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High correlation between the turnover of nucleotides under mutational pressure and the DNA composition.

Kowalczuk M, Mackiewicz P, Mackiewicz D, Nowicka A, Dudkiewicz M, Dudek MR, Cebrat S - BMC Evol. Biol. (2001)

Bottom Line: However, it is important to discriminate between the effect of mutations, and the effect of selection, when studying the phylogenic relations between taxa.We have tested in computer simulations, and analytically, the available substitution matrices for many genomes, and we have found that DNA strands in equilibrium under mutational pressure have unique feature: the fraction of each type of nucleotide is linearly dependent on the time needed for substitution of half of nucleotides of a given type, with a correlation coefficient close to 1.Substitution matrices found for sequences under selection pressure do not have this property.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Microbiology, Wroclaw University, ul Przybyszewskiego 63/77, 51-148 Wroclaw, Poland. kowal@microb.uni.wroc.pl

ABSTRACT

Background: Any DNA sequence is a result of compromise between the selection and mutation pressures exerted on it during evolution. It is difficult to estimate the relative influence of each of these pressures on the rate of accumulation of substitutions. However, it is important to discriminate between the effect of mutations, and the effect of selection, when studying the phylogenic relations between taxa.

Results: We have tested in computer simulations, and analytically, the available substitution matrices for many genomes, and we have found that DNA strands in equilibrium under mutational pressure have unique feature: the fraction of each type of nucleotide is linearly dependent on the time needed for substitution of half of nucleotides of a given type, with a correlation coefficient close to 1. Substitution matrices found for sequences under selection pressure do not have this property. A substitution matrix for the leading strand of the Borrelia burgdorferi genome, having reached equilibrium in computer simulation, gives a DNA sequence with nucleotide composition and asymmetry corresponding precisely to the third positions in codons of protein coding genes located on the leading strand.

Conclusions: Parameters of mutational pressure allow us to count DNA composition in equilibrium with this mutational pressure. Comparing any real DNA sequence with the sequence in equilibrium it is possible to estimate the distance between these sequences, which could be used as a measure of the selection pressure. Furthermore, the parameters of the mutational pressure enable direct estimation of the relative mutation rates in any DNA sequence in the studied genome.

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Related in: MedlinePlus

Changes in the nucleotide composition of the first positions in codons of B. burgdorferi coding sequences from the leading strand under BbTS mutational pressure. Descriptions as for Fig. 1 and 2. Note that the fractions of nucleotides which have not been substituted are exactly as in Fig. 2A but the fractions of nucleotides which substituted other nucleotides are far from being symmetrical to the first ones.
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Figure 3: Changes in the nucleotide composition of the first positions in codons of B. burgdorferi coding sequences from the leading strand under BbTS mutational pressure. Descriptions as for Fig. 1 and 2. Note that the fractions of nucleotides which have not been substituted are exactly as in Fig. 2A but the fractions of nucleotides which substituted other nucleotides are far from being symmetrical to the first ones.

Mentions: The implications of such evolutionary established relations between the DNA composition and the turnover rates of nucleotides would have a great impact on the understanding of the genomes evolution itself. It gives the possibility of estimating the relations between the mutational pressure exerted on specific nucleotides of each genome analytically i.e. by simple computing the nucleotide composition of sequences which are not subject to selection pressure. Having the mutational pressure in terms of nucleotide turnover, one can estimate the selection pressure exerted on any sequence or position in codons. For example, see what would be the fate of the first positions of ORFs from the leading strand of the B. burgdorferi genome under the BbTS molecular pressure, without selection (Fig. 3). Note that the half time of substitutions of each nucleotide is the same as for other sequences under such mutational pressure, but the rate of appearing of new nucleotides is different and the composition of the sequence would change non-linearly during evolution. It is also simple to count, from the results of computer simulations, the corrections for multiple substitutions and reversions, which is important for estimating the real divergence time. It is clear that such corrections should be counted considering different contributions of each nucleotide turnover in the overall frequencies of multiple substitutions. Having precise mutational pressure one can predict not only the selection pressure but also find the history of the sequence.


High correlation between the turnover of nucleotides under mutational pressure and the DNA composition.

Kowalczuk M, Mackiewicz P, Mackiewicz D, Nowicka A, Dudkiewicz M, Dudek MR, Cebrat S - BMC Evol. Biol. (2001)

Changes in the nucleotide composition of the first positions in codons of B. burgdorferi coding sequences from the leading strand under BbTS mutational pressure. Descriptions as for Fig. 1 and 2. Note that the fractions of nucleotides which have not been substituted are exactly as in Fig. 2A but the fractions of nucleotides which substituted other nucleotides are far from being symmetrical to the first ones.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC64649&req=5

Figure 3: Changes in the nucleotide composition of the first positions in codons of B. burgdorferi coding sequences from the leading strand under BbTS mutational pressure. Descriptions as for Fig. 1 and 2. Note that the fractions of nucleotides which have not been substituted are exactly as in Fig. 2A but the fractions of nucleotides which substituted other nucleotides are far from being symmetrical to the first ones.
Mentions: The implications of such evolutionary established relations between the DNA composition and the turnover rates of nucleotides would have a great impact on the understanding of the genomes evolution itself. It gives the possibility of estimating the relations between the mutational pressure exerted on specific nucleotides of each genome analytically i.e. by simple computing the nucleotide composition of sequences which are not subject to selection pressure. Having the mutational pressure in terms of nucleotide turnover, one can estimate the selection pressure exerted on any sequence or position in codons. For example, see what would be the fate of the first positions of ORFs from the leading strand of the B. burgdorferi genome under the BbTS molecular pressure, without selection (Fig. 3). Note that the half time of substitutions of each nucleotide is the same as for other sequences under such mutational pressure, but the rate of appearing of new nucleotides is different and the composition of the sequence would change non-linearly during evolution. It is also simple to count, from the results of computer simulations, the corrections for multiple substitutions and reversions, which is important for estimating the real divergence time. It is clear that such corrections should be counted considering different contributions of each nucleotide turnover in the overall frequencies of multiple substitutions. Having precise mutational pressure one can predict not only the selection pressure but also find the history of the sequence.

Bottom Line: However, it is important to discriminate between the effect of mutations, and the effect of selection, when studying the phylogenic relations between taxa.We have tested in computer simulations, and analytically, the available substitution matrices for many genomes, and we have found that DNA strands in equilibrium under mutational pressure have unique feature: the fraction of each type of nucleotide is linearly dependent on the time needed for substitution of half of nucleotides of a given type, with a correlation coefficient close to 1.Substitution matrices found for sequences under selection pressure do not have this property.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Microbiology, Wroclaw University, ul Przybyszewskiego 63/77, 51-148 Wroclaw, Poland. kowal@microb.uni.wroc.pl

ABSTRACT

Background: Any DNA sequence is a result of compromise between the selection and mutation pressures exerted on it during evolution. It is difficult to estimate the relative influence of each of these pressures on the rate of accumulation of substitutions. However, it is important to discriminate between the effect of mutations, and the effect of selection, when studying the phylogenic relations between taxa.

Results: We have tested in computer simulations, and analytically, the available substitution matrices for many genomes, and we have found that DNA strands in equilibrium under mutational pressure have unique feature: the fraction of each type of nucleotide is linearly dependent on the time needed for substitution of half of nucleotides of a given type, with a correlation coefficient close to 1. Substitution matrices found for sequences under selection pressure do not have this property. A substitution matrix for the leading strand of the Borrelia burgdorferi genome, having reached equilibrium in computer simulation, gives a DNA sequence with nucleotide composition and asymmetry corresponding precisely to the third positions in codons of protein coding genes located on the leading strand.

Conclusions: Parameters of mutational pressure allow us to count DNA composition in equilibrium with this mutational pressure. Comparing any real DNA sequence with the sequence in equilibrium it is possible to estimate the distance between these sequences, which could be used as a measure of the selection pressure. Furthermore, the parameters of the mutational pressure enable direct estimation of the relative mutation rates in any DNA sequence in the studied genome.

Show MeSH
Related in: MedlinePlus