Metallothioneins (MTs) are small, non-enzymatic proteins that are involved in cellular detoxification and metal homeostasis because of their high cysteine content. MTs have also been identified as one of the vast number of adaptive responses to mitochondrial respiratory chain (RC) deficiencies. Aside from this, numerous other studies have linked MTs to several mitochondrion-linked components, including reactive oxygen species (ROS) and oxidative stress, apoptosis, glutathione, energy metabolism and nuclear- and mitochondrial DNA transcription regulation. However, most of the reports concerning the putative link between MTs and mitochondria are from in vitro studies and relatively little supportive in vivo evidence has been reported. Information on the involvement of MTs with respiratory chain function is especially limited. Is was therefore the aim of this study to investigate the involvement of MTs in mitochondrial respiration and respiratory chain enzyme function by using an MT knockout (MTKO) mouse model, which was treated with the irreversible complex I inhibiting reagent, rotenone. The aim was achieved by implementing three objectives: firstly, the RC function was investigated as a complete working unit; secondly, the functional and structural properties of single units (enzymes) of the RC were investigated utilising enzyme activity assays and BN- PAGE/western blot analysis; and thirdly, the possible effect of MTs on mtDNA copy number was investigated. While some tendencies of variation in RC enzyme activity and expression were identified, no significant effect on the overall mitochondrial respiratory function, or any significant differences in the relative mtDNA copy number of MTKO mice were observed. Thus it is concluded, while MTs have in this study revealed relatively small changes in respiratory chain function, which may still prove to have biological ignificance in vivo, the exact nature of the putative role of MTs in mitochondrial respiration or oxidative phosphorylation remains undefined. / Thesis (MSc (Biochemistry))--North-West University, Potchefstroom Campus, 2012.

A Saccharomyces cerevisiae, un increment de la temperatura comporta diversos efectes deleteris en l’organització interna de la cèl∙lula i indueix una inducció ràpida, massiva i transitòria d’expressió gènica, que es controla principalment pels factors de transcripció Hsf1 i Msn2/4. En aquest estudi, fent servir un crivatge genètic a gran escala, hem identificat el conjunt d’activitats que es requereixen per a l’adaptació cel∙lular a l’estrés tèrmic. A més, hem trobat que el complex de desacetilació d’histones de Rpd3 és un component essencial per a l’adaptació i la supervivència a l’estrés tèrmic, i que es requereix per a l’adequada regulació de l’expressió gènica. Concretament, Rpd3 es necessita per a l’activació dels gens depenents de Msn2/4 en resposta a estrés tèrmic. A més, hem trobat que és el complex gran de Rpd3, però no el petit, el qui media l’adaptació cel∙lular. Un increment en l’osmolaritat externa activa la quinasa activada per estrés (SAPK) Hog1, que és essencial per induir diverses respostes adaptatives, com la regulació de l’expressió gènica. Hog1 controla al menys cinc factors de transcripció. Aquí ensenyem que els factors de transcripció Rtg1 i Rtg3 regulen l’expressió d’un conjunt de gens en resposta a estrés osmòtic, d’una manera depenent de Hog1. En resposta a estrés osmòtic, Hog1 es requereix per a l’acumulació nuclear del complex de transcripció de Rtg1/3. Un cop al nucli, Hog1 es recluta als promotors i la seva activitat es requereix per a la unió de Rtg1/3 a la cromatina. A més, la fosforilació de Rtg3 per Hog1 és un pas important per a l’adequada activació transcripcional. / In Saccharomyces cerevisiae, increases in temperature lead to deleterious effects on the internal organization of the cell, and lead to a massive and transient induction of gene expression, mainly controlled by Hsf1 and Msn2/4 transcription factors. In this study, by using a genome‐wide genetic screen, we identified the network of essential activities required for cell adaptation to heat stress. Moreover, we found that the Rpd3 histone deacetylase (HDAC) complex is an essential component for adaptation and survival to heat stress and it is required for proper regulation of gene expression. Specifically, Rpd3 is needed for activation of the Msn2/4‐dependent genes in response to heat stress. Moreover, we found that the large, but not the small Rpd3 complex mediates cell adaptation. Increases in the extracellular osmolarity activate the Hog1 stress‐activated protein kinase (SAPK), which is essential for the induction of diverse osmoadaptive responses, such as regulation of gene expression. At least five transcription factors have been shown to be controlled by Hog1. Here we show that the Rtg1 and Rtg3 transcription factors regulate the expression of a set of genes upon osmostress in a Hog1‐dependent manner. In response to osmostress, Hog1 is required for the nuclear accumulation of the Rtg1/3 transcription complex. Once in the nucleus, Hog1 is recruited at promoters and its activity is required for the binding of Rtg1/3 to chromatin. Moreover, Rtg3 phosphorylation by Hog1 is an important step for proper transcriptional activation.

Le complexe bc₁ de la chaîne respiratoire mitochondriale est une bonne cible thérapeutique pour traiter le paludisme car cette enzyme est essentielle au parasite. Ses deux sites actifs, Qo et Qi, formés par le cytochrome b, ne sont pas totalement conservés entre les espèces, facilitant la découverte d’inhibiteurs à affinité différentielle, ce qui est important dans le développement de médicaments. L’atovaquone est le seul antipaludique ciblant le complexe bc₁ utilisé en médecine. L’émergence de résistance rend urgente l’étude de nouveaux inhibiteurs. Les ELQs (Endochin-like Quinolones) sont une classe d’antipaludiques particulièrement prometteuse.Pour étudier la liaison des inhibiteurs dans les sites actifs et l’effet de mutations de résistance, nous utilisons la levure et des méthodes biochimiques et bio-informatiques. Dans ce travail, nous avons étudié la relation entre mutations de résistance à l’atovaquone dans le site Qo et perte de fonction. Nous avons aussi modifié le site Qo de la levure pour qu’il mime mieux le site de l’enzyme du parasite. Les résidus «Plasmodium» altèrent le fonctionnement du site, résultant en une surproduction d’ions superoxides et une perte de croissance respiratoire, qui est restaurée par la modification d’une autre sous-unité du complexe, ISP, partenaire du site Qo, suggérant que les deux sous-unités doivent s’ajuster pour un fonctionnement correct. Nous avons analysé des polymorphismes de la région Qo observés chez l’Homme et trouvé qu’ils peuvent modifier la sensibilité du complexe à l’atovaquone, ce qui pourrait avoir un impact sur les effets secondaires du traitement. Nous avons ensuite étudié le mode d’action d’ELQ-400 et montré que ce nouvel antipaludique cible les deux sites Qo et Qi, ce qui rend l’apparition de résistance peu probable. Enfin, nous avons commencé la reconstruction du site Qi de la levure pour mimer le site du parasite.Les mutants de levure avec un complexe bc₁ «Plasmodium» semblent être de bons outils pour l’étude des inhibiteurs. Leur étude a aussi permis de comprendre mieux la structure et le fonctionnement du complexe bc₁. / The bc₁ complex of the mitochondrial respiratory chain is a good therapeutic target for the treatment of malaria as the enzyme is essential for pathogen proliferation. The two catalytic sites, Qo and Qi, formed by cytochrome b, are not fully conserved between species, facilitating the development of inhibitors with differential saffinity, which is important for the development of new drugs. At present, Atovaquone is the only antimalarial drug targeting the bc₁ complex used in medicine. The emergence of resistance makes it important to find new inhibitors, and the ELQs (Endochin-like Quinolones) are promising antimalarial candidates.In order to study the inhibitor binding to the active sites and the effect of resistance mutations, we have used yeast and a combination of biochemical and bioinformatic methods. We have studied the relationship between atovaquone resistance mutations in the Qo site and loss of function. We have also modified the yeast Qo site to make it more like the parasite site. The “Plasmodium” residues in the yeast Qo site altered its activity, which resulted in the overproduction of superoxide and the loss of respiratory growth. This could be restored by the modification of another bc₁ complex subunit interacting with the Qo site, ISP, suggesting that both these subunits need to be readjusted for correct activity. We then analyzed polymorphisms of the Qo region reported in Humans and found that they could alter the enzyme sensitivity to atovaquone, which could impact the side-effects linked to atovaquone treatment. We have also studied the mode of action of ELQ-400 and showed that this new antimalarial drug targets both the Qo and Qi sites, which would make the emergence of resistance less likely. Finally, we have started the reconstruction of yeast Qi site to make it resemble the parasite site.The yeast mutants with a “Plasmodium-like” bc₁ complex could be useful tools for the study of antimalarial drugs. These analyses have also resulted in a better understanding of the structure and function of the bc₁ complex.

Inborn errors of metabolism represent a heterogenous group of rare conditions, most having an incidence of less than 1 in 100,000 births. Because of their low prevalence, they are on the margin of attention of general research and even more so of large pharmaceutical companies. Study of rare diseases is the only way to design therapeutic options in order to improve quality of life of affected patients. Present Thesis particularly focuses on disturbances in mitochondrial energy metabolism. The main goals were the characterization of mitochondrial biogenesis within foetal development, as well as in childhood and adulthood. Another aim was to define clinical, biochemical and molecular aspects of mitochondrial optic neuropathies in childhood and adulthood. This work supported the earlier observations that gestational week 22 is the edge of viability, which has to be taken into account in upcoming discussions about guidelines on resuscitation of preterm neonates. Secondly, over last four years, we managed to examine and describe large cohort of patients with optic neuropathies based on a mitochondrial dysfunction. We have managed to characterize the biochemical and molecular-genetic background in more than 200 patients, and both selected cases (LHON/MELAS overlap syndrome) and cohort studies (MELAS,...

Die Infektionskrankheit Malaria wird von einzelligen Parasiten der Gattung Plasmodium verursacht und stellt vor allem im südlichen Afrika eine große Herausforderung dar. Die Zellen der Parasiten enthalten zwei endosymbiontische Organellen, den Apicoplast und das Mitochondrium. Beide Organellen besitzen ein reduziertes Genom. Die Struktur des mitochondrialen Genoms ist ungewöhnlich. Mit nur 6 kb gehört es zu den kleinsten beschriebenen Genomen und enthält neben drei proteinkodierende Gene auch 34 kleine rRNA-Gene. Um das Genom zu exprimieren wird eine Vielzahl von kernkodierten Faktoren benötigt. Die Regulation der Expression, die Prozessierung der polycistronischen Primärtranskripte und die Regulation des RNA-Metabolismus des Mitochondriums ist jedoch weitestgehend unbekannt. In dieser Arbeit konnten kurze RNAs in den Mitochondrien von P. falciparum mittels Hochdurchsatzsequenzierung identifiziert werden. Solche RNA-Akkumulationen an Transkriptenden werden in den Organellen höherer Pflanzen durch PPR-Proteine (Pentatricopeptide repeat) verursacht. Um zu untersuchen, ob in P. falciparum PPR-ähnliche, helikale Proteine vorhanden sind, wurde genomweit nach Proteinen mit repetitiven, helikalen Elementen gesucht. Dabei konnte eine vorher unbekannte Proteinfamilie identifiziert werden, die aufgrund ihrer 37 Aminosäure langen Motive Heptatricopeptide repeat Proteine (HPR) genannt wurde. In P. berghei konnte für 7 HPR-Proteine eine mitochondriale Lokalisation betätigt werden. Außerdem zeigten Deletionsversuche, dass die meisten HPR-Proteine in den Blutstadien essentiell sind. In vitro RNA-Bindestudien konnte für ein rekombinantes HPR-Protein eine unspezifische Interaktion mit mitochondrialen Transkripten nachgewiesen werden, während keine Bindung an DNA erfolgt. Eine breite Suche in verschiedenen phylogenetischen Gruppen zeigte, dass HPR-Proteine in verschiedensten eurkaryotischen Taxa vorhanden sind, mithin früh in der Evolution der eukaryotischen Zelle entstanden sind. / Malaria is caused by a single celled parasite of the genus Plasmodium. Especially in Sub-Saharan Africa, -this disease is a huge challenge for the health system. The cells of the parasites contain two organelles of endosymbiotic origin, the apicoplast and the mitochondrion. Both organelles still contain a reduced genome. For the expression of the genome, the organelles depends on a large set of nuclear encoded proteins. The mitochondrial genome has a unique structure. With only 6 kb it is one of the smallest genomes discovered to date and it contains only three protein coding genes along with 34 small ribosomal genes. The regulation of expression, the processing of the polycistronic primary transcript and the regulation of the RNA metabolism in the mitochondria of Plasmodium remains largely unknown. Through high-throughput sequencing of cellular RNA, we discovered a population of small RNAs originating in the mitochondria of P. falciparum. Similar RNA accumulations can be detected in the organelles of higher plants and are caused by helical-hairpin repeat proteins like PPR proteins (pentatricopeptide repeat). To search for plant-like RNA binding proteins similar to PPR proteins we scanned the nuclear genome of P. falciparum for helical-hairpin repeat proteins. We found a novel protein family with repetitive helical elements of 37 amino acid length we termed heptatricopeptide repeat (HPR) proteins. In the rodent Malaria parasite P. berghei, the mitochondrial localization for 7 HPR-Proteins was verified. In knockout studies, we also showed that almost all HPR proteins are essential for blood stages of P. berghei. In RNA-binding assays, one recombinant HPR protein showed unspecific interaction with mitochondrial transcripts but not with DNA. By broadening the search, we discovered that HPR proteins are found in multiple eukaryotic taxa.

Mitochondrial disorders, with incidence 1:5000 live births children, are one of the most common metabolic diseases. Clinically, it is heterogeneous group of disorders caused by mutations in more than 250 genes. Diagnostic of patients with suspected mitochondrial disorder relies on broad spectrum of biochemical analysis. One of them is a measurement of Mitochondrial Energy Generating Capacity (MEGC). The principle of MEGC analysis is measuring oxidations rate of 14 C - labeled substrates in 10 different incubations. These incubations contain [1-14 C]pyruvate, [U-14 C]malate or [1,4-14 C]succinate, donors and acceptors of Acetyl-CoA and inhibitors of TCA cycle. The results of MEGC analysis provide a variety of information about mitochondrial energy metabolism (MEM) of individual in particular tissue. In diagnostic of patients with suspected mitochondrial disorder is MEGC routinely determined in skeletal muscle. The aim of this study is to optimize MEGC analysis for its use in cultures skin fibroblasts. In sum, MEGC analysis was performed in 23 patients with primary deficiency of oxidative phosphorylation (OXPHOS), in 7 patients with secondary deficiency of OXPHOS and in 15 controls cell lines. The results of MEGC in cultured skin fibroblasts were then compared with results of spectrophotometric...

In the search for the mitochondrion of oxymonads, DNA of Monocercomonoides exilis - an oxymonad isolated from the gut of Chinchilla, was isolated and its genome was sequenced. Sequencing resulted in a fairly complete genome which was extensively searched or genes for mitochondrion related proteins, but no reliable candidate for such gene was identified. Even genes for the ISC pathway, which is responsible for Fe-S cluster assembly and considered to be the only essential function of reduced mitochondrion-like organelles (MROs), were absent. Instead, we were able to detect the presence of a SUF pathway which functionally replaced the ISC pathway. Closer examination of the SUF pathway based on heterologous localisation revealed that this pathway localised in the cytosol. In silico analysis showed that SUF genes are highly conserved at the level of secondary and tertiary structure and most catalytic residues and motifs are present in their sequences. The functionality of these proteins was further indirectly confirmed by complementation experiments in Escherichia coli where SUF proteins of M. exilis were able to restore at least partially Fe-S cluster assembly of strains deficient in the SUF and ISC pathways. We also proved by bacterial adenylate cyclase two-hybrid system that SufB and SufC can form...