Complete Sequence of the Citrus Tristeza Virus RNA Genome

Abstract

The sequence of the entire genome of citrus tristeza virus (CTV), Florida isolate T36, was completed. The 19,296-nt CTV genome encodes 12 open reading frames (ORFs) potentially coding for at least 17 protein products. The 5'-proximal ORF 1a starts at nucleotide 108 and encodes a large polyprotein with calculated MW of 349 kDa containing domains characteristic of (from 5' to 3') two papain-like proteases (P-PRO), a methyltransferase (MT), and a helicase (HEL). Alignment of the putative P-PRO sequences of CTV with the related proteases of beet yellows closterovirus (BYV) and potyviruses allowed the prediction of catalytic cysteine and histidine residues as well as two cleavage sites, namely Val-Gly/Gly for the 5' proximal P-PRO domain and Met-Gly/Gly for the 5' distal P-PRO domain. The autoproteolytic cleavage of the polyprotein at these sites would release two N-terminal leader proteins of 54 and 55 kDa, respectively, and a 240-kDa C-terminal fragment containing MT and HEL domains. The apparent duplication of the leader domain distinguishes CTV from BYV and accounts for most of the size increase in the ORF 1a product of CTV. The downstream ORF 1b encodes a 57-kDa putative RNA-dependent RNA polymerase (RdRp), which is probably expressed via a +1 ribosomal frameshift. Sequence analysis of the frameshift region suggests that this +1 frameshift probably occurs at a rare arginine codon CGG and that elements of the RNA secondary structure are unlikely to be involved in this process. The complete polyprotein resulting from this frameshift event has a calculated MW of 401 kDa and after cleavage of the two N-terminal leaders would yield a 292-kDa protein containing the MT, HEL, and RdRp domains. Phylogenetic analysis of the three replication-associated domains, MT, HEL, and RdRp, indicates that CTV and BYV form a separate closterovirus lineage within the alpha-like supergroup of positive-strand RNA viruses. Two gene blocks or modules can be easily identified in the CTV genome. The first includes the replicative MT, HEL, and RdRp genes and is conserved throughout the entire alpha-like superfamily. The second block consists of five ORFs, 3 to 7, conserved among closteroviruses, including genes for the CTV homolog of HSP70 proteins and a duplicate of the coat protein gene. The 3'-terminal ORFs 8 to 11 encode a putative RNA-binding protein (ORF 11), and three proteins with unknown functions; this gene array is poorly conserved among closteroviruses.(ABSTRACT TRUNCATED AT 400 WORDS)

Evidence of Recombinant Citrus tristeza virus Isolate Occurring in Acid Lime cv. Pant Lemon Orchard in Uttarakhand Terai Region of Northern Himalaya in India

“…CTV infects nearly all the citrus species, cultivars, and inter-generic hybrids and some citrus relatives, inducing symptoms like decline, stem pitting, seedling yellows, vein clearing and flecking [5,6,14,23]. CTV isolates differ in their biological characteristics, types and intensity of symptoms induced in different citrus hosts and aphid transmissibility [12], however, molecular determinant for symptom development in citrus hosts are not yet clearly known.…”

“…The CTV genome contains single stranded RNA of about 19.3 kb with 12 open reading frames (ORFs) encoding at least 19 proteins [12,21]. The ORFs 1a and 1b encode replication related proteins, whereas, the 3 0 end ten ORFs (ORFs 2-ORF11) encodes proteins p33, p6, p65, p61, p27, p25, p18, p13, p20 and p23 [11,22].…”

Prevalence of Citrus tristeza virus in Mandarin of Sikkim Himalayan Region

“…It is probably originated in Asia and has been disseminated to almost all citrus-growing countries mainly by the movement of infected plant material and subsequent spread by aphid vectors with Toxoptera citricida, commonly called the brown citrus aphid, being the most efficient [13]. CTV is a phloem-limited 2000 nm long filamentous virus having single stranded RNA genome [11]. The virus is genetically and biologically diverse and can cause field symptoms ranging from vein clearing, stem pitting, yellowing, slow decline and quick decline, or no symptoms depending on virus isolate, time of infection, rootstocks, citrus cultivars and environmental conditions [4].…”

Complete genome structure and phylogenetic analysis of little cherry virus, a mealybug-transmissible closterovirus.

“…As the anchor ligation method (Keim-Konrad & Jelkmann, 1996) failed to yield PCR products, tailing of the dsRNA with rATP followed by applying a 5h\3h RACE protocol (Boehringer Mannheim) was used. The 5h-terminal residue determined from the minus strand of LChV dsRNA is a C. Genomic RNAs of other closteroviruses start with an A or G (Agranovsky et al, 1994 ;Klaassen et al, 1995 ;Karasev et al, 1995), as is characteristic for the residues next to the 5h-m7G cap in eukaryotic messengers. However, Karasev et al (1995) Local similarity searches were performed using the program ALIGN-2 from the GENEBEE package (Brodsky et al, 1990).…”