Maintenance of genomic integrity and stability is of prime importance for the survival of an organism. Upon exposure to different damaging agents, DNA acquires various lesions such as base modifications, single-strand breaks (SSBs), and double-strand breaks (DSBs). Organisms have evolved specific repair pathways in order to efficiently correct such DNA damages. Among various types of DNA damages, DSBs are the most serious when present inside cells. Unrepaired or misrepaired DSBs account for some of the genetic instabilities that lead to secondary chromosomal rearrangements, such as deletions, inversions, and translocations and consequently to cancer predisposition. Nonhomologous DNA end joining (NHEJ) is one of the major DSB repair pathways in higher organisms. Mitochondrial DNA (mtDNA) deletions identified in humans are flanked by short directly-repeated sequences, however, the mechanism by which these deletions arise are unknown. mtDNA deletions are associated with various types of mitochondrial disorders related to cancer, aging, diabetes, deafness, neurodegenerative disorders, sporadic and inherited diseases. Compared to nuclear DNA (nDNA), mtDNA is highly exposed to oxidative stress due to its proximity to the respiratory chain and the lack of protective histones. DSBs generated by reactive oxygen species, replication stalling or radiation represents a highly dangerous form of damage to both nDNA and mtDNA. However, the repair of DSBs in mitochondria and the proteins involved in this repair are still elusive. Animals deficient for any one of the known Classical-NHEJ factors are immunodeficient. However, DSB repair (DSBR) is not eliminated entirely in these animals suggesting evidence of alternative mechanism, ‘alternative NHEJ’ (A-NHEJ/A-EJ). Several lines of evidence also suggest that alternative and less well-defined backup NHEJ (B-NHEJ) pathways play an important role in physiological and pathological DSBR. We studied NHEJ in different tissue mitochondrial protein extracts using oligomeric DNA substrates which mimics various endogenous DSBs. Results showed A-EJ, as the predominant pathway in mitochondria. Interestingly, immunoprecipitation (IP) studies and specific inhibitor assays suggested, mitochondrial end joining (EJ) was dependent on A-EJ proteins and independent of C-NHEJ proteins. Further, colocalization studies showed A-EJ proteins localize into mitochondria in HeLa cells. More importantly knockdown experiments showed the involvement of DNA LIGASE III in mitochondrial A-EJ. These observations highlight the central role of A-EJ in maintenance of the mammalian mitochondrial genome. By using oligomeric DNA substrates mimicking various endogenous DSBs, NHEJ in different cancer cell lines were studied. We found that the efficiency of NHEJ varies among cancer cells; however, there was no remarkable difference in the mechanism and expression of NHEJ proteins. Interestingly, cancer cells with lower levels of BCL2 possessed efficient NHEJ and vice versa. Removal of BCL2 by immunoprecipitation and protein fractionation using size exclusion column chromatography showed elevated levels of EJ. Most importantly, the overexpression of BCL2 in vivo or the addition of purified BCL2 in vitro led to the downregulation of NHEJ in cancer cells. Further, we found that BCL2 interacts with KU proteins both in vitro and in vivo using immunoprecipitation and immunofluorescence, respectively. Hence, NHEJ in cancer cells is negatively regulated by the anti-apoptotic protein, BCL2, and this may contribute towards increased chromosomal abnormalities in cancer. In summary, our study showed that the efficiency of EJ in cancers could be regulated by the antiapoptotic protein BCL2. However, it may not affect the mechanistic aspect of EJ. BCL2 instead may interfere with EJ by sequestering KU and preventing it from binding to DNA ends. This may help in better understanding towards increased chromosomal abnormalities in cancer. Study of mitochondrial DSBR in mammalian system highlights the central role of microhomology-mediated A-EJ in the maintenance of the mammalian mitochondrial genome and this knowledge will helpful for the development of future therapeutic strategies against variety of mitochondria associated diseases.

Les aminoacyl-ARNt synthétases mitochondriales humaines (aaRS mt) sont des enzymes clés de la traduction mitochondriale. Elles catalysent l'aminoacylation des ARNt par les acides aminés correspondent. Des mutations dans leurs gènes sont corrélées à des pathologies avec un large spectre de phénotypes cliniques, mais aux mécanismes moléculaires sous-jacents encore incompris. L'objectif de ce travail de thèse s'intègre dans les axes scientifiques du laboratoire, mais élargit l'intérêt et les connaissance à un système encore peu exploré: l'arginyl-ARNt synthétase mitochondriale (ArgRS mt). Des mutations dans la ArgRS sont liées à une hypoplasie Pontocérébelleuse (PCH6), une pathologie neurodéveloppementale sévère. Le travail de cette thèse s’articule autour de 3 axes : (I) L’analyse des phénotypes cliniques des pathologies liées aux mutations dans les aaRS mt, (II) La caractérisation des propriétéscellulaires de l’ArgRS mt, et (III) L'étude de l’impact de mutations « pathologiques » sur diverses propriétés de l’ArgRS mt. Combinés avec les travaux précédents, les résultats obtenus sont une contribution importante à l'élargissement des connaissances fondamentales des mt aaRSs, et apportent un nouvel éclairage sur le lien entre les mt-aaRSs-mutations et la maladie. / Human mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are housekeeping enzymes involved in the mitochondrial translation. They catalyze the aminoacylation of tRNAs with their cognate amino acids. Mutations in their nuclear genes are correlated with pathologies with a broad spectrum of clinical phenotypes, but with so far no clear explanations about the underlying molecular mechanism(s). The aim of this PhD work follows the long-standing efforts of the host laboratory but expand the interest and knowledge to an unexplored system: the human mitochondrial arginyl-tRNA synthetase (mt-ArgRS). Mutations in the mt-ArgRS lead to Pontocebellar hypoplasia type 6, a severe neuro-developmental pathology. I thus contributed to i) comprehensively analyze the clinical data reported in pathologies related to mutations on mt-aaRSs, resulting in a categorization according to the affected anatomical system; ii) decipher some cellular properties of the mt-ArgRS; and iii) investigate to impact of disease-associated mutations on mt-aaRSs properties. Combined with previous works, the present results expand the knowledge of the mt-aaRSs, shedding new light on the link between mt-aaRSs-mutations and disease.

<p dir="ltr">Adipose tissue is characterized by the dominant presence of adipocytes, specialized cells adept at lipid metabolism. These adipocytes act as critical nodes, coordinating the complex processes of energy storage and mobilization according to the body's metabolic requirements. Within the adipocyte population of mammals, there are three main subtypes: white, beige, and brown adipocytes. White adipocytes are primarily dedicated to the sequestration of energy in the form of triglycerides. Conversely, beige and brown adipocytes are distinguished by their capacity for thermogenesis, the process of dissipating nutritional energy as heat. The contemporary challenge of chronic overnutrition has precipitated a global surge in obesity and cardiometabolic diseases. Addressing this issue necessitates the maintenance of white adipocyte homeostasis and the enhancement of the quantity and function of thermogenic adipocytes, which are imperative for mitigating the global obesity epidemics.</p><p dir="ltr">Mitochondrion, a multifunctional organelle, is integral to a broad spectrum of cellular processes, including anabolic and catabolic metabolism, bioenergetics, and signal transduction, all of which are essential for maintaining cellular functions and homeostasis. The efficacy of mitochondrial operations is intrinsically linked to their membrane dynamics. In this study, transmission electron microscopy and mass spectrometry were employed to investigate the proteins implicated in the cold-induced mitochondrial membrane remodeling in brown adipocytes. Through this approach, a poorly characterized protein, Family with Sequence Similarity 210 Member A (FAM210A), was identified as a mitochondrial inner membrane protein that is induced by cold stimulation. Subsequent loss-of-function experiments were conducted to elucidate the role of FAM210A in adipocytes. Mice with adipose-specific deletion of <i>Fam210a</i> (<i>Fam210a</i>^<em>AKO</em>) exhibited compromised mitochondrial cristae structure and a reduced thermogenic capacity in brown adipose tissue (BAT), resulting in an increased susceptibility to lethal hypothermia during acute cold challenge. Moreover, in mice with inducible ablation of <i>Fam210a</i> in adipocytes (<i>Fam210</i>^{<em>iAKO</em>}), mitochondrial alterations in BAT were negligible at thermoneutral conditions; however, they exhibited defective cold-induced mitochondrial cristae remodeling, culminating in a progressive loss of cristae and diminished mitochondrial density. Mechanistically, it was determined that FAM210A interacts with mitochondrial protease YME1L and modulates its activity toward OMA1 and OPA1 cleavage, thus compromising cold-induced mitochondrial remodeling in BAT.</p><p dir="ltr">Additionally, this research delved into the role of FAM210A in adipocytes in response to dietary stress by feeding mice with high-fat diet (HFD). The study found a consistent correlation between FAM210A expression and OPA1 cleavage in adipocytes under HFD challenge. Mice lacking FAM210A in all adipocytes and subjected to HFD exhibited lipoatrophy in white adipose tissue (WAT) and a downregulation of genes associated with adipogenesis and lipid metabolism. In contrast, mice with a brown adipocyte-specific ablation of <i>Fam210a </i>(<i>Fam210a</i>^<em>UKO</em>) displayed no significant change in WAT mass but had enlarged livers. Crucially, both <i>Fam210a</i>^<em>AKO</em> and <i>Fam210a</i>^<em>UKO</em> mice presented increased WAT inflammation, deteriorated glucose tolerance, and exacerbated insulin resistance. These findings underscore the pivotal role of FAM210A in brown adipose tissue (BAT) in the preservation of WAT homeostasis and the regulation of systemic glucose clearance in diet-induced obesity.</p><p dir="ltr">In summary, these studies characterize the mitochondrial dynamics in brown adipocytes in response to cold stress, identify a new cold-induced mitochondrial protein, FAM210A, and uncover its functions in adipocytes under cold and dietary stresses. These findings highlight the importance of mitochondrial remodeling in the adaptive response of adipocytes to evolving metabolic demands. This work establishes FAM210A as a key regulator of mitochondrial cristae remodeling, shedding light on the mechanisms that govern mitochondrial plasticity in adipocytes.</p>

No description available.

<p>Mitochondria are responsible for producing the vast majority of cellular ATP, and are therefore critical to organismal health [1]. They contain thir own genomes (mtDNA) which encode 13 proteins that are all subunits of the mitochondrial respiratory chain (MRC) and are essential for oxidative phosphorylation [2]. mtDNA is present in multiple copies per cell, usually between 103 and 104 , though this number is reduced during certain developmental stages [3, 4]. The health of the mitochondrial genome is also important to the health of the organism, as mutations in mtDNA lead to human diseases that collectively affect approximately 1 in 4000 people [5, 6]. mtDNA is more susceptible than nuclear DNA (nucDNA) to damage by many environmental pollutants, for reasons including the absence of Nucleotide Excision Repair (NER) in the mitochondria [7]. NER is a highly functionally conserved DNA repair pathway that removes bulky, helix distorting lesions such as those caused by ultraviolet C (UVC) radiation and also many environmental toxicants, including benzo[a]pyrene (BaP) [8]. While these lesions cannot be repaired, they are slowly removed through a process that involves mitochondrial dynamics and autophagy [9, 10]. However, when present during development in C. elegans, this damage reduces mtDNA copy number and ATP levels [11]. We hypothesize that this damage, when present during development, will result in mitochondrial dysfunction and increase the potential for adverse outcomes later in life.</p><p>To test this hypothesis, 1st larval stage (L1) C. elegans are exposed to 3 doses of 7.5J/m2 ultraviolet C radiation 24 hours apart, leading to the accumulation of mtDNA damage [9, 11]. After exposure, many mitochondrial endpoints are assessed at multiple time points later in life. mtDNA and nucDNA damage levels and genome copy numbers are measured via QPCR and real-time PCR , respectively, every 2 day for 10 days. Steady state ATP levels are measured via luciferase expressing reporter strains and traditional ATP extraction methods. Oxygen consumption is measured using a Seahorse XFe24 extra cellular flux analyzer. Gene expression changes are measured via real time PCR and targeted metabolomics via LC-MS are used to investigate changes in organic acid, amino acid and acyl-carnitine levels. Lastly, nematode developmental delay is assessed as growth, and measured via imaging and COPAS biosort.</p><p>I have found that despite being removed, UVC induced mtDNA damage during development leads to persistent deficits in energy production later in life. mtDNA copy number is permanently reduced, as are ATP levels, though oxygen consumption is increased, indicating inefficient or uncoupled respiration. Metabolomic data and mutant sensitivity indicate a role for NADPH and oxidative stress in these results, and exposed nematodes are more sensitive to the mitochondrial poison rotenone later in life. These results fit with the developmental origin of health and disease hypothesis, and show the potential for environmental exposures to have lasting effects on mitochondrial function.</p><p>Lastly, we are currently working to investigate the potential for irreparable mtDNA lesions to drive mutagenesis in mtDNA. Mutations in mtDNA lead to a wide range of diseases, yet we currently do not understand the environmental component of what causes them. In vitro evidence suggests that UVC induced thymine dimers can be mutagenic [12]. We are using duplex sequencing of C. elegans mtDNA to determine mutation rates in nematodes exposed to our serial UVC protocol. Furthermore, by including mutant strains deficient in mitochondrial fission and mitophagy, we hope to determine if deficiencies in these processes will further increase mtDNA mutation rates, as they are implicated in human diseases.</p> / Dissertation

published_or_final_version / Medicine / Doctoral / Doctor of Philosophy

Asexual species which never incorporate novel genetic material from other lineages will go extinct faster than sexually reproducing species, because adaptive variability may be lower and a larger number of harmful mutations may accumulate. One form of asexuality, androgenesis, results in offspring that are clones of the father. Both androgenetic and sexual species are found in the clam genus Corbicula. I used genetic data to explore why there are multiple species of androgenetic Corbicula, and whether genetic exchange occurs between species. I found that in North American locations where two invasive, androgenetic species co-occur, restriction digest mapping of rDNA failed to detect recent nuclear exchange. However, in these same locations, mitochondrial markers were shared between species. In places where only one species was found, mitochondrial markers were unique to that species. This suggests androgenetic clams are able to parasitize eggs of closely related species. Whereas maternal mitochondria are retained in the fertilized egg, maternal nuclear chromosomes are expelled, and the mother incubates male clones of another species. To look at possible gene exchange over the long term, I compared phylogenetic tree topologies of one mitochondrial and two nuclear markers from multiple sexual and androgenetic species. Since several androgenetic species share similar or identical alleles, androgenesis seems to have evolved relatively recently in Corbicula. However, since different androgenetic species also have divergent alleles not shared between species, genetic capture of maternal nuclear DNA from other species may rarely occur. This rare capture of genetic material from other species may permit the long-term persistence of androgenesis in Corbicula. / text

Mitochondrial DNA encodes thirteen protein subunits in the oxidative phosphorylation system (OXPHOS) that is responsible for cellular energy production. Mitochondrial disorders have been identified to be associated with mtDNA mutations. However, the molecular mechanisms of specific mtDNA mutations are still being explored in order to establish causative links. This study tries to elucidate the mutational effects of mtDNA on OXPHOS complex activities and cell growths. Using mouse 3T3 fibroblasts as a cell model, single-cell clones with different growth rates were isolated. The entire mtDNA genome was sequenced for mutations. The enzymatic activities of OXPHOS complex I to V were analysed. Three growth patterns represented by five clones were identified. Three clones (clone #2, #3, and #6) had the shortest doubling times (11.5 - 14.9 hours). Clone #1 had a medium growth rate (19.2 hous); and clone #5 had a significantly slow growth rate (22 hours). MtDNA sequencing results revealed that clone #5 had several heteroplasmic mutations (one in 16S rRNA, two in tRNAser (UCN), three in tRNAasp, one in tRNAlys, one in COI, five in COII, and one in ATPase8) while the other four clones showed sequence homology. Enzymatic analyses showed that on average clone #5 had significantly low complex III, IV, and V activities (p < 0.05). Changes in biochemical properties and protein structure were analyzed to deduct possible mechanisms for reduced respiration. In conclusion, the slow growth rate is associated with reduced OXPHOS enzyme functions. It is most likely that the combination of COI and COII mutations resulted in the reduction of complex IV function. It is still unclear whether the ATPase8 mutation (T7869A) in the non-conserved region alone can have such a pronounced phenotypic effect. A reduction in complex III also cannot be explained since there were no mutations in the only mtDNA-encoded complex III gene, but it is possible that there are mutations in the nDNA-encoded complex III genes. Mutations in tRNA and rRNA genes may also be responsible for reduced protein syntheses and consequently reduced OXPHOS activities. It is unclear why complex I activity was not affected. Although the mutational effect of individual mtDNA mutation observed cannot be clearly identified, this study establishes a correlation between mtDNA mutation and cell energy production and growth.

Mitochondria were extracted from seedling radicles of Pima S-5 and Pima E-14 cottons and the state 3 respiration, state 4 respiration, ADP:O ratio and respiratory control (RC) ratio were measured in vitro over a range of temperatures from 6 to 18C. Mitochondria from E-14 seedlings exhibited a mean state 3 respiration rate of 13.42 μMO₂/min/gm tissue while mitochondria from S-5 seedlings showed a mean state 3 rate of 17.94 μMO₂/min/gm tissue. Mean state 4 respiration exhibited a similar trend with measurements of 73.4 μMO₂/min/gm tissue and 11.73 μMO₂/min/gm tissue for E-14 and S-5. Mitochondria from E-14 seedlings exhibited a mean ADP:O ratio of 3.73 compared to an ADP:O of 3.28 for S-5, across all assay temperatures. Mean respiratory control ratio was 1.79 for E-14 and 1.53 for S-5. These lower respiration rates of E-14 coupled with higher ADP:O ratios and RC ratios support a greater respiratory efficiency at low temperatures of this variety compared to S-5. Additionally, the E-14 mitochondrial membranes exhibited an ability to remain in a fluid state to a lower temperature than Pima S-5 mitochondrial membranes as judged by Arrhenius plots of respiration. Since mitochondrial respiration is considered to be regulated by membrane-bound enzymes, any change in membrane fluidity would conceivably affect mitochondrial enzyme activity and thus alter respiration rates. Changes in respiration rates will be reflected as a break in an Arrhenius plot. The mean break point temperature of state 3 respiration was 10.7C for E-14 and 13.4C for S-5. The mean break point temperature for state 4 respiration was 10.9C for E-14 and 13.6C for S-5. The ability of E-14 to withstand a greater degree of chilling under field conditions can be attributed, in part, to the greater fluidity of seedling mitochondrial membranes at low temperatures and concomitant conservation of respiratory energy through a lower rate of respiration. Assays of mitochondrial respiration and Arrhenius plots of mitochondrial respiration versus temperatures could be used to select cotton lines more tolerant to chilling temperatures.

No description available.