Mitochondria and chloroplasts are eukaryotic organelles that were acquired through endosymbiosis. In the case of the mitochondrion, a heterotrophic cell engulfed and retained an alpha-proteobacterium. The engulfed bacterium, or endosymbiont, underwent extensive cellular and genetic integration with its host, thereby becoming an organelle. Chloroplasts are derived from the engulfment and retention of a photosynthetic cyanobacterium that also experienced loss of cellular functions and genetic material. Although mitochondria and chloroplasts retain their own genomes, most of the proteins that function in these organelles are encoded by genes that were transferred to the nucleus in a process known as Endosymbiotic Gene Transfer (EGT). Chloroplasts in plants, green algae and red algae are known as primary plastids. Other photosynthetic organisms have secondary plastids that were acquired by engulfing and retaining a primary plastid-bearing alga. In the process, the nucleus of the engulfed alga underwent EGT (and presumably gene loss) to such an extent that it disappeared completely except in two lineages, cryptophytes and chlorarachniophytes, which retain a highly reduced and miniaturized form known as a nucleomorph. To understand the process of EGT and endosymbiosis in general, the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans were sequenced. In the case of G. theta its nucleomorph is of red algal origin while the nucleomorph of B. natans is derived from a green algal endosymbiont. Prior to the nuclear genome projects the genomes of the three organelles – plastid, mitochondrion, nucleomorph – had already been sequenced. This allowed investigation of recent transfers of organellar DNA to the nucleus. Mitochondrial transfers to the nucleus are still occurring in both organisms but transfers of plastid and nucleomorph DNA are not. The nucleomorph genomes of B. natans and G. theta appear ‘frozen’, unable to undergo EGT and thus unable to disappear as they have in all other lineages with secondary plastids. The creation of a spliceosomal intron from transferred organellar DNA was investigated. I also investigated nuclear genes whose encoded proteins appear to function in the mitochondrion. 833 putatively mitochondrial targeted proteins were identified in G. theta and 720 in B. natans.

Studies have discovered higher frequencies of single nucleotide polymorphisms (SNPs) in different mitochondrial genes are associated with subnormozoospermia. However, the frequencies of SNPs in ND1 and ND2 are not unknown. The present research was aimed to determine the frequencies of SNPs in ND1 and ND2 genes of the mitochondrial genome in fertile and subfertile men and whether changes in codon usage was associated with fertility phenotypes. Total genomic DNA from 157 semen samples was extracted using the proteinase K/SDS digestion procedure, followed by phenol/chloroform purification and ethanol precipitation. ND1 and ND2 genes were amplified respectively from 80 and 92 DNA samples from different fertility groups. Each PCR product was sequenced to identify mutations. Codon change resulting from a nucleotide substitution was determined by comparison with a reference mtDNA sequence obtained from the NCBI database. The frequency of codon usage in the reference mtDNA was determined by the computer program MEGA version 2.1. Eleven synonymous nucleotide substitutions and two non-synonymous substitutions were found in this study. Four SNPs were previously characterized; all SNPs were homoplasmic. None of the SNPs were likely to affect the function of the proteins on the basis of the hydrophobicity plots or secondary structure predictions. Sixty two percent of synonymous mutations were found to change from a high to a low relative codon usage values; 37% of synonymous mutations changed from a low to a high relative usage value. Chi-square (χ²) test (χ²= 0.067 with 1 d.f.) showed that there was no significant difference at the 5% level between these changes. Thus, change in codon usage was not related to semen quality in men. Further, there were no statistically significant differences in the observed frequencies of SNPs of fertile and subfertile men. However, the sample size was small and this study was only focused on a single NZ Caucasian population. Further study including larger and more diverse population samples may provide further insight into the functional importance of codon usage and its relevance to fertility

Studies have discovered higher frequencies of single nucleotide polymorphisms (SNPs) in different mitochondrial genes are associated with subnormozoospermia. However, the frequencies of SNPs in ND1 and ND2 are not unknown. The present research was aimed to determine the frequencies of SNPs in ND1 and ND2 genes of the mitochondrial genome in fertile and subfertile men and whether changes in codon usage was associated with fertility phenotypes. Total genomic DNA from 157 semen samples was extracted using the proteinase K/SDS digestion procedure, followed by phenol/chloroform purification and ethanol precipitation. ND1 and ND2 genes were amplified respectively from 80 and 92 DNA samples from different fertility groups. Each PCR product was sequenced to identify mutations. Codon change resulting from a nucleotide substitution was determined by comparison with a reference mtDNA sequence obtained from the NCBI database. The frequency of codon usage in the reference mtDNA was determined by the computer program MEGA version 2.1. Eleven synonymous nucleotide substitutions and two non-synonymous substitutions were found in this study. Four SNPs were previously characterized; all SNPs were homoplasmic. None of the SNPs were likely to affect the function of the proteins on the basis of the hydrophobicity plots or secondary structure predictions. Sixty two percent of synonymous mutations were found to change from a high to a low relative codon usage values; 37% of synonymous mutations changed from a low to a high relative usage value. Chi-square (χ²) test (χ²= 0.067 with 1 d.f.) showed that there was no significant difference at the 5% level between these changes. Thus, change in codon usage was not related to semen quality in men. Further, there were no statistically significant differences in the observed frequencies of SNPs of fertile and subfertile men. However, the sample size was small and this study was only focused on a single NZ Caucasian population. Further study including larger and more diverse population samples may provide further insight into the functional importance of codon usage and its relevance to fertility

La plupart des cellules cancéreuses présentent une reprogrammation métabolique qui favorise la glycolyse et diminue la phosphorylation oxydative. Cette reprogrammation a reçu le nom d’effet Warburg et permet aux cellules tumorales de proliférer même en conditions adverses. Bien que l’effet Warburg ait été, pendant longtemps, associé à un dysfonctionnement mitochondrial, plusieurs études ont montré que dans les cellules cancéreuses les mitochondries ne sont pas dysfonctionnelles et jouent même un rôle important dans la tumorigénèse. Cependant, les mécanismes qui régulent cette reprogrammation métabolique dans le mélanome restent encore à être bien évalués. Dans ce contexte, nous avons montré que les mélanomes présentent une faible activité mitochondriale caractérisée par une diminution de la consommation d’oxygène. Ce profil métabolique est contrôlé au moins en partie par le facteur de transcription HIF-1, via l’expression de la pyruvate déshydrogénase kinase 3 (PDK3). L’inhibition pharmacologique de la PDK3, utilisant le Dichloroacetate (DCA) est suffisante pour réactiver la phosphorylation oxydative et induire la production des espèces réactives de l’oxygène (ROS). Ainsi, la combinaison du DCA avec la molécule pro-oxydant elesclomol permet de potentialiser l’effet antitumural de cette dernière, de manière synergique. Fait intéressant, cette combinaison est également efficace dans les cellules ayant développé une résistance au vemurafenib, un inhibiteur de la protéine BRAFV600E. Dans ce contexte, dans la deuxième partie de cette étude, nous avons évalué si les cellules résistantes au vemurafenib présentent une modification métabolique qui pourrait expliquer leur sensibilité à la combiniasion DCA+eleslclomol. Nous avons montré que le vemurafenib induit une diminution de la glycolyse rendant les cellules dépendantes à la phosphorylation oxydative et augmente la biogénèse mitochondriale de manière dépendante ou indépendante de la réactivation de la voie MITF/PGC1α. En accord avec ces résultats, les cellules résistantes au vemurafenib présentent une augmentation de la consommation d’oxygène et de la production de ROS par rapport aux cellules sensibles. Le nouveau profil métabolique des cellules résistantes les rende plus sensibles aux agents pro-oxydants tels que l’elesclomol Nos résultats ont permis de montré la possibilité de cibler les modifications métaboliques par une approche pro-oxydant dans le but d’éradiquer de manière efficace les cellules de mélanome. / Most cancer cells undergo a metabolic rewiring from oxidative phosphorylation to glycolysis that allows them to proliferate even under stressful conditions. This phenomenon is known as the Warburg Effect and has been often associated to mitochondrial dysfunction. Although, many studies have shown that mitochondria is still active in cancer cells and seems to play a key role in tumorigenesis little is know about the mechanisms that regulate this metabolic swift. In this context, we first focused in the study of melanoma metabolism in different cell lines as in samples coming from patients. We first found that melanoma cells present low mitochondrial activity characterized by low oxidative phosphorylation. This metabolic behavior is at least partially controlled by the hypoxia-inducible factor-1α HIF-1α witch is constitutively express in melanoma cells even under nomoxic conditions. Inhibition of this factor induces a strong decrease in the expression and activity of PDK3. Pharmacological inhibition of PDK3 activity by dichloroacetate (DCA) is enough to reactivate mitochondrial oxidative phosphorylation and reactive oxygen species (ROS) production. Furthermore DCA increases in a synergistic manner elesclomol’s induced ROS production and cell death. Interestingly, BRAF V600E melanoma cells that were resistant to the BRAF inhibitor vemurafenib show were also sensible to this combination. Consequently, as a second part of this work we looked for to understand, why resistant cells were so sensible to these agents and if there were some metabolic modifications that could explain this behavior. We found that vemurafenib BRAFV600E induced inhibition causes an important decrease in glycolysis and renders melanoma cells addicted to oxidative phosphorylation by increasing mitochondria biogenesis dependently or not of MTIF/PCG1 axis. Conversely, vemurafenib resistant melanoma cell lines show higher mitochondrial activity associated with higher ROS production. Thus these cells are more sensible to elesclomol induced cell death than vemurafenib sensible cell lines. Our findings provide new insights into the metabolic pathways that allow cells to adapt to difficult microenvironment, showing that these metabolic modifications, especially in terms of ROS production, can be used to target and eradicate melanoma cells.

In this study the importance of prohibitin1 and prohibitin2 genes for Trypanosoma brucei was examined. RNA interference showed both of them essential for parasites to survive. Knocking down of these genes resulted in altered morphology of the mitochondrion, changes in membrane potential and shut down of mitochondrial translation. No changes were observed in levels of Reactive Oxygen Species and respiration. Both prohibitines are part of big complex present in the mitochondrion.

As mitocôndrias são os principais locais de geração de espécies reativas de oxigênio (ERO), que são produzidos como subprodutos da cadeia de transporte de elétrons. O ferro livre e as ERO podem se envolver em processos potencialmente nocivos, sendo que a desregulação do metabolismo do ferro nessa organela tem sido associada a várias doenças, como a Ataxia de Friedreich (FA). O transporte seletivo de quelantes de ferro a esta organela é proposto como um meio de melhorar sintomas de FA. A desferrioxamina (DFO) é um sideróforo bacteriano com grande afinidade ao ferro, mas baixa penetração celular. Já os peptídeos altamente catiônicos TAT49-57 (Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg), 1A (Fx-Arg-Fx-Lys-Fx-Arg-Fx -Lys), SS02 (Dmt-(D)-Arg-Phe-Lys) e SS20 (Phe-(D)-Arg-Phe-Lys) são conhecidos por permear as membranas citossólicas e mitocondriais. Nós preparamos conjugados de DFO com peptídeos que penetram as mitocôndrias e estudamos suas características de ligação ao ferro in vitro. Eles foram preparados e conjugados em fase sólida com DFO (produzindo quatro mtDFO), que em seguida foram purificados e caracterizados por meio de LC/MS e análise de aminoácidos. Os mtDFO de alta pureza exibiram capacidade de ligação de ferro idêntica à do quelante livre DFO. Os mtDFO também foram capazes de suprimir a oxidação catalisada pelo sistema ferro-ascorbato. A fim de avaliar a localização intracelular dos mtDFO, estes foram marcados com TAMRA (mtDFO-TAMRA). Frente a uma linhagem de carcinoma de ovario, os mtDFO foram em geral pouco tóxicos e altamente localizados nas mitocôndrias. Não foram observados níveis expressivos de danos a DNA, indução de apoptose, geração de ERO na mitocôndria, arraste de ciclo celular ou de apoptose. Resultados preliminares da aplicação dos mtDFO a cardiomiócitos murínicos com baixo nível de frataxina (modelo de FA) indicam um restabelecimento de aproximadamente 60% na morfologia mitocondrial, o que pode ser interpretado como uma melhora nas funções dessa organela. Estes resultados indicam que os mtDFO produzidos podem ser uma parte importante no arsenal terapêutico para FA. / Mitochondria are the main site for the generation of reactive oxygen species (ROS) as sub products of electron transport chain. Free iron and ROS may interact to generate potentially harmful species, and iron homeostasis in this organelle has been linked to several diseases, such as Friedreich Ataxia (FA). Selective targeting of iron chelators to mitochondria has been proposed as a means of alleviating FA symptoms. Desferrioxamine (DFO) is a bacterial siderophore with high affinity for iron, however low cell penetration. Highly charged peptides TAT49-57 Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg), 1A (Fx-Arg-Fx-Lys-Fx-Arg-Fx -Lys), SS02 (Dmt-(D)-Arg-Phe-Lys) and SS20 (Phe-(D)-Arg-Phe-Lys) are known as both cell- and mitochondria-permeant. We prepared conjugates of DFO with mitochondria-penetrating peptides and studied their iron binding characteristics in vitro. They were prepared in solid phase and conjugated to DFO (generating four mtDFO), which were then purified and characterized by LC/MS and Amino acid analysis. MtDFO exhibited iron binding ability identical to free DFO. The mtDFO of high purity were also able to quench the oxidation catalyzed by the iron-ascorbate system. Cell localization studies were performed by tagging mtDFO with TAMRA. In A2780 cells, mtDFO displayed in general low toxicity and high levels of mitochondrial location. No expressive levels of DNA damage, apoptosis, mitochondrial ERO generation or cell cycle arresting were observed. Preliminary results of the application of mtDFO on mouse cardiomiocytes with low levels of frataxin (animal model of FA) indicate a recovery of ca. 60% of mitochondrial morphology. This is interpreted as an improvement of the functions of the organelle. These results indicate that mtDFO may be important allies in the therapy of FA.

As mitocôndrias são os principais locais de geração de espécies reativas de oxigênio (ERO), que são produzidos como subprodutos da cadeia de transporte de elétrons. O ferro livre e as ERO podem se envolver em processos potencialmente nocivos, sendo que a desregulação do metabolismo do ferro nessa organela tem sido associada a várias doenças, como a Ataxia de Friedreich (FA). O transporte seletivo de quelantes de ferro a esta organela é proposto como um meio de melhorar sintomas de FA. A desferrioxamina (DFO) é um sideróforo bacteriano com grande afinidade ao ferro, mas baixa penetração celular. Já os peptídeos altamente catiônicos TAT49-57 (Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg), 1A (Fx-Arg-Fx-Lys-Fx-Arg-Fx -Lys), SS02 (Dmt-(D)-Arg-Phe-Lys) e SS20 (Phe-(D)-Arg-Phe-Lys) são conhecidos por permear as membranas citossólicas e mitocondriais. Nós preparamos conjugados de DFO com peptídeos que penetram as mitocôndrias e estudamos suas características de ligação ao ferro in vitro. Eles foram preparados e conjugados em fase sólida com DFO (produzindo quatro mtDFO), que em seguida foram purificados e caracterizados por meio de LC/MS e análise de aminoácidos. Os mtDFO de alta pureza exibiram capacidade de ligação de ferro idêntica à do quelante livre DFO. Os mtDFO também foram capazes de suprimir a oxidação catalisada pelo sistema ferro-ascorbato. A fim de avaliar a localização intracelular dos mtDFO, estes foram marcados com TAMRA (mtDFO-TAMRA). Frente a uma linhagem de carcinoma de ovario, os mtDFO foram em geral pouco tóxicos e altamente localizados nas mitocôndrias. Não foram observados níveis expressivos de danos a DNA, indução de apoptose, geração de ERO na mitocôndria, arraste de ciclo celular ou de apoptose. Resultados preliminares da aplicação dos mtDFO a cardiomiócitos murínicos com baixo nível de frataxina (modelo de FA) indicam um restabelecimento de aproximadamente 60% na morfologia mitocondrial, o que pode ser interpretado como uma melhora nas funções dessa organela. Estes resultados indicam que os mtDFO produzidos podem ser uma parte importante no arsenal terapêutico para FA. / Mitochondria are the main site for the generation of reactive oxygen species (ROS) as sub products of electron transport chain. Free iron and ROS may interact to generate potentially harmful species, and iron homeostasis in this organelle has been linked to several diseases, such as Friedreich Ataxia (FA). Selective targeting of iron chelators to mitochondria has been proposed as a means of alleviating FA symptoms. Desferrioxamine (DFO) is a bacterial siderophore with high affinity for iron, however low cell penetration. Highly charged peptides TAT49-57 Arg-Lys-Lys-Arg-Arg-Gln-Arg-Arg-Arg), 1A (Fx-Arg-Fx-Lys-Fx-Arg-Fx -Lys), SS02 (Dmt-(D)-Arg-Phe-Lys) and SS20 (Phe-(D)-Arg-Phe-Lys) are known as both cell- and mitochondria-permeant. We prepared conjugates of DFO with mitochondria-penetrating peptides and studied their iron binding characteristics in vitro. They were prepared in solid phase and conjugated to DFO (generating four mtDFO), which were then purified and characterized by LC/MS and Amino acid analysis. MtDFO exhibited iron binding ability identical to free DFO. The mtDFO of high purity were also able to quench the oxidation catalyzed by the iron-ascorbate system. Cell localization studies were performed by tagging mtDFO with TAMRA. In A2780 cells, mtDFO displayed in general low toxicity and high levels of mitochondrial location. No expressive levels of DNA damage, apoptosis, mitochondrial ERO generation or cell cycle arresting were observed. Preliminary results of the application of mtDFO on mouse cardiomiocytes with low levels of frataxin (animal model of FA) indicate a recovery of ca. 60% of mitochondrial morphology. This is interpreted as an improvement of the functions of the organelle. These results indicate that mtDFO may be important allies in the therapy of FA.

The mitochondrial genome (kinetoplast or kDNA) of Trypanosoma brucei is highly complex in terms of structure, content and function. It is composed of two types of molecules: 10-50 copies of identical ~23-kb maxicircles and 5,000-10,000 highly heterogeneous 1-kb minicircles. Maxicircles and minicircles form a concatenated network that resembles chainmail. Maxicircles are the equivalent of mitochondrial DNA in other eukaryotes, but 12 out of the 18 protein-coding genes encoded on the maxicircle require post-transcriptional RNA editing by uridylate insertion and removal before a functional mRNA can be generated. The 1-kb minicircles make up the bulk of the kDNA content and facilitate the editing of the maxicircle-encoded mRNAs by encoding short guide RNAs (gRNAs) that are complementary to blocks of edited sequence. It is estimated that there are at least hundred classes of minicircle, each class encoding a different set of gRNAs. At each cycle of cell division the contents of the kDNA genome must be faithfully copied and segregated into the daughter cells. Mathematical modelling of kDNA replication has shown that failure to segregate evenly will eventually result in loss of low copy number minicircle classes from the population. Depending on the type of minicircle that is lost this can result in immediate parasite death or, if the loss occurred in the bloodstream stage, render the cells unable to complete the canonical life-cycle in the tsetse fly vector. In order to investigate minicircle complexity and replication in T. brucei further we i) first established the true complexity of the kDNA genome using a Illumina short read sequencing and a bespoke assembly pipeline, ii) annotated the minicircles to establish the editing capacity of the cells, iii) analysed expression levels of predicted gRNA gene cassettes using small RNA data, and iv) carried out a long term time course to measure how kDNA complexity changes over time and compared this to preliminary model predictions. The structure of this thesis follows these steps. Using these approaches, 365 unique and complete minicircle sequences were assembled and annotated, representing 99% of the minicircle genome of the differentiation competent (i.e. transmission competent) T. brucei strain AnTat90.13. These minicircles encode 593 canonical gRNAs, defined as having a match in the known editing space, and a further 558 non-canonical gRNAs with unknown function. Transcriptome analysis showed that the non-canonical gRNAs, like the canonical set, have 3' U-tails and showed the same length distribution. Canonical and non-canonical sets differ, however, in their sense to anti-sense transcript ratios. In vitro culturing of bloodstream form T. brucei for ~500 generations resulted in loss of ~30 minicircle classes. After incorporating parameters for network size and minicircle diversity determined above, model fitting to longitudinal kDNA complexity data will provide estimations for the fidelity of kDNA segregation. The refined mathematical model for kDNA segregation will permit insight into time constraints for transmissibility during chronic infections due to progressive minicircle loss. It also has the potential to shed light on the selective pressures that may have led to the apparent co-evolution of the concatenated kDNA network structure and parasitism in kinetoplastids.

I investigated cellular mechanisms of ion and acid-base transport in rainbow trout (Oncorhyncus mykiss), crabs (Neohelice granulata), zebrafish (Danio rerio), Pacific hagfish (Eptatretus stoutii), and mosquito larvae (Aedes aegypti) with a primary focus on discerning the mechanisms governing ion transport and acid base regulation. In rainbow trout I provide the first functional evidence for two physiologically distinct mitochondrion-rich (MR) cells at the gill and demonstrate a new model for transepithelial Na+ uptake from freshwater involving apical Na+ channels and basolateral Na+/HCO3- co-transporters. These data are supported by extensive thermodynamic consideration of Na+ uptake from freshwater. I also demonstrate functional Cl-/HCO3- exchangers in both MR cell subtypes with roles for Cl- uptake and intracellular pH (pHi) regulation respectively and I present the first evidence for a Cl- dependent Na+/H+ exchanger in gill MR cells. Finally I demonstrate a unique Na+ dependent pHi recovery mechanism that requires protein kinase C for activation. A major limiting factor in clarifying the mechanisms of Na+ uptake in freshwater fish is the lack of a typical Na+ channel in any of the fish molecular databases. My work on zebrafish, although preliminary, indicates that a member of the acid-sensing ion channel family could be responsible for Na+ uptake from freshwater. I then expanded my research outside the trout model using an isolated crab gill preparation. I provide a cellular model for H+ secretion in crab gills that supports the transepithelial Na+ transport model that I described in rainbow trout. In Pacific hagfish, I demonstrate that recovery from blood acidosis is dependent on a Na+/H+ exchanger in gill MR cells. This mechanism of regulation involves translocation from the cytoplasm to the apical membrane during acidotic stress. This data combines with other studies demonstrating the mechanisms of acid and base secretion from a single MR cell subtype. Finally, I show that serotonin stimulation alkalinizes the pHi of the anterior midgut cells in the larval mosquito to levels never before observed in cell biology. These data challenge the dogma of pHi regulation in cell biology and demonstrate the power of using a comparative approach to systems physiology. / Physiology, Cell and Developmental Biology

Onchocerciasis, or river blindness, has historically represented one of the significant neglected tropical diseases on the planet in terms of socio-economic impact. The discovery that ivermectin was a safe and effective treatment for onchocerciasis, together with the decision of the manufacturer to donate the drug for the treatment of this disease became the basis for several large international programs to control and eventually eliminate the infection. These programs have managed to virtually eliminate transmission of the parasite causing Onchocerca volvulus from many foci in Africa and the Americas. Verifying that transmission has been halted requires sensitive and specific assays to detect the presence of the parasite. The gold standard to accomplish this has been to employ a PCR assay targeting a specific repeated sequence family encoded in the genome of O. volvulus to screen for the presence of the parasite in pools of vector black flies. While this assay is highly sensitive, obtaining the high specificity required to document an absence of transmission requires an independent confirmatory assay. To meet this need, an independent PCR assay targeting the cytochrome B (cytB) gene of the O. volvulus mitochondrion was developed. This assay could detect O. volvulus mitochondrial DNA purified by magnetic bead capture using the primers for the cytB gene and from the nuclear encoded repeated sequence DNA targeted in the primary assay. These preliminary data suggest that the mitochondrial PCR assay may be employed as a confirmatory assay to detect O. volvulus in pools of vector flies.