Compositional constraints and codon usage

Other factors do, however, play a role in shaping codon usage, even in the case of vertebrates. Indeed, if multivariate analysis is applied to the coding sequences of Xenopus, which are characterized by a rather average GC3 distribution, with very scarce high values, the results obtained (Musto et ah, 2001) show that codon usage, although mainly determined by compositional constraints, is, in fact, also influenced by translational selection 

Our early results on vertebrates led us to consider compositional constraints in microorganisms (and viruses) as another factor determining codon usage next to translational selection. The correlation of GC3 with genome GC exhibited by prokaryotes, showed that, indeed, compositional constraints also played a role in this case (Bemardi and Bernardi, 1985, 1986a Muto and Osawa, 1987). 

Relative Synonymous Codon Usage (RSCU) values of P. falciparum (Pf) and S. aureus (Saf 

To sum up, codon usage is due to two main selective factors 1) compositional constraints (which we visualize as the result of natural selection shaping up the compositional patterns of genomes), and 2) translational selection. When the former are very biased, the latter becomes barely detectable (one should remember that at 100% GC, 50% of codons are not used) and, vice versa, when the eompositional constraints are not biased (and genomes are in middle GC range), translational selection becomes quite visible. 

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