Respiratory complexes are encoded by two genomes (mitochondrial DNA [mtDNA] and nuclear DNA [nDNA]). Although the importance of intergenomic coadaptation is acknowledged, the forces and constraints shaping such coevolution are largely unknown. Previous works using cytochrome c oxidase (COX) as a model enzyme have led to the so-called “optimizing interaction” hypothesis. According to this view, mtDNA-encoded residues close to nDNA-encoded residues evolve faster than the rest of positions, favoring the optimization of protein–protein interfaces. 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. Nevertheless, noncontact residues from the surface of COX I subunit are a remarkable exception, being subjected to an exceptionally high purifying selection that may be related to the maintenance of a suitable heme environment. We also report that mtDNA-encoded residues involved in contacts with other mtDNA-encoded subunits are more constrained than mtDNA-encoded residues interacting with nDNA-encoded polypeptides. 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.

By using a combination of evolutionary and structural data from 231 species, we have addressed the relationship between evolution and structural features of cytochrome b and COX I, two mtDNA-encoded proteins. The interior of cytochrome b, in contrast to that of COX I, exhibits a remarkable tolerance to changes. The higher evolvability of cytochrome b contrasts with the lower rate of synonymous substitutions of its gene when compared to that of COX I, suggesting that the latter is subjected to a stronger purifying selection. We present evidences that the stability effect of mutations (ΔΔG) may be behind these differential behaviour.

Motivation The oxidation of protein-bound methionine to form methionine sulfoxide has traditionally been regarded as an oxidative damage. However, growing evidences support the view of this reversible reaction also as a regulatory post-translational modification. Thus, the oxidation of methionine residues has been reported to have multiple and varied implications for protein function. However, despite the importance of this modification and the abundance of reports, all these data are scattered in the literature. No database/resource on methionine sulfoxidation exists currently. Since this information is useful to gain further insights into the redox regulation of cellular proteins, we have created a primary database of experimentally confirmed sulfoxidation sites. Results MetOSite currently contains 7242 methionine sulfoxide sites found in 3562 different proteins from 23 species, with Homo sapiens, Arabidopsis thaliana and Bacillus cereus as the main contributors. Each collected site has been classified according to the effect of its sulfoxidation on the biological properties of the modified protein. Thus, MetOSite documents cases where the sulfoxidation of methionine leads to (i) gain of activity, (ii) loss of activity, (iii) increased protein–protein interaction susceptibility, (iv) decreased protein–protein interaction susceptibility, (v) changes in protein stability and (vi) changes in subcellular location. Availability and implementation MetOSite is available at https://metosite.uma.es.

During the course of evolution, amino acid shifts might have resulted in mitochondrial proteomes better endowed to resist oxidative stress. However, owing to the problem of distinguishing between functional constraints/adaptations in protein sequences and mutationdriven biases in the composition of these sequences, the adaptive value of such amino acid shifts remains under discussion. We have analyzed the coding sequences of mtDNA from 173 mammalian species, dissecting the effect of nucleotide composition on amino acid usages. We found remarkable cysteine avoidance in mtDNA-encoded proteins. However, no effect of longevity on cysteine content could be detected. On the other hand, nucleotide compositional shifts fully accounted for threonine usages. In spite of a strong effect of mutational bias on methionine abundances, our results suggest a role of selection in determining the composition of methionine. Whether this selective effect is linked or not to protection against oxidative stress is still a subject of debate.

Con la finalidad de evaluar el uso de enzimas comerciales Ronozyme, SSF, VegPro e Hyboteck (Yucca schidigera) en la cría y engorde de pollos broilers en época lluviosa se estableció un ensayo en tres provincias: Los Ríos (Quevedo), Santo Domingo de los Tsáchilas (Santo Domingo de los Colorados) y Cotopaxi (Salcedo), utilizando un total de 1,440 aves de línea Hubbard (480 por localidad). Se empleó un Diseño Completamente al Azar, con cuatro tratamientos (enzimas) y seis repeticiones con 20 pollos como unidad experimental. Las variables evaluadas fueron: consumo de alimento (g), ganancia de peso (g), conversión alimenticia, rendimiento a la canal (%), relación Costo/Beneficio y análisis bromatológicos de las canales. Se observó que los mayores consumo de alimento en las tres localidades se presentó con Hyboteck, (5,181.21; 6,713.42 y 5,680.37 g); la mejor ganancia de peso se observó con VegPro en Quevedo (2,543.34 g), SSF Santo Domingo de los Colorados (3,497.83 g) e Hyboteck en Salcedo (2,286.08 g), la conversión más eficiente se reportó con Ronozyme en Quevedo (1.76), SSF en Santo Domingo de los Colorados (1.88), y VegPro en Salcedo (2.55). La mayor relación costo / beneficio se presentó con SSF en las localidades de Santo Domingo de los Colorados (0.10) y Salcedo (0.21) mientras en Quevedo la mejor fue Ronozyme (0.26). El mejor valor proteico de las canales de pollos se reportaron en las localidades de Quevedo y Salcedo con Ronozyme (26.05 y 22.80% respectivamente), y para la localidad de Santo Domingo de los Colorados fue con SSF (25.35% de proteína).