Biomedical subjects

Christian J Michel

Publications and source records attributed to Christian J Michel.

6 recordsLinked to original sources

PubMed2006

An analytical model of gene evolution with 9 mutation parameters: an application to the amino acids coded by the common circular code.

We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64 x 64 with nine substitution parameters associated with the three types of substitutions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4 x 4 and the trinucleotide mutation matrix 64 x 64 with three and six parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to these nine substitution parameters. An application of this model allows an evolutionary study of the common circular code [Formula: see text] of eukaryotes and prokaryotes and its 12 coded amino acids. The main property of this code [Formula: see text] is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. However, since its identification in 1996, amino acid information coded by [Formula: see text] has never been studied. Very unexpectedly, this evolutionary model demonstrates that random substitutions in this code [Formula: see text] and with particular values for the nine substitutions parameters retrieve after a certain time of evolution a frequency distribution of these 12 amino acids very close to the one coded by the actual genes.

Amino Acids↗

PubMed2006

Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes.

We developed a statistical method that allows each trinucleotide to be associated with a unique frame among the three possible ones in a (protein coding) gene. An extensive gene study in 175 complete bacterial genomes based on this statistical approach resulted in identification of 72 new circular codes. Finding a circular code enables an immediate retrieval of the reading frame locally anywhere in a gene. No knowledge of location of the start codon is required and a short window of only a few nucleotides is sufficient for automatic retrieval. We have therefore developed a factorization method (that explores previously found circular codes) for retrieving the reading frames of bacterial genes. Its principle is new and easy to understand. Neither complex treatment nor specific information on the nucleotide sequences is necessary. Moreover, the method can be used for short regions in nucleotide sequences (less than 25 nucleotides in protein coding genes). Selected additional properties of circular codes and their possible biological consequences are also discussed.

Base Sequence↗

PubMed2006

An analytical model of gene evolution with six mutation parameters: an application to archaeal circular codes.

We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64 x 64 with six substitution parameters associated with the transitions and transversions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4 x 4 and the trinucleotide mutation matrix 64 x 64 with three parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to six substitution parameters. An application of this model allows an evolutionary study of the common circular code COM and the 15 archaeal circular codes X which have been recently identified in several archaeal genomes. The main property of a circular code is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. In genes, the circular code is superimposed on the traditional genetic one. Very unexpectedly, the evolutionary model demonstrates that the archaeal circular codes can derive from the common circular code subjected to random substitutions with particular values for six substitutions parameters. It has a strong correlation with the statistical observations of three archaeal codes in actual genes. Furthermore, the properties of these substitution rates allow proposal of an evolutionary classification of the 15 archaeal codes into three main classes according to this model. In almost all the cases, they agree with the actual degeneracy of the genetic code with substitutions more frequent in the third trinucleotide site and with transitions more frequent that transversions in any trinucleotide site.

Archaea↗

PubMed2004

A stochastic gene evolution model with time dependent mutations.

We develop here a new class of gene evolution models in which the nucleotide mutations are time dependent. These models allow to study nonlinear gene evolution by accelerating or decelerating the mutation rates at different evolutionary times. They generalize the previous ones which are based on constant mutation rates. The stochastic model developed in this class determines at some time t the occurrence probabilities of trinucleotides mutating according to 3 time dependent substitution parameters associated with the 3 trinucleotide sites. Therefore, it allows to simulate the evolution of the circular code recently observed in genes. By varying the class of function for the substitution parameters, 1 among 12 models retrieves after mutation the statistical properties of the observed circular code in the 3 frames of actual genes. In this model, the mutation rate in the 3rd trinucleotide site increases during gene evolution while the mutation rates in the 1st and 2nd sites decrease. This property agrees with the actual degeneracy of the genetic code. This approach can easily be generalized to study evolution of motifs of various lengths, e.g., dicodons, etc., with time dependent mutations.

Codon↗

PubMed2003

Circular codes in archaeal genomes.

A new statistical method associating each trinucleotide with a frame is developed for identifying circular codes. Its sensibility allows the detection of several circular codes in the (protein coding) genes of archaeal genomes. Several properties of these circular codes are described, in particular the lengths of the minimal windows to retrieve the construction frames, a new definition of a parameter for measuring some probabilities of words generated by the circular codes, and the types of nucleotides in the trinucleotide sites. Some biological consequences are presented in Discussion.

Archaea↗

PubMedDate not supplied

Identification of protein coding genes in genomes with statistical functions based on the circular code.

A new statistical approach using functions based on the circular code classifies correctly more than 93% of bases in protein (coding) genes and non-coding genes of human sequences. Based on this statistical study, a research software called 'Analysis of Coding Genes' (ACG) has been developed for identifying protein genes in the genomes and for determining their frame. Furthermore, the software ACG also allows an evaluation of the length of protein genes, their position in the genome, their relative position between themselves, and the prediction of internal frames in protein genes.

Base Sequence↗