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Nucleic Acids Research, 1993, Vol. 21, No. 15 3529-3535
© 1993

GENOME STRUCTURE AND MAPPING

Prominent polypurine and polypyrimidine tracts in plant viroids and in RNA of the human hepatitis delta agent

Andrea D. Branch, Susan E. Lee, Olivia D. Neel and Hugh D. Robertson

Center for Studies of the Biological Correlates of Addiction, The Rockefeller University and The Cornell University Medical College New York, NY 10021, USA

Received March 17, 1993. Revised June 17, 1993. Accepted June 17, 1993.

To seek patterns of nucleotlde usage in the three types of circular subviral RNA pathogens, trimer frequencies and nearest-neighbor biases were studied in 12 plant virold sequences; five sequences of circular plant viral satellite RNAs; and the sequence of RNA from the human hepatitis delta agent. The viroids and RNA of the delta agent contain tracts of polypurines and polypyrimidines which make up substantial portions of their genomes. Such tracts are not common in the virusoids or in the satellite RNA of tobacco ringspot virus. Viroids, the delta hepatitis agent, and the circular satellite RNAs of certain plant viruses have several features in common: all have circular genomic RNA and replicate through an RNA to RNA rolling circle replication cycle. However, virusoids and related satellite RNAs are directly or indirectly dependent on their helper viruses for replication, while the delta agent and viroids are not. The difference in the pattern of nucleotide usage between the plant viral satellite RNAs on the one hand, and virolds and delta RNA on the other, may relate to this difference in replication strategy.


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