scholarly journals Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10096
Author(s):  
Yahya Zakaria Abdou Gaafar ◽  
Heiko Ziebell
Keyword(s):  
In Silico ◽  
Viral Infections ◽  
Control Strategies ◽  
Plant Viruses ◽  
Open Reading Frames ◽  
Tomato Production ◽  
Tomato Plants ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle ◽  
Tomato Microrna

Background Physostegia chlorotic mottle virus (PhCMoV; genus: Alphanucleorhabdovirus, family: Rhabdoviridae) and tomato brown rugose fruit virus (ToBRFV; genus: Tobamovirus, family: Virgaviridae) are newly emerging plant viruses that have a dramatic effect on tomato production. Among various known virus-control strategies, RNAi-mediated defence has shown the potential to protect plants against various pathogens including viral infections. Micro(mi)RNAs play a major role in RNAi-mediated defence. Methods Using in silico analyses, we investigated the possibility of tomato-encoded miRNAs (TomiRNA) to target PhCMoV and ToBRFV genomes using five different algorithms, i.e., miRanda, RNAhybrid, RNA22, Tapirhybrid and psRNATarget. Results The results revealed that 14 loci on PhCMoV and 10 loci on ToBRFV can be targeted by the TomiRNAs based on the prediction of at least three algorithms. Interestingly, one TomiRNA, miR6026, can target open reading frames from both viruses, i.e., the phosphoprotein encoding gene of PhCMoV, and the two replicase components of ToBRFV. There are currently no commercially available PhCMoV- or ToBRFV-resistant tomato varieties, therefore the predicted data provide useful information for the development of PhCMoV- and ToBFRV-resistant tomato plants.

scholarly journals Characterization of Cestrum yellow leaf curling virus: a new member of the family Caulimoviridae

2003 ◽  
Vol 84 (12) ◽  
pp. 3459-3464 ◽  
Author(s):  
Livia Stavolone ◽  
Antonio Ragozzino ◽  
Thomas Hohn
Keyword(s):  
Genomic Sequence ◽  
Infected Plant ◽  
Virus Genome ◽  
Mosaic Disease ◽  
Open Reading Frames ◽  
Primer Binding Site ◽  
Yellow Leaf ◽  
Leaf Curling ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle

Cestrum yellow leaf curling virus (CmYLCV) has been characterized as the aetiological agent of the Cestrum parqui mosaic disease. The virus genome was cloned and the clone was proven to be infectious to C. parqui. The presence of typical viroplasms in virus-infected plant tissue and the information obtained from the complete genomic sequence confirmed CmYLCV as a member of the Caulimoviridae family. All characteristic domains conserved in plant pararetroviruses were found in CmYLCV. Its genome is 8253 bp long and contains seven open reading frames (ORFs). Phylogenetic analysis of the relationships with other members of the Caulimoviridae revealed that CmYLCV is closely related to the Soybean chlorotic mottle virus (SbCMV)-like genus and particularly to SbCMV. However, in contrast to the other members of this genus, the primer-binding site is located in the intercistronic region following ORF Ib rather than within this ORF, and an ORF corresponding to ORF VII is missing.

scholarly journals Responses of Tomatoes Grafting Using Variation of Rootstock against Virus Infection and Tomato Yields

2020 ◽  
Vol 24 (1) ◽  
pp. 98
Author(s):  
Tri Retno Widyastuti ◽  
Sri Sulandari ◽  
Sedyo Hartono ◽  
Triwidodo Arwiyanto
Keyword(s):  
Viral Infection ◽  
Viral Infections ◽  
Field Research ◽  
Viral Diseases ◽  
Specific Primer ◽  
Resistance Response ◽  
Tomato Production ◽  
Tomato Plants ◽  
Randomized Design ◽  
Tomato Chlorosis Virus

Grafting methods on tomato have been done to reduce the infection rate of various pathogens. Begomovirus and Crinivirus are important viruses in tomato plants. The research aimed to determine the resistance response of tomato plants to viral infection, and tomato production. Field research was conducted in Harjobinangun, Pakem, Sleman, Yogyakarta in the endemic area of the viral diseases transmitted by Bemisia tabaci. This experiment used a Completely Randomized Design non-factorial with “Servo” as scion and “Amelia”, “H-7996”, “Mawar” as rootstock. The disease development, presence of viral diseases, and tomato yields were observed. PCR detection using Krusty & Hommr primer successfully amplified Begomovirus DNA bands with an approximate size of 580 bp in tomato plant with interveinal chlorosis, curling, thick, rigid, and stunt symptoms. Chlorotic spots and yellowing symptoms successfully amplified using ToCV-CF/ToCV-CR specific primer for the amplification of Tomato chlorosis virus with DNA band approximately size of 360 bp, whereas using TICV-CF/TICV-CR specific primer could not amplify the virus cDNA. The leaves roll upward with purple interveinal symptoms that were not infected by both viruses. Both viral infections affected the quality of the fruit which indicated by a higher number of abnormal fruits. “Servo” grafted onto “Amelia” and non-grafted Servo were tolerant to viral infection, “Servo” grafted onto “H-7996” or to “Mawar variety were susceptible to viral infection, self-grafted Servo were very susceptible to viral infection. 

scholarly journals Structural Transitions and Energy Landscape for Cowpea Chlorotic Mottle Virus Capsid Mechanics from Nanomanipulation in Vitro and in Silico

2013 ◽  
Vol 105 (8) ◽  
pp. 1893-1903 ◽  
Author(s):  
Olga Kononova ◽  
Joost Snijder ◽  
Melanie Brasch ◽  
Jeroen Cornelissen ◽  
Ruxandra I. Dima ◽  
...  
Keyword(s):  
In Silico ◽  
Energy Landscape ◽  
Mottle Virus ◽  
Structural Transitions ◽  
Virus Capsid ◽  
Cowpea Chlorotic Mottle Virus ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle

scholarly journals Controlling the surface charge of simple viruses

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0255820
Author(s):  
A. L. Duran-Meza ◽  
M. V. Villagrana-Escareño ◽  
J. Ruiz-García ◽  
C. M. Knobler ◽  
W. M. Gelbart
Keyword(s):  
Ionic Strength ◽  
Surface Charge ◽  
Lipid Bilayer ◽  
Colloidal Particles ◽  
Plant Viruses ◽  
Brome Mosaic Virus ◽  
Host Cells ◽  
Cowpea Chlorotic Mottle Virus ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle

The vast majority of plant viruses are unenveloped, i.e., they lack a lipid bilayer that is characteristic of most animal viruses. The interactions between plant viruses, and between viruses and surfaces, properties that are essential for understanding their infectivity and to their use as bionanomaterials, are largely controlled by their surface charge, which depends on pH and ionic strength. They may also depend on the charge of their contents, i.e., of their genes or–in the instance of virus-like particles–encapsidated cargo such as nucleic acid molecules, nanoparticles or drugs. In the case of enveloped viruses, the surface charge of the capsid is equally important for controlling its interaction with the lipid bilayer that it acquires and loses upon leaving and entering host cells. We have previously investigated the charge on the unenveloped plant virus Cowpea Chlorotic Mottle Virus (CCMV) by measurements of its electrophoretic mobility. Here we examine the electrophoretic properties of a structurally and genetically closely related bromovirus, Brome Mosaic Virus (BMV), of its capsid protein, and of its empty viral shells, as functions of pH and ionic strength, and compare them with those of CCMV. From measurements of both solution and gel electrophoretic mobilities (EMs) we find that the isoelectric point (pI) of BMV (5.2) is significantly higher than that of CCMV (3.7), that virion EMs are essentially the same as those of the corresponding empty capsids, and that the same is true for the pIs of the virions and of their cleaved protein subunits. We discuss these results in terms of current theories of charged colloidal particles and relate them to biological processes and the role of surface charge in the design of new classes of drug and gene delivery systems.

scholarly journals Application of Plant Viruses as a Biotemplate for Nanomaterial Fabrication

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2311 ◽  
Author(s):  
Yu Zhang ◽  
Yixin Dong ◽  
Jinhua Zhou ◽  
Xun Li ◽  
Fei Wang
Keyword(s):  
Tobacco Mosaic Virus ◽  
Mosaic Virus ◽  
Size Distribution ◽  
Plant Viruses ◽  
Brome Mosaic Virus ◽  
Cowpea Chlorotic Mottle Virus ◽  
High Uniformity ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle ◽  
Wide Range

Viruses are widely used to fabricate nanomaterials in the field of nanotechnology. Plant viruses are of great interest to the nanotechnology field because of their symmetry, polyvalency, homogeneous size distribution, and ability to self-assemble. This homogeneity can be used to obtain the high uniformity of the templated material and its related properties. In this paper, the variety of nanomaterials generated in rod-like and spherical plant viruses is highlighted for the cowpea chlorotic mottle virus (CCMV), cowpea mosaic virus (CPMV), brome mosaic virus (BMV), and tobacco mosaic virus (TMV). Their recent studies on developing nanomaterials in a wide range of applications from biomedicine and catalysts to biosensors are reviewed.

scholarly journals Genes Ia, II, III, IV and V of Soybean chlorotic mottle virus are essential but the gene Ib product is non-essential for systemic infection

2001 ◽  
Vol 82 (6) ◽  
pp. 1481-1489 ◽  
Author(s):  
Yutaka Takemoto ◽  
Tadaaki Hibi
Keyword(s):  
Mutational Analysis ◽  
Systemic Infection ◽  
Peptide Sequencing ◽  
Cauliflower Mosaic Virus ◽  
Open Reading Frames ◽  
Mottle Virus ◽  
Primer Binding Site ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle ◽  
Infected Cells

Soybean chlorotic mottle virus (SbCMV) is the type species of the genus ‘Soybean chlorotic mottle-like viruses’, within the family Caulimoviridae. The double-stranded DNA genome of SbCMV (8178 bp) contains eight major open reading frames (ORFs). Viral genes essential and non-essential for the replication and movement of SbCMV were investigated by mutational analysis of an infectious 1·3-mer DNA clone. The results indicated that ORFs Ia, II, III, IV and V were essential for systemic infection. The product of ORF Ib was non-essential, although the putative tRNAMet primer-binding site in ORF Ib was proved to be essential. Immunoselection PCR revealed that an ORF Ia deletion mutant was encapsidated in primarily infected cells, indicating that ORF Ia is required for virus movement but not for replication. ORF IV was confirmed to encode a capsid protein by peptide sequencing of the capsid. Analysis of the viral transcripts showed that the SbCMV DNA genome gives rise to a pregenomic RNA and an ORF VI mRNA, as shown in the case of Cauliflower mosaic virus.

scholarly journals A naturally occurring recombinant DNA-A of a typical bipartite begomovirus does not require the cognate DNA-B to infect Nicotiana benthamiana systemically

2003 ◽  
Vol 84 (3) ◽  
pp. 715-726 ◽  
Author(s):  
Rafaelo M. Galvão ◽  
Andrea C. Mariano ◽  
Dirce F. Luz ◽  
Poliane F. Alfenas ◽  
Eduardo C. Andrade ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Recombinant Dna ◽  
Western Hemisphere ◽  
Bipartite Begomovirus ◽  
Virus Species ◽  
Tomato Plants ◽  
Chlorotic Mottle Virus ◽  
Bipartite Genome ◽  
Chlorotic Mottle ◽  
Hybrid Genome

Species of the genus Begomovirus (family Geminiviridae) found in the western hemisphere typically have a bipartite genome that consists of two 2·6 kb DNA genomic components, DNA-A and DNA-B. We have identified and cloned genomic components of a new tomato-infecting begomovirus from Brazil, for which the name Tomato crinkle leaf yellows virus (TCrLYV) is proposed, and a DNA-A variant of Tomato chlorotic mottle virus (ToCMV-[MG-Bt1]). Sequence analysis revealed that TCrLYV was most closely related to ToCMV, although it was sufficiently divergent to be considered a distinct virus species. Furthermore, these closely related viruses induce distinguishable symptoms in tomato plants. With respect to ToCMV-[MG-Bt1] DNA-A, evidence is presented that suggests a recombinant origin. It possesses a hybrid genome on which the replication compatible module (AC1 and replication origin) was probably donated by ToCMV-[BA-Se1] and the remaining sequences appear to have originated from Tomato rugose mosaic virus (ToRMV). Despite the high degree of sequence conservation with its predecessors, ToCMV-[MG-Bt1] differs significantly in its biological properties. Although ToCMV-[MG-Bt1] DNA-A did not infect tomato plants, it systemically infected Nicotiana benthamiana, induced symptoms of mottling and accumulated viral DNA in the apical leaves in the absence of a cognate DNA-B. The modular rearrangement that resulted in ToCMV-[MG-Bt1] DNA-A may have provided this virus with a more aggressive nature. Our results further support the notion that interspecies recombination may play a significant role in geminivirus diversity and their emergence as agriculturally important pathogens.

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