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Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force.

Aledo JC, Valverde H, Ruíz-Camacho M, Morilla I, López FD - Genome Biol Evol (2014)

Bottom Line: Herein, using evolutionary data in combination with structural information of COX, we show that failing to discern the effects of interaction from other structural and functional effects can lead to deceptive conclusions such as the "optimizing hypothesis." Once spurious factors have been accounted for, data analysis shows that mtDNA-encoded residues engaged in contacts are, in general, more constrained than their noncontact counterparts.This differential behavior cannot be explained on the basis of predicted thermodynamic stability, as interactions between mtDNA-encoded subunits contribute more weakly to the complex stability than those interactions between subunits encoded by different genomes.Therefore, the higher conservation observed among mtDNA-encoded residues involved in intragenome interactions is likely due to factors other than structural stability.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain caledo@uma.es.

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Residues involved in Mt–mt interactions are broadly conserved through phylogeny. The phylogenetic relationship among the 371 mammalian species of this study was reconstructed. The obtained tree was used to calculate the number of nonsynonymous substitutions per nonsynonymous site on a lineage-by-lineage basis, using the program “codeml” from the PAML package. In this way, within each category of codons, the dN was computed for each of the 739 branches. To assess whether the dN values within a codon category tend to be higher or lower than the dN values computed for other codon category, we proceeded in the following way. For a given branch, the difference dNMt–nu − dNMt–mt was calculated. Afterwards, using data from all the branches, an abundance histogram was plotted.
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evu240-F8: Residues involved in Mt–mt interactions are broadly conserved through phylogeny. The phylogenetic relationship among the 371 mammalian species of this study was reconstructed. The obtained tree was used to calculate the number of nonsynonymous substitutions per nonsynonymous site on a lineage-by-lineage basis, using the program “codeml” from the PAML package. In this way, within each category of codons, the dN was computed for each of the 739 branches. To assess whether the dN values within a codon category tend to be higher or lower than the dN values computed for other codon category, we proceeded in the following way. For a given branch, the difference dNMt–nu − dNMt–mt was calculated. Afterwards, using data from all the branches, an abundance histogram was plotted.

Mentions: As it can be observed in figure 3, among all exposed residues, those involved in interactions between different mtDNA-encoded chains were the most constrained, showing both the lowest ω and ΣdN values, regardless of the mtDNA-encoded subunit being considered. This observation indicates a much stronger purifying selection among Mt–mt Contact residues than among Mt–nu Contact amino acids. To substantiate this conclusion, we next assessed whether this differential behavior of the two subsets of contact residues had a broad phylogenetic distribution and was present in most mammalian lineages. To this end, we used the reconstructed tree to apportion the COX I nonsynonymous substitutions for the two categories of contact sites. Figure 8 shows the distribution of the statistic dNMt–nu − dNMt–mt among the phylogenetic tree branches, which was clearly biased toward positive values. Overall, these results suggest that those mtDNA-encoded residues in contact with mtDNA-encoded residues from a different chain are subjected to stronger constraints than those involved in interactions with nDNA-encoded subunits. In addition, this behavior seems to have a broad phylogenetic distribution and is valid for most mammalian lineages. To the best of our knowledge, this is the first quantitative study supporting such a conclusion.Fig. 8.—


Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force.

Aledo JC, Valverde H, Ruíz-Camacho M, Morilla I, López FD - Genome Biol Evol (2014)

Residues involved in Mt–mt interactions are broadly conserved through phylogeny. The phylogenetic relationship among the 371 mammalian species of this study was reconstructed. The obtained tree was used to calculate the number of nonsynonymous substitutions per nonsynonymous site on a lineage-by-lineage basis, using the program “codeml” from the PAML package. In this way, within each category of codons, the dN was computed for each of the 739 branches. To assess whether the dN values within a codon category tend to be higher or lower than the dN values computed for other codon category, we proceeded in the following way. For a given branch, the difference dNMt–nu − dNMt–mt was calculated. Afterwards, using data from all the branches, an abundance histogram was plotted.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4255772&req=5

evu240-F8: Residues involved in Mt–mt interactions are broadly conserved through phylogeny. The phylogenetic relationship among the 371 mammalian species of this study was reconstructed. The obtained tree was used to calculate the number of nonsynonymous substitutions per nonsynonymous site on a lineage-by-lineage basis, using the program “codeml” from the PAML package. In this way, within each category of codons, the dN was computed for each of the 739 branches. To assess whether the dN values within a codon category tend to be higher or lower than the dN values computed for other codon category, we proceeded in the following way. For a given branch, the difference dNMt–nu − dNMt–mt was calculated. Afterwards, using data from all the branches, an abundance histogram was plotted.
Mentions: As it can be observed in figure 3, among all exposed residues, those involved in interactions between different mtDNA-encoded chains were the most constrained, showing both the lowest ω and ΣdN values, regardless of the mtDNA-encoded subunit being considered. This observation indicates a much stronger purifying selection among Mt–mt Contact residues than among Mt–nu Contact amino acids. To substantiate this conclusion, we next assessed whether this differential behavior of the two subsets of contact residues had a broad phylogenetic distribution and was present in most mammalian lineages. To this end, we used the reconstructed tree to apportion the COX I nonsynonymous substitutions for the two categories of contact sites. Figure 8 shows the distribution of the statistic dNMt–nu − dNMt–mt among the phylogenetic tree branches, which was clearly biased toward positive values. Overall, these results suggest that those mtDNA-encoded residues in contact with mtDNA-encoded residues from a different chain are subjected to stronger constraints than those involved in interactions with nDNA-encoded subunits. In addition, this behavior seems to have a broad phylogenetic distribution and is valid for most mammalian lineages. To the best of our knowledge, this is the first quantitative study supporting such a conclusion.Fig. 8.—

Bottom Line: Herein, using evolutionary data in combination with structural information of COX, we show that failing to discern the effects of interaction from other structural and functional effects can lead to deceptive conclusions such as the "optimizing hypothesis." Once spurious factors have been accounted for, data analysis shows that mtDNA-encoded residues engaged in contacts are, in general, more constrained than their noncontact counterparts.This differential behavior cannot be explained on the basis of predicted thermodynamic stability, as interactions between mtDNA-encoded subunits contribute more weakly to the complex stability than those interactions between subunits encoded by different genomes.Therefore, the higher conservation observed among mtDNA-encoded residues involved in intragenome interactions is likely due to factors other than structural stability.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain caledo@uma.es.

Show MeSH