Limits...
Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes?

Zhang F, Broughton RE - Genome Biol Evol (2013)

Bottom Line: The results from a combined analysis of all OXPHOS subunits fit the predictions of the hypothesis.However, results from two OXPHOS complexes did not fit this pattern when analyzed separately.We found that the d(N) of nu OXPHOS genes for "core" subunits (those involved in the major catalytic activity) was lower than that of "noncore" subunits, whereas there was no significant difference in d(N) between genes for nu non-OXPHOS and core subunits.

View Article: PubMed Central - PubMed

Affiliation: Oklahoma Biological Survey and Department of Biology, University of Oklahoma.

ABSTRACT
Oxidative phosphorylation (OXPHOS), the major energy-producing pathway in aerobic organisms, includes protein subunits encoded by both mitochondrial (mt) and nuclear (nu) genomes. How these independent genomes have coevolved is a long-standing question in evolutionary biology. Although mt genes evolve faster than most nu genes, maintenance of OXPHOS structural stability and functional efficiency may involve correlated evolution of mt and nu OXPHOS genes. The nu OXPHOS genes might be predicted to exhibit accelerated evolutionary rates to accommodate the elevated substitution rates of mt OXPHOS subunits with which they interact. Evolutionary rates of nu OXPHOS genes should, therefore, be higher than that of nu genes that are not involved in OXPHOS (nu non-OXPHOS). We tested the compensatory evolution hypothesis by comparing the evolutionary rates (synonymous substitution rate dS and nonsynonymous substitution rate dN) among 13 mt OXPHOS genes, 60 nu OXPHOS genes, and 77 nu non-OXPHOS genes in vertebrates (7 fish and 40 mammal species). The results from a combined analysis of all OXPHOS subunits fit the predictions of the hypothesis. However, results from two OXPHOS complexes did not fit this pattern when analyzed separately. We found that the d(N) of nu OXPHOS genes for "core" subunits (those involved in the major catalytic activity) was lower than that of "noncore" subunits, whereas there was no significant difference in d(N) between genes for nu non-OXPHOS and core subunits. This latter finding suggests that compensatory changes play a minor role in the evolution of OXPHOS genes and that the observed accelerated nu substitution rates are due largely to reduced functional constraint on noncore subunits.

Show MeSH

Related in: MedlinePlus

Comparison of synonymous substitution rate (dS) and nonsynonymous substitution rate (dN) among mitochondrial oxidative phosphorylation (mt OXPHOS), nuclear core OXPHOS (nu core OXPHOS), nuclear noncore OXPHOS (nu noncore OXPHOS), and non-OXPHOS genes in 7 fishes (A, B) and 40 mammals (C, D). Whisker-ends are at the 5th and 95th percentiles. *P < 0.05, **P < 0.01, ***P < 0.001.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3814189&req=5

evt129-F4: Comparison of synonymous substitution rate (dS) and nonsynonymous substitution rate (dN) among mitochondrial oxidative phosphorylation (mt OXPHOS), nuclear core OXPHOS (nu core OXPHOS), nuclear noncore OXPHOS (nu noncore OXPHOS), and non-OXPHOS genes in 7 fishes (A, B) and 40 mammals (C, D). Whisker-ends are at the 5th and 95th percentiles. *P < 0.05, **P < 0.01, ***P < 0.001.

Mentions: Because of their different functions and interactions, OXPHOS genes may be under different levels of functional constraint, so we separated them into core and noncore groups. Core subunits were defined as those that have bacterial homologs and that participate directly in electron transport or ATP synthesis. After partitioning, dS of mt OXPHOS genes was found to be significantly higher than that of all nu gene groups (fig. 4A and C), whereas the dN of noncore OXPHOS genes was higher than that of core OXPHOS genes (fig. 4B and D). There were no significant differences in dN between nu non-OXPHOS genes and nu core OXPHOS genes (fig. 4B and D, table 2).Fig. 4.—


Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes?

Zhang F, Broughton RE - Genome Biol Evol (2013)

Comparison of synonymous substitution rate (dS) and nonsynonymous substitution rate (dN) among mitochondrial oxidative phosphorylation (mt OXPHOS), nuclear core OXPHOS (nu core OXPHOS), nuclear noncore OXPHOS (nu noncore OXPHOS), and non-OXPHOS genes in 7 fishes (A, B) and 40 mammals (C, D). Whisker-ends are at the 5th and 95th percentiles. *P < 0.05, **P < 0.01, ***P < 0.001.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814189&req=5

evt129-F4: Comparison of synonymous substitution rate (dS) and nonsynonymous substitution rate (dN) among mitochondrial oxidative phosphorylation (mt OXPHOS), nuclear core OXPHOS (nu core OXPHOS), nuclear noncore OXPHOS (nu noncore OXPHOS), and non-OXPHOS genes in 7 fishes (A, B) and 40 mammals (C, D). Whisker-ends are at the 5th and 95th percentiles. *P < 0.05, **P < 0.01, ***P < 0.001.
Mentions: Because of their different functions and interactions, OXPHOS genes may be under different levels of functional constraint, so we separated them into core and noncore groups. Core subunits were defined as those that have bacterial homologs and that participate directly in electron transport or ATP synthesis. After partitioning, dS of mt OXPHOS genes was found to be significantly higher than that of all nu gene groups (fig. 4A and C), whereas the dN of noncore OXPHOS genes was higher than that of core OXPHOS genes (fig. 4B and D). There were no significant differences in dN between nu non-OXPHOS genes and nu core OXPHOS genes (fig. 4B and D, table 2).Fig. 4.—

Bottom Line: The results from a combined analysis of all OXPHOS subunits fit the predictions of the hypothesis.However, results from two OXPHOS complexes did not fit this pattern when analyzed separately.We found that the d(N) of nu OXPHOS genes for "core" subunits (those involved in the major catalytic activity) was lower than that of "noncore" subunits, whereas there was no significant difference in d(N) between genes for nu non-OXPHOS and core subunits.

View Article: PubMed Central - PubMed

Affiliation: Oklahoma Biological Survey and Department of Biology, University of Oklahoma.

ABSTRACT
Oxidative phosphorylation (OXPHOS), the major energy-producing pathway in aerobic organisms, includes protein subunits encoded by both mitochondrial (mt) and nuclear (nu) genomes. How these independent genomes have coevolved is a long-standing question in evolutionary biology. Although mt genes evolve faster than most nu genes, maintenance of OXPHOS structural stability and functional efficiency may involve correlated evolution of mt and nu OXPHOS genes. The nu OXPHOS genes might be predicted to exhibit accelerated evolutionary rates to accommodate the elevated substitution rates of mt OXPHOS subunits with which they interact. Evolutionary rates of nu OXPHOS genes should, therefore, be higher than that of nu genes that are not involved in OXPHOS (nu non-OXPHOS). We tested the compensatory evolution hypothesis by comparing the evolutionary rates (synonymous substitution rate dS and nonsynonymous substitution rate dN) among 13 mt OXPHOS genes, 60 nu OXPHOS genes, and 77 nu non-OXPHOS genes in vertebrates (7 fish and 40 mammal species). The results from a combined analysis of all OXPHOS subunits fit the predictions of the hypothesis. However, results from two OXPHOS complexes did not fit this pattern when analyzed separately. We found that the d(N) of nu OXPHOS genes for "core" subunits (those involved in the major catalytic activity) was lower than that of "noncore" subunits, whereas there was no significant difference in d(N) between genes for nu non-OXPHOS and core subunits. This latter finding suggests that compensatory changes play a minor role in the evolution of OXPHOS genes and that the observed accelerated nu substitution rates are due largely to reduced functional constraint on noncore subunits.

Show MeSH
Related in: MedlinePlus