The alphavirus 3'-nontranslated region: size heterogeneity and arrangement of repeated sequence elements.
The 3'-nontranslated region (NTR) of representative strains of all known alphavirus species was amplified by reverse transcription-polymerase chain reaction. For 23 of them, the 3'-NTR sequence was determined. Together with previously published data, this allowed an analysis of the 3'-NTR of the viruses in the genus Alphavirus. The length of the 3'-NTRs varied from 77 nt for Pixuna virus to 609 nt for Bebaru virus. The 19-nt conserved sequence element directly adjacent to the poly(A) tract was found in all viruses, supporting the hypothesis that this region is a cis-acting sequence element during viral replication and essential for virus growth in vitro. Within the 3'-NTR of all alphaviruses, repeated sequence elements of various numbers and lengths were found. Their composition was very consistent in both the Venezuelan equine encephalitis (VEE) and the Sindbis-like viruses, although their number was constant only within the latter group. For the VEE viruses, our data suggested that insertion events rather than deletions from an ancestor with a long 3'-NTR created the various number of repeated sequence elements. Among the remaining viruses, both the number and the composition of repeated sequence elements varied remarkedly.
Pfeffer
M
M
Institute for Medical Microbiology, Epidemic and Infectious Diseases, Veterinary Faculty, Ludwig-Maximilians University, Munich, Germany. Martin.Pfeffer@micro.vetmed.uni-muenchen.de
Kinney
R M
RM
Kaaden
O R
OR
D000524:Alphavirus / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D017931:DNA Primers; D004666:Encephalitis Virus, Venezuelan Equine / Q000235:genetics; D016679:Genome, Viral; D006736:Horses; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D012845:Sindbis Virus / Q000235:genetics
D017931:DNA Primers; D012367:RNA, Viral