scholarly journals Noncoding RNAs of Plant Viruses and Viroids: Sponges of Host Translation and RNA Interference Machinery

2016 ◽  
Vol 29 (3) ◽  
pp. 156-164 ◽  
Author(s):  
W. Allen Miller ◽  
Ruizhong Shen ◽  
William Staplin ◽  
Pulkit Kanodia
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Mosaic Virus ◽  
Barley Yellow Dwarf Virus ◽  
Plant Viruses ◽  
Cauliflower Mosaic Virus ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Noncoding Sequences ◽  
Yellow Dwarf Virus

Noncoding sequences in plant viral genomes are well-known to control viral replication and gene expression in cis. However, plant viral and viroid noncoding (nc)RNA sequences can also regulate gene expression acting in trans, often acting like ‘sponges’ that bind and sequester host cellular machinery to favor viral infection. Noncoding sequences of small subgenomic (sg)RNAs of Barley yellow dwarf virus (BYDV) and Red clover necrotic mosaic virus (RCNMV) contain a cap-independent translation element that binds translation initiation factor eIF4G. We provide new evidence that a sgRNA of BYDV can globally attenuate host translation, probably by sponging eIF4G. Subgenomic ncRNA of RCNMV is generated via 5′ to 3′ degradation by a host exonuclease. The similar noncoding subgenomic flavivirus (sf)RNA, inhibits the innate immune response, enhancing viral pathogenesis. Cauliflower mosaic virus transcribes massive amounts of a 600-nt ncRNA, which is processed into small RNAs that overwhelm the host’s RNA interference (RNAi) system. Viroids use the host RNAi machinery to generate viroid-derived ncRNAs that inhibit expression of host defense genes by mimicking a microRNA. More examples of plant viral and viroid ncRNAs are likely to be discovered, revealing fascinating new weaponry in the host-virus arms race.

Viruses of New Zealand pasture grasses and legumes: a review

2014 ◽  
Vol 65 (9) ◽  
pp. 841 ◽  
Author(s):  
P. L. Guy
Keyword(s):  
New Zealand ◽  
Mosaic Virus ◽  
Resistance Genes ◽  
Barley Yellow Dwarf Virus ◽  
Cropping Systems ◽  
Alfalfa Mosaic Virus ◽  
Plant Viruses ◽  
Future Research ◽  
Pasture Grasses ◽  
Yellow Dwarf Virus

This article reviews knowledge of 23 plant viruses infecting pasture grasses and legumes in New Zealand. The incidence, ecology and impact of each virus and prospects for control using natural or artificial resistance genes or by vector control is discussed. The most prevalent viruses are Alfalfa mosaic virus and White clover mosaic virus in pasture legumes and Cocksfoot mottle virus, Ryegrass mosaic virus and Barley yellow dwarf virus in pasture grasses. Lucerne Australian latent virus is restricted to the North Island and Red clover necrotic mosaic virus is largely restricted to the South Island. These patterns are likely to be dynamic with ongoing changes in weather patterns, land use, the spread of insect vectors and the continuing introduction of viruses and vectors. The existing and potential threats to 12 pasture species are tabulated and the knowledge gaps for each species highlighted. Control of vectors including aphids, eriophyid mites and soil-borne fungi is probably not economic per se but could be an additional benefit of integrated pest management in pasture and cropping systems. The most cost-effective and practical preventative measures are likely to be the use of virus-tested seed to establish new pastures and the incorporation of resistance genes by conventional breeding or by genetic engineering. Finally, recommendations are made for future research for New Zealand, which is also relevant to other temperate regions of the world.

scholarly journals Identification and Validation of Reference Genes for Normalization of Transcripts from Virus-Infected Arabidopsis thaliana

2011 ◽  
Vol 24 (3) ◽  
pp. 294-304 ◽  
Author(s):  
S. T. Lilly ◽  
R. S. M. Drummond ◽  
M. N. Pearson ◽  
R. M. MacDiarmid
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Mosaic Virus ◽  
Reference Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Plant Viruses ◽  
Cauliflower Mosaic Virus ◽  
Yellow Mosaic Virus ◽  
Complementary Dna ◽  
Family Protein

Real-time quantitative polymerase chain reaction (qPCR) of complementary DNA is now a standard method for studies of gene expression. However, qPCR can identify genuine variation only when transcript quantities are accurately normalized to an appropriate reference. To identify the most reliable reference genes for transcript quantification by qPCR, we describe a systematic evaluation of candidate reference genes of Arabidopsis thaliana ecotype Columbia-0 (Col-0). Twelve genes were selected for transcript stability studies by qPCR of complementary DNA prepared from Arabidopsis leaf tissue infected with one of five plant viruses (Cauliflower mosaic virus, Tobacco mosaic virus, Tomato spotted wilt virus, Turnip mosaic virus, and Turnip yellow mosaic virus). The F-box family protein, elongation factor 1-α, sand family protein, and protodermal factor 2 gene transcripts showed the most stable accumulation, whereas a traditionally used reference gene, Actin8, showed the least stable accumulation as measured by the geNorm algorithm. The data furnish plant virologists with reference genes for normalization of qPCR-derived gene expression in virus-infected Arabidopsis and will be beneficial to the selection and design of primers targeting orthologous genes in other plant species.

Differential inhibition of downstream gene expression by the cauliflower mosaic virus 35S RNA leader

Virus Genes ◽  
1989 ◽  
Vol 3 (1) ◽  
pp. 45-55 ◽  
Author(s):  
Johannes F�tterer ◽  
Karl Gordon ◽  
Pierre Pfeiffer ◽  
H�l�lene Sanfa�on ◽  
Barbara Pisan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mosaic Virus ◽  
Cauliflower Mosaic Virus ◽  
Differential Inhibition ◽  
Downstream Gene Expression ◽  
Cauliflower Mosaic Virus 35S

scholarly journals First Report of Soilborne Wheat Mosaic Virus in the United Kingdom

Plant Disease ◽  
1999 ◽  
Vol 83 (9) ◽  
pp. 880-880 ◽  
Author(s):  
G. R. G. Clover ◽  
D. M. Wright ◽  
C. M. Henry
Keyword(s):  
United Kingdom ◽  
Mosaic Virus ◽  
Barley Yellow Dwarf Virus ◽  
Protein A ◽  
The United States ◽  
Enzyme Linked Immunosorbent Assay ◽  
Barley Yellow Dwarf ◽  
The United Kingdom ◽  
Field Samples ◽  
Yellow Dwarf Virus

In April 1999, severe soilborne wheat mosaic virus (SBWMV) symptoms were observed in five fields of winter wheat (Triticum aestivum, cvs. Consort, Equinox, and Savannah) on one farm in Wiltshire, UK. Affected plants were markedly stunted and had a pale mosaic on their leaf sheaths that developed into bright yellow, parallel streaks on the leaves as they unfolded. Symptomatic plants were found in discrete, elliptical patches ranging in size from a few square meters to nearly a hectare. During May and June, symptoms became less marked as temperatures increased and were restricted to lower leaves. SBWMV was positively identified in all five fields (60 to 170 plants per field) by double (W. Huth, BBA-Braunschweig, Germany; Sanofi Phyto-Diagnostics, Paris) and triple (T. Wilson, SCRI, Dundee, UK) antibody sandwich enzyme-linked immunosorbent assay and by reversetranscription polymerase chain reaction (2). Identification was confirmed by immunoelectron microscopy, including protein-A gold labeling, which revealed bipartite, rod-shaped particles typical of SBWMV. Neither wheat spindle streak mosaic virus nor barley yellow dwarf virus was detected in the field samples, nor was SBWMV detected in any other field subsequently sampled, despite a survey of the surrounding area. Wheat is the most important economic crop in the United Kingdom (≈1.9 million hectares are grown annually, yielding ≈16 million tonnes), but its position is threatened by the economic impact of SBWMV, which has decreased yields by up to 50% in the United States (1). References: (1) T. A. Kucharek and J. H. Walker. Plant Dis. Rep. 58:763, 1974. (2) R. E. Pennington et al. Plant Dis. 77:1202, 1993.

scholarly journals Altered Patterns of Gene Expression in Arabidopsis Elicited by Cauliflower Mosaic Virus (CaMV) Infection and by a CaMV Gene VI Transgene

1999 ◽  
Vol 12 (5) ◽  
pp. 377-384 ◽  
Author(s):  
Chiara Geri ◽  
Edi Cecchini ◽  
Maria E. Giannakou ◽  
Simon N. Covey ◽  
Joel J. Milner
Keyword(s):  
Gene Expression ◽  
Transgenic Plants ◽  
Mosaic Virus ◽  
Rna Binding ◽  
Important Determinant ◽  
Blot Hybridization ◽  
Cauliflower Mosaic Virus ◽  
Slot Blot Hybridization ◽  
Pcr Products ◽  
Polymerase Chain

Cauliflower mosaic virus (CaMV) gene VI protein (P6) is an important determinant of symptom expression. Differential display polymerase chain reaction (PCR) was used to identify changes in gene expression in Arabidopsis elicited by a P6 transgene that causes a symptomatic phenotype. We used slot blot hybridization to measure the abundance of mRNAs complementary to 66 candidate PCR products in transgenic, CaMV-infected, and uninfected Arabidopsis plants. CaMV-infected and P6 transgenic plants showed broadly similar changes in abundance of mRNA species. In P6 transgenic plants we detected 18 PCR products that showed unambiguous changes in abundance plus another 15 that showed more limited changes (approximately twofold). CaMV-infected plants showed 17 unambiguous and 13 limited changes. Down-regulated species include those encoding a novel, phenol-like sulfotransferase, and a glycine-rich, RNA-binding protein. Up-regulated species included ones encoding an myb protein, glycine-rich and stress-inducible proteins, and a member of a previously unreported gene family. CaMV infection causes alterations in expression of many Arabidopsis genes. Transgene-mediated expression of P6 mimics virus infection in its effect on host gene expression, providing a potential mechanism for this process.

scholarly journals Barley yellow dwarf virus-GAV-derived vsiRNAs are involved in the production of wheat leaf yellowing symptoms by targeting chlorophyll synthase

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Chuan Shen ◽  
Caiyan Wei ◽  
Jingyuan Li ◽  
Xudong Zhang ◽  
Qinrong Zhong ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Barley Yellow Dwarf Virus ◽  
Plant Viruses ◽  
Yellow Dwarf ◽  
Dwarf Virus ◽  
Small Rna Sequencing ◽  
Symptom Development ◽  
Barley Yellow Dwarf ◽  
Leaf Yellowing ◽  
Yellow Dwarf Virus

Abstract Background Wheat yellow dwarf virus disease is infected by barley yellow dwarf virus (BYDV), which causes leaf yellowing and dwarfing symptoms in wheat, thereby posing a serious threat to China's food production. The infection of plant viruses can produce large numbers of vsiRNAs, which can target host transcripts and cause symptom development. However, few studies have been conducted to explore the role played by vsiRNAs in the interaction between BYDV-GAV and host wheat plants. Methods In this study, small RNA sequencing was conducted to profile vsiRNAs in BYDV-GAV-infected wheat plants. The putative targets of vsiRNAs were predicted by the bioinformatics software psRNATarget. RT-qPCR and VIGS were employed to identify the function of selected target transcripts. To confirm the interaction between vsiRNA and the target, 5′ RACE was performed to analyze the specific cleavage sites. Results From the sequencing data, we obtained a total of 11,384 detected vsiRNAs. The length distribution of these vsiRNAs was mostly 21 and 22 nt, and an A/U bias was observed at the 5′ terminus. We also observed that the production region of vsiRNAs had no strand polarity. The vsiRNAs were predicted to target 23,719 wheat transcripts. GO and KEGG enrichment analysis demonstrated that these targets were mostly involved in cell components, catalytic activity and plant-pathogen interactions. The results of RT-qPCR analysis showed that most chloroplast-related genes were downregulated in BYDV-GAV-infected wheat plants. Silencing of a chlorophyll synthase gene caused leaf yellowing that was similar to the symptoms exhibited by BYDV-GAV-inoculated wheat plants. A vsiRNA from an overlapping region of BYDV-GAV MP and CP was observed to target chlorophyll synthase for gene silencing. Next, 5′ RACE validated that vsiRNA8856 could cleave the chlorophyll synthase transcript in a sequence-specific manner. Conclusions This report is the first to demonstrate that BYDV-GAV-derived vsiRNAs can target wheat transcripts for symptom development, and the results of this study help to elucidate the molecular mechanisms underlying leaf yellowing after viral infection.

Virus-Dependent and -Independent Responses of Sitobion avenae (Homoptera: Aphididae) Feeding on Wheat Infected by Transmitted and Nontransmitted Viruses at Transcriptomic Level

2019 ◽  
Vol 112 (5) ◽  
pp. 2067-2076
Author(s):  
Dandan Li ◽  
Dan Su ◽  
Zeqian Tong ◽  
Chi Zhang ◽  
Gaisheng Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Barley Yellow Dwarf Virus ◽  
Plant Viruses ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Dwarf Virus ◽  
Illumina Hiseq ◽  
Sequencing Platform ◽  
Yellow Dwarf Virus ◽  
Transcriptomic Level

Abstract Most plant viruses maintain complex interactions with their vector or nonvector insects and can indirectly (via host plants) or directly affect the fitness of insects. However, little is known about the genes involved in the interactions between insects and transmitted or nontransmitted viruses, particularly nontransmitted viruses. Sitobion avenae (Fabricius) is a vector of barley yellow dwarf virus GAV strains (BYDV-GAV), but not a vector of wheat dwarf virus (WDV), which is transmitted by the leafhopper [Psammotettix alienus (Dahlbom)]. In this study, S. avenae was utilized to determine the transcriptomic responses after feeding on wheat infected by each of the two viruses, respectively, using an Illumina Hiseq sequencing platform. The transcriptomic data presented 61,508 genes, of which 854 differentially expressed. Moreover, in addition to sharing 208 genes, the number of differentially expressed genes (DEGs) in S. avenae exposed to BYDV was higher (800) than that when exposed to WDV (262). The DEGs related to the immune system and fitness of S. avenae in response to BYDV-/WDV-infected plants were identified and analyzed using Gene Ontologies (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the number of related DEGs was lower as nonvector than as vector. This study provides the baseline information to further examine molecular mechanisms of how wheat viruses affect S. avenae fitness and immune response either as a vector for BYDV-GAV or as a nonvector for WDV.

Occurrence of Viruses in Wheat in the Great Plains Region, 2008

2009 ◽  
Vol 10 (1) ◽  
pp. 14 ◽  
Author(s):  
Mary Burrows ◽  
Gary Franc ◽  
Charlie Rush ◽  
Tamla Blunt ◽  
Dai Ito ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Great Plains ◽  
Barley Yellow Dwarf Virus ◽  
Average Frequency ◽  
Yellow Dwarf ◽  
Dwarf Virus ◽  
High Plains ◽  
Virus Infections ◽  
Yellow Dwarf Virus ◽  
First Time

Field surveys in 2008 determined the prevalence and diversity of viruses present in the Great Plains wheat crops. Symptomatic plants (n = 754) in nine states were tested for Wheat streak mosaic virus (WSMV), Wheat mosaic virus (WMoV, formerly known as High Plains virus), Triticum mosaic virus (TriMV), Barley yellow dwarf virus-PAV (BYDV-PAV), and Cereal yellow dwarf virus-RPV (CYDV-RPV), using indirect ELISA. Virus prevalence varied greatly, with average frequency of detection highest for WSMV (47%), followed by WMoV (19%), TriMV (17%), BYDV-PAV (7%), and lowest for CYDV-RPV (2%). Most positive plant samples (37%) had one virus present, with decreasing frequencies for co-infection by two (19%), three (5%), or four viruses (1%). TriMV was detected for the first time in Colorado, Nebraska, Oklahoma, South Dakota, Texas, and Wyoming. WMoV was identified for the first time in Montana and Wyoming. Chlorotic streaks were more frequently associated with WSMV, WMoV, and TriMV (R = 0.166 to 0.342; P < 0.05), and stunting was more frequently associated with WMoV (R = 0.142; P = 0.004) or TriMV (R = 0.107; P = 0.033) than WSMV. Symptom severity did not increase with co-infection as compared to single virus infections, with the exception of plants co-infected with mite transmitted viruses in Texas. Accepted for publication 1 May 2009. Published 6 July 2009.

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