Regulated intramembrane proteolysis is an interesting process involved in a multitude of cellular pathways. Enzymes which catalyse this are termed intramembrane proteases (IMPRs), cleaving proteins passing through the membrane within their transmembrane domain. Rhomboid proteases are serine IMPRs. They are widely distributed among organisms and evolutionarily conserved, but despite many efforts, their physiological roles are largely unexplored. RHBDL4 is a mammalian rhomboid protease localised to the endoplasmic reticulum. It is involved in the development of colorectal cancer, which makes it an important focus of research, but its physiological function is not well understood. In order to explore it, I established and employed a proximity proteomics approach, termed APEX2. It is based on biotinylation of proteins in the spatial proximity of the target in the physiological environment of intact living cells. Labelled proteins are subsequently purified, identified and quantified by mass spectrometry. Exploring the physiological vicinity of RHBDL4, its interaction partners and substrates can be revealed and the detailed subcellular compartment, where RHBDL4 resides, can thus be inferred. During three independent experiments in HCT116 cell line, three proteins emerged repeatedly in the RHBDL4...

Au cours des dernières décennies, le régime alimentaire a subi une transition sans précédent, avec une augmentation de la consommation de protéines, de lipides et de glucides simples, et la diminution des apports en fibres. Par ailleurs, au-delà de la composition, la structure des aliments joue un rôle essentiel sur les cinétiques de digestibilité et la biodisponibilité des nutriments, modulant ainsi leur accessibilité pour microbiote dans le côlon. L’impact de la structure d’une matrice alimentaire complexe, formée de protéines et de lipides, sur le microbiote a été analysé de façon intégrée et a montré in vivo que la structure seule, dans le contexte d’un régime équilibré, pouvait altérer la composition du microbiote dans les zones distales et proximales que sont l’iléon et le cæcum. L’émulsion de protéines natives en phase liquide continue avec de fines gouttelettes protéolipidiques a arboré des protéines moins digestibles que l’émulsion de protéines dénaturées, en phase gélifiée, solide, avec de grandes gouttelettes. D’autre part, les lipides de l’émulsion solide étaient, à l’inverse, moins digestibles. Les protéines non digérées de l’émulsion liquide ont favorisé in vivo, les communautés de Lactobacillus et de Copprococcus tout en activant plus fortement les métabolismes de protéolyse. Inversement, les communautés de Bifidobacterium et d’Akkermansia muciniphila ont vu leurs abondances augmenter chez les rats consommant l’émulsion solide. Le deuxième objectif de ce travail de thèse a alors été d'analyser la capacité d'espèces prévalentes du microbiote intestinal humain à métaboliser des protéines non digérées. Nous avons montré, par le suivi des cinétiques de croissance et des productions de métabolites spécifiques, que les protéines du lait étaient une source d'énergie pour B. caccae, P. distasonis, B. longum et B. cocccoides en milieu pauvre ainsi qu'en milieu riche. Dans ces mêmes conditions, le transcriptome de B. caccae a montré la sur-expression de gènes codant pour des peptidases de specifités différentes, pour la production d'indoles, de GABA et de fimbriae. Ces travaux apportent des informations nouvelles sur l'impact de la structure sur l'écosystème digestif, et ouvre des portes pour le développement de nouveaux aliments. / Over the past decades, diet in developed countries has undergone an unprecedented transition, with increased intakes of protein, fat and high glycemic index carbohydrates. The first goal of this PhD work was to investigate how, beyond its composition, the food structure itself could play a part in nutrient digestibility and bioavailability, and consequently modulate the microbiota. We showed in vivo that the structure of proteino-lipidic emulsions modulated peptides transporters, and protein fermentation. The native proteins emulsion in a continuous liquid phase, with fine proteolipid droplets, was less digestible and led to more protein fermentation. It modified the gut microbiota composition in the distal and proximal intestinal sections and increased Lactobacillus and Coprococcus communities. A second in vivo study, using 15N labelled emulsions allowed us to disentangle the digestibility from the transit time effect. The second objective of the PhD was to characterize the capacity of prevalent human gut bacterial species to use undigested proteins as energy source. By monitoring growth kinetics and the production of specific metabolites, we showed that B. caccae, P. distasonis, B. longum et B. cocccoides could use whey protein as energy source. In addition we measured in B. caccae transcriptome, the over-expression of genes encoding for distinct peptidases, but also of GABA and indole pathways, and fimbriae biosynthesis. These data provide new insights on the relationships between food structure and the digestive ecosystem and could lead to the design of new functional food.

Rhomboids are intramembrane serine proteases that belong to the evolutionarily widespread rhomboid superfamily. Rhomboids developed a slightly different catalytic mechanism compared to classical serine proteases; they utilise a catalytic dyad (Ser/His) instead of the common triad (Ser/His/Asp), and the rhomboid active site is buried in the membrane. This, coupled with their hydrophobicity, makes them quite difficult to study. Therefore, even though they are known to be involved in several important biological processes it is still not clear how exactly most of them are involved in the regulation of or in the pathologies of diseases related to these processes (such as malaria, Parkinson's disease or cancer). Our understanding is hindered by the lack of tools for their characterisation both in vitro and in vivo. In my thesis I present new fluorogenic substrates based on the LacYTM2 sequence, which is hydrolysed by several different rhomboid proteases. Using Förster resonance energy transfer (FRET)-based methods, these substrates are suitable for continuous monitoring of rhomboid activity in vitro. Modifications in the P5-P1 residues can improve selectivity for a specific rhomboid, the choice of FRET pair of fluorophores that absorbes light of longer wavelengths makes them suitable for high throughput...

It is well-known that the large diversity of protein functions and structures derives from the broad spectrum of physicochemical properties of the 20 canonical amino acids that constitute modern proteins. According to the generally accepted coevolution theory of the genetic code, evolution of protein structures and functions was continuously associated with enrichment of the genetic code, with aromatic amino acids being considered the latest addition to the genetic code to increase structural stability of proteins and diversification of their catalytic functions. The main objective of this master thesis was to test whether enzymatic catalysis could precede the appearance of aromatic amino acids in the standard genetic code. For that purpose, the effect of amino acid alphabet reduction on structure and function of dephosphocoenzyme A kinase (DPCK) was studied. Dephosphocoenzyme A kinase catalyses the final step in the biosynthesis of coenzyme A, a very conserved cofactor. Two aromatic amino acid-lacking mutants of DPCK from a thermophilic bacterium, Aquifex aeolicus, were designed by substituting aromatic amino acid residues by (i) leucines and (ii) various non-aromatic amino acids to best preserve the structural stability of the protein. Wild type protein and the two mutants were cloned and...

The Calvin – Benson cycle is the most widespread metabolic pathway capable of fixing CO2 in nature and a target of very high interest to metabolic engineers worldwide. In this study, 12 metabolites (ATP, AMP, NADP, NADPH, 2PG, 3PGA, FBP, RuBP, PEP, AKG, Ac-CoA and phenylalanine) were tested for protein – metabolite interactions against the proteome of Cupriavidus necator (previously Ralstonia eutropha) in the hopes of finding potential examples of allosteric regulation of the Calvin – Benson cycle. This is accomplished through the use of the LiP-SMap method, a recently developed shotgun proteomics method described by Piazza et al. capable of testing a metabolite of interest for interactions with the entire proteome of an organism at once. A functional protocol was developed and 234 protein – metabolite interactions between ATP and the proteome of C. necator are identified, 103 of which are potentially novel. Due to time constraints and setbacks in the lab, significant results were not produced for the other 11 metabolites tested. C. necator is an industrially relevant chemolithoautotroph that can be engineered to produce many valuable products and is capable of growth on CO2 and hydrogen gas. The bacteria were grown in continuous cultures after which the proteome was extracted while retaining its native state. Subsequently, the proteome was incubated with a metabolite of interest and subjected to limited, non-specific proteolysis. The resulting peptide mix was analyzed by liquid chromatography coupled tandem mass spectrometry (LC – MS/MS). / Calvin-Benson-cykeln är den mest utbredda metaboliska processen i naturen med vilken det är möjligt att fixera CO2 och en måltavla av högsta intresse för bioteknologer världen över. I den här studien testades 12 metaboliter (ATP, AMP, NADP, NADPH, 2PG, 3PGA, FBP, RuBP, PEP, AKG, Ac-CoA and phenylalanine) för interaktioner mot proteomet från Cupriavidus necator (tidigare Ralstonia eutropha) i hopp om att hitta potentiella exempel på allosterisk reglering av Calvin-Benson-cykeln. Detta uppnåddes genom användning av LiP-SMap-metoden, en nyligen utvecklad proteomikmetod beskriven av Piazza et al. kapabel av att testa en metabolit av intresse mot en organisms hela proteom simultant. Ett funktionellt protokoll utvecklades och 234 interaktioner mellan ATP och proteomet av C. necator identifierades, varav 103 potentiellt är nyupptäckta. På grund av tidsbrist och motgångar i labbet producerades inga signifikanta resultat för de resterande 11 metaboliterna som testades. C. necator är en industriellt relevant kemolitoautotrof som kan växa på CO2 och vätgas, samt manipuleras till att producera många värdefulla produkter. Bakterierna odlades i kemostater varefter proteomet extraherades i sitt naturliga tillstånd. Sedan inkuberades proteomet med en metabolit av intresse och utsattes för begränsad, icke-specifik proteolys. Den resulterande peptidblandningen analyserades via tandem masspektrometri kopplad till vätskekromatografi (LC – MS/MS).

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Introduction Adhesion GPCRs (aGPCRs) constitute the second largest family of the GPCR superfamily, and yet their properties are also the least understood. Growing research on the biological functions of aGPCRs suggest their implications in various (patho)physiological processes, such as cell migration, organ development and cancers. Moreover, due to the unique architecture of a large extracellular region (ECR) containing a plethora of adhesion motifs, aGPCRs are vital as a mechanosensor which transduces extracellular mechanical stimuli into intracellular signal transduction. One distinct feature of aGPCRs among the GPCR superfamily is the possession of a conserved extracellular fold termed GPCR autoproteolysis-inducing (GAIN) domain in perhaps all members within the class. The cleavage at the last loop of the GAIN domain leads to the formation of two non-covalently associated N- and C-terminal fragments (NTF/CTF). A peptide stretch in the start of the CTF acts as a tethered agonist (TA) which is responsible for at least part of the signaling volumes of an activated receptor. Despite the strict conservation of the GAIN domain and its importance in the activation mechanism of aGPCRs, some other fundamental properties of the receptors, with reference to GAIN domain cleavage, have not been rigorously analysed in a biological context. Thus, this study aims to: 1. Explore the structural and molecular determinants that affects GAIN domain cleavage; 2. Investigate the consequences of GAIN domain cleavage towards (i) surface trafficking, and (ii) phosphorylation of receptors. Results Abolishment of GAIN domain cleavage in Polycystin-1, the only other protein family possessing the GAIN domain, was found to eliminate its surface expression, which is a cause of polycystic kidney/liver disease. However, whether such relationship is also true for aGPCRs has not been systematically analysed. Therefore, the study started with profiling the kinetics of surface delivery of several members of aGPCRs. Mutations on the -2 or +1 residues of the GPCR proteolytic site (GPS) (thereby abolishing GAIN domain cleavage) affected the steady-state surface and total expressions of the receptors differently, and had variable effect towards different receptor members. However, the observations from steady-state kinetics are also a resultant output from numerous processes involved in proteostasis. To further dissect whether GPS mutations affect the surface trafficking of the receptors, a pulse-chase assay called the ‘Retention Upon Selective Hook’ (RUSH) assay was employed, wherein the synthesised receptor molecules conjugated to a streptavidin-binding peptide are withheld in the ER by the co-expressed, ER-resident streptavidin, and are only released upon the addition of biotin that outcompete the receptor-streptavidin binding, creating a synchronised transport. By adapting the RUSH assay on some aGPCR members, the attenuation of surface trafficking by GPS mutations has become more apparent. The tested receptors were found to have a deficit in the quantity of surface population, rather than a change in rate of trafficking, upon the introduction of GPS mutations. This implies that the cells may utilise GAIN domain cleavage as a quality checkpoint for ER exit of aGPCRs. As the GAIN domains of at least some aGPCRs were found to be cleaved before ER exit, and as the rate of surface delivery was generally not affected by GAIN domain cleavage, the influence of GAIN domain cleavage may arise earlier during the receptor maturation in the ER. However, while the mechanisms of GAIN domain cleavage have been elucidated previously, they rely heavily on purified domains. The fundamental questions of when exactly the GAIN domain is cleaved and what additional determinants apart from the GPS sequence contribute to GAIN domain cleavage during receptor biogenesis have still not been answered. In combination with molecular dynamics (MD) simulation studies on the GAIN domain of rat isoform of ADGRL1, F803 was found to be crucial in the proteolysis by forming an edge-π interaction with H836 (-2 position of the cleavage site), such that H836 is in close proximity to the hydroxyl group of T838 for the initiation of the nucleophilic attack. Reconstruction of the edge-π interaction into ADGRB3, a naturally uncleavable receptor, partially reinstates its GAIN domain cleavage; but similar reintroduction on ADGRB2 has no effect on restoring the proteolysis. Nonetheless, this observation highlights the vitality of a proper folding of the GAIN domain, specifically the microenvironment of the cleavage site, in assisting in cleavage. The study continued with a systematic series of experiments that ultimately discover the roles of the CTF towards GAIN domain cleavage of aGPCRs. Firstly, to mimic the biogenesis of the receptor, the seven transmembrane (7TM) region of ADGRE2 (E2) was stepwisely truncated and then analysed for GAIN domain cleavage. It was observed that the extent of GAIN domain cleavage increases when the ECR of E2 precedes with more number of TMs. The proteolysis occurs, although less efficiently, as early as the first TM is synthesised. Interestingly, GAIN domain cleavage is unaffected when the TM region of the E2-1TM mutant was replaced by other single-pass TM, and whether it is trafficked to the surface or held in the ER, while the proteolysis of TM-less ECR mutants is largely impeded. Based on this observation, the ECR and the TM region was spaced either by a fluorophore moiety or a variable number of helical turns. Remarkably, the extent of GAIN domain cleavage of all tested receptors declined upon the increase in displacement with the lumenal side of the ER membrane, defining the importance of membrane proximity in the completion of proteolysis during the maturation of GAIN domain. In that, a new model of GAIN domain cleavage during biogenesis has been proposed, with appreciation of the GAIN domain as part of a higher-order stuctural organisation rather than an independent domain. A physiological extent of GAIN domain cleavage does not only require the folding of the GAIN domain, but also the membrane tethering property of the CTF, allowing a partial cleavage as little as one TM is generated, and a dynamic stability provided by the full CTF. In some aGPCRs, the contributions from CTF are more significant than the autonomous GAIN domain folding. The findings implicate more complex requirements for GAIN domain cleavage in a biological context, and hence supporting a possibility that GAIN domain cleavage is the rate-determining step for ER exit of the receptor, leading to the observations obtained in the kinetic study. Phosphorylation of L3 by PKC activated by distant signaling cascade(s) The last part of the study focused on characterising the mechanism of phosphorylation of ADGRL3 (L3) at Thr1140 (pT1140), which is a poorly explored field of aGPCRs. It was made possible by exploiting a phosphospecific antibody developed in collaboration. Coincidently, pT1140 was not dependent on the examined GPCR properties of the receptor, such as G protein coupling, dependence of the TA, and GRK-mediated phosphorylation. Instead, by series of pharmacological inhibitions, it was discovered that pT1140 originates from the action of novel PKCs (nPKCs). Co-expression of L3 and dominant-negative mutants or the catalytic domains of individual members of nPKCs reveals that PKC acts as a master regulator of the phosphorylation event, by directly phosphorylating the receptor and priming other members of the nPKCs for pT1140. Finally, possible origins of the PKC activation were explored. It was found that the stimulation of PKC occurs via actin disassembly, which can act downstreams of VEGF-A/VEGFR2 signaling, although the physiological relevance is still yet to be deciphered. Nonetheless, the observations opened up new directions of research in the aspect of crosstalks between different signaling cascades and the possible modulations of the signaling fidelity of aGPCRs. Additionally, the complexity of aGPCR signaling has been clearly demonstrated. Conclusion This study has further defined the importance of GAIN domain cleavage for surface trafficking of aGPCRs, a process crucial for extracellular interactions. Moreover, a novel mechanistic model of GAIN domain cleavage in relevance to biogenesis and maturation of the receptors has been postulated. Characterisation of a site-specific phosphorylation mechanism of L3 has illustrated the potential of complex interactions of aGPCRs with other signaling pathways in cells. The results collectively shed light on the structure-function relationship of aGPCRs, and pave ways for numerous potential areas for explorations in the future.

Programmed cell death in animals, plants and protists is in part regulated by a variety of proteases, including cysteine aspartyl proteases, (caspases, paracaspases and metacaspases), cathepsins, subtilisin-like serine proteases, vacuolar processing enzymes and the proteasome. The role of different proteases in the cell death responses of the fungi is however largely unknown. A greater understanding of the fungal cell death machinery may provide new insights into the mechanisms and evolution of PCD and potentially reveal novel targets for a new generation of antifungal drugs. The role of a metacaspase encoding gene, MCA1, in the cell death response of the human pathogen Candida albicans pathogen has been investigated by functional analysis. MCA1 deletion not only alters the sensitivity of cells to a number of cell death stimuli, it also enhances virulence in an insect model. C. albicans shows altered cell and colony morphology on Lee’s medium. Evidence is presented to suggest that these functions appear to be dependent upon active mitochondria. In this study it has also been shown that key caspase substrates may be conserved between humans and the yeasts Saccharomyces cerevisiae and Candida albicans. Many substrates, particularly those which are essential, have retained their caspase cleavage motifs. 14 protease mutants displayed altered activity against caspase 1, 3, 6 or 8 substrates during acetic acid-induced PCD and caspase 1-like activity appeared to be particularly associated with PCD. Using a novel bioinformatic analysis of experimental LC-MS/MS data, changes in the degradation patterns of the proteome (destructome) following acetic acid-induced cell death have been investigated in wild-type yeast. In addition, potential native substrates of the yeast Mca1 have also been identified. The future challenge is to characterise the destructome of different proteases under a range of cell death conditions. In this way it may be possible to identify key components of the cell death machinery and their substrates and so reveal the most promising targets for future therapeutics.

Thesis (MSc (Physiological Sciences))--Stellenbosch University, 2008. / Introduction: Skeletal muscle atrophy is a mitigating complication that is characterized by a reduction in muscle fibre cross-sectional area as well as protein content, reduced force, elevated fatigability and insulin resistance. It seems to be a highly ordered and regulated process and signs of this condition are often seen in inflammatory conditions such as cancer, AIDS, diabetes and chronic heart failure (CHF). It has long been understood that an imbalance between protein degradation (increase) and protein synthesis (decrease) both contribute to the overall loss of muscle protein. Although the triggers that cause atrophy are different, the loss of muscle mass in each case involves a common phenomenon that induces muscle proteolysis. It is becoming evident that interactions among known proteolytic systems (ubiquitin-proteosome) are actively involved in muscle proteolysis during atrophy. Factors such as TNF-α and ROS are elevated in a wide variety of chronic inflammatory diseases in which skeletal muscle proteolysis presents a lethal threat. There is an increasing body of evidence that implies TNF-α may play a critical role in skeletal muscle atrophy in a number of clinical settings but the mechanisms mediating its effects are not completely understood. It is also now apparent that the transcription factor NF-κB is a key intracellular signal transducer in muscle catabolic conditions. This study investigated the various proposed signalling pathways that are modulated by increasing levels of TNF-α in a skeletal muscle cell line, in order to synthesize our current understanding of the molecular regulation of muscle atrophy. Materials and Methods: L6 (rat skeletal muscle) cells were cultured under standard conditions where after reaching ± 60-65% confluency levels, differentiation was induced for a maximum of 8 days. During the last 2 days, myotubes were incubated with increasing concentrations of recombinant TNF-α (1, 3, 6 and 10 ng/ml) for a period of 40 minutes, 24 and 48 hours. The effects of TNF-α on proliferation and cell viability were measured by MTT assay and Trypan Blue exclusion technique. Morphological assessment of cell death was conducted using the Hoechst 33342 and Propidium Iodide staining method. Detection of apoptosis was assessed by DNA isolation and fragmentation assay. The HE stain was used for the measurement of cell size. In order to determine the source and amount of ROS production, MitoTracker Red CM-H2 X ROS was utilised. Ubiquitin expression was assessed by immunohistochemistry. PI3-K activity was calculated by using an ELISA assay and the expression of signalling proteins was analysed by Western Blotting using phospho-specific and total antibodies. Additionally, the antioxidant Oxiprovin was used to investigate the quantity of ROS production in TNF-α-induced muscle atrophy. Results and Discussion: Incubation of L6 myotubes with increasing concentrations of recombinant TNF-α revealed that the lower concentrations of TNF-α used were not toxic to the cells but data analysis of cell death showed that 10 ng/ml TNF-α induced apoptosis and necrosis. Long-term treatment with TNF-α resulted in an increase in the upregulation of TNF- α receptors, specifically TNF-R1. The transcription factors NF-κB and FKHR were rapidly activated thus resulting in the induction of the ubiquitin-proteosome pathway. Activation of this pathway produced significant increases in the expression of E3 ubiquitin ligases MuRF-1 and MAFbx. Muscle fibre diameter appeared to have decreased with increasing TNF-α concentrations in part due to the suppressed activity of the PI3-K/Akt pathway as well as significant reductions in differentiation markers. Western blot analysis also showed that certain MAPKs are activated in response to TNF-α. No profound changes were observed with ROS production. Finally, the use Oxiprovin significantly lowered cell viability and ROS production. These findings suggest that TNF-α may elicit strong catabolic effects on L6 myotubes in a dose and time dependent manner. Conclusion: These observations suggest that TNF-α might have beneficial effects in skeletal muscle in certain circumstances. This beneficial effect however is limited by several aspects which include the concentration of TNF-α, cell type, time of exposure, culture conditions, state of the cell (disturbed or normal) and the cells stage of differentiation. The effect of TNF-α can be positive or negative depending on the concentration and time points analysed. This action is mediated by various signal transduction pathways that are thought to cooperate with each other. More understanding of these pathways as well as their subsequent upstream and downstream constituents is obligatory to clarify the central mechanism/s that control physiological and pathophysiological effects of TNF-α in skeletal muscle.