The adaptive evolution of the mammalian mitochondrial genome
Open Access
- 4 March 2008
- journal article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 9 (1), 119
- https://doi.org/10.1186/1471-2164-9-119
Abstract
The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures. Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas). Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas. Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.This publication has 87 references indexed in Scilit:
- Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as OutgroupPLoS Biology, 2007
- Analysis of mitochondrial DNA sequences in patients with isolated or combined oxidative phosphorylation system deficiencyJournal of Medical Genetics, 2006
- Surface-modulated motion switch: Capture and release of iron–sulfur protein in the cytochrome bc 1 complexProceedings of the National Academy of Sciences of the United States of America, 2006
- The three-dimensional structure of complex I from Yarrowia lipolytica: A highly dynamic enzymeJournal of Structural Biology, 2006
- Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial bc1 Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-bonding PatternJournal of Molecular Biology, 2005
- Effects of Purifying and Adaptive Selection on Regional Variation in Human mtDNAScience, 2004
- Predicting transmembrane protein topology with a hidden markov model: application to complete genomesJournal of Molecular Biology, 2001
- Exercise Intolerance Due to Mutations in the CytochromebGene of Mitochondrial DNAThe New England Journal of Medicine, 1999
- VMD: Visual molecular dynamicsJournal of Molecular Graphics, 1996
- Possible molecular mechanisms of the protonmotive function of cytochrome systemsJournal of Theoretical Biology, 1976