Characterization of the 5′- and 3′-terminal subgenomic RNAs produced by a capillovirus: Evidence for a CP subgenomic RNA

The members of Capillovirus genus encode two overlapping open reading frames (ORFs): ORF1 encodes a large polyprotein containing the replication-associated proteins plus a coat protein (CP), and ORF2 encodes a movement protein (MP), located within ORF1 in a different reading frame. Organization of the CP sequence as part of the replicase ORF is unusual in capilloviruses. In this study, we examined the capillovirus genome expression strategy by characterizing viral RNAs produced by Citrus tatter leaf virus (CTLV), isolate ML, a Capillovirus. CTLV-ML produced a genome-length RNA of ∼ 6.5-kb and two 3′-terminal sgRNAs in infected tissue that contain the MP and CP coding sequences (3′-sgRNA1), and the CP coding sequence (3′-sgRNA2), respectively. Both 3′-sgRNAs initiate at a conserved octanucleotide (UUGAAAGA), and are 1826 (3′-sgRNA1) and 869 (3′-sgRNA2) nts with 119 and 15 nt leader sequences, respectively, suggesting that these two 3′-sgRNAs could serve to express the MP and CP. Additionally, accumulation of two 5′-terminal sgRNAs of 5586 (5′-sgRNA1) and 4625 (5′-sgRNA2) nts was observed, and their 3′-termini mapped to 38–44 nts upstream of the transcription start sites of 3′-sgRNAs. The presence of a separate 3′-sgRNA corresponding to the CP coding sequence and its cognate 5′-terminal sgRNA (5′-sgRNA1) suggests that CTLV-ML produces a dedicated sg mRNA for the expression of its CP.