On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses |
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Authors: | Angelo Pavesi Bettina De Iaco Maria Ilde Granero Alfredo Porati |
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Institution: | (1) Department of Evolutionary Biology, University of Parma, Viale delle Scienze, I-43100, Parma, Italy, IT;(2) Institute of Biomathematics, University of Parma, Viale delle Scienze, I-43100, Parma, Italy, IT;(3) Department of Physics, University of Parma, Via del Taglio, I-43100, Parma, Italy, IT |
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Abstract: | In genetic language a peculiar arrangement of biological information is provided by overlapping genes in which the same region
of DNA can code for functionally unrelated messages. In this work, the informational content of overlapping genes belonging
to prokaryotic and eukaryotic viruses was analyzed. Using information theory indices, we identified in the regions of overlap
a first pattern, exhibiting a more uniform base composition and more severe constraints in base ordering with respect to the
nonoverlapping regions. This pattern was found to be peculiar to coliphage, avian hepatitis B virus, human lentivirus, and
plant luteovirus families. A second pattern, characterized by the occurrence of similar compositional constraints in both
types of coding regions, was found to be limited to plant tymoviruses. At the level of codon usage, a low degree of correlation
between overlapping and nonoverlapping coding regions characterized the first pattern, whereas a close link was found in tymoviruses,
indicating a fine adaptation of the overlapping frame to the original codon choice of the virus. As a result of codon usage
correlation analysis, deductions concerning the origin and evolution of several overlapping frames were also proposed. Comparison
of amino acid composition revealed an increased frequency of amino acid residues with a high level of degeneracy (arginine,
leucine, and serine) in the proteins encoded by overlapping genes; this peculiar feature of overlapping genes can be viewed
as a way with which they may expand their coding ability and gain new, specialized functions.
Received: 28 October 1996 / Accepted: 29 January 1997 |
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Keywords: | : Overlapping genes — Information Theory — Codon usage — Amino acid composition |
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