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An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences.

Carels N, Ponce de Leon M - Bioinform Biol Insights (2015)

Bottom Line: We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins.Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller's spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth.These amino acids match the hydropathy and secondary structures of modern proteins.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Modelagem de Sistemas Biológicos, National Institute for Science and Technology on Innovation in Neglected Diseases (INCT/IDN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.

ABSTRACT
Purine bias, which is usually referred to as an "ancestral codon", is known to result in short-range correlations between nucleotides in coding sequences, and it is common in all species. We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins. Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller's spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth. These amino acids match the hydropathy and secondary structures of modern proteins.

No MeSH data available.


Distribution of CDSs according to G (average G1, G2, G3), G1, G2 in C. reinhardtii (A) and P. falciparum (B). Bold lines are for G, thin lines are for G1, and dash lines are for G2.
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f1-bbi-9-2015-037: Distribution of CDSs according to G (average G1, G2, G3), G1, G2 in C. reinhardtii (A) and P. falciparum (B). Bold lines are for G, thin lines are for G1, and dash lines are for G2.

Mentions: Short-range correlations among nucleotides in CDSs can be analyzed in heterogeneous genomes, ie, genomes whose CDSs cover a wide range of GC variation (>50%) in third codon position (GC3), such as the Homo sapiens and Oryza sativa genomes, or homogeneous genomes (GC3 variation <50%) at different positions of the universal correlation regression line (see Fig. 1 in Ref. 39). The universal correlation, shown for the first time by Sueoka,40 describes the linear relationship that species display when their genomes are plotted for the average GC3 versus GC in the second codon position (GC2) of their CDSs. In eukaryotes, the genomes at both boundaries of this relationship are Plasmodium falciparum (AT-rich) and Chlamydomonas reinhardtii (GC-rich).


An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences.

Carels N, Ponce de Leon M - Bioinform Biol Insights (2015)

Distribution of CDSs according to G (average G1, G2, G3), G1, G2 in C. reinhardtii (A) and P. falciparum (B). Bold lines are for G, thin lines are for G1, and dash lines are for G2.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4401237&req=5

f1-bbi-9-2015-037: Distribution of CDSs according to G (average G1, G2, G3), G1, G2 in C. reinhardtii (A) and P. falciparum (B). Bold lines are for G, thin lines are for G1, and dash lines are for G2.
Mentions: Short-range correlations among nucleotides in CDSs can be analyzed in heterogeneous genomes, ie, genomes whose CDSs cover a wide range of GC variation (>50%) in third codon position (GC3), such as the Homo sapiens and Oryza sativa genomes, or homogeneous genomes (GC3 variation <50%) at different positions of the universal correlation regression line (see Fig. 1 in Ref. 39). The universal correlation, shown for the first time by Sueoka,40 describes the linear relationship that species display when their genomes are plotted for the average GC3 versus GC in the second codon position (GC2) of their CDSs. In eukaryotes, the genomes at both boundaries of this relationship are Plasmodium falciparum (AT-rich) and Chlamydomonas reinhardtii (GC-rich).

Bottom Line: We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins.Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller's spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth.These amino acids match the hydropathy and secondary structures of modern proteins.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Modelagem de Sistemas Biológicos, National Institute for Science and Technology on Innovation in Neglected Diseases (INCT/IDN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.

ABSTRACT
Purine bias, which is usually referred to as an "ancestral codon", is known to result in short-range correlations between nucleotides in coding sequences, and it is common in all species. We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins. Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller's spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth. These amino acids match the hydropathy and secondary structures of modern proteins.

No MeSH data available.