Adaptive Threonine Increase in Transmembrane Regions of Mitochondrial Proteins in Higher Primates

BACKGROUND: The mitochondrial (mt) gene tree of placental mammals reveals a very strong acceleration of the amino acid (AA) replacement rate and a change in AA compositional bias in the lineage leading to the higher primates (simians), in contrast to the nuclear gene tree. Whether this acceleration and compositional bias were caused by adaptive evolution at the AA level or directional mutation pressure at the DNA level has been vigorously debated. METHODOLOGY/PRINCIPAL FINDINGS: Our phylogenetic analysis indicates that the rate acceleration in the simian lineage is accompanied by a marked increase in threonine (Thr) residues in the transmembrane helix regions of mt DNA-encoded proteins. This Thr increase involved the replacement of hydrophobic AAs in the membrane interior. Even after accounting for lack of independence due to phylogeny, a regression analysis reveals a statistical significant positive correlation between Thr composition and longevity in primates. CONCLUSION/SIGNIFICANCE: Because crucial roles of Thr and Ser in membrane proteins have been proposed to be the formation of hydrogen bonds enhancing helix-helix interactions, the Thr increase detected in the higher primates might be adaptive by serving to reinforce stability of mt proteins in the inner membrane. The correlation between Thr composition in the membrane interior and the longevity of animals is striking, especially because some mt functions are thought to be involved in aging

Core set approach to reduce uncertainty of gene trees

BACKGROUND: A genealogy based on gene sequences within a species plays an essential role in the estimation of the character, structure, and evolutionary history of that species. Because intraspecific sequences are more closely related than interspecific ones, detailed information on the evolutionary process may be available by determining all the node sequences of trees and provide insight into functional constraints and adaptations. However, strong evolutionary correlations on a few lineages make this determination difficult as a whole, and the maximum parsimony (MP) method frequently allows a number of topologies with a same total branching length. RESULTS: Kitazoe et al. developed multidimensional vector-space representation of phylogeny. It converts additivity of evolutionary distances to orthogonality among the vectors expressing branches, and provides a unified index to measure deviations from the orthogoality. In this paper, this index is used to detect and exclude sequences with large deviations from orthogonality, and then selects a maximum subset ("core set") of sequences for which MP generates a single solution. Once the core set tree is formed whose all the node sequences are given, the excluded sequences are found to have basically two phylogenetic positions on this tree, respectively. Fortunately, since multiple substitutions are rare in intra-species sequences, the variance of nucleotide transitions is confined to a small range. By applying the core set approach to 38 partial env sequences of HIV-1 in a single patient and also 198 mitochondrial COI and COII DNA sequences of Anopheles dirus, we demonstrate how consistently this approach constructs the tree. CONCLUSION: In the HIV dataset, we confirmed that the obtained core set tree is the unique maximum set for which MP proposes a single tree. In the mosquito data set, the fluctuation of nucleotide transitions caused by the sequences excluded from the core set was very small. We reproduced this core-set tree by simulation based on random process, and applied our approach to many sets of the obtained endpoint sequences. Consequently, the ninety percent of the endpoint sequences was identified as the core sets and the obtained node sequences were perfectly identical to the true ones

Robust Time Estimation Reconciles Views of the Antiquity of Placental Mammals

BACKGROUND: Molecular studies have reported divergence times of modern placental orders long before the Cretaceous–Tertiary boundary and far older than paleontological data. However, this discrepancy may not be real, but rather appear because of the violation of implicit assumptions in the estimation procedures, such as non-gradual change of evolutionary rate and failure to correct for convergent evolution. METHODOLOGY/PRINCIPAL FINDINGS: New procedures for divergence-time estimation robust to abrupt changes in the rate of molecular evolution are described. We used a variant of the multidimensional vector space (MVS) procedure to take account of possible convergent evolution. Numerical simulations of abrupt rate change and convergent evolution showed good performance of the new procedures in contrast to current methods. Application to complete mitochondrial genomes identified marked rate accelerations and decelerations, which are not obtained with current methods. The root of placental mammals is estimated to be ∼18 million years more recent than when assuming a log Brownian motion model. Correcting the pairwise distances for convergent evolution using MVS lowers the age of the root about another 20 million years compared to using standard maximum likelihood tree branch lengths. These two procedures combined revise the root time of placental mammals from around 122 million years ago to close to 84 million years ago. As a result, the estimated distribution of molecular divergence times is broadly consistent with quantitative analysis of the North American fossil record and traditional morphological views. CONCLUSIONS/SIGNIFICANCE: By including the dual effects of abrupt rate change and directly accounting for convergent evolution at the molecular level, these estimates provide congruence between the molecular results, paleontological analyses and morphological expectations. The programs developed here are provided along with sample data that reproduce the results of this study and are especially applicable studies using genome-scale sequence lengths

Stability of Mitochondrial Membrane Proteins in Terrestrial Vertebrates Predicts Aerobic Capacity and Longevity

The cellular energy produced by mitochondria is a fundamental currency of life. However, the extent to which mitochondrial (mt) performance (power and endurance) is adapted to habitats and life strategies of vertebrates is not well understood. A global analysis of mt genomes revealed that hydrophobicity (HYD) of mt membrane proteins (MMPs) is much lower in terrestrial vertebrates than in fishes and shows a strong negative correlation with serine/threonine composition (STC). Here, we present evidence that this systematic feature of MMPs was crucial for the evolution of large terrestrial vertebrates with high aerobic capacity. An Arrhenius-type equation gave positive correlations between STC and maximum life span (MLS) in terrestrial vertebrates (with a few exceptions relating to the lifestyle of small animals with a high resting metabolic rate [RMR]) and negative correlations in secondary marine vertebrates, such as cetaceans and alligators (which returned from land to water, utilizing buoyancy with increased body size). In particular, marked STC increases in primates (especially hominoids) among placentals were associated with very high MLS values. We connected these STC increases in MMPs with greater stability of respiratory complexes by estimating the degradation of the Arrhenius plot given by accelerating mtRMR up to mt maximum metabolic rate. Both mtRMR and HYD in terrestrial vertebrates decreased with increasing body mass. Decreases in mtRMR raise MMP stability when high mobility is not required, whereas decreased HYD may weaken this stability under the hydrophobic environment of lipid bilayer. High maximal metabolic rates (5-10 RMR), which we postulate require high MMP mobility, presumably render MMPs more unstable. A marked rise in STC may therefore be essential to stabilize MMPs, perhaps as dynamic supercomplexes, via hydrogen bonds associated with serine/threonine motifs

Evolution of Mitochondrial Power in Vertebrate Metazoans

<div><p>Background</p><p>Basal metabolic rate (<i>BMR</i>) has a very strong body-mass (<i>M</i>) dependence in an individual animal group, and <i>BMR</i> per unit mass (<i>msBMR</i>) converges on a markedly narrow range even across major taxonomic groups. However, it is here a basic question in metazoan biology how much <i>BMR</i> per unit mitochondrion (<i>mtBMR</i>) changes, and then whether <i>mtBMR</i> can be related to the original molecular mechanism of action of mt-encoded membrane proteins (MMPs) playing a central role in cellular energy production.</p><p>Methodology/Principal Findings</p><p>Analyzing variations of amino-acid compositions of MMPs across 13 metazoan animal groups, incorporating 2022 sequences, we found a strong inverse correlation between Ser/Thr composition (<i>STC</i>) and hydrophobicity (<i>HYD</i>). A majority of animal groups showed an evolutionary pathway of a gradual increase in <i>HYD</i> and decrease in <i>STC</i>, whereas only the deuterostome lineage revealed a rapid decrease in <i>HYD</i> and increase in <i>STC</i>. The strongest correlations appeared in 5 large subunits (ND4, ND5, ND2, CO1, and CO3) undergoing dynamic conformational changes for the proton-pumping function. The pathway of the majority groups is well understood as reflecting natural selection to reduce <i>mtBMR</i>, since simply raising <i>HYD</i> in MMPs (surrounded by the lipid bilayer) weakens their mobility and strengthens their stability. On the other hand, the marked decrease in <i>HYD</i> of the deuterostome elevates <i>mtBMR</i>, but is accompanied with their instability heightening a turnover rate of mitochondria and then cells. Interestingly, cooperative networks of interhelical hydrogen-bonds between motifs involving Ser and Thr residues can enhance MMP stability.</p><p>Conclusion/Significance</p><p>This stability enhancement lowers turnover rates of mitochondria/cells and may prolong even longevity, and was indeed founded by strong positive correlations of <i>STC</i> with both <i>mtBMR</i> and longevity. The lowest <i>HYD</i> and highest <i>STC</i> in Aves and Mammals are congruent with their very high <i>mtBMR</i> and long longevity.</p></div

Global relationship between <i>TC</i> and <i>HYD</i> in MMPs of metazoan animals.

<p>Solid circles represent the average values of <i>HYD</i> and <i>TC</i> in each animal group, with the hydrophobic score S>0 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098188#s2" target="_blank">Materials and Methods</a>). The red circles show the <i>STC</i> values, which well describe the vertebrate lineage <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098188#pone.0098188-Kitazoe1" target="_blank">[16]</a>. Such a strong correlation was also obtained by analyzing all 13 proteins (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098188#pone.0098188.s001" target="_blank">Figure S1</a>). The correlation is totally well reproduced by a non-linear function (<b>A</b>: <i>TC</i> = 0.429•<i>HYD</i>^−4.2045 with R² = 0.901), but it can be separately expressed by 2 regression lines with different slopes (<b>B</b>: the dotted line for the deuterostomes with R² = 0.918) and (<b>C</b>: the dotted line for the other groups with R² = 0.890). The error range of the x-axis (<i>HYD</i>) in an animal group can be estimated by moving the regression curve <b>A</b> in parallel along the y-axis so that the y-value of this curve may be equal to that of the solid circle of the group, since this error range of <i>HYD</i> may be roughly given by the x-axis values of the curve corresponding to the error range of the y-axis (<i>STC</i>).</p

<i>HYD</i> and <i>TC</i> versus <i>TSN</i>.

<p>The regression lines for Deuterostomes and those for Protostomes were estimated separately. <i>HYD</i> and <i>TC</i> are expressed on the left and right ordinates, respectively.</p

<i>HYD</i>-<i>TC</i> and <i>TC</i>-<i>CC</i> correlations (R²) within respective proteins.

<p>The * symbol denotes 2 subunits with weak correlations (ATP6 and ND6) and 4 subunits with small numbers (3 or less in humans) of helices (ND3, ATP8, ND4L, and CO2). The analysis includes the following 13 metazoan animal groups: Porifera, Cnidaria, Mollusca, Crustacea, Hexapoda, Chelicerata, Nematoda, Platyhelminthes, Echinodermata, Fishes, Amphibia, Eutheria, and Aves.</p

<i>HYD</i> and <i>TC</i> distributions in the mt inner membrane of ND2, ND4 and ND5.

<p>Four animal groups were selected as providing extreme situations of the hydrophobic distribution. This result was obtained by using SOSUI WWW server <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098188#pone.0098188-SOSUI1" target="_blank">[19]</a> and TMHMM Server <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098188#pone.0098188-TMHMM1" target="_blank">[20]</a> for the prediction of the secondary structure of proteins.</p

Correlations (R²) between the pairs of variables (<i>HYD</i>, <i>TC</i>, <i>STC</i>, <i>CC</i>, <i>TSN</i>, <i>mtBMR</i>, <i>msBMR</i> and <i>MLS</i>).

<p> denotes that <i>TSN</i> of each protein set occupies the n % of that of the complete amino acid sequence in Human. P and N stand for the positive and negative correlations, respectively. The best results in the respective correlation croups are denoted by italics.</p