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Computational study of translation elongation features in Mycoplasma V.S. Sokolov
Institute of Cytology and Genetics SB RAS, Novosibirsk, e-mail: sokovlad1@bionet.nsc.ru

V.A. Likhoshvai, Y.G. Matushkin
Institute of Cytology and Genetics SB RAS, Novosibirsk

In a modern bio logy, study of genes expressio n efficiency and its optimizat ion is timely and significant problem both for theory and for practice. From the fundamental po int of view, a solut ion of this problem is important for theoretical est imation o f expressio n level of genes, which experimental data is not available yet. The results o f this research can also be helpful in pract ical bio logy, for instance in planning genet ic engineering experiments or increasing producers (genetically modified organisms) productivit y. It is known, that for unicellular and many mult icellular organisms level of genes expressio n depends on such factors as gene codon composit ion, presence and distribut ion of secondary structures in mRNA and their stabilit y [1]. According to various co mbinat ions o f these factors five groups of organisms, that optimized the primary structure of their genes in different ways during the evolut ion, are ident ified [2]. We have implemented the algorithm for research of completely sequenced geno mes. For each gene in a geno me, the algorithm calculates parameters associated with mRNA codon composit ion and stabilit y o f its secondary structures. Consequent ly, so-called elongat ion efficiency index (EEI) is assigned to each gene. We have analyzed genomes o f 42 various Mycoplasma strains. It was found, that genes expressio n level in almo st all organisms depends on number of mRNA secondar y structure and doesn't depend on codon co mpositio n. Also three strains which significant ly differed fro m others were revealed (Mycoplasma haemocanis Illinois, Mycoplasma haemofelis Ohio2 and Mycoplasma haemofelis Langford1). Geno mes o f these part icular organisms are dist inguished by much lower average number of local inverted repeats, which can form secondary structures in mRNA. For addit ional invest igat ion we have constructed


and analyzed the average profiles o f local inverted repeats localizat ion in mRNA for all Mycoplasma geno mes. Based on our data and information available in literature about Mycoplasma phylogeny we suppose, that particular Mycoplasma strains evo lved in the line of reducing number of mRNA secondary structures for increasing genes expressio n level. Parasit ic life style o f these organisms can be the main cause of such changes. 1. N.V.Vladimirov, V.A.Likhoshvai, Y.G.Matushkin. (2007) Correlat ion o f codon biases and potential secondary structures with mRNA translat ion efficiency in unicellular organisms, Molecular Bio logy, V. 41. 5. P. 843-850. 2. V.A.Likhoshvai, Y.G.Matushkin. (2002) Different iat ion of single-cell organisms according to elongation stages crucial for gene expressio n efficacy, FEBS.