Analysis of the complete genome of peach chlorotic mottle virus: identification of non-AUG start codons, in vitro coat protein expression, and elucidation of serological cross-reactions

Abstract

The entire genome of peach chlorotic mottle virus (PCMV), originally identified as Prunus persica cv. Agua virus (4N6), was sequenced and analysed. PCMV cross-reacts with antisera to diverse viruses, such as plum pox virus (PPV), genus Potyvirus, family Potyviridae; and apple stem pitting virus (ASPV), genus Foveavirus, family Flexiviridae. The PCMV genome consists of 9005 nucleotides (nts), excluding a poly(A) tail at the 3' end of the genome. Five open reading frames (ORFs) were identified with four untranslated regions (UTR) including a 5', a 3', and two intergenic UTRs. The genome organisation of PCMV is similar to that of ASPV and the two genomes share a nucleotide (nt) sequence identity of 58%. PCMV ORF1 encodes the replication-associated protein complex (Mr 241,503), ORF2-ORF4 code for the triple gene block proteins (TGBp; Mr 24,802, 12,370, and 7320, respectively), and ORF5 encodes the coat protein (CP) (Mr 42,505). Two non-AUG start codons participate in the initiation of translation: 35AUC and 7676AUA initiate translation of ORF1 and ORF5. In vitro expression with subsequent Western blot analysis confirmed ORF5 as the CP-encoding gene and confirmed that the codon AUA is able to initiate translation of the CP. Expression of a truncated CP fragment (Mr 39, 689) was demonstrated, and both proteins are expressed in vivo, since both were observed in Western blot analysis of PCMV-infected peach and Nicotiana occidentalis. The expressed proteins cross-reacted with an antiserum against ASPV. The amino acid sequences of the CPs of PCMV and ASPV CP share only 37% identity, but there are 11 shared peptides 4-8 aa residues long. These may constitute linear epitopes responsible for ASPV antiserum cross reactions. No significant common linear epitopes were associated with PPV. Extensive phylogenetic analysis indicates that PCMV is closely related to ASPV and is a new and distinct member of the genus Foveavirus.

Molecular Characterization and Detection of African Oil Palm Ringspot Virus

“…However, the genome organization of these viruses differs from that of AOPRV in that the cherry viruses have more than five ORFs. The other unassigned viruses in the Flexiviridae : APruV‐1, ‐2 and ‐3, and PCMV seem to be closely related to the definitive species of the genus Foveavirus , although they form a separate cluster (Marais et al., 2006; James et al., 2007).…”

List of non‐EU viruses and viroids of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L.

“…() Peach chlorotic mottle virus PeCMVXNot reported to be present in the EUIt might be present but not reported in the EUJames et al. () Peach enation (?) nepovirus PENVXNot reported to be present in the EUVirus very poorly characterised, only mentioned in one 1973 abstract.…”

Lolium latent virus (Alphaflexiviridae) coat proteins: expression and functions in infected plant tissue

“…are expressed in infected tissues (James et al, 2007). Among the family Alphaflexiviridae (which includes LoLV), the presence of two conserved in-frame AUGs has been reported for the CP of Plantago asiatica mosaic virus (PlAMV; genus Potexvirus) (Ozeki et al, 2009); however, the virus is thought to have a single type of CP (Solovyev et al, 1994) with the first AUG as the major initiation codon for CP translation.…”

“…Within the genus Marafivirus , maize rayado fino virus (MRFV) and oat blue dwarf virus each produce carboxy-coterminal CPs (Hammond & Hammond, 2010; Hammond & Ramirez, 2001). Within the family Betaflexiviridae , peach chlorotic mottle virus (PCMV; genus Foveavirus ) utilizes AUA as an upstream CP alternative start codon in addition to a supplementary in-frame downstream AUG; both CPs are expressed in infected tissues (James et al , 2007). Among the family Alphaflexiviridae (which includes LoLV), the presence of two conserved in-frame AUGs has been reported for the CP of Plantago asiatica mosaic virus (PlAMV; genus Potexvirus ) (Ozeki et al , 2009); however, the virus is thought to have a single type of CP (Solovyev et al , 1994) with the first AUG as the major initiation codon for CP translation.…”