L'exposition aux ultraviolets solaires constitue un facteur de risque majeur dans le développement de cancers cutanés. L'initiation de ces cancers est cependant pondérée par des mécanismes cellulaires de protection qui contrecarrent l'instabilité génomique éventuellement promue par les UV. Dans ces mécanismes, le suppresseur de tumeur p53 joue un rôle fondamental en régulant l'expression de nombreux gènes permettant de bloquer le cycle cellulaire et de réparer l'ADN ou, si les dommages cellulaires sont trop importants, d'activer l'apoptose. Les régulateurs de la stabilité de la protéine p53 en réponse au stress UV sont ainsi capitaux pour assurer la stabilité du génome. En réponse au stress UV in vivo et in vitro, nous mettons en évidence que le facteur de transcription USF1 est primordial à l'activation du programme génétique contrôlé par la protéine p53. Nos données convergent vers un modèle dans lequel USF1 agit sur la voie p53 par deux moyens. D'une part, USF1, assure par interaction physique la stabilité de p53 en contrecarrant de manière mutuellement exclusive l'association du suppresseur de tumeur à MDM2 son inhibiteur physiologique. D'autre part, USF1 agit synergiquement avec le suppresseur de tumeur pour transcrire certains gènes cibles de p53 comme le régulateur du cycle cellulaire CDKN1A (p21). Ces deux niveaux de régulation dépendent étroitement du niveau de stress et permettent d'assurer un contrôle optimal de l'arrêt du cycle cellulaire en réponse à l'exposition UV. Collectivement, nos données montrent qu'USF1, par le contrôle de la voie p53, est un facteur essentiel contre l'instabilité génomique induite par les UV. / Ultraviolets (UV) solar exposure is a critical risk factor in skin cancers development. Initiation of these cancers is however lowered by cellular protective mechanisms that counteract the genomic instability potentially promoted by UV. In these mechanisms p53 protein is critical in regulating a large number of genes that blocks the cell cycle to allow DNA repair or, if damages are beyond repair, to activate apoptosis. The regulators of p53 stability in response to UV are thus crucial to ensure genomic stability. In response to UV stress, we found by in vivo and in vitro studies that USF1 is essential in the activation of p53 genetic program. Our data converge to a model whereby USF1 acts on p53 pathway by two means. On one hand, USF1 stabilizes p53 from MDM2 mediated degradation by a physical association to the tumor suppressor in a MDM2 mutually exclusive manner. On the other hand USF1 synergizes with the tumor suppressor in the transcription of several targets of p53 protein and particularly the CDKN1A inhibitor of the cell cycle. These two levels of regulation are closely dependent in the stress level and ensure an optimal control of the cell cycle progression in response to UV. Collectively, our results show that USF1, by controlling p53 pathway, is a critical factor against the genomic instability promoted by UV.

The evolution and adaptation of microorganisms is so rapid it can be seen in the time frame of days. The root cause for their evolution comes from selective environmental pressures that see organisms with beneficial mutations survive otherwise deadly encounters or outperform members of its population who fail to adapt. This does not always result in strict improvement of the individual as in the case of antibiotic resistant bacteria who often display fitness tradeoffs to avoid death (see Reviews [1-3]). For example, when an ampicillin resistance gene (ampC) containing plasmid that is occasionally found in the wild was transformed into S. typhimurium the bacteria had slower growth and impaired invasiveness [4]. In another example, capreomycin use with mycobacteria resulted in lower binding of the drug to the ribosome through mutations in rRNA methylase TlyA 16S rRNA, which decreases the overall fitness of the mycobacteria [5]. The evolutionary interactomes between bacteria and antibiotics do not end there, as antibiotic resistant bacteria often accumulate compensatory mechanisms to regain fitness. These range in effect with some altering individual cellular pathways and others having systemic affects [1]. My work has focused on the intersection of diabetes and related antibiotic resistant bacterial infections. Diabetes is one of the leading health issues in the United States, with over 10% of the adult population and over 26% of the elderly diagnosed (American Diabetes Association) [6]. Herein I further characterize the molecular pathways involved in diabetes, through the study of PAS kinase (PASK) function. PAS kinase is a serine-threonine protein kinase which regulates the pathways disrupted in diabetes, namely triglyceride accumulation, metabolic rate (respiration), adiposity and insulin production and sensitivity [7-9]. In this study I specifically focus on the effects of PAS kinase and its substrate, USF1/Cbf1p, and how their altered metabolic deficiencies can be suppressed using yeast cells. Through this study I further characterized the molecular function of USF1/Cbf1p through the identification of putative co-transcriptional regulators, identify novel genes involved in the regulation of respiration, and uncover a function or a previous uncharacterized protein, Pal1p. Part of the diabetes healthcare challenge results from the wide range of diseases that are associated with diabetes, including obesity [10, 11], renal failure [12, 13], neuropathies and neurodegeneration [14, 15], endocrine dysfunctions [16, 17], and cancers [18]. In addition, diabetes is a leading cause of lower limb amputations, due to poor circulation and the prevalence of ulcers [19-21], many of which are antibiotic resistant [22-25]. Phage therapy, based on the administration of bacterial viruses, is a viable option for the treatment of these diseases, with our lab recently isolating bacteriophages for several clinical cases. In the second half of my thesis, I present the study of the adaptation of bacteriophages to their hosts as well as report contributions of local ecology to their evolution.

The second identified substrate of PAS kinase discussed is Pbp1. The human homolog of Pbp1 is ataxin-2, mutations in which are a known risk factor for amyotrophic lateral sclerosis (ALS). As diet and sex have been shown to be important factors regarding PAS kinase function, they also are strong contributing factors to ALS and are extensively reviewed herein. Pbp1 is known to be sequestered by PAS kinase under glucose depravation, and it can sequester additional proteins along with it to regulate different cellular pathways. To shed light on the pathways affected by Pbp1, we performed a yeast two-hybrid assay and mass spectrometry, identifying 32 novel interacting partners of Pbp1 (ataxin-2). We provide further analysis of the direct binding partner Ptc6, measuring mitophagy, mitochondrial content, colocalization, and respiration. This work elucidates novel molecular mechanisms behind the function of PAS kinase and yields valuable insights into the role of PAS kinase in disease.

Nutrient sensing kinases lie at the heart of cellular health and homeostasis, allowing cells to quickly adapt to changing environments. Target of Rapamycin (TOR) and PAS kinase (PASK, or PASKIN) are two such nutrient kinases, conserved from yeast to man. In yeast, these kinases each have paralogs. The two TOR paralogs in yeast mimic the mammalian TORC1 and TORC2 complexes, except both Tor1 and Tor2 may contribute to TORC1 or TORC2 function. The two PAS kinase paralogs are paired with the TOR paralogs, meaning that both Psk1 and Psk2 regulate TORC1, while Psk2 suppresses a temperature-sensitive allele of Tor2. Herein we review the evolutionary models for these paralogs, their function in yeast and mammalian cells, as well as the overlapping function of PAS kinase and TOR. We also use Rice University’s Direct Coupling Analysis algorithms to analyze co-evolutionary relationships and identify potential interaction sites between PAS kinase and several of its substrates.