STRUCTURE, FUNCTION, AND EVOLUTION OF ADENOVIRUS-ASSOCIATED RNA - A PHYLOGENETIC APPROACH

To explore the structure and function of a small regulatory RNA, we ex amined the virus-associated (VA) RNA species of all 47 known human ade novirus serotypes and of one simian virus, SA7. The VA RNA gene region s of 43 human adenoviruses were amplified and sequenced, and the struc tures of 10 representative VA RNAs were probed by nuclease sensitivity analysis. Most human viruses have two VA RNA species, VA RNA(I) and V A RNA(II), but nine viruses (19%) have a single VA RNA gene. Sequence alignments classified the RNAs into eight families, corresponding broa dly to the known virus groups, and three superfamilies. One superfamil y contains the single VA RNAs of groups A and F and the VA RNA(I) spec ies 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), a s well as the single VA RNAs of group B2; and the third contains all V A RNA(II) species. Fourteen regions of homology occur throughout the m olecule. The longest of these correspond to transcription signals; mos t of the others participate in RNA secondary structure. The previously identified tetranucleotide pair, GGGU:ACCC, is nearly invariant, dive rging slightly (to GGGU:ACCU) only in the two group F viruses and form ing a stem in the central domain that is critical for VA RNA structure and function. Secondary structure models which accommodate the nuclea se sensitivity data and sequence variations within each family were ge nerated. 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 RN A(II) species. Sequence analysis suggests that an ancestral VA RNA gen e underwent duplication during the evolution of viruses containing two VARNA genes. Although the VA RNA(II) gene seems to have been lost or inactivated by secondary deletion events in some viruses, the high deg ree 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.