Secondary structure of the 3' untranslated region of flaviviruses: similarities and differences.

Genetic algorithm-based RNA secondary structure prediction was used in combination with comparative sequence analysis to construct models of folding for the distal part of the 3'-untranslated region of flaviviruses belonging to four serological groups. Elements of RNA secondary structure that are preserved among all the flaviviruses studied were revealed, despite the high degree of sequence divergence between them. At the same time, structural elements were observed that distinguish members of different serological groups and, in particular, a region of remarkable structural divergence between the tick-borne and mosquito-borne flaviviruses was found. Application of the genetic algorithm also revealed that the 3'-terminus of flaviviral genomic RNA may take on alternative conformations, which are not observed in the 3'-terminus of complementary minus strand RNA. These alternative folding patterns may have roles in the regulation of transcription and translation initiation and in the switch between them.

[1]  C. Pleij,et al.  The computer simulation of RNA folding pathways using a genetic algorithm. , 1995, Journal of molecular biology.

[2]  J. Puglisi,et al.  Conformation of the TAR RNA-arginine complex by NMR spectroscopy. , 1992, Science.

[3]  E. Gould,et al.  Phylogeny of TYU, SRE, and CFA virus: different evolutionary rates in the genus Flavivirus. , 1995, Virology.

[4]  T. E. Ryan,et al.  Identification and characterization of type 2 dengue virus replicative intermediate and replicative form RNAs. , 1981, Virology.

[5]  M. Brinton,et al.  BHK cell proteins that bind to the 3' stem-loop structure of the West Nile virus genome RNA , 1995, Journal of virology.

[6]  C. Pleij,et al.  An APL-programmed genetic algorithm for the prediction of RNA secondary structure. , 1995, Journal of theoretical biology.

[7]  G. Wengler,et al.  Analysis of structural properties which possibly are characteristic for the 3'-terminal sequence of the genome RNA of flaviviruses. , 1986, The Journal of general virology.

[8]  C. Mandl,et al.  Presence of poly(A) in a flavivirus: significant differences between the 3' noncoding regions of the genomic RNAs of tick-borne encephalitis virus strains , 1991, Journal of virology.

[9]  C. Pleij,et al.  The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics. , 1995, Nucleic acids research.

[10]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[11]  M. Brinton,et al.  The 3'-nucleotides of flavivirus genomic RNA form a conserved secondary structure. , 1986, Virology.

[12]  M. Poidinger,et al.  Molecular characterization of the Japanese encephalitis serocomplex of the flavivirus genus. , 1996, Virology.

[13]  M. Zuker.  On finding all suboptimal foldings of an RNA molecule. , 1989, Science.

[14]  W D Wilson,et al.  Evidence for the existence of a pseudoknot structure at the 3' terminus of the flavivirus genomic RNA. , 1996, Biochemistry.

[15]  J. H. Strauss,et al.  Conserved elements in the 3' untranslated region of flavivirus RNAs and potential cyclization sequences. , 1987, Journal of molecular biology.

[16]  M. Byrne,et al.  Nucleotide and complete amino acid sequences of Kunjin virus: definitive gene order and characteristics of the virus-specified proteins. , 1988, The Journal of general virology.

[17]  C. Rice,et al.  Flavivirus genome organization, expression, and replication. , 1990, Annual review of microbiology.

[18]  N. Karabatsos,et al.  Antigenic relationships between flaviviruses as determined by cross-neutralization tests with polyclonal antisera. , 1989, The Journal of general virology.

[19]  E. Geiduschek,et al.  Analysis of RNA chain elongation and termination by Saccharomyces cerevisiae RNA polymerase III. , 1994, Journal of molecular biology.

[20]  M. Bouloy,et al.  Stable secondary structures at the 3'‐end of the genome of yellow fever virus (17 D vaccine strain) , 1985, FEBS letters.

[21]  V. Stollar,et al.  Studies on the nature of dengue viruses. III. RNA synthesis in cells infected with type 2 dengue virus. , 1967, Virology.

[22]  C. Mandl,et al.  Complete genomic sequence of Powassan virus: evaluation of genetic elements in tick-borne versus mosquito-borne flaviviruses. , 1993, Virology.

[23]  J. Williamson,et al.  Binding of an HIV Rev peptide to Rev responsive element RNA induces formation of purine-purine base pairs. , 1994, Biochemistry.

[24]  C. Mandl,et al.  The flavivirus 3'-noncoding region: extensive size heterogeneity independent of evolutionary relationships among strains of tick-borne encephalitis virus. , 1995, Virology.

[25]  J. H. Strauss,et al.  Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution. , 1985, Science.