scholarly journals Molecular Characterization, Phylogenetic Relationships, and Specific Detection of Peach mosaic virus

2006 ◽  
Vol 96 (2) ◽  
pp. 137-144 ◽  
Author(s):  
D. James ◽  
A. Varga ◽  
H. Croft ◽  
H. Rast ◽  
D. Thompson ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Open Reading Frames ◽  
Nucleic Acid Binding ◽  
Specific Detection ◽  
Deletion Event ◽  
Polymerase Chain ◽  
Similar Genome Organization ◽  
Leaf Virus

Peach mosaic virus (PcMV) and Cherry mottle leaf virus (CMLV) are serologically related viruses that cause distinct diseases, have a different host range, and are vectored by different eriophyid mites. Sequence analysis of the genome of PcMV indicates that it is closely related genetically to CMLV but distinct, with similar genome organization and a member of the genus Trichovirus. The genome of PcMV consists of 7,988 nucleotides, excluding a poly(A) tail at the 3′ end of the genome. Four putative open reading frames (ORF1 to 4) were identified coding for proteins of 216.3, 47.2, 21.7, and 15.7 kDa, respectively. Also, three noncoding regions were identified, including an intergenic region separating ORF3 and ORF4. The complete nucleotide sequence of PcMV shares 73% identity with CMLV. The CP amino acid sequence identity between isolates of PcMV ranged from 97 to 99% versus 83% identity when compared with the CP of CMLV. In vitro expression and subsequent western blot analysis confirmed ORF3 as encoding the CP gene of PcMV. Phylogenetic analysis supports classification of PcMV and CMLV as members of the genus Trichovirus. They are unique members of this genus with an extra ORF (ORF4). PcMV ORF4 appears to code for a putative nucleic acid-binding (NB) protein which has identity with the NB protein of CMLV and members of the genera Allexivirus, Carlavirus, and Vitivirus. PcMV and CMLV appear to be the products of recombination between members of the genus Trichovirus and a virus group containing the putative NB protein. Alternatively, PcMV and CMLV may represent the intact genome, with a deletion event producing members that lack ORF4. A reverse transcription-polymerase chain reaction procedure was developed for reliable and specific detection of PcMV. This will be an asset for stone fruit virus certification.

scholarly journals Partial Molecular Characterization of Dahlia mosaic virus and Its Detection by PCR

Plant Disease ◽  
2003 ◽  
Vol 87 (8) ◽  
pp. 945-948 ◽  
Author(s):  
M. Nicolaisen
Keyword(s):  
Nucleotide Sequence ◽  
Mosaic Virus ◽  
Real Time ◽  
Real Time Pcr ◽  
Open Reading Frames ◽  
Dahlia Mosaic Virus ◽  
Polymerase Chain ◽  
Pcr Assays

Dahlia mosaic virus (DMV) is the causal agent of one of the most important diseases of Dahlia pinnata. The nucleotide sequence of a 1,195-bp fragment of its genome was amplified and characterized. Based on this sequence, polymerase chain reaction (PCR) assays were developed for detection of DMV. The nucleotide sequence confirmed the classification of DMV as a member of genus Caulimovirus since it was similar to a region covering partly open reading frames (ORFs) IV and V found in caulimoviruses. The two most closely related viruses on the basis of comparison of ORF V fragments were shown to be Figwort mosaic virus and Mirabilis mosaic virus with 66.6 and 68.1% identity, respectively. Two PCR assays were developed using identical primer pairs: a real-time PCR based on SYBR green chemistry and a conventional PCR. Both methods clearly discriminated DMV-infected and healthy dahlia. The real-time PCR assay detected DMV-infected material that was diluted 105-fold in healthy material.

scholarly journals A New Tymovirus Isolated From Solanum quitoense: Characterization and Prevalence in Two Solanaceous Crops in Ecuador

Plant Disease ◽  
2019 ◽  
Vol 103 (9) ◽  
pp. 2246-2251 ◽  
Author(s):  
Juan F. Cornejo-Franco ◽  
Robert A. Alvarez-Quinto ◽  
Samuel Grinstead ◽  
Dimitre Mollov ◽  
Alexander V. Karasev ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Open Reading Frames ◽  
Yellow Mosaic Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Mild Mosaic ◽  
Fresh Market ◽  
Certification Programs ◽  
Mild Mosaic Virus ◽  
Polymerase Chain ◽  
Production Areas

Naranjilla (Solanum quitoense Lam.) and tamarillo (S. betaceum Cav.) are two important perennial solanaceous crops grown in Ecuador for the fresh market and juice production. Viruses infecting tamarillo and naranjilla are currently poorly studied, and no clean stock program exists in Ecuador. Here, we report a new virus, provisionally named as naranjilla mild mosaic virus (NarMMV) (genus Tymovirus, family Tymoviridae), isolated from naranjilla grown in an orchard in Pichincha Province, Ecuador. The complete genome of the virus consists of 6,348 nucleotides and encodes three open reading frames typical for members of the genus Tymovirus. Phylogenetically, Chiltepin yellow mosaic virus, Eggplant mosaic virus, and the recently characterized naranjilla chlorotic mosaic virus (NarCMV) were found to be the closest relatives of NarMMV. Unlike NarCMV, the new virus induced mild mosaic in naranjilla and more severe symptoms in tamarillo. Similar to NarCMV, NarMMV was unable to systemically infect potato. Virus surveys found NarMMV prevalent in naranjilla production areas of two provinces of Ecuador, especially where hybrid cultivars of naranjilla were cultivated. NarMMV was also found in field-grown tamarillo. The new virus cross-reacted with antibodies developed against NarCMV. Hence, this antibody will be useful for its field diagnosis using enzyme-linked immunosorbent assay or immunocapture reverse transcription polymerase chain reaction in future virus-free certification programs.

RHD gene deletion occurred in the Rhesus box

Blood ◽  
2000 ◽  
Vol 95 (12) ◽  
pp. 3662-3668 ◽  
Author(s):  
Franz F. Wagner ◽  
Willy A. Flegel
Keyword(s):  
Open Reading Frames ◽  
Chromosome 1 ◽  
Nucleotide Sequencing ◽  
Blood Group Antigens ◽  
Specific Detection ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Specific Priming ◽  
Rh Blood Group ◽  
Reading Frames

Abstract The Rh blood group antigens derive from 2 genes,RHD and RHCE, that are located at chromosomal position 1p34.1-1p36 (chromosome 1, short arm, region 3, band 4, subband 1, through band 6). In whites, a cde haplotype with a deletion of the whole RHD gene occurs with a frequency of approximately 40%. The relative position of the 2 RH genes and the location of the RHD deletion was previously unknown. A model has been developed for the RH locus using RHD- and RHCE-related nucleotide sequences deposited in nucleotide sequence databases along with polymerase chain reaction (PCR) and nucleotide sequencing. The open reading frames of bothRH genes had opposite orientations. The 3′ ends of the genes faced each other and were separated by about 30 000 base pair (bp) that contained the SMP1 gene. The RHD gene was flanked by 2 DNA segments, dubbed Rhesus boxes, with a length of approximately 9000 bp, 98.6% homology, and identical orientation. The Rhesus box contained the RHD deletion occurring within a stretch of 1463 bp of identity. PCR with sequence-specific priming (PCR-SSP) and PCR with restriction fragment length polymorphism (PCR-RFLP) were used for specific detection of the RHDdeletion. The molecular structure of the RH gene locus explains the mechanisms for generating RHD/RHCE hybrid alleles and the RHD deletion. Specific detection of theRHD− genotype is now possible.

Control of translation reinitiation on the cauliflower mosaic virus (CaMV) polycistronic RNA

2004 ◽  
Vol 32 (4) ◽  
pp. 592-596 ◽  
Author(s):  
L. Ryabova ◽  
H.-S. Park ◽  
T. Hohn
Keyword(s):  
Mosaic Virus ◽  
Cauliflower Mosaic Virus ◽  
Open Reading Frames ◽  
Initiation Factor ◽  
Plant Protoplasts ◽  
Translational Machinery ◽  
Infected Cells ◽  
Transient Overexpression ◽  
Polycistronic Rna

Translation of the polycistronic 35S RNA of CaMV (cauliflower mosaic virus) occurs via a reinitiation mechanism, which requires TAV (transactivator/viroplasmin). To allow translation reinitiation of the major open reading frames on the polycistronic RNA, TAV interacts with the host translational machinery via eIF3 (eukaryotic initiation factor 3) and the 60S ribosome. Accumulation of TAV and eIF3 in the polysomal fraction isolated from CaMV-infected cells suggested that TAV prevents loss of eIF3 from the translating ribosomes during the first initiation event. The TAV–eIF3–80S complex could be detected in vitro by sucrose-gradient-sedimentation analysis. The question is whether TAV interacts directly with the 48S preinitiation complex or enters polysomes after the first initiation event. eIF4B, a component of the 48S initiation complex, can preclude formation of the TAV–eIF3 complex via competition with TAV for eIF3 binding; the eIF4B- and TAV-binding sites on eIF3g overlap. eIF4B out-competes TAV for binding to eIF3 and to the eIF3–40S complex. Transient overexpression of eIF4B in plant protoplasts specifically inhibits TAV-mediated transactivation of polycistronic translation. Our results thus indicate that eIF4B precludes TAV–eIF3–40S complex formation during the first initiation event. Consequently, overexpression of TAV in plant protoplasts affects only the second and subsequent initiation events. We propose a model in which TAV enters the host translational machinery at the eIF4B-removal step to stabilize eIF3 within polysomes.

RHD gene deletion occurred in the Rhesus box

Blood ◽  
2000 ◽  
Vol 95 (12) ◽  
pp. 3662-3668 ◽  
Author(s):  
Franz F. Wagner ◽  
Willy A. Flegel
Keyword(s):  
Open Reading Frames ◽  
Chromosome 1 ◽  
Nucleotide Sequencing ◽  
Blood Group Antigens ◽  
Specific Detection ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Specific Priming ◽  
Rh Blood Group ◽  
Reading Frames

The Rh blood group antigens derive from 2 genes,RHD and RHCE, that are located at chromosomal position 1p34.1-1p36 (chromosome 1, short arm, region 3, band 4, subband 1, through band 6). In whites, a cde haplotype with a deletion of the whole RHD gene occurs with a frequency of approximately 40%. The relative position of the 2 RH genes and the location of the RHD deletion was previously unknown. A model has been developed for the RH locus using RHD- and RHCE-related nucleotide sequences deposited in nucleotide sequence databases along with polymerase chain reaction (PCR) and nucleotide sequencing. The open reading frames of bothRH genes had opposite orientations. The 3′ ends of the genes faced each other and were separated by about 30 000 base pair (bp) that contained the SMP1 gene. The RHD gene was flanked by 2 DNA segments, dubbed Rhesus boxes, with a length of approximately 9000 bp, 98.6% homology, and identical orientation. The Rhesus box contained the RHD deletion occurring within a stretch of 1463 bp of identity. PCR with sequence-specific priming (PCR-SSP) and PCR with restriction fragment length polymorphism (PCR-RFLP) were used for specific detection of the RHDdeletion. The molecular structure of the RH gene locus explains the mechanisms for generating RHD/RHCE hybrid alleles and the RHD deletion. Specific detection of theRHD− genotype is now possible.

scholarly journals Insertion Sequences

1998 ◽  
Vol 62 (3) ◽  
pp. 725-774 ◽  
Author(s):  
Jacques Mahillon ◽  
Michael Chandler
Keyword(s):  
Open Reading Frames ◽  
Insertion Sequences ◽  
Bacterial Genomes ◽  
Or Groups ◽  
Direct Target ◽  
Transposition Mechanism ◽  
The Individual ◽  
And Function

SUMMARY Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available.

scholarly journals Characterization of a New Tymovirus Causing Stunting and Chlorotic Mosaic in Naranjilla (Solanum quitoense)

Plant Disease ◽  
2018 ◽  
Vol 102 (5) ◽  
pp. 911-918 ◽  
Author(s):  
Kelsie J. Green ◽  
Dimitre Mollov ◽  
Lisa T. Tran ◽  
Robert A. Alvarez-Quinto ◽  
Jose B. Ochoa ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
High Throughput Sequencing ◽  
Infectious Agent ◽  
Open Reading Frames ◽  
Spherical Particles ◽  
The Andes ◽  
Perennial Shrub ◽  
Original Plant ◽  
Polymerase Chain

Naranjilla (“little orange”), also known as lulo (Solanum quitoense Lam.), is a perennial shrub species cultivated in the Andes for fresh fruit and juice production. In 2015, a naranjilla plant exhibiting stunting, mosaic, and chlorotic spots was sampled in the Pastaza province of Ecuador and maintained under greenhouse conditions. An infectious agent was mechanically transmitted to indicator plants and was subjected to biological and molecular characterization. Spherical particles approximately 30 nm in diameter, composed of a single 20-kDa capsid protein, were observed under an electron microscope in infected naranjilla plants. High-throughput sequencing conducted on inoculated Nicotiana benthamiana plants produced a single sequence contig sharing the closest relationship with several tymoviruses. The entire 6,245-nucleotide genome of a new tymovirus was amplified using reverse-transcription polymerase chain reaction and resequenced with the Sanger methodology. The genome had three open reading frames typical of tymoviruses, and displayed a whole-genome nucleotide identity level with the closest tymovirus, Eggplant mosaic virus, at 71% (90% coverage). This tymovirus from naranjilla was able to systemically infect eggplant, tamarillo, N. benthamiana, and naranjilla. In naranjilla, it produced mosaic, chlorotic spots, and stunting, similar to the symptoms observed in the original plant. The virus was unable to infect potato and tobacco and unable to systemically infect pepper plants, replicating only in inoculated leaves. We concluded that this virus represented a new tymovirus infecting naranjilla, and proposed the tentative name Naranjilla chlorotic mosaic virus (NarCMV).

scholarly journals Biological properties and relative fitness of inter-subgroup cucumber mosaic virus RNA 3 recombinants produced in vitro

2007 ◽  
Vol 88 (10) ◽  
pp. 2852-2861 ◽  
Author(s):  
Olivier Pierrugues ◽  
Laurent Guilbaud ◽  
Isabelle Fernandez-Delmond ◽  
Frédéric Fabre ◽  
Mark Tepfer ◽  
...  
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Point Mutations ◽  
Biological Properties ◽  
Open Reading Frames ◽  
Relative Fitness ◽  
Coding Region ◽  
Virus Rna ◽  
Viral Cdna

In vitro reverse transcription of a mixture of total RNA from plants infected with the I17F or R strains of cucumber mosaic virus (CMV), representative of subgroups IA and II, respectively, results in viral cDNA populations including rare recombinant RNA 3 molecules, some of which also have point mutations. The biological properties of 17 recombinants in the capsid gene or the 3′ non-coding region of RNA 3 were evaluated when associated with I17F RNAs 1 and 2. Six viruses displayed deficiencies (non-viability, deficiencies for movement and/or replication, delayed infection, loss of aphid transmissibility). Nine induced symptoms close to those of I17F-CMV on tobacco and pepper plants. All recombinants bearing the movement protein (MP) of R-CMV and part or most of the capsid protein (CP) of I17F-CMV, as well as the recombinant created in vitro by exchanging the corresponding open reading frames, also induced filiformism on tobacco, but induced only faint symptoms on melon. Two recombinants induced atypically severe symptoms on both tobacco and pepper. Most of the recombinants generally accumulated to lower levels than the wild-type I17F strain in tobacco. Three recombinants, however, including one responsible for severe symptoms, accumulated to generally higher levels than I17F-CMV. When two of these were tested in co-infection experiments with I17F RNA 3, they proved to be poorly competitive, suggesting that they would be unlikely to emerge in the field.

Sign in / Sign up

Export Citation Format

Share Document