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Does codon bias have an evolutionary origin?

Biro JC - Theor Biol Med Model (2008)

Bottom Line: Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB.Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise.The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Homulus Foundation, 612 S Flower St, Los Angeles, CA 90017, USA. jan.biro@att.net

ABSTRACT

Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information about the origin and evolution of this bias.

Results: Codon Usage Bias (CUB, defined here as deviation from equal usage of synonymous codons) was studied in 113 species. The average CUB was 29.3 +/- 1.1% (S.E.M, n = 113) of the theoretical maximum and declined progressively with evolution and increasing genome complexity. A Pan-Genomic Codon Usage Frequency (CUF) Table was constructed to describe genome-wide relationships among codons. Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB. Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise. These strong correlations made it possible to predict missing synonymous codons (wobble bases) reliably from the remaining codons or codon residues.

Conclusion: The results put the concept of "codon bias" into a novel perspective. The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.

Show MeSH
Correlation between Codon Bases in Codons of 113 Species. The frequency of the four possible nucleotide bases (A, T, G, G) in the 3 possible codons positions (1st. 2nd, 3rd) were counted in 113 codon usage tables and plotted against each other. A1+T1 > A3 means the correlation between the sum of the 1st A plus 1st T frequencies and the 3rd A frequency (n = 113).
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Figure 7: Correlation between Codon Bases in Codons of 113 Species. The frequency of the four possible nucleotide bases (A, T, G, G) in the 3 possible codons positions (1st. 2nd, 3rd) were counted in 113 codon usage tables and plotted against each other. A1+T1 > A3 means the correlation between the sum of the 1st A plus 1st T frequencies and the 3rd A frequency (n = 113).

Mentions: I used the correlation between the sum of complementary codon pairs in the 1st and 2nd codon positions to predict the wobble bases using the frequencies for 113 different species (Table 4, Figure 7). This is of course a prediction of the frequencies of the four wobble bases in all 64 possible codons and has no predictive value for individual wobble bases belonging to individual amino acids. All these correlation were of course carefully compared to corresponding random controls. Care was taken to ensure that the randomized control samples had the same size and distribution as the test samples. The sum of randomized fractions was kept equal to 1, as in the test samples. There were no correlations between the corresponding nucleotides in the control samples.


Does codon bias have an evolutionary origin?

Biro JC - Theor Biol Med Model (2008)

Correlation between Codon Bases in Codons of 113 Species. The frequency of the four possible nucleotide bases (A, T, G, G) in the 3 possible codons positions (1st. 2nd, 3rd) were counted in 113 codon usage tables and plotted against each other. A1+T1 > A3 means the correlation between the sum of the 1st A plus 1st T frequencies and the 3rd A frequency (n = 113).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2519059&req=5

Figure 7: Correlation between Codon Bases in Codons of 113 Species. The frequency of the four possible nucleotide bases (A, T, G, G) in the 3 possible codons positions (1st. 2nd, 3rd) were counted in 113 codon usage tables and plotted against each other. A1+T1 > A3 means the correlation between the sum of the 1st A plus 1st T frequencies and the 3rd A frequency (n = 113).
Mentions: I used the correlation between the sum of complementary codon pairs in the 1st and 2nd codon positions to predict the wobble bases using the frequencies for 113 different species (Table 4, Figure 7). This is of course a prediction of the frequencies of the four wobble bases in all 64 possible codons and has no predictive value for individual wobble bases belonging to individual amino acids. All these correlation were of course carefully compared to corresponding random controls. Care was taken to ensure that the randomized control samples had the same size and distribution as the test samples. The sum of randomized fractions was kept equal to 1, as in the test samples. There were no correlations between the corresponding nucleotides in the control samples.

Bottom Line: Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB.Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise.The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Homulus Foundation, 612 S Flower St, Los Angeles, CA 90017, USA. jan.biro@att.net

ABSTRACT

Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information about the origin and evolution of this bias.

Results: Codon Usage Bias (CUB, defined here as deviation from equal usage of synonymous codons) was studied in 113 species. The average CUB was 29.3 +/- 1.1% (S.E.M, n = 113) of the theoretical maximum and declined progressively with evolution and increasing genome complexity. A Pan-Genomic Codon Usage Frequency (CUF) Table was constructed to describe genome-wide relationships among codons. Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB. Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise. These strong correlations made it possible to predict missing synonymous codons (wobble bases) reliably from the remaining codons or codon residues.

Conclusion: The results put the concept of "codon bias" into a novel perspective. The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.

Show MeSH