scholarly journals Molecular Variability of the 5′- and 3′-Terminal Regions of Citrus Tristeza Virus RNA

1998 ◽  
Vol 88 (7) ◽  
pp. 685-691 ◽  
Author(s):  
C. López ◽  
M. A. Ayllón ◽  
J. Navas-Castillo ◽  
J. Guerri ◽  
P. Moreno ◽  
...  
Keyword(s):  
Citrus Tristeza Virus ◽  
Biological Properties ◽  
Terminal Region ◽  
Cdna Clones ◽  
Reading Frame ◽  
Group Iii ◽  
Sequence Identity ◽  
Virus Rna ◽  
Tristeza Virus ◽  
Citrus Tristeza

Isolates of citrus tristeza virus (CTV) differ widely in their biological properties. These properties may depend on the structure of viral RNA populations comprising the different isolates. As a first approach to study the molecular basis of the biological variability, we have compared the sequences of multiple cDNA clones of the two terminal regions of the RNA from different CTV isolates. The polymorphism of the 5′ untranslated region (UTR) allowed the classification of the sequences into three groups, with intragroup sequence identity higher than 88% and intergroup sequence identity as low as 44%. The variability of an open reading frame (ORF) 1a segment adjacent to the 5′ UTR supports the same grouping. Some CTV isolates contained sequences of more than one group. Most sequences from Spanish isolates belonged to group III, whereas a Japanese isolate was composed mostly of sequences of groups I and II. The mildest isolates contained only sequences of group III, whereas the most severe isolates also contained sequences of groups I, II, or both. The most stable secondary structure predicted for the 5′ UTR was composed of two stem-loops and remained essentially unchanged as a result of compensatory mutations in the stems and accommodation of most of the variability in the loops. In contrast to the 5′-terminal region, the variability of the 3′-terminal region of CTV RNA was very much restricted, with nucleotide identity values higher than 90%. The presence of a conserved putative “zinc-finger” domain adjacent to a basic region in p23, the predicted product of ORF 11, suggests that this protein might act as a regulatory factor during virus replication.

scholarly journals Citrus Tristeza Virus Isolates of the Same Genotype Differ in Stem Pitting Severity in Grapefruit

Plant Disease ◽  
2020 ◽  
Vol 104 (9) ◽  
pp. 2362-2368
Author(s):  
Glynnis Cook ◽  
Beatrix Coetzee ◽  
Rachelle Bester ◽  
Johannes H. J. Breytenbach ◽  
Chanel Steyn ◽  
...  
Keyword(s):  
Citrus Tristeza Virus ◽  
Aphid Transmission ◽  
Common Source ◽  
Citrus Paradisi ◽  
Full Genome ◽  
Full Genome Sequencing ◽  
Reading Frame ◽  
Tristeza Virus ◽  
Stem Pitting ◽  
Citrus Tristeza

Two isolates of the T68 genotype of citrus tristeza virus (CTV) were derived from a common source, GFMS12, by single aphid transmission. These isolates, named GFMS12-8 and GFMS12-1.3, induced stem pitting with differing severity in ‘Duncan’ grapefruit (Citrus × paradisi [Macfad.]). Full-genome sequencing of these isolates showed only minor nucleotide sequence differences totaling 45 polymorphisms. Numerous nucleotide changes, in relatively close proximity, were detected in the p33 open reading frame (ORF) and the leader protease domains of ORF1a. This is the first report of full-genome characterization of CTV isolates of a single genotype, derived from the same source, but showing differences in pathogenicity. The results demonstrate the development of intragenotype heterogeneity known to occur with single-stranded RNA viruses. Identification of genetic variability between isolates showing different pathogenicity will enable interrogation of specific genome regions for potential stem pitting determinants.

scholarly journals Transcription Strategy in a Closterovirus: a Novel 5′-Proximal Controller Element of Citrus Tristeza Virus Produces 5′- and 3′-Terminal Subgenomic RNAs and Differs from 3′ Open Reading Frame Controller Elements

2003 ◽  
Vol 77 (1) ◽  
pp. 340-352 ◽  
Author(s):  
Siddarame Gowda ◽  
María A. Ayllón ◽  
Tatineni Satyanarayana ◽  
Moshe Bar-Joseph ◽  
William O. Dawson
Keyword(s):  
Promoter Activity ◽  
Citrus Tristeza Virus ◽  
Open Reading Frames ◽  
Stem Loop ◽  
Reading Frame ◽  
Subgenomic Rnas ◽  
Modular Evolution ◽  
Different Origins ◽  
Tristeza Virus ◽  
Citrus Tristeza

ABSTRACT Citrus tristeza virus (CTV) produces more than thirty 3′- or 5′-terminal subgenomic RNAs (sgRNAs) that accumulate to various extents during replication in protoplasts and plants. Among the most unusual species are two abundant populations of small 5′-terminal sgRNAs of approximately 800 nucleotides (nt) termed low-molecular-weight tristeza (LMT1 and LMT2) RNAs. Remarkably, CTV replicons with all 10 3′ genes deleted produce only the larger LMT1 RNAs. These 5′-terminal positive-sense sgRNAs do not have corresponding negative strands and were hypothesized to be produced by premature termination during plus-strand genomic RNA synthesis. We characterized a cis-acting element that controls the production of the LMT1 RNAs. Since manipulation of this cis-acting element in its native position (the L-ProI region of replicase) was not possible because the mutations negatively affect replication, a region (5′TR) surrounding the putative termination sites (nt ∼550 to 1000) was duplicated in the 3′ end of a CTV replicon to allow characterization. The duplicated sequence continued to produce a 5′-terminal plus-strand sgRNA, here much larger (∼11 kb), apparently by termination. Surprisingly, a new 3′-terminal sgRNA was observed from the duplicated 5′TR. A large 3′-terminal sgRNA resulting from the putative promoter activity of the native 5′TR was not observed, possibly because of the down-regulation of a promoter ∼19 kb from the 3′ terminus. However, we were able to observe a sgRNA produced from the native 5′TR of a small defective RNA, which placed the native 5′TR closer to the 3′ terminus, demonstrating sgRNA promoter activity of the native 5′TR. Deletion mutagenesis mapped the promoter and the terminator activities of the 5′TR (in the 3′ position in the CTV replicon) to a 57-nt region, which was folded by the MFOLD computer program into two stem-loops. Mutations in the putative stem-loop structures equally reduced or prevented production of both the 3′- and 5′-terminal sgRNAs. These mutations, when introduced in frame in the native 5′TR, similarly abolished the synthesis of the LMT1 RNAs and presumably the large 3′-terminal sgRNA while having no impact on replication, demonstrating that neither 5′- nor 3′-terminal sgRNA is necessary for replication of the replicon or full-length CTV in protoplasts. Differences between the 5′TR, which produced two plus-strand sgRNAs, and the cis-acting elements controlling the 3′ open reading frames, which produced additional minus-strand sgRNAs corresponding to the 3′-terminal mRNAs, suggest that the different sgRNA controller elements had different origins in the modular evolution of closteroviruses.

scholarly journals Identification and Characterization of Citrus tristeza virus Isolates Breaking Resistance in Trifoliate Orange in California

2017 ◽  
Vol 107 (7) ◽  
pp. 901-908 ◽  
Author(s):  
Raymond K. Yokomi ◽  
Vijayanandraj Selvaraj ◽  
Yogita Maheshwari ◽  
Maria Saponari ◽  
Annalisa Giampetruzzi ◽  
...  
Keyword(s):  
Citrus Tristeza Virus ◽  
Aphid Transmission ◽  
Poncirus Trifoliata ◽  
Trifoliate Orange ◽  
In Planta ◽  
Sequence Identity ◽  
Group I ◽  
Genetic Profiles ◽  
Tristeza Virus ◽  
Citrus Tristeza

Most Citrus tristeza virus (CTV) isolates in California are biologically mild and symptomless in commercial cultivars on CTV tolerant rootstocks. However, to better define California CTV isolates showing divergent serological and genetic profiles, selected isolates were subjected to deep sequencing of small RNAs. Full-length sequences were assembled, annotated and trifoliate orange resistance-breaking (RB) isolates of CTV were identified. Phylogenetic relationships based on their full genomes placed three isolates in the RB clade: CA-RB-115, CA-RB-AT25, and CA-RB-AT35. The latter two isolates were obtained by aphid transmission from Murcott and Dekopon trees, respectively, containing CTV mixtures. The California RB isolates were further distinguished into two subclades. Group I included CA-RB-115 and CA-RB-AT25 with 99% nucleotide sequence identity with RB type strain NZRB-G90; and group II included CA-RB-AT35 with 99 and 96% sequence identity with Taiwan Pumelo/SP/T1 and HA18-9, respectively. The RB phenotype was confirmed by detecting CTV replication in graft-inoculated Poncirus trifoliata and transmission from P. trifoliata to sweet orange. The California RB isolates induced mild symptoms compared with severe isolates in greenhouse indexing tests. Further examination of 570 CTV accessions, acquired from approximately 1960 and maintained in planta at the Central California Tristeza Eradication Agency, revealed 16 RB positive isolates based on partial p65 sequences. Six isolates collected from 1992 to 2011 from Tulare and Kern counties were CA-RB-115-like; and 10 isolates collected from 1968 to 2010 from Riverside, Fresno, and Kern counties were CA-RB-AT35-like. The presence of the RB genotype is relevant because P. trifoliata and its hybrids are the most popular rootstocks in California.

scholarly journals Complete Sequence of the Citrus Tristeza Virus RNA Genome

Virology ◽  
1995 ◽  
Vol 208 (2) ◽  
pp. 511-520 ◽  
Author(s):  
A.V. Karasev ◽  
V.P. Boyko ◽  
S. Gowda ◽  
O.V. Nikolaeva ◽  
M.E. Hilf ◽  
...  
Keyword(s):  
Citrus Tristeza Virus ◽  
Complete Sequence ◽  
Virus Rna ◽  
Rna Genome ◽  
Tristeza Virus ◽  
Citrus Tristeza
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