Biomedical subjects

S Cruveiller

Publications and source records attributed to S Cruveiller.

4 recordsLinked to original sources

PubMed2001

Translational selection on codon usage in Xenopus laevis.

A correspondence analysis of codon usage in Xenopus laevis revealed that the first axis is strongly correlated with the base composition at third codon positions. The second axis discriminates between putatively highly expressed genes and the other coding sequences, with expression levels being confirmed by the analysis of Expressed sequence tag frequencies. The comparison of codon usage of the sequences displaying the extreme values on the second axis indicates that several codons are statistically more frequent among the highly expressed (mainly housekeeping) genes. Translational selection appears, therefore, to influence synonymous codon usage in Xenopus.

Amino Acids↗

PubMed2000

The compositional transition between the genomes of cold- and warm-blooded vertebrates: codon frequencies in orthologous genes.

The genomes of the ancestors of mammals and birds underwent a compositional change in which the gene-richest regions increased their GC levels. Here we investigated this compositional transition by analyzing the levels of G and C in third codon positions, as well as the codon frequencies of orthologous genes from human, chicken and Xenopus. The results may be summed up as follows: (i) GC-poor genes, that did not undergo the compositional transition, showed only minor differences in orthologous sets from Xenopus, human and chicken; this is remarkable in view of the very many nucleotide substitutions that occurred over the long evolutionary times separating these species; (ii) GC-rich genes, that underwent the compositional transition, showed large differences between Xenopus and warm-blooded vertebrates, but not between chicken and human. In other words, the independent changes that occurred in avian and mammalian genes, on the average, were the same.

Amino Acids↗

PubMed1999

Different hydrophobicities of orthologous proteins from Xenopus and human.

A compositional transition was previously detected by comparing orthologous coding sequences from cold- and warm-blooded vertebrates (see Bernardi, G., Hughes, S., Mouchiroud, D., 1997. The major compositional transitions in the vertebrate genome. J. Mol. Evol. 44, S44-S51 for a review). The transition is characterized by higher GC levels (GC is the molar ratio of guanine+cytosine in DNA) and, especially, by higher GC3 levels (GC3 is the GC level of third codon positions) in coding sequences from warm-blooded vertebrates. This transition essentially affects GC-rich genes, although the nucleotide substitution rate is of the same order of magnitude in both GC-poor and GC-rich genes. In order to understand the evolutionary basis of the changes, we have compared the hydrophobicity of orthologous proteins from Xenopus and human. Although the differences are small in proteins encoded by coding sequences ranging from 0 to 65% in GC3, they are large in the proteins encoded by sequences characterized by GC3 values higher than 65%. The latter proteins are more hydrophobic in human than in Xenopus.

Amino Acid Sequence↗

PubMed1999

Evolutionary genomics of vertebrates and its implications.

The discovery that the vertebrate genomes of warm-blooded vertebrates are mosaics of isochores, long DNA segments homogeneous in base composition, yet belonging to families covering a broad spectrum of GC levels, has led to two major observations. The first is that gene density is strikingly non-uniform in the genome of all vertebrates, gene concentration increasing with increasing GC levels. (Although the genomes of cold-blooded vertebrates are characterized by smaller compositional heterogeneities than those of warm-blooded vertebrates and high GC levels are not attained, their gene distribution is basically similar to that of warm-blooded vertebrates.) The second observation is that the GC-richest and gene-richest isochores underwent a compositional transition (characterized by a strong increase in GC level) between cold- and warm-blooded vertebrates. Evidence to be discussed favors the idea that this compositional transition and the ensuing highly heterogeneous compositional pattern was due to, and was maintained by, natural selection.

Animals↗