Comparative analysis of mitochondrial genotype and aging

Towards understanding the evolutionary dynamics of mtDNA

Historically, mtDNA was considered a selectively neutral marker that was useful for estimating the population genetic history of the maternal lineage. Over time there has been an increasing appreciation of mtDNA and mitochondria in maintaining cellular and organismal health. Beyond energy production, mtDNA and mitochondria have critical cellular roles in signalling. Here we briefly review the structure of mtDNA and the role of the mitochondrion in energy production. We then discuss the predictions that can be obtained from quaternary structure modelling and focus on mitochondrial complex I. Complex I is the primary entry point for electrons into the electron transport system is the largest respiratory complex of the chain and produces about 40% of the proton flux used to synthesize ATP. A focus of the review is Drosophila's utility as a model organism to study the selective advantage of specific mutations. However, we note that the incorporation of insights from a multitude of systems is necessary to fully understand the range of roles that mtDNA has in organismal fitness. We speculate that dietary changes can illicit stress responses that influence the selective advantage of specific mtDNA mutations and cause spatial and temporal fluctuations in the frequencies of mutations. We conclude that developing our understanding of the roles mtDNA has in determining organismal fitness will enable increased evolutionary insight and propose we can no longer assume it is evolving as a strictly neutral marker without testing this hypothesis.

The Paradox of Coenzyme Q10 in Aging

Coenzyme Q (CoQ) is an essential endogenously synthesized molecule that links different metabolic pathways to mitochondrial energy production thanks to its location in the mitochondrial inner membrane and its redox capacity, which also provide it with the capability to work as an antioxidant. Although defects in CoQ biosynthesis in human and mouse models cause CoQ deficiency syndrome, some animals models with particular defects in the CoQ biosynthetic pathway have shown an increase in life span, a fact that has been attributed to the concept of mitohormesis. Paradoxically, CoQ levels decline in some tissues in human and rodents during aging and coenzyme Q₁₀ (CoQ₁₀) supplementation has shown benefits as an anti-aging agent, especially under certain conditions associated with increased oxidative stress. Also, CoQ₁₀ has shown therapeutic benefits in aging-related disorders, particularly in cardiovascular and metabolic diseases. Thus, we discuss the paradox of health benefits due to a defect in the CoQ biosynthetic pathway or exogenous supplementation of CoQ₁₀.

Mitochondrial haplogroup H is related to CD4+ T cell recovery in HIV infected patients starting combination antiretroviral therapy

Background

The mitochondrial DNA (mtDNA) seems to influence in a large number of diseases, including HIV infection. Moreover, there is a substantial inter-individual variability in the CD4+ recovery in HIV-infected patients on combination antiretroviral therapy (cART). Our study aimed to analyze the association between mtDNA haplogroups and CD4+ recovery in HIV-infected patients on cART.

Methods

This is a retrospective study of 324 naïve cART patients with CD4+ < 200 cells/mm³, who were followed-up during 24 months after initiating cART. All patients had undetectable HIV viral load during the follow-up. Besides, we included 141 healthy controls. MtDNA genotyping was performed by using Sequenom’s MassARRAY platform. The primary outcome variable was the slope of CD4+ recovery. Patients were stratified into two groups by the median slope value of CD4+ (9.65 CD4+ cells/mm³/month). Logistic regression analyses were performed to calculate the odds of CD4+ recovery according to mtDNA haplogroups.

Results

Our study included European HIV-infected patients within the N macro-cluster. The baseline values of CD4+ T-cells were similar between groups of patients stratified by the P50th of the slope of CD4+ T-cells recovery. Patients in the low CD4+ T-cells recovery group were older (p = 0.001), but this variable was included in the multivariate models. When we analyzed the frequencies of mtDNA haplogroups, no significant differences between HIV-infected individuals and healthy controls were found. We did not find any significant association between mtDNA haplogroups and the slope of CD4+ T-cells recovery by linear regression analysis. However, Patients carrying haplogroup H had a higher odds of having a better CD4+ recovery (> 9.65 CD4+ cells/mm³/month) than patients without haplogroup H (p = 0.032). The adjusted logistic regression showed that patients carrying haplogroup H had a higher likelihood of achieving a CD4+ recovery > 9.65 CD4+ cells/mm³/month [adjusted odds ratio (aOR) = 1.75 (95% CI = 1.04; 2.95); p = 0.035].

Conclusions

European mitochondrial haplogroup H was associated with the improved CD4+ recovery in HIV-infected patients starting cART with CD4+ < 200 cells/mm³.

Electronic supplementary material

The online version of this article (10.1186/s12967-018-1717-y) contains supplementary material, which is available to authorized users.

[Carbohydrate restriction in the larval diet causes oxidative stress in adult insects of Drosophila melanogaster]

The influence of 20 and 1% glucose and fructose, which were components of larval diet, on the level of oxidized proteins and lipids, low molecular mass antioxidant content as well as activities of antioxidant and associated enzymes in adult fruit fly Drosophila melanogaster were investigated. The restriction of carbohydrates in larval diet leads to oxidative stress in adult insects. It is supported by 40-50% increased content of protein carbonyl groups and by 60-70% decreased level of protein thiol groups as well as by a 4-fold increase of lipid peroxide content in 2-day-old flies of both sexes, developed on the diet with 1% carbohydrates. Oxidative stress, induced by carbohydrate restriction of the larval diet, caused the activation of antioxidant defence, differently exhibited in male and female fruit flies. Caloric restriction increased activity of superoxide dismutase and thioredoxin reductase associating only in males with 2-fold higher activity of NADPH-producing enzymes--glucose-6-phosphate dehydrogenase and isocitrate dehydrogenase. Carbohydrate restriction in the larval diet caused the increase of uric acid content, but the decrease in catalase activity in males. In females the values of these parameters were changed in opposite direction compared with males. The obtained results let us conclude the different involvement of low molecular mass antioxidants, glutathione and uric acid, and antioxidant enzyme catalase in the protection of male and female fruit fly macromolecules against oxidative damages, caused by calorie restriction of larval diet.

Mitochondrial haplogroups are associated with clinical pattern of AIDS progression in HIV-infected patients

We performed a cross-sectional study in 469 HIV-infected patients, whose mitochondrial haplogroups were genotyped to study their association with the clinical pattern of AIDS progression. The chance of not having an AIDS progression was 1.45 [95% of confidence interval (CI) = 1.02 to 2.05, P = 0.035) times greater in patients with cluster HV and 1.51 (95% CI = 1.06 to 2.18, P = 0.021) times greater in patients with haplogroup H. However, we only found significant values for haplogroup H (odds ratio = 1.52, 95% CI = 1.01 to 2.32, P = 0.049) in an ordinal logistic regression adjusted by gender, age at HIV infection, intravenous drug users, and hepatitis C virus infection. These data suggest that mitochondrial haplogroups might play a significant role in AIDS progression.

European mitochondrial haplogroups are associated with CD4+ T cell recovery in HIV-infected patients on combination antiretroviral therapy

BACKGROUND

There is substantial interindividual variability in the rate and extent of CD4+ T cell recovery after starting combination antiretroviral therapy (cART). The aim of our study was to determine whether mitochondrial DNA (mtDNA) haplogroups are associated with recovery of CD4+ in HIV-infected patients on cART.

METHODS

We carried out a retrospective study on 275 cART-naive patients with CD4+ counts <350 cells/mm(3), who were followed-up during at least 24 months after initiating cART. mtDNA genotyping was performed by Sequenom's MassARRAY platform.

RESULTS

Patients within cluster JT and haplogroup J had a lower chance of achieving a CD4+ count ≥500 cells/mm(3) than patients within cluster HV and haplogroup H [hazard ratio (HR) = 0.68 (P = 0.058) and HR = 0.48 (P = 0.010), respectively]. The time of follow-up during which the CD4+ count was ≥500 cells/mm(3) was longer in haplogroups HV and H than in haplogroups JT and J [20 months versus 6.2 months (P = 0.029) and 20 months versus 0 months (P = 0.024), respectively]. Additionally, haplogroups HV and H had greater chances of achieving a CD4+ count ≥500 cells/mm(3) during at least 12, 36, 48 and 60 months post-cART initiation compared with patients within haplogroups JT and J. Patients within haplogroup T only had a lesser chance of achieving a CD4+ count ≥500 cells/mm(3) during at least 48 months and 60 months post-cART initiation.

CONCLUSION

European mitochondrial haplogroups might influence CD4+ recovery in HIV-infected patients following initiation with cART. Haplogroups J and T appear to be associated with a worse profile of CD4+ recovery, whereas haplogroup H was associated with a better CD4+ reconstitution.

Using near-infrared spectroscopy to resolve the species, gender, age, and the presence of Wolbachia infection in laboratory-reared Drosophila

The aim of the study was to determine the accuracy of near-infrared spectroscopy (NIRS) in determining species, gender, age, and the presence of the common endosymbiont Wolbachia in laboratory-reared Drosophila. NIRS measures the absorption of light by organic molecules. Initially, a calibration model was developed for each study. An independent set with flies not involved in initial cross-validation was then used to validate the accuracy of each calibration model. Flies from the independent sets were correctly classified into Drosophila melanogaster and Drosophila simulans with 94% and 82% accuracy, respectively, whereas flies were successfully classified by gender with accuracy greater than 90%. In the age grading test, correlation plots of the actual and predicted age for males and females of D. melanogaster and D. simulans were shown to be overlapping between the adjacent age groups. It is, however, possible to predict the age of flies as less than 9 days of age with 62–88% accuracy and flies that are equal to or older than 9 days of age with 91–98% accuracy. Finally, we used NIRS to detect the presence of Wolbachia in flies. Flies from the independent sets were successfully identified as infected or not infected with Wolbachia with approximately 90% accuracy. These results suggest that NIRS has the potential to quantify the species, gender, and presence of Wolbachia in fly populations. However, additional optimization of the protocol may be necessary before the technique can reliably estimate fly age.

European mitochondrial DNA haplogroups and liver fibrosis in HIV and hepatitis C virus coinfected patients

BACKGROUND

HIV infection, hepatitis C virus (HCV) liver disease, and mitochondrial DNA (mtDNA) polymorphisms are three possibly interrelated factors that might be associated with progression of liver disease. The aim of this study was to investigate whether mtDNA haplogroups had any influence on liver fibrosis progression in HIV/HCV coinfected patients.

METHODS

We carried out a cross-sectional study in 231 patients who were genotyped via Sequenom's MassARRAY platform (San Diego, California, USA). Liver fibrosis was estimated based on the METAVIR score. In each patient, fibrosis progression rate (FPR) was calculated by dividing the fibrosis stage (0-4) by the estimated duration of HCV infection in years.

RESULTS

The cluster or major haplogroup HV was significantly associated with reduced odds ratios (OR) for advanced fibrosis [OR 0.35, 95% confidence interval (CI) 0.16-0.77, P = 0.009], cirrhosis (OR 0.16, 95% CI 0.04-0.60, P = 0.007), or high FPR (OR 0.43, 95% CI 0.21-0.84, P = 0.015). Within the major haplogroup HV, haplogroup H was significantly associated with an absence of advanced fibrosis (OR 0.40, 95% CI 0.18-0.91, P = 0.029), cirrhosis (OR 0.14, 95% CI 0.03-0.67, P = 0.014), or high FPR (OR 0.47, 95% CI 0.23-0.95, P = 0.035). We also found a significant association with increased odds of cirrhosis (OR 5.25, 95% CI 1.76-15.64, P = 0.003) in the closely related major haplogroup U.

CONCLUSION

The mtDNA haplogroups HV and H were associated with slower fibrosis progression, and the haplogroup U was associated with faster fibrosis progression in HIV/HCV coinfected patients. These data suggest that mtDNA haplogroup may play a significant role in liver fibrogenesis during HCV infection.

Starvation resistance is positively correlated with body lipid proportion in five wild caught Drosophila simulans populations

Stress resistance traits in Drosophila often show clinal variation, suggesting that selection affects resistance traits either directly or indirectly. One of the most common causes of stress for animals is the shortage or suboptimal quality of food, and individuals within many species must survive periods of starvation or exposure to nutritionally imbalanced diets. This study determines the relationship between starvation resistance, body lipid content, and lifespan in five recently collected Drosophila simulans populations from four distinct geographic localities. Despite rearing under standard nutritional conditions, we observed significant differences in starvation resistance between sexes and between localities. If body lipid proportion is included as a covariate in statistical analysis the difference between the sexes remains (slopes are parallel, with males more susceptible than females to starvation across all lipid proportions) but the effect of locality disappears. This result suggests that flies from different localities differ in their susceptibility to starvation because of differences in their propensity to store body lipid. We observed a negative relationship between lifespan and starvation resistance in both males and females, suggesting a fitness cost to increasing lipid reserves. These data raise issues about the role of diet in maintaining life history trait variation within and among populations. In conclusion, we show many similarities and surprising differences in life history traits between D. simulans and Drosophila melanogaster.

Early mitochondrial dysfunction in long-lived Mclk1+/- mice

Reduced activity of CLK-1/MCLK1 (also known as COQ7), a mitochondrial enzyme that is necessary for ubiquinone biosynthesis, prolongs the lifespan of nematodes and mice by a mechanism that is distinct from that of the insulin signaling pathway. Here we show that 2-fold reduction of MCLK1 expression in mice reveals an additional function for the protein, as this level of reduction does not affect ubiquinone levels yet affects mitochondrial function substantially. Indeed, we observe that the phenotype of young Mclk1(+/-) mutants includes a severe reduction of mitochondrial electron transport, ATP synthesis, and total nicotinamide adenine dinucleotide (NAD(tot)) pool size as well as an alteration in the activity of key enzymes of the tricarboxylic acid cycle. Surprisingly, we also find that Mclk1 heterozygosity leads to a dramatic increase in mitochondrial oxidative stress by a variety of measures. Furthermore, we find that the mitochondrial dysfunction is accompanied by a decrease in oxidative damage to cytosolic proteins as well as by a decrease in plasma isoprostanes, a systemic biomarker of oxidative stress and aging. We propose a mechanism for the conjunction of low ATP levels, high mitochondrial oxidative stress, and low non-mitochondrial oxidative damage in a long-lived mutant. Our model helps to clarify the relationship between energy metabolism and the aging process and suggests the need for a reformulation of the mitochondrial oxidative stress theory of aging.

A candidate complex approach to study functional mitochondrial DNA changes: sequence variation and quaternary structure modeling of Drosophila simulans cytochrome c oxidase

A problem with studying evolutionary dynamics of mitochondrial (mt) DNA is that classical population genetic techniques cannot identify selected substitutions because of genetic hitchhiking. We circumvented this problem by employing a candidate complex approach to study sequence variation in cytochrome c oxidase (COX) genes within and among three distinct Drosophila simulans mtDNA haplogroups. First, we determined sequence variation in complete coding regions for all COX mtDNA and nuclear loci and their isoforms. Second, we constructed a quaternary structure model of D. simulans COX. Third, we predicted that six of nine amino acid changes in D. simulans mtDNA are likely to be functionally important. Of these seven, genetic crosses can experimentally determine the functional significance of three. Fourth, we identified two single amino acid changes and a deletion of two consecutive amino acids in nuclear encoded COX loci that are likely to influence cytochrome c oxidase activity. These data show that linking population genetics and quaternary structure modeling can lead to functional predictions of specific mtDNA amino acid mutations and validate the candidate complex approach.

Sex differences in survival and mitochondrial bioenergetics during aging in Drosophila

The goal of this study is to test the role of mitochondria and of mitochondrial metabolism in determining the processes that influence aging of female and male Drosophila. We observe that Drosophila simulans females tended to have shorter lifespan, higher levels of hydrogen peroxide production and significantly lower levels of catalase but not superoxide dismutase compared to males. In contrast, mammalian females tend to be longer lived, have lower rates of reactive oxygen species production and higher antioxidant activity. In both Drosophila and mammals, mitochondria extracted from females consume a higher quantity of oxygen when provided with adenosine diphosphate and have a greater mtDNA copy number than males. Combined, these data illustrate important similarities between the parameters that influence aging and mitochondrial metabolism in Drosophila and in mammals but also show surprising differences.