engleski

Palindromic sequences - boogeymen in the genes

Perfect inverted repeats, or palindromes, are present in the DNA of natural plasmids, viral and bacterial genomes and eukaryotic chromosomes and organelles. Their significance was first acknowledged in the context of the bacterial type II restriction– modification systems and a number of regulatory proteins were shown to bind palindromic sequences as homo- or hetero-dimers. Further important property of palindromes is their intrinsic potential to form intra-strand hydrogen bonds, giving rise to secondary structures known as hairpins and cruciforms. Both protein binding and secondary structure formation make palindromic sequences important constituents of different cis-acting genetic elements like promoters, operators, attenuators, viral and plasmid origins of replication. However, in spite of their importance and functional versatility, palindromes are also known to provoke different types of potentially deleterious genetic alterations, such as deletions or translocations. Thus, the importance of palindromic sequences in regulation of different cellular processes on one side and their influence on genetic stability on the other, makes them an especially attractive target for systematic study at the whole genome level. In our previous work we developed a computer program that may identify, locate and count palindromes in a given sequence in a strictly defined way, and we used this program to investigate the palindrome content of the entire genome of the yeast Saccharomyces cerevisiae. This analysis revealed that there is a strong avoidance of palindromic sequences in the coding regions of the yeast genome. To explain the underrepresentation of palindromes in yeast genes, we have hypothesised that intragenic variations in codon usage could be a way to control the amount of palindromes within genes. To test this hypothesis, we have first developed a new computer program for shuffling of synonymous codons within genes. This program was then used to shuffle the codons in ~3200 well-characterized genes of the yeast Saccharomyces cerevisiae, while keeping the amino acid sequence of the translation product constant. Palindromes were then counted in shuffled sequences and their number compared with the reference sequence. This analysis demonstrated that the number of palindromes in yeast genes is lower than the amount of palindromes in shuffled genes and points to the existence of a process which operates to reduce the number of palindromes. In other words, the succession of codons appears to be a manner in which the cell controls the number of palindromes within genes. Additionally, the preliminary results suggest a possible relationship between the representation of palindromes in genes and their expression.

Perfect inverted repeats; Palindromes; Yeast; Saccharomyces cerevisiae; Synonymous codons

nije evidentirano