Maize Chlorotic Mottle Machlomovirus Expresses Its Coat Protein from a 1.47-kb Subgenomic RNA and Makes a 0.34-kb Subgenomic RNA

Abstract

Analysis of double-stranded RNAs produced in maize plants infected with maize chlorotic mottle machlomovirus (MCMV) and Northern blots of total RNA from infected plants or protoplasts showed two subgenomic RNAs (sgRNAs). Primer extension was used to map these sgRNAs, which are 1.47 and 0.34 kb long. The transcription start sites are nucleotide (nt) 2970 or 2971 for sgRNA1 and nt 4101 for sgRNA2. The 5' ends of the sgRNAs are similar to one another and to the 5' end of genomic RNA, and 11 nt sequences immediately upstream of their transcription start sites are similar. The location of the sgRNA1 transcription start site indicates that MCMV expresses a 7-kDa open reading frame (ORF) from nt 2995 to 3202 instead of the predicted 9-kDa ORF from nt 2959 to 3202. In protoplast inoculation experiments, a silent mutation at nt 2965 and a 4-nt change at nt 2959-2962 stopped the synthesis of sgRNA1 and expression of the coat protein ORF, which begins more than 400 nt downstream. Replication of MCMV does not require the expression of any of the ORFs encoded on sgRNA1. SgRNA2 has the potential to encode 2.3-, 2.7-, and 4. 6-kDa peptides, but the function, if any, of sgRNA2 is unknown.

Pelarspovirus, a proposed new genus in the family Tombusviridae

“…However, in contrast to carmoviruses, which produce two sgRNAs to express genes in the 3 0 half of their genomes, pelarspoviruses are known (PLPV, ELV, PCRPV, PelRSV) [5,[14][15][16] or predicted (RrLDV) [24] to generate only one sgRNA (Fig. 1), similar to that reported for panicoviruses [39] and maize chlorotic mottle virus, the only member of the genus Machlomovirus [31]. The synthesis of a single sgRNA was initially suggested by the presence of two virus-specific dsRNA species in pelarspovirus-infected plants, compared to the expected three dsRNA species found in carmovirus infections [14,16,20].…”

Effects of Modification of the Transcription Initiation Site Context on Citrus Tristeza Virus Subgenomic RNA Synthesis

“…Thus, all CTV sgRNAs mapped so far have an adenylate as the 5Ј terminus, suggesting that initiation of RNA synthesis from a uridylate on the minus strand is preferred by the CTV replicase complex. Sequence similarity at the 5Ј ends of the genomic RNA and the 5Ј leaders of sgRNAs is a characteristic of numerous viruses (7,48,56,60,61,65,67), including other members of the Closteroviridae such as BYV (5) and Sweet potato chlorotic stunt virus (28). This sequence similarity has been proposed to be involved in assisting the viral replicase complex to recognize and interact with specific minus-strand signals for the initiation of synthesis of plus-strand genomic RNA and sgRNAs.…”

“…In general, alpha-like viruses are expected to follow the ϩ1 pyrimidine and ϩ2 adenylate rule (in reference to the negative strand of the genome) as initiation nucleotides for the genomic positive strand and sgRNA (3), and usually within each virus the same first nucleotide is found for both types of RNAs (3,34). Most of the small RNA viruses of plants have guanylates as 5Ј termini of the genomic and sgRNAs (8,13,16,18,23,25,26,48,55,56,60,61,63,65). Adenylate, however, is a common 5Ј terminus of RNAs for animal alpha-like viruses and members of the Nidovirales (12,31,38,53,59) but infrequent for plant viruses (30,43,67).…”

Subgenomic mRNA transcription in Tombusviridae

“…17 of Tombusviridae, a small non-coding sg RNA corresponding roughly to the genomic 3'UTR is observed in infections. [8][9][10] In Red clover necrotic mosaic virus (RCNMV), this RNA has been shown to be generated by host ribonucleolytic cleavage, rather than by viral RdRp-mediated transcription, and it functions to help regulate the translation of viral mRNAs. 10 The focus of this review, however, will be on the genesis and function of RdRp-transcribed sg mRNAs that act as messages for the translation of viral proteins.…”