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https://www.readbyqxmd.com/read/27915129/nicotiana-benthamiana-plants-asymptomatically-infected-by-pelargonium-line-pattern-virus-show-unusually-high-accumulation-of-viral-small-rnas-that-is-neither-associated-with-dcl-induction-nor-rdr6-activity
#1
Miryam Pérez-Cañamás, Marta Blanco-Pérez, Javier Forment, Carmen Hernández
Pelargonium line pattern virus (PLPV, Tombusviridae) normally establishes systemic, low-titered and asymptomatic infections in its hosts. This type of interaction may be largely determined by events related to RNA silencing, a major antiviral mechanism in plants. This mechanism is triggered by double or quasi double-stranded (ds) viral RNAs which are cut by DCL ribonucleases into virus small RNAs (vsRNAs). Such vsRNAs are at the core of the silencing process as they guide sequence-specific RNA degradation Host RNA dependent-RNA polymerases (RDRs), and particularly RDR6, strengthen antiviral silencing by promoting biosynthesis of secondary vsRNAs...
December 1, 2016: Virology
https://www.readbyqxmd.com/read/27693919/differential-response-of-cassava-genotypes-to-infection-by-cassava-mosaic-geminiviruses
#2
Paul Kuria, Muhammad Ilyas, Elijah Ateka, Douglas Miano, Justus Onguso, James C Carrington, Nigel J Taylor
Mitigation of cassava mosaic disease (CMD) focuses on the introgression of resistance imparted by the polygenic recessive (CMD1), dominant monogenic (CMD2) and CMD3 loci. The mechanism(s) of resistance they impart, however, remain unknown. Two CMD susceptible and nine CMD resistant cassava genotypes were inoculated by microparticle bombardment with infectious clones of African cassava mosaic virus Cameroon strain (ACMV-CM) and the Kenyan strain K201 of East African cassava mosaic virus (EACMV KE2 [K201]). Genotypes carrying the CMD1 (TMS 30572), CMD2 (TME 3, TME 204 and Oko-iyawo) and CMD3 (TMS 97/0505) resistance mechanisms showed high levels of resistance to ACMV-CM, with viral DNA undetectable by PCR beyond 7days post inoculation (dpi)...
January 2, 2017: Virus Research
https://www.readbyqxmd.com/read/27586073/small-rna-and-methylation-responses-in-susceptible-and-tolerant-landraces-of-cassava-infected-with-south-african-cassava-mosaic-virus
#3
Sarah Jane Rogans, Farhahna Allie, Jason Edward Tirant, Marie Emma Chrissie Rey
Endogenous small RNAs (sRNAs) associated with gene regulatory mechanisms respond to virus infection, and virus-derived small RNAs (vsRNAs) have been implicated in recovery or symptom remission in some geminivirus-host interactions. Transcriptional gene silencing (TGS) (24 nt vsRNAs) and post transcriptional gene silencing (PTGS) (21-23 nt vsRNAs) have been associated with geminivirus intergenic (IR) and coding regions, respectively. In this Illumina deep sequencing study, we compared for the first time, the small RNA response to South African cassava mosaic virus (SACMV) of cassava landrace TME3 which shows a recovery and tolerant phenotype, and T200, a highly susceptible landrace...
October 2, 2016: Virus Research
https://www.readbyqxmd.com/read/27030271/differential-inductions-of-rna-silencing-among-encapsidated-double-stranded-rna-mycoviruses-in-the-white-root-rot-fungus-rosellinia-necatrix
#4
Hajime Yaegashi, Takeo Shimizu, Tsutae Ito, Satoko Kanematsu
UNLABELLED: RNA silencing acts as a defense mechanism against virus infection in a wide variety of organisms. Here, we investigated inductions of RNA silencing against encapsidated double-stranded RNA (dsRNA) fungal viruses (mycoviruses), including a partitivirus (RnPV1), a quadrivirus (RnQV1), a victorivirus (RnVV1), a mycoreovirus (RnMyRV3), and a megabirnavirus (RnMBV1) in the phytopathogenic fungus Rosellinia necatrix Expression profiling of RNA silencing-related genes revealed that a dicer-like gene, an Argonaute-like gene, and two RNA-dependent RNA polymerase genes were upregulated by RnMyRV3 or RnMBV1 infection but not by other virus infections or by constitutive expression of dsRNA in R...
June 15, 2016: Journal of Virology
https://www.readbyqxmd.com/read/26175068/deep-sequencing-and-analysis-of-small-rnas-in-sweet-orange-grafted-on-sour-orange-infected-with-two-citrus-tristeza-virus-isolates-prevalent-in-sicily
#5
Grazia Licciardello, Giuseppe Scuderi, Rosario Ferraro, Annalisa Giampetruzzi, Marcella Russo, Alessandro Lombardo, Domenico Raspagliesi, Moshe Bar-Joseph, Antonino Catara
Two representative isolates of a citrus tristeza virus population in Sicily, SG29 (aggressive) and Bau282 (mild), were sequenced via viral small RNAs (vsRNA) produced in budlings of sweet orange grafted on sour orange. Phylogenetic relationships with Mediterranean and exotic isolates revealed that SG29 clustered within the "VT-Asian" subtype, whereas Bau282 belonged to the cluster T30. The study confirms that molecular data need to be integrated with bio-indexing in order to obtain adequate information for risk assessment...
October 2015: Archives of Virology
https://www.readbyqxmd.com/read/26047586/small-rna-profiles-of-wild-type-and-silencing-suppressor-deficient-tomato-spotted-wilt-virus-infected-nicotiana-benthamiana
#6
Paolo Margaria, Laura Miozzi, Cristina Rosa, Michael J Axtell, Hanu R Pappu, Massimo Turina
Tospoviruses are plant-infecting viruses belonging to the family Bunyaviridae. We used a collection of wild-type, phylogenetically distinct tomato spotted wilt virus isolates and related silencing-suppressor defective mutants to study the effects on the small RNA (sRNA) accumulation during infection of Nicotiana benthamiana. Our data showed that absence of a functional silencing suppressor determined a marked increase of the total amount of viral sRNAs (vsRNAs), and specifically of the 21 nt class. We observed a common under-representation of vsRNAs mapping to the intergenic region of S and M genomic segments, and preferential mapping of the reads against the viral sense open reading frames, with the exception of the NSs gene...
October 2, 2015: Virus Research
https://www.readbyqxmd.com/read/25980760/mammalian-rna-virus-derived-small-rna-biogenesis-and-functional-activity
#7
REVIEW
Kuo-Feng Weng, Po-Ting Hsieh, Hsing-I Huang, Shin-Ru Shih
The role of virus-derived small RNAs (vsRNAs) has been identified as an antiviral mechanism in plants, arthropods, and nematodes. Although mammalian DNA viruses have been observed to encode functional miRNAs, whether RNA virus infection generates functional vsRNAs remains under discussion. This article reviews the most recent reports regarding pathways for generating vsRNAs and the identified vsRNA activity in mammalian cells infected with RNA viruses. We also discuss several hypotheses regarding the roles of mammalian vsRNAs and comment on the potential directions for this research field...
August 2015: Microbes and Infection
https://www.readbyqxmd.com/read/25765188/comparative-analysis-among-the-small-rna-populations-of-source-sink-and-conductive-tissues-in-two-different-plant-virus-pathosystems
#8
Mari Carmen Herranz, Jose Antonio Navarro, Evelien Sommen, Vicente Pallas
BACKGROUND: In plants, RNA silencing plays a fundamental role as defence mechanism against viruses. During last years deep-sequencing technology has allowed to analyze the sRNA profile of a large variety of virus-infected tissues. Nevertheless, the majority of these studies have been restricted to a unique tissue and no comparative analysis between phloem and source/sink tissues has been conducted. In the present work, we compared the sRNA populations of source, sink and conductive (phloem) tissues in two different plant virus pathosystems...
2015: BMC Genomics
https://www.readbyqxmd.com/read/25352551/a-cytoplasmic-rna-virus-generates-functional-viral-small-rnas-and-regulates-viral-ires-activity-in-mammalian-cells
#9
Kuo-Feng Weng, Chuan-Tien Hung, Po-Ting Hsieh, Mei-Ling Li, Guang-Wu Chen, Yu-An Kung, Peng-Nien Huang, Rei-Lin Kuo, Li-Lien Chen, Jing-Yi Lin, Robert Yung-Liang Wang, Shu-Jen Chen, Petrus Tang, Jim-Tong Horng, Hsing-I Huang, Jen-Ren Wang, David M Ojcius, Gary Brewer, Shin-Ru Shih
The roles of virus-derived small RNAs (vsRNAs) have been studied in plants and insects. However, the generation and function of small RNAs from cytoplasmic RNA viruses in mammalian cells remain unexplored. This study describes four vsRNAs that were detected in enterovirus 71-infected cells using next-generation sequencing and northern blots. Viral infection produced substantial levels (>10(5) copy numbers per cell) of vsRNA1, one of the four vsRNAs. We also demonstrated that Dicer is involved in vsRNA1 generation in infected cells...
November 10, 2014: Nucleic Acids Research
https://www.readbyqxmd.com/read/24751798/characterization-of-complete-genome-and-small-rna-profile-of-pagoda-yellow-mosaic-associated-virus-a-novel-badnavirus-in-china
#10
Yilun Wang, Xiaofei Cheng, Xiaoxia Wu, Aiming Wang, Xiaoyun Wu
A new badnavirus was discovered from pagoda trees showing yellow mosaic symptoms on the leaves by high throughput sequencing of small RNAs. The complete genome of this virus was determined to comprise 7424 nucleotides, and the virus shared 40.4-45.1% identity with that of other badnaviruses. The genome encodes five open reading frames (ORFs) on the plus strand, which includes three conserved badnaviral ORFs. These results suggest that this virus is a new member of the genus Badnavirus in the family Caulimoviridae...
August 8, 2014: Virus Research
https://www.readbyqxmd.com/read/24550303/microrna-like-viral-small-rna-from-dengue-virus-2-autoregulates-its-replication-in-mosquito-cells
#11
Mazhar Hussain, Sassan Asgari
MicroRNAs (miRNAs) are small regulatory RNAs that play significant roles in most cellular processes. In the seemingly endless arms race between hosts and pathogens, viruses also encode miRNAs that facilitate successful infection. In search of functional miRNAs or viral small RNAs (vsRNAs) encoded by Dengue virus (DENV), deep sequencing data of virus-infected Aedes aegypti mosquitoes were used. From six vsRNAs, with candidate stem-loop structures in the 5' and 3' untranslated regions of the viral genomic RNA, inhibition of DENV-vsRNA-5 led to significant increases in viral replication...
February 18, 2014: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/24091361/analysis-of-small-rnas-derived-from-tomato-yellow-leaf-curl-sardinia-virus-reveals-a-cross-reaction-between-the-major-viral-hotspot-and-the-plant-host-genome
#12
Laura Miozzi, Vitantonio Pantaleo, József Burgyán, Gian Paolo Accotto, Emanuela Noris
RNA silencing is a defense mechanism exploited by plants against viruses. Upon infection, viral genomes and their transcripts are processed by Dicer-like (DCL) ribonucleases into viral small interfering RNAs (vsRNAs) of 21-24 nucleotides that further guide silencing of viral transcripts. To get an insight into the molecular interaction between tomato and the monopartite phloem-limited begomovirus tomato yellow leaf curl Sardinia virus (TYLCSV), a pathogen inducing a devastating disease of tomato in the Mediterranean region, we characterized by deep sequencing the vsRNA population in virus-infected tomato plants, using a Solexa/Illumina platform...
December 26, 2013: Virus Research
https://www.readbyqxmd.com/read/23642540/small-rna-populations-for-two-unrelated-viruses-exhibit-different-biases-in-strand-polarity-and-proximity-to-terminal-sequences-in-the-insect-host-homalodisca-vitripennis
#13
Raja Sekhar Nandety, Viacheslav Y Fofanov, Heather Koshinsky, Drake C Stenger, Bryce W Falk
Next generation sequence analyses were used to assess virus-derived small RNA (vsRNA) profiles for Homalodisca coagulata virus-1 (HoCV-1), family Dicistroviridae, and Homalodisca vitripennis reovirus (HoVRV), family Reoviridae, from virus-infected H. vitripennis, the glassy-winged sharpshooter. The vsRNA reads were mapped against the monopartite genome of HoCV-1 and all 12 genome segments of HoVRV, and 21nt vsRNAs were most common. However, strikingly contrasting patterns for the HoCV-1 and HoVRV genomic RNAs were observed...
July 20, 2013: Virology
https://www.readbyqxmd.com/read/22944665/biological-and-molecular-analysis-of-the-pathogenic-variant-c3-of-potato-spindle-tuber-viroid-pstvd-evolved-during-adaptation-to-chamomile-matricaria-chamomilla
#14
Jaroslav Matoušek, Jan Stehlík, Jitka Procházková, Lidmila Orctová, Julia Wullenweber, Zoltan Füssy, Josef Kováčik, Ganesh S Duraisamy, Angelika Ziegler, Jörg Schubert, Gerhard Steger
Viroid-caused pathogenesis is a specific process dependent on viroid and host genotype(s), and may involve viroid-specific small RNAs (vsRNAs). We describe a new PSTVd variant C3, evolved through sequence adaptation to the host chamomile (Matricaria chamomilla) after biolistic inoculation with PSTVd-KF440-2, which causes extraordinary strong ('lethal') symptoms. The deletion of a single adenine A in the oligoA stretch of the pathogenicity (P) domain appears characteristic of PSTVd-C3. The pathogenicity and the vsRNA pool of PSTVd-C3 were compared to those of lethal variant PSTVd-AS1, from which PSTVd-C3 differs by five mutations located in the P domain...
July 2012: Biological Chemistry
https://www.readbyqxmd.com/read/22617880/viroid-specific-small-rna-in-plant-disease
#15
REVIEW
Christian Hammann, Gerhard Steger
Viroids are the smallest autonomous infectious nucleic acids known today. They are non-coding, unencapsidated, circular RNAs with sizes ranging from 250 to 400 nucleotides and infect certain plants. These RNAs are transcribed by rolling-circle mechanisms in the plant host's nuclei (Pospiviroidae) or chloroplasts (Avsunviroidae). Since viroids lack any open reading frame, their pathogenicity has for a long time been a conundrum. Recent findings, however, show that viroid infection is associated with the appearance of viroid-specific small RNA (vsRNA)...
June 2012: RNA Biology
https://www.readbyqxmd.com/read/21378120/massive-production-of-small-rnas-from-a-non-coding-region-of-cauliflower-mosaic-virus-in-plant-defense-and-viral-counter-defense
#16
Todd Blevins, Rajendran Rajeswaran, Michael Aregger, Basanta K Borah, Mikhail Schepetilnikov, Loïc Baerlocher, Laurent Farinelli, Frederick Meins, Thomas Hohn, Mikhail M Pooggin
To successfully infect plants, viruses must counteract small RNA-based host defense responses. During infection of Arabidopsis, Cauliflower mosaic pararetrovirus (CaMV) is transcribed into pregenomic 35S and subgenomic 19S RNAs. The 35S RNA is both reverse transcribed and also used as an mRNA with highly structured 600 nt leader. We found that this leader region is transcribed into long sense- and antisense-RNAs and spawns a massive quantity of 21, 22 and 24 nt viral small RNAs (vsRNAs), comparable to the entire complement of host-encoded small-interfering RNAs and microRNAs...
July 2011: Nucleic Acids Research
https://www.readbyqxmd.com/read/21087089/characterization-of-plant-mirnas-and-small-rnas-derived-from-potato-spindle-tuber-viroid-pstvd-in-infected-tomato
#17
Natalie Diermann, Jaroslav Matoušek, Markus Junge, Detlev Riesner, Gerhard Steger
To defend against invading pathogens, plants possess RNA silencing mechanisms involving small RNAs (miRNAs, siRNAs). Also viroids - plant infectious, non-coding, unencapsidated RNA - cause the production of viroid-specific small RNAs (vsRNA), but viroids do escape the cytoplasmic silencing mechanism. Viroids with minor sequence variations can produce different symptoms in infected plants, suggesting an involvement of vsRNAs in symptom production. We analyzed by deep sequencing the spectrum of vsRNAs induced by the PSTVd strain AS1, which causes strong symptoms such as dwarfing and necrosis upon infection of tomato plants cv Rutgers...
December 2010: Biological Chemistry
https://www.readbyqxmd.com/read/20831405/antiviral-role-of-plant-encoded-rna-dependent-rna-polymerases-revisited-with-deep-sequencing-of-small-interfering-rnas-of-virus-origin
#18
REVIEW
Feng Qu
Several recent studies profiled virus-specific small interfering RNAs (vsRNAs) using next generation sequencing platforms and compellingly implicated plant-encoded RNA-dependent RNA polymerases (RDR) in vsRNA biogenesis and vsRNA-mediated antiviral defense. Specifically, both RDR1 and RDR6 were found to contribute to the accumulation of vsRNAs in virus-infected cells. While RDR1 was responsible for the majority of vsRNAs in plants infected with three different viruses, RDR6 acted as a surrogate when RDR1 function was disrupted...
October 2010: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/19665162/deep-sequencing-of-plant-viral-small-rnas-reveals-effective-and-widespread-targeting-of-viral-genomes
#19
Livia Donaire, Yu Wang, Daniel Gonzalez-Ibeas, Klaus F Mayer, Miguel A Aranda, César Llave
Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the data set...
September 30, 2009: Virology
https://www.readbyqxmd.com/read/2160856/a-site-specific-self-cleavage-reaction-performed-by-a-novel-rna-in-neurospora-mitochondria
#20
B J Saville, R A Collins
We describe a novel DNA and RNA found in the mitochondria of the Varkud-1c natural isolate of Neurospora. The majority of the RNA, termed VSRNA, is an 881 nucleotide single-stranded circular molecule complementary to one strand of a low copy, double-stranded circular DNA, VSDNA. VSRNA combines some features of the human hepatitis delta virus, group I introns, retroelements, and plant viral satellite RNAs. VSRNA synthesized in vitro performs a self-cleavage reaction whose products terminate with a 5' hydroxyl and a 2',3' cyclic phosphate...
May 18, 1990: Cell
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