Mitochondria are a key organelle within human cells, with functions ranging from ATP synthesis to apoptosis. Changes in mitochondrial function are associated with many diseases, as well as 'natural' processes like ageing. Mitochondria have a unique evolutionary origin, as the result of an endosymbiotic relationship between a bacterium and an archaeal cell. Therefore, the phylogenetic history of the mitochondrial proteome is also unique within the total human proteome. A new description of the genes encoding the human mitochondrial proteome - IMPI (Integrated Mitochondrial Protein Index) 2017 - provided an opportunity for exploration of mitochondrial proteome history and the application of this knowledge to the understanding of gene function, disease and ageing. To facilitate the exploration of the mitochondrial proteome, I created a manually curated dataset of 190,097 predicted orthologues of the 1,550 IMPI 2017 human genes across 359 species, using reciprocal best hit analysis as the basis for orthologue prediction. I used this to explore gene history and the potential for phylogenetic profiling to predict the function of uncharacterised genes. This inspired the use of phylogenetic profiling within two phyla of animals, to link presence and absence of metabolic genes to the function of mitochondrial transporters. Potential transport substrates were predicted for two groups of uncharacterised mitochondrial carriers. I also used the dataset to identify features of genes associated with monogenetic disease, as well as differences between recessive and dominant disease genes. A similar orthologue identification method was used to explore the total sequenced viral proteome for potential orthologues of mitochondrial proteins. This showed that a range of mitochondrial proteins are shared with viruses, potentially facilitating the co-opting of mitochondrial function during viral infection of eukaryotic cells. I then used orthology to explore the conservation of residues linked to protein acetylation and identify a link with lifespan in warm-blooded vertebrates. In conclusion, I have used orthology to further the understanding of human mitochondrial proteome history and developed applications of this information. For example, phylogenetic features of disease genes are being used as part of a wider pipeline to predict mitochondrial disease genes. Furthermore, predicted substrates of the SLC25A14/30 mitochondrial carriers are being tested. My dataset provides further opportunities to explore the evolution and function of the mitochondrion.

O grau de acetilação (GA) da quitosana é um parâmetro que influi nas interações inter e intramoleculares deste polímero e, portanto, em suas propriedades. É comum a incorporação de compostos a filmes de quitosana para melhora de suas propriedades, contudo, não há relatos da incorporação da resina de jatobá, composto natural com potencial atividade biológica, a estes filmes. Portanto, esta pesquisa buscou estudar a influência do grau de acetilação da quitosana e da inclusão da resina de jatobá sobre as propriedades de filmes de quitosana/gelatina, visando uma possível aplicação em cicatrização de feridas cutâneas. Foram produzidas amostras de quitosana a partir de gládios de lula com três diferentes valores de GA, variáveis de 7 a 35%. As soluções formadoras de filme apresentaram redução no valor de concentração inibitória mínima contra Staphylococcus aureus tanto com a redução no GA quanto com a incorporação da resina de jatobá, apesar da resina isoladamente não ter apresentado atividade antimicrobiana nas concentrações estudadas. Os ensaios reológicos demonstraram que a inclusão da resina de jatobá e maiores valores de GA reduziram os valores de viscosidade das soluções, enquanto a temperatura de gelificação também diminuiu com a inclusão da resina de jatobá. Os filmes apresentaram uma superfície lisa e compacta para as blendas quitosana/gelatina e uma morfologia rugosa e irregular após adição da resina de jatobá, quando analisados por MEV. A adição de resina de jatobá levou também a redução na estabilidade térmica dos filmes. Nos testes de absorção em PBS ficou evidente o efeito do GA da quitosana sobre a propriedade, exibindo valores de intumescimento consideravelmente maiores para os filmes conforme o aumento no GA, fator relacionado ao aumento do número de grupos acetila. Por outro lado, a adição de resina de jatobá e o processo de neutralização reduziram consideravelmente o grau de intumescimento dos filmes. Foi observado também que a redução no GA e a inclusão da resina de jatobá tanto aumentaram a permeação ao vapor de água dos filmes, quanto levaram a uma redução da solubilidade destes materiais. / The degree of acetylation (DA) of chitosan is a parameter that influences the inter and intramolecular interactions of this polymer and, therefore, its properties. In addition, it is common the incorporation of other compounds to chitosan films to improve their properties. However, there are no reports of the incorporation of jatoba resin, a natural compound with potential biological activity. Therefore, this research aimed to study the influence of the degree of chitosan acetylation and the inclusion of the jatoba resin on the properties of chitosan/gelatin films, with potential applications in wound healing. Samples of chitosan were produced from squid pens with three different DA values, ranging from 7 to 35%. The reduction in DA of chitosan and incorporation of the jatoba resin into the film-forming solutions resulted in reductions in the minimum inhibitory concentration against Staphylococcus aureus, although the isolated resin did not exhibit antimicrobial activity at the concentrations studied. The rheological tests showed that the inclusion of the jatoba resin and higher DA values reduced the viscosity of the solutions, while gelation temperature values decreased with the jatoba resin addition. The films presented a smooth and compact surface for the chitosan/gelatin blends and a rough and irregular morphology after addition of the jatoba resin. The addition of jatoba resin also led to the reduction in thermal stability of the films. The effect of the DA of chitosan on the absorption of PBS was evident, exhibiting considerably higher swelling values for the films as a function of the DA increase, a factor related to the increase in the number of acetyl groups. Moreover, the addition of jatoba resin and neutralization process considerably reduced the degree of swelling of the films. The water vapor permeability of the films increased due to both the reduction in DA and the inclusion of the jatoba resin, whereas these changes led to the reduction of the solubility of these materials.

Many mutations in superoxide dismutase 1 (SOD1) cause destabilization and misfolding of the protein and are implicated in amyotrophic lateral sclerosis. Likewise, a few post-translational modifications (PTMs) on SOD1 have been shown to cause the same phenotype. However, relatively few PTMs on SOD1 have been studied in depth and, in particular, very few studies have demonstrated how these PTMs affect SOD1's various biological roles. SOD1 is traditionally known for its role in reactive oxygen species (ROS)-scavenging but has also been found to have a few other biological roles, including transcription factor activity to promote genomic stability, preservation of cytoskeletal activity, maintaining zinc and copper homeostasis, and suppressing respiration. We have used the computational analysis tool, SAPH-ire, to find PTM 'hotspots' on SOD1 that have a high likelihood of affecting its biological functions. Interestingly, the top seven ranked PTM 'hotspots' were found in a small region of SOD1, between S98-K128. We focused our studies on one of the PTM 'hotspots' found in this region, lysine-122 (K122). K122 is found in the electrostatic loop of SOD1, a loop that is important for shuttling in superoxide radicals to be neutralized. According to our data, and other studies, this lysine is both succinylated and acetylated. We found that acetyl and succinyl-mimetics (K122Q and K122E, respectively) of this site do not affect its ROS scavenging activity but do prevent SOD1 from suppressing respiration and decrease its localization to the mitochondria. Further, when cells are depleted of SIRT5 (the desuccinylase for K122), SOD1 can no longer suppress respiration. Additionally, we found that SOD1 appears to suppress respiration at complex I, whether directly or through an indirect pathway is unknown. When HCT116 colon cancer cells were depleted of endogenous SOD1, the overexpressed succinyl K122-mimetic (K122E) could not recover growth as well as overexpressed WT SOD1. The K122E SOD1 expressing cells also exhibited increased mitochondrial ROS and unhealthier mitochondria. We propose a mechanism whereby SOD1 suppression of respiration acts as an additional regulator of oxidative stress: SOD1 suppresses the electron transport chain to decrease reactive oxygen species leakage and to promote healthier mitochondria and growth.

Salicylic Acid Binding Protein2 (SABP2) is an enzyme known to play important role in SA mediated pathway. SBIP-428 (SABP2 Interacting Protein-428), a SIR2 like deacetylase, has been found to interact with SABP2. We demonstrate that SBIP-428 functions as a Sirtuin deacetylase. We show that SBIP-428 itself is lysine acetylated. Interactions of a SBIP-428 with SABP2 also raised the possibility of SABP2 itself being lysine acetylated. The recombinant purified SABP2 or native partially purified SABP2 displayed no acetylation. In response to TMV infection, the expression of SBIP-428 was down regulated at 48 hpi. In addition, SBIP-428 was up regulated in plant known to accumulate less SA. Taken together expression of SBIP-428 is negatively correlated to the levels of SA in plants. The AtSRT2 plants exhibit no altered growth phenotype but exhibit a higher pathogen resistance against bacterial pathogen. Our results indicate that SBIP-428 is an important regulator in plant defense pathway.

Cyclooxygenase (COX) is the rate limiting enzyme that catalyses the production of prostanoids, which are crucial to vascular homeostasis. Evidence suggests that endothelial dysfunction and inflammation play a role in vascular complications in aging and diabetes. Previous animal studies by our laboratory at RMIT University reported enhanced COX expression with aging in rat aortas, platelets and monocytes. Potentially, alteration in COX expression may result in an imbalanced prostanoid production favoring the synthesis of vasoconstrictors and hence increase the risk of cardiovascular events in the aging population. The regulation of altered COX expression in aging, however, is not clear. It has been suggested that histone hyperacetylation may be an important mechanism that regulates COX levels during the aging process as increased histone acetylation has been shown to occur with aging. Thus, we hypothesized that COX expression is modulated by histone hyperacetylati on. This was investigated by measuring COX expression in histone hyperacetylated cultured endothelial cells. In the case of diabetes, studies have reported that the development of diabetes and its complications is associated with persistent inflammatory activity, evident with increased inflammatory markers in the circulation. COX-mediated pathways may be involved in this inflammatory process in diabetes. Furthermore, the formation of advanced glycation end products (AGEs) is accelerated in diabetes. AGEs can bind to receptors for AGEs (RAGE), which has also been suggested to play a role in inflammation in diabetes. We hypothesized that COX- and RAGE-mediated pathways contribute to increased inflammation in diabetes and potentiate the development of diabetic vascular complications. This was investigated by measuring changes in COX-mediated pathways in both rat and human diabetic models. The current thesis reports: 1) in cultured endothelial cells, histone hyperacetylation was associated with increased COX expression; 2) an overall increase in inflammation was observed in diabetes involving COX- and RAGE-mediated pathways. This was supported by increased platelet COX-1 and monocyte COX-2 levels in Zucker rats, increased monocyte COX-2 in human Type 1 diabetes and elevated plasma TXB2 and PGE2 levels in both human Type 1 and Type 2 diabetic subjects. Up-regulation of RAGE expression was further found in platelets and monocytes in both human diabetes types. When treated with NSAIDs, plasma prostanoid levels, COX and RAGE expression were reduced significantly in both platelets and monocytes in human diabetic subjects. 3) It is unclear how COX and RAGE expression was regulated, but histone modifications may be one of the mechanisms. Data from cultured cells indicated that increased COX expression was associated with increased histone acetylation levels induced by TSA. Concurrent increases in histone acetylation and COX-2 levels were also observed in human Type 1 diabetes, but similar findings were not observed in human Type 2 diabetes. In addition, we failed to find an age-dependent increase in monocyte histone H4 acetylation in human Type 2 diabetes despite an age-dependent increase in monocyte COX-2 expression. Thus, whether histone hyperacetylation modulates COX expression and in what conditions require further investigation.

Il apparait de nos jours évident que les cancers ne peuvent se réduire uniquement à des aberrations génétiques, et qu'un nouveau paramètre est à prendre en considération, l'épigénétique. Au cours de ma thèse je me suis efforcé de caractériser la protéine fusion BRD4-NUT. Cette protéine résulte d'une translocation t(15;19) observée dans les carcinomes de la ligne médiane (NMC), extrêmement agressifs et létaux. La protéine BRD4 possède un double bromodomaine capable de s'associer à la chromatine acétylée, et recrute divers facteurs sur la chromatine. NUT est une protéine de fonction inconnue exprimée exclusivement au cours de la spermatogenèse. J'ai pu démontrer que la protéine fusion BRD4-NUT était suffisante pour induire la tumorigenèse, par un mécanisme de séquestration de la proteine histone acétyltransférase (HAT) CBP/p300. NUT interagit avec CBP/p300 et suractive son activité d'acétylation, créant des foci hyperacétylés de chromatine. BRD4-NUT empêche ainsi CBP/p300 d'aller co-activer la transcription de nombreux gènes, et bloque notamment la réponse apoptotique p53-dépendante. Une inhibition de BRD4-NUT – par siRNA, mutation des bromodomaines ou dérégulation de l'acétylation des foci par des inhibiteurs des histones déacétylases (HDAC) – réenclenche la voie d'apoptose et la mort de ces cellules tumorales. Cette étude est un exemple précis de l'impact qu'une dérégulation épigénétique peut avoir sur l'homéostasie cellulaire et son mécanisme d'induction de la tumorigenèse. Je me suis également interessé à caracteriser la protéine NUT lors de son contexte physiologique, la spermatogenèse, ou lors de son expression illégitime dans des lignées tumorales sans fusion avec BRD4. La protéine NUT est exprimée au niveau des stades de maturation des cellules germinales spermatides, et pourrait participer au remodelage du génome et à l'établissement de l'épigénome final du spermatozoïde. Nut semble également conférer un avantage prolifératif lors de son expression anormale dans au moins trois lignées cellulaires, U2OS, A549 et A7R5. Ainsi, la protéine NUT, seule ou fusionnée avec BRD4, est un facteur Cancer/Testiculaire capable d'influer négativement sur l'homéostasie des cellules somatiques dans lesquelles ses fonctions, normalement restreintes à la spermatogenèse, participent à la tumorigenèse.

<p>The human tumour suppressor protein p53 is an effective inhibitor of cell growth, by inducing cell cycle arrest and apoptosis. However, p53-induced cell growth inhibition can be detrimental for virus multiplication. Therefore, viruses encode for proteins, which can interfere with the functions of the p53 protein. Human adenoviruses encode for a transcription repressor protein named E1B-55K, which inhibits the activity of the p53 protein during a lytic adenovirus infection.</p><p>In this thesis, we have studied the biochemical characteristics of the E1B-55K protein and how the E1B-55K protein interferes with the function of p53 as a transcription factor.</p><p>Our data show that the E1B-55K protein interacts with the Sin3 co-repressor complex in adenovirus transformed and in adenovirus infected cells. Furthermore, the E1B-55K protein recruites a histone deacetylase activity, indicating that the E1B-55K protein is associated with a functional chromatin modifying complex. We also show that in addition to repressing p53-activated transcription, E1B-55K could also relieve p53-mediated repression of the survivin and Map4 promoters.</p><p>Previous results have shown that E1B-55K inhibits p53 as a transcriptional activator of the p21/CDKN1A promoter. Here we show that the E1B-55K protein prevents p53 from inducing histone H3 and H4 acetylation on p21/CDKN1A promoter, which coincided with the inhibition of p21/CDKN1A protein expression. Notably, the Sin3 complex was detected in the vicinity of the p53 binding site on the p21/CDKN1A promoter, suggesting that the E1B-55K protein blocked p53-mediated histone acetylation by recruitment of a histone deacetylase activity. Inhibition of p21/CDKN1A protein expression might be the reason, why the E1B-55K protein alleviates p53-dependent transcriptional repression of the survivin promoter. </p><p>Finally, we show that oligomerisation of the E1B-55K protein is important for the defined subcellular localization of the protein and for its function as a repressor of p53-activated transcription.</p>

Biobased materials made from renewable resources, such as wood, play an important role in the sustainable development of society. One main challenge of biobased building materials is their inherent moisture sensitivity, a major cause for fungal decay, mold growth and dimensional instability, resulting in decreased service life as well as costly maintenance. A new building material known as wood-plastic composites (WPCs) has emerged. WPCs are a combination of a thermoplastic matrix and a wood component, the former is usually recycled polyethylene or polypropylene, and the latter a wood processing residual, e.g. sawdust and wood shavings. The objective of this thesis was to gain more insight about characteristics of WPCs containing a modified wood component. The hypothesis was that a modified wood component in WPCs would increase the moisture resistance and durability in outdoor applications. The study comprises both injection molded and extruded WPC samples made with an unmodified, acetylated, thermally modified or furfurylated wood component in a polypropylene (PP), high density polyethylene (HDPE), cellulose ester (CAP, a cellulose ester containing both acetate and propionate substituents) or polylactate (PLA) matrix. The WPCs were prepared with 50-70 weight-% wood. The emphasis was on studying the moisture sorption, fungal resistance and micromorphological features of these new types of composites. Water sorption in both liquid and vapor phases was studied, and the biological performance was studied both in laboratory and in long term outdoor field tests. Micromorphological features were assessed by analyzing of the wood component prior to and after processing, and by studying the composite microstructure by means of a new sample preparation technique based on UV excimer laser ablation combined with scanning electron microscopy (SEM). Results showed that the WPCs with a modified wood component had a distinctly lower hygroscopicity than the WPCs with unmodified wood, which resulted in less wood-plastic interfacial cracks when subjected to a moisture soaking-drying cycle. Durability assessments in field and marine tests showed that WPCs with PP or CAP as a matrix and 70 weight-% unmodified wood degraded severely within a few years, whereas the corresponding WPCs with a modified wood component were sound after 7 years in field tests and 6 years in marine tests. Accelerated durability tests of WPCs with PLA as a matrix showed only low mass losses due to decay. However, strength losses due to moisture sorption suggest that the compatibility between the PLA and the different wood components must be improved. The micromorphological studies showed that WPC processing distinctly reduces the size and changes the shape of the wood component. The change was most pronounced in the thermally modified wood component which became significantly reduced in size. The disintegration of the modified wood components during processing also creates a more homogeneous micromorphology of the WPCs, which may be beneficial from a mechanical performance perspective. Future studies are suggested to include analyses of the surface composition, the surface energy and the surface energy heterogeneity of both wood and polymer components in order to tailor new compatible wood-polymer combinations in WPCs and biocomposites. / <p>QC 20121119</p>

The human tumour suppressor protein p53 is an effective inhibitor of cell growth, by inducing cell cycle arrest and apoptosis. However, p53-induced cell growth inhibition can be detrimental for virus multiplication. Therefore, viruses encode for proteins, which can interfere with the functions of the p53 protein. Human adenoviruses encode for a transcription repressor protein named E1B-55K, which inhibits the activity of the p53 protein during a lytic adenovirus infection. In this thesis, we have studied the biochemical characteristics of the E1B-55K protein and how the E1B-55K protein interferes with the function of p53 as a transcription factor. Our data show that the E1B-55K protein interacts with the Sin3 co-repressor complex in adenovirus transformed and in adenovirus infected cells. Furthermore, the E1B-55K protein recruites a histone deacetylase activity, indicating that the E1B-55K protein is associated with a functional chromatin modifying complex. We also show that in addition to repressing p53-activated transcription, E1B-55K could also relieve p53-mediated repression of the survivin and Map4 promoters. Previous results have shown that E1B-55K inhibits p53 as a transcriptional activator of the p21/CDKN1A promoter. Here we show that the E1B-55K protein prevents p53 from inducing histone H3 and H4 acetylation on p21/CDKN1A promoter, which coincided with the inhibition of p21/CDKN1A protein expression. Notably, the Sin3 complex was detected in the vicinity of the p53 binding site on the p21/CDKN1A promoter, suggesting that the E1B-55K protein blocked p53-mediated histone acetylation by recruitment of a histone deacetylase activity. Inhibition of p21/CDKN1A protein expression might be the reason, why the E1B-55K protein alleviates p53-dependent transcriptional repression of the survivin promoter. Finally, we show that oligomerisation of the E1B-55K protein is important for the defined subcellular localization of the protein and for its function as a repressor of p53-activated transcription.

Transforming growth factor β (TGF-β) is a member of a large family of cytokines that regulate many crucial events in cells, including proliferation, differentiation, migration and apoptosis. Deregulated TGF-β signaling is associated with various forms of cancers and developmental disorders. TGF-β binds to a receptor complex at the surface of cells and activates a signaling cascade involving specific intracellular signaling proteins, known as Smads. Following receptor activation, the Smads are activated by phosphorylation and translocate to the nucleus, where they activate or repress the expression of specific genes. Posttranslational modifications regulate the function of proteins in a number of ways, including their activity, stability, localization, and/or interactions with other proteins. These modifications are important to modulate the strength and specificity of cellular signal transduction. Smad7, an important negative modulator of TGF-β signaling, has been shown to be acetylated by the acetyltransferase p300. My aim was to further explore the involvement of protein acetylation in TGF-β-dependent signaling. We could show that the acetylation of Smad7 is a reversible process. Interestingly, earlier work had shown that the acetylation of Smad7 prevented its degradation. In agreement with this observation, we found that the ubiquitylation and degradation of Smad7 was increased following cotransfection with HDAC1, a protein deacetylase. Based on our observations, we propose a model in which the stability of Smad7 is controlled by the balance between its acetylation, deacetylation and ubiquitylation. In a separate study, we found that also Smad2 and Smad3 are acetylated by p300/CBP and P/CAF upon TGF-β stimulation. Moreover, we found that the acetylation of the short isoform of Smad2 promoted its DNA binding activity, resulting in an increased transcriptional activity. Our results suggest that the increased DNA binding in response to acetylation is due to a conformational change in Smad2.