Talk:Molecular Development - Rubella Genome

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1990

Sequence of the genome RNA of rubella virus: evidence for genetic rearrangement during toga virus evolution

Virology. 1990 Jul;177(1):225-38.

Dominguez G, Wang CY, Frey TK. Source Department of Biology, Georgia State University, Atlanta 30302-4010.

Abstract

The nucleotide sequence of the rubella virus (RUB) genomic RNA was determined. The RUB genomic RNA is 9757 nucleotides in length [excluding the poly(A) tail] and has a G/C content of 69.5%, the highest of any RNA virus sequenced to date. The RUB genomic RNA contains two long open reading frames (ORFs), a 5'-proximal ORF of 6656 nucleotides and a 3'-proximal ORF of 3189 nucleotides which encodes the structural proteins. Thus, the genomic organization of RUB is similar to that of alphaviruses, the other genus of the Togavirus family, and the 5'-proximal ORF of RUB therefore putatively codes for the nonstructural proteins. Sequences homologous to three regions of nucleotide sequence highly conserved among alphaviruses (a stem-and-loop structure at the 5' end of the genome, a 51-nucleotide conserved sequence near the 5' end of the genome, and a 20-nucleotide conserved sequence at the subgenomic RNA start site) were found in the RUB genomic RNA. Amino acid sequence comparisons between the nonstructural ORF of RUB and alphaviruses revealed only one short (122 amino acids) region of significant homology, indicating that these viruses are only distantly related. This region of homology is located at the NH2 terminus of nsP3 in the alphavirus genome. The RUB nonstructural protein ORF contains two global amino acid motifs conserved in a large number of positive-polarity RNA viruses, a motif indicative of helicase activity and a motif indicative of replicase activity. The order of the helicase motif and the nsP3 homology region in the RUB genome is reversed with respect to the alphavirus genome indicating that a genetic rearrangement has occurred during the evolution of these viruses.

PMID 2353453



REFERENCE 1 (bases 8155 to 9754)
AUTHORS Frey,T.K., Marr,L.D., Hemphill,M.L. and Dominguez,G.
TITLE Molecular cloning and sequencing of the region of the rubella virus
genome coding for glycoprotein E1
JOURNAL Virology 154 (1), 228-232 (1986)
MEDLINE 86317717
REFERENCE 2 (bases 5917 to 9754)
AUTHORS Frey,T.K. and Marr,L.D.
JOURNAL Unpublished (1987)
REFERENCE 3 (bases 5247 to 8366)
AUTHORS Frey,T.K. and Marr,L.D.
TITLE Sequence of the region coding for virion proteins C and E2 and the
carboxy terminus of the nonstructural proteins of rubella virus:
comparison with alphaviruses
JOURNAL Gene 62 (1), 85-99 (1988)
MEDLINE 88226020
REFERENCE 4 (bases 1 to 9755)
AUTHORS Dominguez,G., Wang,C.Y. and Frey,T.K.
TITLE Sequence of the genome RNA of rubella virus: evidence for genetic
rearrangement during togavirus evolution
JOURNAL Virology 177 (1), 225-238 (1990)
MEDLINE 90281585
COMMENT [2] revises [1].
Draft entry and computer-readable copy of sequence in [2] kindly
provided by T.K.Frey, 01-JUN-1987.
Draft entry and computer-readable sequence for [4] kindly submitted
by G.Dominguez, 09-MAR-1990, for release after publication.
Glycoprotein E1 contains the viral hemagglutinin activity. Multiple
copies of the C protein comprise the nucleocapsid.
FEATURES Location/Qualifiers