effective against any viral disease of plants. Here, we show the importance of the search for endophytes with protease and RNase activity combined with the capacity to prime antiviral plant defense responses for their protection against viruses. This review discusses the possible mechanisms used to suppress a viral attack as well as the use of local endophytic bacteria for antiviral control in crops.

APA, Harvard, Vancouver, ISO, and other styles

24

Singh, Khushwant, Chris Dardick, and Jiban Kumar Kundu. "RNAi-Mediated Resistance Against Viruses in Perennial Fruit Plants." Plants 8, no. 10 (September 22, 2019): 359. http://dx.doi.org/10.3390/plants8100359.

Full text

Abstract:

Small RNAs (sRNAs) are 20–30-nucleotide-long, regulatory, noncoding RNAs that induce silencing of target genes at the transcriptional and posttranscriptional levels. They are key components for cellular functions during plant development, hormone signaling, and stress responses. Generated from the cleavage of double-stranded RNAs (dsRNAs) or RNAs with hairpin structures by Dicer-like proteins (DCLs), they are loaded onto Argonaute (AGO) protein complexes to induce gene silencing of their complementary targets by promoting messenger RNA (mRNA) cleavage or degradation, translation inhibition, DNA methylation, and/or histone modifications. This mechanism of regulating RNA activity, collectively referred to as RNA interference (RNAi), which is an evolutionarily conserved process in eukaryotes. Plant RNAi pathways play a fundamental role in plant immunity against viruses and have been exploited via genetic engineering to control disease. Plant viruses of RNA origin that contain double-stranded RNA are targeted by the RNA-silencing machinery to produce virus-derived small RNAs (vsRNAs). Some vsRNAs serve as an effector to repress host immunity by capturing host RNAi pathways. High-throughput sequencing (HTS) strategies have been used to identify endogenous sRNA profiles, the “sRNAome”, and analyze expression in various perennial plants. Therefore, the review examines the current knowledge of sRNAs in perennial plants and fruits, describes the development and implementation of RNA interference (RNAi) in providing resistance against economically important viruses, and explores sRNA targets that are important in regulating a variety of biological processes.

APA, Harvard, Vancouver, ISO, and other styles

25

Herath, Venura, Gustavo Romay, Cesar D. Urrutia, and Jeanmarie Verchot. "Family Level Phylogenies Reveal Relationships of Plant Viruses within the Order Bunyavirales." Viruses 12, no. 9 (September 10, 2020): 1010. http://dx.doi.org/10.3390/v12091010.

Full text

Abstract:

Bunyavirales are negative-sense segmented RNA viruses infecting arthropods, protozoans, plants, and animals. This study examines the phylogenetic relationships of plant viruses within this order, many of which are recently classified species. Comprehensive phylogenetic analyses of the viral RNA dependent RNA polymerase (RdRp), precursor glycoprotein (preGP), the nucleocapsid (N) proteins point toward common progenitor viruses. The RdRp of Fimoviridae and Tospoviridae show a close evolutional relationship while the preGP of Fimoviridae and Phenuiviridae show a closed relationship. The N proteins of Fimoviridae were closer to the Phasmaviridae, the Tospoviridae were close to some Phenuiviridae members and the Peribunyaviridae. The plant viral movement proteins of species within the Tospoviridae and Phenuiviridae were more closely related to each other than to members of the Fimoviridae. Interestingly, distal ends of 3′ and 5′ untranslated regions of species within the Fimoviridae shared similarity to arthropod and vertebrate infecting members of the Cruliviridae and Peribunyaviridae compared to other plant virus families. Co-phylogeny analysis of the plant infecting viruses indicates that duplication and host switching were more common than co-divergence with a host species.

APA, Harvard, Vancouver, ISO, and other styles

26

Roossinck, Marilyn J., Darren P. Martin, and Philippe Roumagnac. "Plant Virus Metagenomics: Advances in Virus Discovery." Phytopathology® 105, no. 6 (June 2015): 716–27. http://dx.doi.org/10.1094/phyto-12-14-0356-rvw.

Full text

Abstract:

In recent years plant viruses have been detected from many environments, including domestic and wild plants and interfaces between these systems—aquatic sources, feces of various animals, and insects. A variety of methods have been employed to study plant virus biodiversity, including enrichment for virus-like particles or virus-specific RNA or DNA, or the extraction of total nucleic acids, followed by next-generation deep sequencing and bioinformatic analyses. All of the methods have some shortcomings, but taken together these studies reveal our surprising lack of knowledge about plant viruses and point to the need for more comprehensive studies. In addition, many new viruses have been discovered, with most virus infections in wild plants appearing asymptomatic, suggesting that virus disease may be a byproduct of domestication. For plant pathologists these studies are providing useful tools to detect viruses, and perhaps to predict future problems that could threaten cultivated plants.

APA, Harvard, Vancouver, ISO, and other styles

27

German, Thomas L., Marcé D. Lorenzen, Nathaniel Grubbs, and Anna E. Whitfield. "New Technologies for Studying Negative-Strand RNA Viruses in Plant and Arthropod Hosts." Molecular Plant-Microbe Interactions® 33, no. 3 (March 2020): 382–93. http://dx.doi.org/10.1094/mpmi-10-19-0281-fi.

Full text

Abstract:

The plant viruses in the phylum Negarnaviricota, orders Bunyavirales and Mononegavirales, have common features of single-stranded, negative-sense RNA genomes and replication in the biological vector. Due to the similarities in biology, comparative functional analysis in plant and vector hosts is helpful for understanding host–virus interactions for negative-strand RNA viruses. In this review, we will highlight recent technological advances that are breaking new ground in the study of these recalcitrant virus systems. The development of infectious clones for plant rhabdoviruses and bunyaviruses is enabling unprecedented examination of gene function in plants and these advances are also being transferred to study virus biology in the vector. In addition, genome and transcriptome projects for critical nonmodel arthropods has enabled characterization of insect response to viruses and identification of interacting proteins. Functional analysis of genes using genome editing will provide future pathways for further study of the transmission cycle and new control strategies for these viruses and their vectors.

APA, Harvard, Vancouver, ISO, and other styles

28

Bucher, Etienne, Dick Lohuis, Pieter M. J. A. van Poppel, Christina Geerts-Dimitriadou, Rob Goldbach, and Marcel Prins. "Multiple virus resistance at a high frequency using a single transgene construct." Journal of General Virology 87, no. 12 (December 1, 2006): 3697–701. http://dx.doi.org/10.1099/vir.0.82276-0.

Full text

Abstract:

RNA silencing is a natural antiviral defence in plants, which can be exploited in transgenic plants for preprogramming virus recognition and ensuring enhanced resistance. By arranging viral transgenes as inverted repeats it is thus possible to obtain strong repression of incoming viruses. Due to the high sequence specificity of RNA silencing, this technology has hitherto been limited to the targeting of single viruses. Here it is shown that efficient simultaneous targeting of four different tospoviruses can be achieved by using a single small transgene based on the production of minimal sized chimaeric cassettes. Due to simultaneous RNA silencing, as demonstrated by specific siRNA accumulation, the transgenic expression of these cassettes rendered up to 82 % of the transformed plant lines heritably resistant against all four viruses. Thus RNA silencing can be further improved for high frequency multiple virus resistance by combining small RNA fragments from a series of target viruses.

APA, Harvard, Vancouver, ISO, and other styles

29

Valkonen, J. P. T. "Mechanisms of resistance to viruses." Plant Protection Science 38, SI 1 - 6th Conf EFPP 2002 (January 1, 2002): S132—S135. http://dx.doi.org/10.17221/10337-pps.

Full text

Abstract:

Resistance associated with a hypersensitive response (HR) and subsequent development of necrotic lesions (cell death) at the sites of virus infection can restrict virus movement in plants. Genes for HR are dominant and act on a gene-for-gene basis. Many viral proteins triggering HR have been identified. Also, several genes for HR-based virus resistance, or virus-induced cell death without resistance, have been isolated and characterized in plants, which provides novel insights to the mechanisms of virus resistance. Another international, major research frontier has formed more recently around RNA silencing, a universal RNA surveillance system and inducible virus defence mechanism in multicellular organisms. Many viral proteins interfere with different phases of RNA silencing. The data provide novel insights to break-down of resistance in mixed virus infections (viral synergism), resistance to virus movement, and recovery of plants from virus infection.

APA, Harvard, Vancouver, ISO, and other styles

30

Lewsey, Mathew G., and John P. Carr. "Effects of DICER-like proteins 2, 3 and 4 on cucumber mosaic virus and tobacco mosaic virus infections in salicylic acid-treated plants." Journal of General Virology 90, no. 12 (December 1, 2009): 3010–14. http://dx.doi.org/10.1099/vir.0.014555-0.

Full text

Abstract:

Salicylic acid (SA)-mediated resistance and RNA silencing are both important plant antiviral defence mechanisms. To investigate overlap between these resistance phenomena, we examined the ability of mutant Arabidopsis thaliana plants lacking DICER-like (DCL) endoribonucleases 2, 3 and 4 to exhibit SA-induced defence. We found that in dcl2/3/4 triple mutant plants, treatment with exogenous SA stimulated resistance to two positive-sense RNA viruses: cucumber mosaic virus and tobacco mosaic virus. We conclude that DCLs 2, 3 and 4, which are the predominant DCL endoribonucleases involved in silencing of positive-sense RNA viruses, are not required for effective SA-induced resistance to these viruses. However, the findings do not exclude RNA silencing from making a contribution to SA-mediated resistance in wild-type plants.

APA, Harvard, Vancouver, ISO, and other styles

31

Pinheiro, Patricia V., Jennifer R. Wilson, Yi Xu, Yi Zheng, Ana Rita Rebelo, Somayeh Fattah-Hosseini, Angela Kruse, et al. "Plant Viruses Transmitted in Two Different Modes Produce Differing Effects on Small RNA-Mediated Processes in Their Aphid Vector." Phytobiomes Journal 3, no. 1 (January 2019): 71–81. http://dx.doi.org/10.1094/pbiomes-10-18-0045-r.

Full text

Abstract:

Transmission of plant viruses by aphids involves multitrophic interactions among host plants, aphid vectors, and plant viruses. Here, we used small RNA (sRNA) sequencing to visualize the sRNA response of Myzus persicae to two plant viruses that M. persicae transmits in different modes: the nonpersistent Potato virus Y (PVY) versus the persistent Potato leafroll virus (PLRV). Aphids exposed to PLRV produced significantly less 22 mers aligned to the aphid genome, and an abundance of 26 to 27 mers, many of which were predicted to be piRNA. Additionally, expression of Buchnera aphidicola tRNA-derived sRNAs was influenced by PLRV and, to a lesser extent, PVY, suggesting that plant viruses alter the aphid-endosymbiont relationship. Finally, aphids exposed to PLRV-infected plants generated an abundance of unusually long sRNAs and a reduced number of 22 mers against an aphid virus, Myzus persicae densovirus (MpDNV) and had higher MpDNV titer. Expression of the PLRV silencing suppressor P0 in plants recapitulated the increase in MpDNV titer in the absence of PLRV infection. Our results show that plant viruses transmitted in two different modes cause distinct effects on their vector with regards to post-transcriptional gene regulation, symbiosis with Buchnera, and the antiviral immune response of aphids to an aphid-infecting densovirus.

APA, Harvard, Vancouver, ISO, and other styles

32

Kashif, M., S. Pietilä, K. Artola, R. A. C. Jones, A. K. Tugume, V. Mäkinen, and J. P. T. Valkonen. "Detection of Viruses in Sweetpotato from Honduras and Guatemala Augmented by Deep-Sequencing of Small-RNAs." Plant Disease 96, no. 10 (October 2012): 1430–37. http://dx.doi.org/10.1094/pdis-03-12-0268-re.

Full text

Abstract:

Sweetpotato (Ipomoea batatas) plants become infected with over 30 RNA or DNA viruses in different parts of the world but little is known about viruses infecting sweetpotato crops in Central America, the center of sweetpotato domestication. Small-RNA deep-sequencing (SRDS) analysis was used to detect viruses in sweetpotato in Honduras and Guatemala, which detected Sweet potato feathery mottle virus strain RC and Sweet potato virus C (Potyvirus spp.), Sweet potato chlorotic stunt virus strain WA (SPCSV-WA; Crinivirus sp.), Sweet potato leaf curl Georgia virus (Begomovirus sp.), and Sweet potato pakakuy virus strain B (synonym: Sweet potato badnavirus B). Results were confirmed by polymerase chain reaction and sequencing of the amplicons. Four viruses were detected in a sweetpotato sample from the Galapagos Islands. Serological assays available to two of the five viruses gave results consistent with those obtained by SRDS, and were negative for six additional sweetpotato viruses tested. Plants coinfected with SPCSV-WA and one to two other viruses displayed severe foliar symptoms of epinasty and leaf malformation, purpling, vein banding, or chlorosis. The results suggest that SRDS is suitable for use as a universal, robust, and reliable method for detection of plant viruses, and especially useful for determining virus infections in crops infected with a wide range of unrelated viruses.

APA, Harvard, Vancouver, ISO, and other styles

33

Hong, Hao, Chunli Wang, Ying Huang, Min Xu, Jiaoling Yan, Mingfeng Feng, Jia Li, et al. "Antiviral RISC mainly targets viral mRNA but not genomic RNA of tospovirus." PLOS Pathogens 17, no. 7 (July 28, 2021): e1009757. http://dx.doi.org/10.1371/journal.ppat.1009757.

Full text

Abstract:

Antiviral RNA silencing/interference (RNAi) of negative-strand (-) RNA plant viruses (NSVs) has been studied less than for single-stranded, positive-sense (+)RNA plant viruses. From the latter, genomic and subgenomic mRNA molecules are targeted by RNAi. However, genomic RNA strands from plant NSVs are generally wrapped tightly within viral nucleocapsid (N) protein to form ribonucleoproteins (RNPs), the core unit for viral replication, transcription and movement. In this study, the targeting of the NSV tospoviral genomic RNA and mRNA molecules by antiviral RNA-induced silencing complexes (RISC) was investigated, in vitro and in planta. RISC fractions isolated from tospovirus-infected N. benthamiana plants specifically cleaved naked, purified tospoviral genomic RNAs in vitro, but not genomic RNAs complexed with viral N protein. In planta RISC complexes, activated by a tobacco rattle virus (TRV) carrying tospovirus NSs or Gn gene fragments, mainly targeted the corresponding viral mRNAs and hardly genomic (viral and viral-complementary strands) RNA assembled into RNPs. In contrast, for the (+)ssRNA cucumber mosaic virus (CMV), RISC complexes, activated by TRV carrying CMV 2a or 2b gene fragments, targeted CMV genomic RNA. Altogether, the results indicated that antiviral RNAi primarily targets tospoviral mRNAs whilst their genomic RNA is well protected in RNPs against RISC-mediated cleavage. Considering the important role of RNPs in the replication cycle of all NSVs, the findings made in this study are likely applicable to all viruses belonging to this group.

APA, Harvard, Vancouver, ISO, and other styles

34

Li, Lulu, Hehong Zhang, Changhai Chen, Haijian Huang, Xiaoxiang Tan, Zhongyan Wei, Junmin Li, et al. "A class of independently evolved transcriptional repressors in plant RNA viruses facilitates viral infection and vector feeding." Proceedings of the National Academy of Sciences 118, no. 11 (March 8, 2021): e2016673118. http://dx.doi.org/10.1073/pnas.2016673118.

Full text

Abstract:

Plant viruses employ diverse virulence strategies to achieve successful infection, but there are few known general strategies of viral pathogenicity and transmission used by widely different plant viruses. Here, we report a class of independently evolved virulence factors in different plant RNA viruses which possess active transcriptional repressor activity. Rice viruses in the genera Fijivirus, Tenuivirus, and Cytorhabdovirus all have transcriptional repressors that interact in plants with the key components of jasmonic acid (JA) signaling, namely mediator subunit OsMED25, OsJAZ proteins, and OsMYC transcription factors. These transcriptional repressors can directly disassociate the OsMED25-OsMYC complex, inhibit the transcriptional activation of OsMYC, and then combine with OsJAZ proteins to cooperatively attenuate the JA pathway in a way that benefits viral infection. At the same time, these transcriptional repressors efficiently enhanced feeding by the virus insect vectors by repressing JA signaling. Our findings reveal a common strategy in unrelated plant viruses in which viral transcriptional repressors hijack and repress the JA pathway in favor of both viral pathogenicity and vector transmission.

APA, Harvard, Vancouver, ISO, and other styles

35

Foong, Siew-Liang, and Kyung-Hee Paek. "Capsicum annum Hsp26.5 promotes defense responses against RNA viruses via ATAF2 but is hijacked as a chaperone for tobamovirus movement protein." Journal of Experimental Botany 71, no. 19 (July 8, 2020): 6142–58. http://dx.doi.org/10.1093/jxb/eraa320.

Full text

Abstract:

Abstract The expression of Capsicum annuum HEAT SHOCK PROTEIN 26.5 (CaHsp26.5) was triggered by the inoculation of Tobacco mosaic virus pathotype P0 (TMV-P0) but its function in the defense response of plants is unknown. We used gene silencing and overexpression approaches to investigate the effect of CaHsp26.5 expression on different plant RNA viruses. Moreover, we performed protein–protein and protein–RNA interaction assays to study the mechanism of CaHsp26.5 function. CaHsp26.5 binding to a short poly-cytosine motif in the 3'-untranslated region of the genome of some viruses triggers the expression of several defense-related genes such as PATHOGENESIS-RELATED GENE 1 with the help of a transcription factor, NAC DOMAIN-CONTAINING PROTEIN 81 (ATAF2). Thus, an elevated CaHsp26.5 level was accompanied by increased plant resistance against plant viruses such as Cucumber mosaic virus strain Korea. However, the movement proteins of Pepper mild mottle virus pathotype P1,2,3 and TMV-P0 were shown to be able to interact with CaHsp26.5 to maintain the integrity of their proteins. Our work shows CaHsp26.5 as a positive player in the plant defense response against several plant RNA viruses. However, some tobamoviruses can hijack CaHsp26.5’s chaperone activity for their own benefit.

APA, Harvard, Vancouver, ISO, and other styles

36

OKUNO, T. "Replication mechanisms of plant RNA viruses —Current understanding and perspective—." Japanese Journal of Phytopathology 78, no. 3 (2012): 141–44. http://dx.doi.org/10.3186/jjphytopath.78.141.

Full text

APA, Harvard, Vancouver, ISO, and other styles

37

VOINNET, O. "RNA silencing as a plant immune system against viruses." Trends in Genetics 17, no. 8 (August 1, 2001): 449–59. http://dx.doi.org/10.1016/s0168-9525(01)02367-8.

Full text

APA, Harvard, Vancouver, ISO, and other styles

38

Carrington, James C., Kristin D. Kasschau, and Lisa K. Johansen. "Activation and Suppression of RNA Silencing by Plant Viruses." Virology 281, no. 1 (March 2001): 1–5. http://dx.doi.org/10.1006/viro.2000.0812.

Full text

APA, Harvard, Vancouver, ISO, and other styles

39

Xu, Min, Magdalena J. Mazur, Xiaorong Tao, and Richard Kormelink. "Cellular RNA Hubs: Friends and Foes of Plant Viruses." Molecular Plant-Microbe Interactions® 33, no. 1 (January 2020): 40–54. http://dx.doi.org/10.1094/mpmi-06-19-0161-fi.

Full text

Abstract:

RNA granules are dynamic cellular foci that are widely spread in eukaryotic cells and play essential roles in cell growth and development, and immune and stress responses. Different types of granules can be distinguished, each with a specific function and playing a role in, for example, RNA transcription, modification, processing, decay, translation, and arrest. By means of communication and exchange of (shared) components, they form a large regulatory network in cells. Viruses have been reported to interact with one or more of these either cytoplasmic or nuclear granules, and act either proviral, to enable and support viral infection and facilitate viral movement, or antiviral, protecting or clearing hosts from viral infection. This review describes an overview and recent progress on cytoplasmic and nuclear RNA granules and their interplay with virus infection, first in animal systems and as a prelude to the status and current developments on plant viruses, which have been less well studied on this thus far.

APA, Harvard, Vancouver, ISO, and other styles

40

Kim, Nam-Yeon, Hyo-Jeong Lee, Hong-Sup Kim, Su-Heon Lee, Jae-Sun Moon, and Rae-Dong Jeong. "Identification of Plant Viruses Infecting Pear Using RNA Sequencing." Plant Pathology Journal 37, no. 3 (June 1, 2021): 258–67. http://dx.doi.org/10.5423/ppj.oa.01.2021.0009.

Full text

APA, Harvard, Vancouver, ISO, and other styles

41

Gaffar, Fatima Yousif, and Aline Koch. "Catch Me If You Can! RNA Silencing-Based Improvement of Antiviral Plant Immunity." Viruses 11, no. 7 (July 23, 2019): 673. http://dx.doi.org/10.3390/v11070673.

Full text

Abstract:

Viruses are obligate parasites which cause a range of severe plant diseases that affect farm productivity around the world, resulting in immense annual losses of yield. Therefore, control of viral pathogens continues to be an agronomic and scientific challenge requiring innovative and ground-breaking strategies to meet the demands of a growing world population. Over the last decade, RNA silencing has been employed to develop plants with an improved resistance to biotic stresses based on their function to provide protection from invasion by foreign nucleic acids, such as viruses. This natural phenomenon can be exploited to control agronomically relevant plant diseases. Recent evidence argues that this biotechnological method, called host-induced gene silencing, is effective against sucking insects, nematodes, and pathogenic fungi, as well as bacteria and viruses on their plant hosts. Here, we review recent studies which reveal the enormous potential that RNA-silencing strategies hold for providing an environmentally friendly mechanism to protect crop plants from viral diseases.

APA, Harvard, Vancouver, ISO, and other styles

42

Shrestha, Nipin, and Józef J. Bujarski. "Long Noncoding RNAs in Plant Viroids and Viruses: A Review." Pathogens 9, no. 9 (September 18, 2020): 765. http://dx.doi.org/10.3390/pathogens9090765.

Full text

Abstract:

Infectious long-noncoding (lnc) RNAs related to plants can be of both viral and non-viral origin. Viroids are infectious plant lncRNAs that are not related to viruses and carry the circular, single-stranded, non-coding RNAs that replicate with host enzymatic activities via a rolling circle mechanism. Viroids interact with host processes in complex ways, emerging as one of the most productive tools for studying the functions of lncRNAs. Defective (D) RNAs, another category of lnc RNAs, are found in a variety of plant RNA viruses, most of which are noncoding. These are derived from and are replicated by the helper virus. D RNA-virus interactions evolve into mutually beneficial combinations, enhancing virus fitness via competitive advantages of moderated symptoms. Yet the satellite RNAs are single-stranded and include either large linear protein-coding ss RNAs, small linear ss RNAs, or small circular ss RNAs (virusoids). The satellite RNAs lack sequence homology to the helper virus, but unlike viroids need a helper virus to replicate and encapsidate. They can attenuate symptoms via RNA silencing and enhancement of host defense, but some can be lethal as RNA silencing suppressor antagonists. Moreover, selected viruses produce lncRNAs by incomplete degradation of genomic RNAs. They do not replicate but may impact viral infection, gene regulation, and cellular functions. Finally, the host plant lncRNAs can also contribute during plant-virus interactions, inducing plant defense and the regulation of gene expression, often in conjunction with micro and/or circRNAs.

APA, Harvard, Vancouver, ISO, and other styles

43

Zhang, L., and W. G. Langenberg. "Unusual Mitochondrial Aggregation with Virus in Infected Transgenic Plants." Microscopy and Microanalysis 4, S2 (July 1998): 1178–79. http://dx.doi.org/10.1017/s1431927600026015.

Full text

Abstract:

Viruses grouped in the family Potyviridaeare long flexious rod-shaped viruses and cause the most damage of all plant vims groups. They possess a single stranded positive sense RNA genome that encodes a single polyprotein product which yields eight or more proteins by secondary processing. Considerable efforts have been made to transform plants with DNA or RNA sequences of these proteins in hopes of obtaining pathogen-derived resistant plants. Hull has suggested that a close assessment of the risks involved in field release of transformed plants would be desirable. However, to our knowledge, there have been no published reports regarding properties of viruses that do infect some transformed plants. We describe here an ultrastructural appearance of transgenic plant cells infected by potato virus Y (PVY) (ATCC PV No. 50; PVY-50) and unusual mitochondrial aggregation with the virus.

APA, Harvard, Vancouver, ISO, and other styles

44

Varanda, Carla M. R., Maria do Rosário Félix, Maria Doroteia Campos, Mariana Patanita, and Patrick Materatski. "Plant Viruses: From Targets to Tools for CRISPR." Viruses 13, no. 1 (January 19, 2021): 141. http://dx.doi.org/10.3390/v13010141.

Full text

Abstract:

Plant viruses cause devastating diseases in many agriculture systems, being a serious threat for the provision of adequate nourishment to a continuous growing population. At the present, there are no chemical products that directly target the viruses, and their control rely mainly on preventive sanitary measures to reduce viral infections that, although important, have proved to be far from enough. The current most effective and sustainable solution is the use of virus-resistant varieties, but which require too much work and time to obtain. In the recent years, the versatile gene editing technology known as CRISPR/Cas has simplified the engineering of crops and has successfully been used for the development of viral resistant plants. CRISPR stands for ‘clustered regularly interspaced short palindromic repeats’ and CRISPR-associated (Cas) proteins, and is based on a natural adaptive immune system that most archaeal and some bacterial species present to defend themselves against invading bacteriophages. Plant viral resistance using CRISPR/Cas technology can been achieved either through manipulation of plant genome (plant-mediated resistance), by mutating host factors required for viral infection; or through manipulation of virus genome (virus-mediated resistance), for which CRISPR/Cas systems must specifically target and cleave viral DNA or RNA. Viruses present an efficient machinery and comprehensive genome structure and, in a different, beneficial perspective, they have been used as biotechnological tools in several areas such as medicine, materials industry, and agriculture with several purposes. Due to all this potential, it is not surprising that viruses have also been used as vectors for CRISPR technology; namely, to deliver CRISPR components into plants, a crucial step for the success of CRISPR technology. Here we discuss the basic principles of CRISPR/Cas technology, with a special focus on the advances of CRISPR/Cas to engineer plant resistance against DNA and RNA viruses. We also describe several strategies for the delivery of these systems into plant cells, focusing on the advantages and disadvantages of the use of plant viruses as vectors. We conclude by discussing some of the constrains faced by the application of CRISPR/Cas technology in agriculture and future prospects.

APA, Harvard, Vancouver, ISO, and other styles

45

Newburn, Laura R., and K. Andrew White. "Trans-Acting RNA–RNA Interactions in Segmented RNA Viruses." Viruses 11, no. 8 (August 14, 2019): 751. http://dx.doi.org/10.3390/v11080751.

Full text

Abstract:

RNA viruses represent a large and important group of pathogens that infect a broad range of hosts. Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single virus particle. These divided genomes come in different forms, including double-stranded RNA, coding-sense single-stranded RNA, and noncoding single-stranded RNA. Genera that possess these genome types include, respectively, Orbivirus (e.g., Bluetongue virus), Dianthovirus (e.g., Red clover necrotic mosaic virus) and Alphainfluenzavirus (e.g., Influenza A virus). Despite their distinct genomic features and diverse host ranges (i.e., animals, plants, and humans, respectively) each of these viruses uses trans-acting RNA–RNA interactions (tRRIs) to facilitate co-packaging of their segmented genome. The tRRIs occur between different viral genome segments and direct the selective packaging of a complete genome complement. Here we explore the current state of understanding of tRRI-mediated co-packaging in the abovementioned viruses and examine other known and potential functions for this class of RNA–RNA interaction.

APA, Harvard, Vancouver, ISO, and other styles

46

Wang, Xiao-Wei, and Stéphane Blanc. "Insect Transmission of Plant Single-Stranded DNA Viruses." Annual Review of Entomology 66, no. 1 (January 7, 2021): 389–405. http://dx.doi.org/10.1146/annurev-ento-060920-094531.

Full text

Abstract:

Of the approximately 1,200 plant virus species that have been described to date, nearly one-third are single-stranded DNA (ssDNA) viruses, and all are transmitted by insect vectors. However, most studies of vector transmission of plant viruses have focused on RNA viruses. All known plant ssDNA viruses belong to two economically important families, Geminiviridae and Nanoviridae, and in recent years, there have been increased efforts to understand whether they have evolved similar relationships with their respective insect vectors. This review describes the current understanding of ssDNA virus–vector interactions, including how these viruses cross insect vector cellular barriers, the responses of vectors to virus circulation, the possible existence of viral replication within insect vectors, and the three-way virus–vector–plant interactions. Despite recent breakthroughs in our understanding of these viruses, many aspects of plant ssDNA virus transmission remain elusive. More effort is needed to identify insect proteins that mediate the transmission of plant ssDNA viruses and to understand the complex virus–insect–plant three-way interactions in the field during natural infection.

APA, Harvard, Vancouver, ISO, and other styles

47

Wolf, Yuri I., Sukrit Silas, Yongjie Wang, Shuang Wu, Michael Bocek, Darius Kazlauskas, Mart Krupovic, Andrew Fire, Valerian V. Dolja, and Eugene V. Koonin. "Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome." Nature Microbiology 5, no. 10 (July 20, 2020): 1262–70. http://dx.doi.org/10.1038/s41564-020-0755-4.

Full text

Abstract:

Abstract RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.

APA, Harvard, Vancouver, ISO, and other styles

48

Hill, Sam R., Reidun Twarock, and Eric C. Dykeman. "The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus." PLOS Computational Biology 17, no. 8 (August 24, 2021): e1009306. http://dx.doi.org/10.1371/journal.pcbi.1009306.

Full text

Abstract:

The vast majority of viruses consist of a nucleic acid surrounded by a protective icosahedral protein shell called the capsid. During viral infection of a host cell, the timing and efficiency of the assembly process is important for ensuring the production of infectious new progeny virus particles. In the class of single-stranded RNA (ssRNA) viruses, the assembly of the capsid takes place in tandem with packaging of the ssRNA genome in a highly cooperative co-assembly process. In simple ssRNA viruses such as the bacteriophage MS2 and small RNA plant viruses such as STNV, this cooperative process results from multiple interactions between the protein shell and sites in the RNA genome which have been termed packaging signals. Using a stochastic assembly algorithm which includes cooperative interactions between the protein shell and packaging signals in the RNA genome, we demonstrate that highly efficient assembly of STNV capsids arises from a set of simple local rules. Altering the local assembly rules results in different nucleation scenarios with varying assembly efficiencies, which in some cases depend strongly on interactions with RNA packaging signals. Our results provide a potential simple explanation based on local assembly rules for the ability of some ssRNA viruses to spontaneously assemble around charged polymers and other non-viral RNAs in vitro.

APA, Harvard, Vancouver, ISO, and other styles

49

Shanmugam, Ganesh, Prasad L. Polavarapu, Amy Kendall, and Gerald Stubbs. "Structures of plant viruses from vibrational circular dichroism." Journal of General Virology 86, no. 8 (August 1, 2005): 2371–77. http://dx.doi.org/10.1099/vir.0.81055-0.

Full text

Abstract:

Vibrational circular dichroism (VCD) spectra in the amide I and II regions have been measured for viruses for the first time. VCD spectra were recorded for films prepared from aqueous buffer solutions and also for solutions using D2O buffers at pH 8. Investigations of four filamentous plant viruses, Tobacco mosaic virus (TMV), Papaya mosaic virus, Narcissus mosaic virus (NMV) and Potato virus X (PVX), as well as a deletion mutant of PVX, are described in this paper. The film VCD spectra of the viruses clearly revealed helical structures in the virus coat proteins; the nucleic acid bases present in the single-stranded RNA could also be characterized. In contrast, the solution VCD spectra showed the characteristic VCD bands for α-helical structures in the coat proteins but not for RNA. Both sets of results clearly indicated that the coat protein conformations are dominated by helical structures, in agreement with earlier reports. VCD results also indicated that the coat protein structures in PVX and NMV are similar to each other and somewhat different from that of TMV. The present study demonstrates the feasibility of measuring VCD spectra for viruses and extracting structural information from these spectra.

APA, Harvard, Vancouver, ISO, and other styles

50

Jooste, T. L., M. Visser, G. Cook, J. T. Burger, and H. J. Maree. "In Silico Probe-Based Detection of Citrus Viruses in NGS Data." Phytopathology® 107, no. 8 (August 2017): 988–93. http://dx.doi.org/10.1094/phyto-10-16-0379-r.

Full text

Abstract:

The conservation of plant biosecurity relies on the rapid identification of pathogenic organisms, including viruses. With next-generation sequencing (NGS), it is possible to identify multiple viruses within a metagenomic sample. In this study, we explored the use of electronic probes (e-probes) for the simultaneous detection of 11 recognized citrus viruses. E-probes were designed and screened against raw sequencing data to minimize the bioinformatic processing time required. The e-probes were able to accurately detect their cognate viruses in simulated datasets, without any false negatives or positives. The efficiency of the e-probe-based approach was validated with NGS datasets generated from different RNA preparations: double-stranded RNA (dsRNA) from ‘Mexican’ lime infected with different Citrus tristeza virus (CTV) genotypes, dsRNA from field samples, and small RNA and total RNA from grapefruit infected with the CTV T3 genotype. A set of probes was made available that is able to accurately detect CTV in sequence data regardless of the input dataset or the genotype that plants are infected with.

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'RNA viruses Plant viruses'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles