The adaptive evolution of the mammalian mitochondrial genome

Abstract

Background: 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.

Results: 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.

Conclusion: 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.

Figure 1

The mammalian mitochondrial genome and its protein-coding gene repertoire involved in the oxidative phosphorylation pathway. (A) Schematic representation of genes within mammalian mitochondrial genome (~7,000 bp). Genes on the outer circle are transcribed from the light-strand. Location of the tRNAs (red boxes) conform to the canonical placental mammalian arrangement. Abbreviations: HSP, putative heavy-strand promoter; OHR, origin of heavy-strand replication; OLR, origin of light-strand replication. (B) Simplified view of the mitochondrial oxidative phosphorylation machinery. Complexes I (NADH dehydrogenase) and II (succinate dehydrogenase) receive electrons from either NADH or FADH₂. Electrons are then carried between complexes by the carrier molecules coenzyme Q/ubiquinone (UQ) and cytochrome c (CYC). The potential energy of these electron transfer events is used to pump protons against the gradient, from the mitochondrial matrix into the intermembrane space [Complexes I and III (cytochrome bc₁) and IV (cytochrome c oxidase)]. ATP synthesis by Complex V (ATP synthase) is driven by the proton gradient, and occurs in the mitochondrial matrix. MM: mitochondria matrix; IM: intermembrane space.

Figure 2

Mammalian mitogenomic phylogenetic tree. Consensus phylogenetic tree (50 percent majority rule) constructed from the combined set of MCMC runs resulting topologies in MrBayes. Numbers give the percentage of posterior probability support for each clade averaged over the runs.

Figure 3

Radical physicochemical amino acid changes varying across the mammalian mitogenomic phylogenetic tree. Representation of the standardized number of strong positively selected amino acid properties across mitochondrial protein-coding genes varying within the branches of the mammalian mitochondrial tree (see Methods for details).

Figure 4

Radical physicochemical amino acid changes among residues in mammalian mitochondrial protein-coding genes. Number of strong positively selected amino acid properties in the mammalian mtDNA protein-coding genes of the oxidative phosphorylation chain.

Figure 5

Correlation between amino acid property variation and genetic distance. Correlation between the number of positively selected amino acid properties and the branch length (genetic distance) in mammalian NDs, CytB, COXs, and ATPs protein-coding genes.

Figure 6

Amino acid properties under positive (blue) and negative (red) selection in mammalian mitochondrial protein-coding genes. Conservative changes correspond to conservative categories 1 and 2 and radical changes to categories 7 and 8 (P ≤ 0.001). (C: chemical; S: structural; O: other [1])

Figure 7

Amino acid properties under positive (blue) and negative (red) selection in transmembrane and loop regions. Conservative changes correspond to conservative categories 1 and 2 and radical changes to categories 7 and 8 (P ≤ 0.001). (C: chemical; S: structural; O: other [1])

Figure 8

Amino acid property variation in NADH dehydrogenase subunits ND2/3/5. Topological assignment of the sites that present a high number of radically changing properties under positive-destabilizing selection in three subunits of the NADH dehydrogenase complex that are suggested to be proton pumping devices. The transmembrane domain average prediction is shown in grey (for details see Material and Methods section). MM: mitochondria matrix; IM: intermembrane space.

Figure 9

Three-dimensional representation of relevant variable amino acids in mammalian cytochrome b. Illustrative representation of some of the amino acid variable sites (see Figure 10) located in relevant functional spots of the bovine CytB structure (pdb code: 1PPJ [66]). The prosthetic groups in CytB are represented in black, and the Q_i and Q_P bound inhibitors in orange (ant: antimycin; stig: stigmatellin). Mutations in sites shown in red have been related to exercise intolerance in humans (see Table 1). Mutations in sites shown in pink are under strong positive selection according to the TreeSAAP analysis (over 5 positively selected properties). In site 277, the alanine present in the bovine structure is shown as ball and stick and the van der Waals surface for the arginine found in dugong is also depicted. MM: mitochondria matrix; IM: intermembrane space.

Figure 10

Amino acid variation in functional sites of mammalian cytochrome b. Amino acid variation in the selected sites of CytB presented in Figure 9 across all the mammalian species surveyed in this study.

Figure 11

Three-dimensional representation of variable amino acid in mammalian cytochrome c oxidase subunits I, II and III. Sites within COX subunits showing a high number of amino acid properties positive selected [see Additional file 1, Fig. S4] mapped into the bovine structure (pdb code: 1V54 [67]). Side-chains with over 5 amino acid properties positive selected are presented as black spheres. Sites showing particular mutational trends are shown in white (see text for further details). Mutations in sites shown in red have been related to exercise intolerance in humans (see Table 1). Prosthetic groups are presented as grey spheres. The side chains of the hydrophobic loop in COXII that is involved in cytochrome c docking and electron transfer are depicted as sticks together with their van der Waals surface. The nuclear encoded subunits of Complex IV are shown as in silver. MM: mitochondria matrix; IM: intermembrane space.

Figure 12

Rotary model for E. coli F₁F₀ ATPase and variation in the mammalian ATP6 subunit. A) Rotary model for E. coli F₁F₀ ATPase (see text for details); B) Topological assignment of the sites that present a high number of strong positively selected amino acid properties under positive-destabilizing selection in ATP6 (corresponds to the a subunit in E. coli). The transmembrane domains location is shown in grey (for details see Material and Methods section). The dark grey domain was only predicted by one of the three methods used.

Figure 13

Basal metabolic rate vs log₁₀ (body mass). The basal metabolic rate (BMR) is presented in three categories (low, intermediate and high). When the BMR value was not available for the species in study, either that of a close relative (indicated in parenthesis) or the average values of several closely related species (AVE) were used (together with the corresponding body mass value). The increase in BMR with the body mass can be easily observed by comparing the average values for each category (dotted lines).