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. 2018 Apr:517:38-43.
doi: 10.1016/j.virol.2018.01.026. Epub 2018 Feb 21.

New insights about the regulation of Nidovirus subgenomic mRNA synthesis

Han Di  1 , Ayisha A McIntyre  1 , Margo A Brinton  2
Affiliations

New insights about the regulation of Nidovirus subgenomic mRNA synthesis

Han Di et al. Virology. 2018 Apr.

Abstract

The members of the Order Nidovirales share a similar genome organization with two overlapping nonstructural polyproteins encoded in the 5' two-thirds and the structural proteins encoded in the 3' third. They also express their 3' region proteins from a nested set of 3' co-terminal subgenomic messenger RNAs (sg mRNAs). Some but not all of the Nidovirus sg mRNAs also have a common 5' leader sequence that is acquired by a discontinuous RNA synthesis mechanism regulated by multiple 3' body transcription regulating sequences (TRSs) and the 5' leader TRS. Initial studies detected a single major body TRS for each 3' sg mRNA with a few alternative functional TRSs reported. The recent application of advanced techniques, such as next generation sequencing and ribosomal profiling, in studies of arteriviruses and coronaviruses has revealed an expanded sg mRNA transcriptome and coding capacity.

Keywords: Arterivirus; Coronavirus; Discontinuous RNA synthesis; Leader-body junction sequences; Next generation sequencing; Nidovirus; Subgenomic mRNAs; Transcription regulatory sequences.

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Figures

Fig. 1
Fig. 1
Diagrams of models of nidovirus sg RNA generation. A. Leader-primed transcription model. Short leader fragments synthesized from the 3′ region of the anti-genomic RNA function as primers for the synthesis of the sg mRNAs at multiple complementary anti-TRSs in the 5′ region of the anti-genome. B. Discontinuous minus strand synthesis model. Minus strand synthesis from the genomic RNA template terminates at various genomic body TRSs and after the nascent minus strand anneals to the complementary genomic leader TRS, minus strand sg RNA synthesis is completed. The minus sg RNAs are then used as templates for sg mRNA synthesis.
Fig. 2
Fig. 2
Diagram of the SHFV transcriptome. The ORFs are represented by white boxes. Identified functional TRSs are indicated by vertical lines to the left each ORF. Red vertical lines represent the nine major SHFV body TRSs published prior to the recent SHFV NGS study. For ORFs with multiple functional TRSs, an asterisk indicates the TRS that produces the highest abundance of sg mRNA for that ORF. (Published in Di et al., 2017. Proc Natl Acad Sci USA 114(42): E8895-E8904).
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