Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: Fermentation in Zymomonas mobilis has been described as a catabolic highway, with 50 % of soluble protein comprising glycolytic and fermentative enzymes. In conjunction with one of the fastest observed fermentations, the conversion of glucose to ethanol forms one of the least efficient energy extractions found in nature. The low energy yield of fermentation in Z. mobilis is a result of the usage of the Entner-Doudoroff glycolytic pathway, which has half the energy yield per mol substrate compared to the well known Embden-Meyerhof-Parnas glycolytic pathway. The work presented in this thesis forms part of a larger project to compare glycolytic regulation in different micro-organisms (i.e., Z. mobilis, Escherichia coli, Saccharomyces cerevisiae and Lactococcus lactis). These organisms were chosen based on their usage of different glycolytic mechanisms. By using supply-demand analysis for quantifying glycolytic regulation as well as similar experimental conditions (e.g. using non-growing cell cultures), we can compare the regulatory behaviour of mechanistically distinct freeenergy supplies. The aim of this thesis was to quantify the importance of anaerobic free-energy generation for the regulation of the Entner-Doudoroff glycolytic pathway in Z. mobilis. We used metabolic control analysis (MCA) and supply-demand analysis to realize this goal. The central message of MCA is that when a metabolic parameter (e.g., a conserved metabolic moiety) is deemed important for affecting a particular steady-state variable (i.e., fermentation flux), its effect on the steady state variable should be tested. An extension to MCA, supply-demand analysis, provides a quantitative framework for analyzing the regulatory importance of cellular commodities such as anaerobic free-energy. This is done through comparing the elasticities of anaerobic free-energy supply and demand, which yields the degree to which the respective reaction blocks control the flux through anaerobic free-energy metabolism, as well as determine the cellular free-energy state (ATP/ADP ratio). The regulation of anaerobic free-energy metabolism in Z. mobilis was investigated with an experimental approach. The key features of our experimental setup were the use of NMR spectroscopy for detecting metabolites, as well as employing non-growing conditions for supply-demand experiments. With NMR spectroscopy metabolites could be detected in real time without using invasive sampling techniques; the use of nongrowing conditions further simplified the analysis by enabling us to correlate fermentative behaviour exclusively with the anaerobic free-energy state. Fermentation of glucose was investigated in the wild type Z. mobilis, a recombinant containing a non-expressing plasmid, or expressing plasmids for over-expressing the glucose facilitator (TCDB 2.A.1.1.4) or glucose-6-phosphate dehydrogenase (EC 1.1.1.49). In addition, ATP demand in the non-expressing recombinant and wild type was perturbed by titrating with the uncoupler acetic acid. Our results show that the anaerobic free-energy demand, the glucose facilitator and glucose-6-phospate dehydrogenase all control the flux of ethanol production in Z. mobilis. The Entner-Doudoroff glycolytic supply activity was found to be sensitive to changes in the ratios of ATP/ADP (elasticity varied between –0.31 and –0.49) and NTP/NDP (elasticity varied between –0.31 and – 0.50). / AFRIKAANSE OPSOMMING: Fermentasie in Zymomonas mobilis word beskryf as ‘n kataboliese snelweg, waar glikolitiese en fermentatiewe ensieme 50% van totale oplosbare proteïene in die sel uitmaak. Hoewel dié fermentasie een van die vinnigstes is wat tot op hede waargeneem is, is die omskakeling van glukose na etanol een van die mees ondoeltreffende energieekstraksies in die natuur. Dié lae energie-opbrengs, soos waarneembaar in fermentasie in Zymomonas mobilis, kan toegeskryf word aan die Entner-Doudoroff metaboliese pad. Hierdie metaboliese pad lewer slegs die helfte van die energie-opbrengs per mol substraat vergeleke met die meer bekende Embden-Meyerhof-Parnas glikolitiese pad. Die navorsing in hierdie tesis is deel van ‘n omvattende projek wat poog om die regulering van glikolise in verskillende mikro-organismes (Z. mobilis, Escherichia coli, Saccharomyces cerevisiae en Lactococcus lactis) te vergelyk. Dié organismes is gekies op grond van die uiteenlopende glikolitiese meganismes waarvan hulle gebruik maak. Ten einde die reguleringsgedrag van meganisties verskillende vry-energie produksieweë m.b.v. vraag-aanbod analise te vergelyk, moet glikolitiese regulering eers onder eenderse eksperimentele kondisies (b.v. nie-groeiende selkulture) gekwantifiseer kan word. Die hoofdoel van hierdie tesis was om die belang van anaerobiese vry-energie produksie vir die regulering van die Entner-Doudoroff glikolitiese pad in Z. mobilis te kwantifiseer. Hiervoor is van Metaboliese kontrole-analise (MKA) en vraag-aanbodanalise (‘n uitbreiding van MKA) gebruik gemaak. MKA is ‘n tegniek waarmee die effek wat ‘n metaboliese parameter (soos metaboliese deel-konservering) op ‘n spesifieke bestendige toestand-veranderlike (soos fermentasiefluksie) het, gekwantifiseer kan word. Vraagaanbodanalise daarenteen, bied ‘n kwantitatiewe raamwerk waardeur die regulatoriese belang van sellulêre kommoditeite (byvoorbeeld anaerobiese vry-energie) geanaliseer kan word. Tydens laasgenoemde proses word die elastisiteit van die anaerobiese vry-energie aanbod en die elastisiteit van die vraag vergelyk. Op hierdie manier kan die mate van beheer wat die onderskeie reaksieblokkie oor die fluksie deur anaerobiese vry-energie metaboliese paaie, sowel as oor die sellulêre vry-energie toestand (ATP/ADP verhouding), bepaal word. In hierdie werk is die regulering van anaerobiese vry-energie metabolisme in Z. mobilis ondersoek deur van ‘n eksperimentele benadering gebruik te maak. Die sleuteleienskappe van dié benadering was om kernmagnetiese-resonansiespektroskopie (KMR spektroskopie) te gebruik om metabolietkonsentrasies te meet, en om van niegroeiende kondisies gebruik te maak vir die vraag-aanbod eksperimente. Metabolietkonsenstrasies kon aaneenlopend bepaal word sonder die gebruik van monsternemingstegnieke wat die reaksie sou kon beïnvloed. Eksterne invloede op die fermentasiegedrag kon ook uitgesluit word deur van nie-groeiende kondisies gebruik te maak, sodat die waargenome fermentasiegedrag uitsluitelik aan die anaerobiese vryenergie toestand toegeskryf kan word. Glukose fermentasie was ondersoek in wilde tipe Z. mobilis, en in drie rekombinante wat onderskeidelik ‘n glukose fasiliteerder ooruitdrukkingsplasmied (TCDB 2.A.1.1.4), ‘n glukose-6-fosfaat dehidrogenase ooruitdrukkingsplasmied (EC 1.1.1.49), en ‘n nieuitdrukkingsplasmied bevat het. Die ATP vraag in die wilde tipe en die nieuitdrukkingsrekombinant is geperturbeer deur titrasies met asynsuur as ontkoppelaar. Die resultate toon dan die anaerobiese vry-energievraag, sowel as die glukose fasiliteerder en glukose-6-fosfaat dehidrogenase, die fluksie van etanolproduksie in Z. mobilis beheer. Die Entner-Doudoroff glikolitiese produksie-aktiwiteit was sensitief vir veranderinge in die ATP/ADP verhouding (elastisiteite was tussen -0.31 en -0.49) en die NTP/NDP verhouding (elastisiteite was tussen -0.31 en -0.50).

Identifying molecular mechanisms regulating cellular energy utilization may lead to increased understanding of maintenance energy cost and improved feed efficiency in beef cows. Three experiments were conducted to characterize measures of residual feed intake (RFI) in pregnant beef cows; to examine the effects of moderate dietary restriction on visceral organ mass and proteins relating to energy metabolism; and to investigate the influence of pregnancy on visceral organ mass and proteins relating to energy metabolism. The first experiment combined data from five experiments using 321 pregnant Angus × Simmental cows. Including ultrasound fat measures and diet/management information increased the feed intake prediction model R2 by 7.3% and > 20%, respectively. Individual experiment RFI models varied greatly in accuracy. In the second experiment, 22 pregnant beef cows were fed at 85% (LOW; n=11) or 140% (HIGH; n=11) of net energy requirements during mid- to late-gestation. Tissue samples from liver, kidney, muscle, ruminal papillae, pancreas, and small intestinal muscosa were collected. Western blots were conducted to quantify abundance of: proliferating cell nuclear antigen, ATP synthase, ubiquitin, and Na/K+ ATPase for all tissues; peroxisome proliferator-activated receptor gamma, peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α), and 5’-adenosine monophosphate-activated protein kinase and phosphorylated-AMPK (pAMPK) for liver, muscle, and rumen; phosphoenolpyruvate carboxykinase for liver and kidney; and uncoupling protein 2 for liver. Cows fed HIGH had greater (P ≤ 0.04) ADG and final BW than cows fed LOW. Ubiquitin abundance in muscle was greater (P = 0.009) in cows fed LOW, and PCG-1α in liver was greater (P = 0.03) in cows fed HIGH. In the third experiment, 18 pregnant (PREG; n =9) or non-pregnant (OPEN; n=9) Angus × Simmental cows were fed for ad libitum intake during mid- to late-gestation. Tissues were weighed and collected and analyzed for protein abundance as described in the second experiment. Liver mass was lower (P ≤ 0.02), abundance of Na+/K+-ATPase was greater (P =0.04) and rumen pAMPK abundance was increased (P = 0.006) in PREG cows. These experiments indicate that measuring RFI in pregnant cows may pose some challenges, and nutrient restriction and pregnancy can influence molecular factors influencing feed efficiency. / Financial support was provided by Canadian Beef Cattle Industry Science Cluster, through funding provided by the Beef Cattle Research Council and Agriculture and Agri-Food Canada, Agriculture Adaptation Council-Farm Innovation Program, Ontario Ministry of Agriculture, Food and Rural Affairs, and the Ontario Cattleman’s Association.

Energy production is a very important function for the cells to maintain homeostasis, survive and proliferate. Cellular energy can be produced either through oxidative phosphorylation (OXPHOS) in the presence of oxygen or glycolysis in its absence. Cancer cells, even in the presence of oxygen prefer to produce energy through glycolysis and this confers them a survival advantage. Energy metabolism has recently attracted the interest of several laboratories as targeting the pathways for energy production in cancer cells could be an efficient anticancer treatment. For that purpose the role of various transcription factors in determining the pathway of energy production has been investigated extensively and there is evidence to suggest that oncogenic transcription factors promote glycolysis whereas tumour suppressors demote it. In line with this notion, the master regulator of cellular response to hypoxia, the Hypoxia Inducible Factor 1 (HIF-1) has been shown to induce the expression of a variety of genes encoding enzymes involved in glucose metabolism as well as OXPHOS favouring energy production through glucose metabolism in hypoxic cells. The tumour suppressor p53 on the other hand inhibits glycolysis and stimulates OXPHOS. One of the pathways through which p53 exerts these effects, is by inducing the inhibitor of glycolysis TIGAR and the cytochrome c oxidase assembly factor SCO2 gene expression under DNA damage conditions. However, the regulation of the expression of these genes in hypoxic conditions has been only partially elucidated. We hypothesised that under hypoxic conditions, TIGAR and SCO2 gene expression might be differentially regulated in cells bearing mutated p53 and in these cells the involvement of HIF-1 could be crucial. Indeed under hypoxia mimicking conditions, the TIGAR and SCO2 protein and mRNA levels were found to be modulated differentially in p53 wild type and mutant cell lines. The bioinformatics analysis revealed the presence of hypoxia responsive elements (HREs) within the regulatory region of the promoters of TIGAR and SCO2 genes. Firefly reporter assays and chromatin immunoprecipitation (ChIP) assays have indicated that HIF-1 plays a crucial role in the regulation of TIGAR gene expression. The direct involvement of HIF-1 in the regulation of SCO2 gene expression requires further investigation. We and others have recently reported that PCAF is a common cofactor for p53 and HIF-1α, regulating the protein stability and transcription target selectivity of both transcription factors thereby orchestrating the balance between life and death in cancer cells. We hypothesised that PCAF plays a similar role in the regulation of cellular energy metabolism by differentially targeting HIF-1α and p53 to the promoter of TIGAR and SCO2 genes. In this study we present evidence to support the notion that PCAF plays an import role in the regulation of TIGAR and SCO2 gene expression under hypoxic mimicking conditions. This conclusion was supported by assessing the functional consequences of PCAFwt and PCAFΔHAT overexpression on the intracellular lactate production, cellular oxygen consumption, NAD+/NADH ratio and ROS generation in cells under hypoxia mimicking conditions.

LKB1 est un gène suppresseur de tumeur qui code une kinase « maitre » dont l’activité contrôle la polarité et la prolifération cellulaire en les coordonnant avec l’état métabolique de la cellule. Ce travail a abouti à l’identification d’une nouvelle isoforme LKB1 appelée ∆N-LKB1 qui est générée par transcription alternative et initiation interne de la traduction de l'ARNm LKB1. La protéine ∆N-LKB1 est délétée de sa partie N-terminale incluant une partie de son domaine kinase. Bien que la protéine N-LKB1 soit catalytiquement inactive, elle potentialise l'effet activateur de la protéine LKB1 sur sa cible principale l’APMK, senseur énergétique de la cellule, via une interaction directe avec le domaine d'auto-inhibition de l’AMPK. En revanche, ∆N-LKB1 interfère négativement avec la capacité de LKB1 à induire la polarité cellulaire. Enfin, en utilisant des approches in vitro et in vivo, nous avons montré que N-LKB1 possède une propriété oncogénique intrinsèque. N-LKB1 est exprimée seule dans la lignée NCI-H460 issue du cancer du poumon. L’inhibition de l’expression de N-LKB1 dans les cellules NCI-H460 induit une diminution de la survie de ces cellules et inhibe leur pouvoir oncogénique quand elles sont greffées dans la souris nude. Nous avons donc identifié une nouvelle isoforme LKB1 qui stimule l’adaptation métabolique LKB1-dépendante, mais qui inhibe la polarité cellulaire contrôlée par LKB1. Le suppresseur de tumeur LKB1 ainsi que l’oncogène N-LKB1 sont codé par le même gène, ce qui peut expliquer certains des effets paradoxaux de LKB1 durant la tumorigenèse. / The LKB1 tumor suppressor gene encodes a master kinase that coordinates the regulation of energetic metabolism, cell growth and cell polarity. We now report the identification of a novel isoform of LKB1 named N-LKB1 that is generated through alternative transcription and internal initiation of translation of the LKB1 mRNA. The N-LKB1 protein lacks the N-terminal region and a portion of the kinase domain. Although N-LKB1 is catalytically inactive, it potentiates the stimulating effect of LKB1 on the AMP-activated protein kinase (AMPK) metabolic sensor through a direct interaction with the regulatory auto-inhibitory domain of AMPK. Contrasting, N-LKB1 negatively interferes with the LKB1 polarizing activity. Finally, combining in vitro and in vivo approaches, we showedthat N-LKB1 has an intrinsic oncogenic property. N-LKB1 is expressed solely in the lung cancer cell line, NCI-H460. Silencing of N-LKB1 decreased survival of NCI-H460 cells and inhibited their tumorigenicity when engrafted in nude mice. In conclusion, we have identified a novel LKB1 isoform that enhances the LKB1-controlled AMPK metabolic activity but inhibits LKB1-induced polarizing activity. Both, the LKB1 tumor suppressor and the oncogene, N-LKB1, are expressed from the same locus and this may account for some of the paradoxical effects of LKB1 during tumorigenesis.

Hintergrund: Die Funktion von Immunzellen hängt von einer konstanten und ausreichenden Energieversorgung ab, die über die OXPHOS in den Mitochondrien und die Glykolyse im Zytosol realisiert wird. Die wichtigsten Substrate dafür sind Sauerstoff und Glukose. Fragestellung: Bei schweren Erkrankungen oder in Entzündungsgebieten ist die zelluläre Energieversorgung stark beeinträchtigt, weil in der Mikroumgebung der Zelle Sauerstoff und Nährstoffe inadäquat bereitgestellt werden. Ziel war herauszufinden, ob und wie humane Immunzellen ihre Lebensfähigkeit und funktionellen Aktivitäten unter solchen Umständen aufrechterhalten. Methoden: Humane CD4+ T-Zellen und CD14+ Monozyten wurden durch MACS aus peripherem Blut gesunder Spender isoliert. Die Sauerstoffverbrauchsmessung mittels Clark-Elektrode war Maß der oxidativen Energiebildung, die mit Myxothiazol und Glukoseentzug gehemmt wurde. Die CD3/CD28-stimulierte T-Zell-Proliferation wurde durchflußzytometrisch mittels CFDA SE analysiert. Basierend auf dem Paraformaldehyd-Saponin-Prozedere wurde die Zytokinsynthese ebenfalls am FACS bewertet, nachdem die T-Zellen in Anwesenheit von Brefeldin A mit PMA/Ionomycin stimuliert wurden. Mit einem käuflichen Testsystem (FACS-Technik) wurde die monozytäre Phagozytose untersucht. Die HIF-1alpha-Expression wurde nach PMA-Ionomycin-Stimulation von Myxothiazol-behandelten T-Zellen auf mRNA- und Proteinebene gemessen. Ergebnisse: Bei Glukoseanwesenheit waren alle untersuchten Immunfunktionen trotz vollständig gehemmter OXPHOS unbeeinträchtigt. Erst bei gleichzeitigem Glukoseentzug, der per sé Proliferation und Phagozytose signifikant beeinträchtigte, waren sie signifikant vermindert. Es wird vermutet, daß T-Zellen die Energieverluste mit einem überschießenden Effekt ihres Sauerstoffverbrauchs und stark angetriebener Glykolyse kompensieren. HIF-1alpha ist dabei nicht entscheidend für die Umschaltung auf anaerobe Energiesynthese. Schlußfolgerung: Die Daten quantifizieren die Energieanforderungen der funktionellen Aktivität in hochgereinigten humanen Immunzellfraktionen. Es wurde nachgewiesen, daß sich Immunzellen unerwartet lange an eine massiv beeinträchtigte Energetik adaptieren können und ihre spezifischen Funktionen aufrechterhalten. / Background: The function of immune cells is dependent upon a constant and adequate supply of energy. Energy is formed via OXPHOS in the mitochondria and via cytosolic glycolysis. Oxygen and glucose are the main substrates for energy synthesis. Objective: In severe diseases or in inflamed areas cellular energy supply is significantly impaired due to inadequate supply of cellular microenvironment with oxygen and nutrients. The aim of this study was to answer the question, whether and how human immune cells maintain viability and functional activity under these circumstances. Methods: Human CD4+ T cells and CD14+ monocytes were isolated by MACS from peripheral blood of healthy donors. The extent of oxidative energy formation was determined via measurement of oxygen consumption using a Clark type electrode. Energy production was restricted in glucose-free cell culture medium and by gradually inhibited OXPHOS using myxothiazol. T cell proliferation was flow-cytometrically analysed using CFDA SE after stimulation with CD3 and CD28 antibodies. Cytokine synthesis was assessed by flow-cytometrical immunofluorescence and the paraformaldehyde-saponin procedure after stimulation of T cells with PMA/ionomycin in the presence of brefeldin A. Phagocytosis of monocytes was measured using a commercial test system (FACS technique). HIF-1alpha expression was assessed by semiquantitative PCR and immunoblot after the stimulation of myxothiazol treated T cells with PMA/ionomycin. Results: In glucose-containing medium all investigated immune functions were unaffected even under complete suppression of OXPHOS. Only when OXPHOS and glycolysis were simultaneously and almost completely suppressed a significant decrease was found. Glucose deprivation per se caused both a significantly reduced proliferation and phagocytosis. It is supposed, that T cells are able to compensate for an energy deficit by an excess of oxygen consumption and strongly induced glycolysis. However, HIF-1alpha was found to be not crucial for switching to anaerobic energy synthesis. Conclusion: These data quantify the energy requirement of functional activity in highly purified human immune cell fractions. An unexpectedly high adaptive potential of immune cells to maintain specific functions even under massively impaired energetic conditions could be demonstrated.