Evolution of the primary and secondary structures of the E1a mRNAs of the adenovirus.

In this paper we investigate and compare (evolutionary) patterns in the primary and secondary structure of four homologous E1a mRNAs of the adenovirus. Our main results are as follows: (1) The similarity of the coding regions of the mRNA sequences reflects both similarity in function (i.e., oncogenicity) and evolutionary divergence. (2) The similarity of the leader and the trailer regions reflects host specificity (i.e., human or simian) and must therefore arise from convergence. (3) Minimal energy foldings of the mRNAs show similar secondary structures (in particular around the splice sites). The conservation of pre-mRNA secondary structure shows that mRNAs are subject to selection constraints in addition to those associated with proteins. (4) The conserved secondary (helical) structures consist of nonhomologous subsequences, i.e., shifts have occurred. The observed shifts near the splice sites seem to be the simplest way of dealing with the dual constraints.

[1]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[2]  D. Konings,et al.  The nucleotide sequence of the leftmost XhoI fragment (6%) of simian adenovirus SA7P. , 1984, The Journal of general virology.

[3]  S. Fields,et al.  Sequence of chicken ovalbumin mRNA , 1978, Nature.

[4]  W. Fitch.  Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .

[5]  W. Rutter,et al.  Splice junctions: association with variation in protein structure. , 1983, Science.

[6]  R. Dijkema,et al.  Gene organization of the transforming region of adenovirus type 7 DNA. , 1982, Gene.

[7]  J. Darnell,et al.  Control of messenger RNA concentration by differential cytoplasmic half-life. Adenovirus messenger RNAs from transcription units 1A and 1B. , 1981, Journal of molecular biology.

[8]  Manolo Gouy,et al.  An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules , 1984, Nucleic Acids Res..

[9]  P. Sharp,et al.  Expression of early adenovirus genes requires a viral encoded acidic polypeptide. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[10]  R. Dijkema,et al.  Comparison of nucleotide sequences of the early E1a regions for subgroups A, B and C of human adenoviruses. , 1980, Gene.

[11]  M. Perricaudet,et al.  Structure of two adenovirus type 12 transforming polypeptides and their evolutionary implications , 1980, Nature.

[12]  R. Nussinov,et al.  Fast algorithm for predicting the secondary structure of single-stranded RNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Craig Montell,et al.  Resolving the functions of overlapping viral genes by site-specific mutagenesis at a mRNA splice site , 1982, Nature.

[14]  T. Smith,et al.  Optimal sequence alignments. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[15]  D. Spector,et al.  Regulation of the appearance of cytoplasmic RNAs from region 1 of the adenovirus 2 genome. , 1978, Journal of molecular biology.

[16]  W. Salser.  Globin mRNA sequences: analysis of base pairing and evolutionary implications. , 1978, Cold Spring Harbor symposia on quantitative biology.

[17]  N. Rosenthal,et al.  The structure and evolution of the two nonallelic rat preproinsulin genes , 1979, Cell.

[18]  S. B. Needleman,et al.  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 1989 .

[19]  David Sankoff,et al.  A strategy for sequence phylogeny research , 1982, Nucleic Acids Res..

[20]  E. Ziff.  Transcription and RNA processing by the DNA tumour viruses , 1980, Nature.

[21]  D. Turner,et al.  Improved free energies for G.C base-pairs. , 1985, Journal of molecular biology.

[22]  J. Nevins,et al.  Steps in the processing of Ad2 mRNA: Poly(A)+ Nuclear sequences are conserved and poly(A) addition precedes splicing , 1978, Cell.

[23]  R Nussinov,et al.  Sequential folding of a messenger RNA molecule. , 1981, Journal of molecular biology.

[24]  Paulien Hogeweg,et al.  Energy directed folding of RNA sequences , 1984, Nucleic Acids Res..

[25]  A. van der Eb,et al.  Transformation and oncogenicity by adenoviruses. , 1984, Current topics in microbiology and immunology.

[26]  C. V. van Beveren,et al.  The nucleotide sequence of the transforming early region E1 of adenovirus type 5 DNA. , 1980, Gene.

[27]  P. Hogeweg,et al.  Minimal energy foldings of eukaryotic mRNAs form a separate leader domain. , 1987, Journal of theoretical biology.

[28]  L. Chow,et al.  Complex splicing patterns of RNAs from the early regions of adenovirus-2. , 1979, Journal of molecular biology.

[29]  K. Sugimoto,et al.  Structure and gene organization in the transforming Hind III-G fragment of Ad12 , 1980, Cell.

[30]  M. Perricaudet,et al.  Structure of two spliced mRNAs from the transforming region of human subgroup C adenoviruses , 1979, Nature.