The 5' and 3' ends of alphavirus RNAs--Non-coding is not non-functional

Abstract

The non-coding regions found at the 5' and 3' ends of alphavirus genomes regulate viral gene expression, replication, translation and virus-host interactions, which have significant implications for viral evolution, host range, and pathogenesis. The functions of these non-coding regions are mediated by a combination of linear sequence and structural elements. The capped 5' untranslated region (UTR) contains promoter elements, translational regulatory sequences that modulate dependence on cellular translation factors, and structures that help to avoid innate immune defenses. The polyadenylated 3' UTR contains highly conserved sequence elements for viral replication, binding sites for cellular miRNAs that determine cell tropism, host range, and pathogenesis, and conserved binding regions for a cellular protein that influences viral RNA stability. Nonetheless, there are additional conserved elements in non-coding regions of the virus (e.g., the repeated sequence elements in the 3' UTR) whose function remains obscure. Thus, key questions remain as to the function of these short yet influential untranslated segments of alphavirus RNAs.

Keywords: Polyadenylation; Protein–RNA interactions; Translation regulation; Viral pathogenesis; mRNA capping; miRNAs.

Fig. 1

Organization and regulatory landmarks of the alphavirus genome. Major RNA regulatory elements and open reading frames are indicated. The positions of the 51 base CSE and subgenomic promoter are given relative to the start site of their associated open reading frame. These latter elements are based solely on studies performed in Sindbis virus.

Fig. 2

Evolution of alphaviruses and the lengths of their untranslated regions. The phylogenetic tree is modified from the Bayesian tree based on structural protein coding regions (Nasar et al., 2012). Posterior probabilities higher than 0.9 are labeled along the branches. UTR lengths were determined from alignments of available viral sequence information (as of September 2014) in GenBank.

Fig. 3

Evolutionary history and lineage-specific structures of the CHIKV 3′ UTR, from (Chen et al., 2013). On the left is the Maximum Clade Credibility tree based on the complete concatenated ORF sequences, with the branches in each lineage collapsed. The estimated year of the most recent common ancestor (MRCA: mean and the 95% HPD values) of each clade is labeled left to the node. The 3′ UTR structures, based on sequence alignment, are shown next to each lineage. Direct repeats are illustrated by different colored blocks, and each of the four colors represents a different homologous sequence region. Sequence gaps in the alignment are indicated by white blocks. In the Asian lineage, two distinct derived differences are observed: (1) duplication of DR3, and; (2) duplication the of DR(1 + 2) region.

Fig. 4

A comparison between mRNA capping of cellular and alphavirus mRNAs. The methyl donor S-adenosyl methionine (SAM) is indicated in green. In alphavirus capping, the nsP1 protein methylates GMP prior to covalently attaching the modified GMP to the diphosphate at the 5′ end of the pre-mRNA generated by triphosphatase activity associated with nsP2. Cellular mRNAs generally contain a 2′-O-methyl modification (2′-O me) of the first nucleotide downstream of the N-7^meGppp cap that is not seen in alphavirus transcripts.