- Article -
| In Silico Biology 3, 0015 (2003); ©2003, Bioinformation Systems e.V. |
In silico search for functionally similar proteins involved in meiosis and recombination in evolutionarily distant organisms
Yuri F. Bogdanov, Sergei Y. Dadashev and Tatiana M. Grishaeva
N. I. Vavilov Institute of General Genetics, Russian Academy of
Sciences, Moscow
Email: bogdanov@vigg.ru
* corresponding author
Edited by E. Wingender; received September 30, 2002; revised and accepted January 28, 2003; published March 01, 2003
Abstract
Evolutionarily distant organisms have not only orthologs, but also nonhomologous proteins that build functionally similar subcellular structures. For instance, this is true with protein components of the synaptonemal complex (SC), a universal ultrastructure that ensures the successful pairing and recombination of homologous chromosomes during meiosis. We aimed at developing a method to search databases for genes that code for such nonhomologous but functionally analogous proteins. Advantage was taken of the ultrastructural parameters of SC and the conformation of SC proteins responsible for these. Proteins involved in SC central space are known to be similar in secondary structure. Using published data, we found a highly significant correlation between the width of the SC central space and the length of rod-shaped central domain of mammalian and yeast intermediate proteins forming transversal filaments in the SC central space. Basing on this, we suggested a method for searching genome databases of distant organisms for genes whose virtual proteins meet the above correlation requirement. Our recent finding of the Drosophila melanogaster CG17604 gene coding for synaptonemal complex transversal filament protein received experimental support from another lab. With the same strategy, we showed that the Arabidopsis thaliana and Caenorhabditis elegans genomes contain unique genes coding for such proteins.
Key words: databases, computer analysis, functional proteomics, meiosis, cell ultrastructure, synaptonemal complex, coiled coil, Arabidopsis thaliana, Caenorhabditis elegans