engleski

Intragenic synonymous codon shuffling as a tool for studying palindrome abundance in protein coding genes

Successful deciphering of the genetic code in the mid-1960s has demonstrated that the large majority of amino acids are encoded by more than one codon. Additionally, synonymous codons are used with different frequencies in different organisms, and the apparent codon usage bias has alredy been extensively discussed and studied in a number of different organisms. However, the factors affecting the consecutive order of synonymous codons whithin a given gene are still largely under-investigated. Previously, we habe performed a comprehensive analysis of palindromic sequences in the genetic material of yeast Saccharomyces cerevisiae and discovered a strong biag in favor of their placement in the non-coding regions of the genome. Based on this result, we have speculated that the order of the synonimous could be selected for in sucha way to control the number of palindromes not only in yeast genes, but also in the genes of other organisms. To test this hypothesis, we have developed Synonymous Codon Shuffler (SCS), a new GUI-supported computational tool which can generate, and analyize the palindrome content in a large number of permuted gene sequences having different order of synonimous codons but the same amino acid sequence and codon usage as the original, existing gene(s). Using SCS, we have then performed a preliminary analysis of the palindrome abundance in the genes of two model organisms, yeast Saccharomyces cerevisiae and bacterium Deinococcus radiodurans. Initial results suggest that the genes of both organisms generally contain fewer palindromes than their permuted variants, implying the existance of a selective preassure which operates to reduce the number of palindromes in the protein coding regions in the genomes of these two organisms.

palindrome abundance; codon usage; codon shuffling; Saccharomyces cerevisiae; Deinococcus radiodurans

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