Elucidating sequence codes: three codes for evolution.

The sequences are related to evolution in several ways. First, they carry traces of a distant past. Two sequence features point to the earliest sequence organization. The universal hidden GCU-periodical pattern in mRNA suggests the earliest codons: GCU and its nine-point-change derivatives. They code for seven amino acids that by several criteria are also the oldest. Together it makes the earliest form of the triplet code, still recognizable in the extant sequences. Another feature present in the sequences, apparently, since separation of prokaryotes and eukaryotes, is hidden genome segmentation. Both protein-coding and noncoding sequences appear to have been formed by fusion of standard size units, about 360 bp (120 aa) in eukaryotes and 450 bp (150 aa) in prokaryotes. Presumably, the units have been functioning at some stage of evolution as autonomous single-gene size elements. There are sequence designs that promote evolution. One such design suitable for fast adaptation is the tandem repetition of identical sequences, so that their copy numbers in the repeat arrays would modulate (tune) the expression of nearby genes. The tandem repeat expansion diseases illustrate this mechanism in a dramatic way: overtuning of the respective gene expression leads to the disease.