From low complexity sequences to function: a new interpretation of evolutionary dynamics.

Since the origin of life coding sequences have been selected according to the functional value of the coded proteins, while the fixation of non random sequences in non coding regions is a consequence of other, still partially unknown features. Deviation from randomness in DNA sequences can be considered as a record of the evolutionary history of organisms. We have been developed an algorithm to measure the low complexity relative weight in a set of genomes from organisms wich are located at different position in the phylogenetic tree of life. We have shown that the weight of low complexity sequences in genomes greatly increases with evolution from Archaea to multicellular eukaryotes. Furthermore non-coding and coding regions show a different evolutionary behaviour: low complexity weight is higher and increases much faster in non-coding than in coding sequences. Low complexity analysis of prokaryotic, eukaryotic and organellar genomes led to a phylogenetic reconstruction generally consistent with known molecular phylogeny. All this prompted us to carry out a series of experiments to test the functional role of these sequences for evolution and variation on Lycopersicon and Nicotiana spp. Low complexity DNA regions were PCR amplified in promoters of hormone related genes such as ACC-synthase, ACC-oxydase involved in ethylene synthesis, and non-coding regions in Nicotiana spp chloroplast genomes. Sequencing of the amplified fragments always uncovered polymorphisms wich are due to rearrangements of low complexity sequences. We found preliminary evidence that this variation is correlated to varying levels of ethylene synthesis and, through it, to the phenotypic variation in tomato. We perfomed cluster analysis of the low complexity regions on the amplified sequences. The detected patterns suggest a role for this class of sequences in the control of gene expression and evolution.