Structure, function, and evolution of adenovirus-associated RNA: a phylogenetic approach

Abstract

To explore the structure and function of a small regulatory RNA, we examined the virus-associated (VA) RNA species of all 47 known human adenovirus serotypes and of one simian virus, SA7. The VA RNA gene regions of 43 human adenoviruses were amplified and sequenced, and the structures of 10 representative VA RNAs were probed by nuclease sensitivity analysis. Most human viruses have two VA RNA species, VA RNA I and VA RNA II , but nine viruses (19%) have a single VA RNA gene. Sequence alignments classified the RNAs into eight families, corresponding broadly to the known virus groups, and three superfamilies. One superfamily contains the single VA RNAs of groups A and F and the VA RNA I species of group C; the second contains the VA RNA I species of groups B1, D, and E and the unclassified viruses (adenovirus types 42 to 47), as well as the single VA RNAs of group B2; and the third contains all VA RNA II species. Fourteen regions of homology occur throughout the molecule. The longest of these correspond to transcription signals; most of the others participate in RNA secondary structure. The previously identified tetranucleotide pair, GGGU:ACCC, is nearly invariant, diverging slightly (to GGGU:ACCU) only in the two group F viruses and forming a stem in the central domain that is critical for VA RNA structure and function. Secondary structure models which accommodate the nuclease sensitivity data and sequence variations within each family were generated. The major structural features-the terminal stem, apical stem-loop, and central domain-are conserved in all VA RNAs, but differences exist in the apical stem and central domains, especially of the VA RNA II species. Sequence analysis suggests that an ancestral VA RNA gene underwent duplication during the evolution of viruses containing two VA RNA genes. Although the VA RNA II gene seems to have been lost or inactivated by secondary deletion events in some viruses, the high degree of homology among the VA RNA II species implies that this RNA may play an undiscovered role in virus survival. We speculate that the VA RNA genes originated from cellular sequences containing multiple tRNA genes.

Adenovirus and miRNAs

“…The nucleotide sequences between VAI and VAII RNAs of a particular virus are significantly different from one another. The same diversity can be observed when analyzing VAI or VAII among different serotypes, especially if they belong to different groups (A to F) [44,45]. Comparison of adenovirus serotypes has shown conserved regions in the 5′ end and near the 3′ terminus.…”

“…It has been shown that these sequences are required for VA RNA transcription initiation and termination. Besides these homologies, highly conserved sequences up to 4 nucleotides are present throughout the VA gene that seem to be required for maintenance of the VA RNA secondary structure [44,45].…”

“…Secondary structure models for VA RNA have been based on extensive mutagenesis and structure probing studies together with comparative sequence analysis [44][45][46][47][48][49][50]. The results of these analyses clearly show that VA RNAs fold into a stem-loop structure (Fig.…”

“…Since the silencing suppressor function of VA RNAs is intimately related to VA RNA biogenesis, a detailed description is provided here. VA RNAs are transcribed by RNA polymerase III in the nucleus of infected cells [45]. VAI synthesis starts during the early phase of infection and rapidly accelerates during late phase.…”

Genomic analysis of HAdV-B14 isolate from the outbreak of febrile respiratory infection in China

“…Virus-associated RNAs (VA RNAs) in AdVs are short, non-coding RNAs transcribed by RNA polymerase III to form double-stranded (ds) RNAlike secondary structures [14,15]. The number of VA RNA genes varies among different AdV species.…”