Purifying and directional selection in overlapping prokaryotic genes.

In overlapping genes, the same DNA sequence codes for two proteins using different reading frames. Analysis of overlapping genes can help in understanding the mode of evolution of a coding region from noncoding DNA. We identified 71 pairs of convergent genes, with overlapping 3' ends longer than 15 nucleotides, that are conserved in at least two prokaryotic genomes. Among the overlap regions, we observed a statistically significant bias towards the 123:132 phase (i.e. the second codon base in one gene facing the degenerate third position in the second gene). This phase ensures the least mutual constraint on nonconservative amino acid replacements in both overlapping coding sequences. The excess of this phase is compatible with directional (positive) selection acting on the overlapping coding regions. This could be a general evolutionary mode for genes emerging from noncoding sequences, in which the protein sequence has not been subject to selection.

[1]  R. Lamb,et al.  Diversity of coding strategies in influenza viruses , 1991, Trends in Genetics.

[2]  B. Barrell,et al.  Overlapping genes in bacteriophage phiX174. , 1976, Nature.

[3]  M. B. Garber,et al.  [Overlapping genes in bacterial and bacteriophage genomes]. , 2000, Molekuliarnaia biologiia.

[4]  A. Pavesi,et al.  On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses , 1997, Journal of Molecular Evolution.

[5]  M S Waterman,et al.  Overlapping genes and information theory. , 1981, Journal of theoretical biology.

[6]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[7]  T. Grundström,et al.  Overlapping genes. , 1983, Annual review of genetics.

[8]  D. Krakauer,et al.  STABILITY AND EVOLUTION OF OVERLAPPING GENES , 2000, Evolution; international journal of organic evolution.

[9]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[10]  C. Samuel,et al.  Polycistronic Animal Virus mRNAs , 1989, Progress in Nucleic Acid Research and Molecular Biology.

[11]  Michael Y. Galperin,et al.  Using the COG Database to Improve Gene Recognition in Complete Genomes , 2004, Genetica.

[12]  M. Tomita,et al.  Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. , 1999, Nucleic acids research.

[13]  P. Keese,et al.  Origins of genes: "big bang" or continuous creation? , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[14]  M. A. McClure,et al.  Molecular evolution of the Paramyxoviridae and Rhabdoviridae multiple-protein-encoding P gene. , 2000, Molecular biology and evolution.

[15]  Masaru Tomita,et al.  Evolution of Overlapping Genes: Comparative Genomics of Mycoplasma genitalium and Mycoplasma pneumoniae , 1998 .

[16]  Shcherbakov Dv,et al.  Overlapping genes in bacterial and bacteriophage genomes , 2000 .

[17]  C. A. Hutchison,et al.  Overlapping genes in bacteriophage φX174 , 1976, Nature.

[18]  Jotun Hein,et al.  A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frames , 1995, Journal of Molecular Evolution.

[19]  G D Schuler,et al.  A workbench for multiple alignment construction and analysis , 1991, Proteins.