The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes

Fluctuations and increments of both C3 and G3 levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC3 levels, the second shows considerable increments of the GC3 levels in the human genes. In both data sets, the fluctuations of C3 and G3 levels along the coding sequences correlated with the secondary structures of the encoded proteins. The human genes that underwent the compositional transition showed a different increment of the C3 and G3 levels within and among the structural units of the proteins. The relative synonymous codon usage (RSCU) of several amino acids were also affected during the compositional transition, showing that there exists a correlation between RSCU and protein secondary structures in human genes. The importance of natural selection for the formation of isochore organization of the human genome has been discussed on the basis of these results.