La protéine de fonction inconnue, YvcK, est vitale chez Staphylococcus aureus mais non essentielle chez les bactéries modèles Bacillus subtilis ou Escherichia coli. Chez B. subtilis, les bactéries délétées du gène yvcK, sont sérieusement affectées dans leur croissance et leur morphologie dans des conditions de croissance gluconéogéniques. Les défauts observés peuvent être compensés par l’ajout de fortes concentrations de magnésium ou par l’inactivation de gènes impliqués dans le métabolisme. Ceci suggère que, les mutants yvcK présentent des altérations au niveau de la paroi bactérienne qui sont probablement dues à un désordre du métabolisme. Le phénotype lié à l’absence d’YvcK est similaire à celui observé chez des souches mutées au niveau de gènes impliqués dans la synthèse du peptidoglycane ou constituant le cytosquelette. La protéine MreB, composant majeur du cytosquelette bactérien, forme une structure hélicoïdale sous la membrane cytoplasmique pour positionner les enzymes de synthèse et la maturation du peptidoglycane. In vivo, la protéine YvcK est également localisée sous la forme d’une hélice. Par ailleurs, la surexpression de YvcK supprime le défaut de morphologie du mutant mreB et vice versa. Il a été montré que, chez B. subtilis, la localisation de la protéine membranaire PBP1 était dépendante de MreB. Une délétion de ponA, gène codant pour PBP1, rétablit la viabilité d’un mutant mreB et celle du mutant yvcK dans des conditions de croissance gluconéogéniques. La protéine de fusion GFP-PBP1 dans une souche délétée du gène yvcK, cultivée en milieu liquide CE-gluconate est délocalisée expliquant le gonflement des cellules. Ce résultat suggère que la localisation normale de PBP1 au septum due à la surproduction de YvcK dans un mutant mreB (et réciproquement) permet la restauration de la croissance et de la morphologie. De plus, nous avons montré que, comme son homologue présent chez Mycobacterium tuberculosis, YvcK est phosphorylée in vitro. Nous avons caractérisé la phosphorylation d’YvcK par la protéine kinase PrkC et nous avons identifié la Thr 304 comme site unique de phosphorylation. Cette phosphorylation semblerait jouer un rôle important dans la complémentation du mutant mreB et du repositionnement de la PBP1. / The YvcK protein is a bacterial conserved protein of unknown function. It is essential in Staphylococcus aureus but not essential in both Bacillus subtilis and Escherichia coli. In B. subtilis, inactivation of the yvcK gene seriously affects growth and morphology on neoglucogenic carbon sources. The defects observed in a yvcK mutant can be offset by the addition of high concentrations of magnesium or by inactivation of genes involved in metabolism. This suggests that, when grown on some carbon sources, yvcK mutants display alterations in their cell wall probably due to a disorder in this metabolism. The phenotype associated with the absence of YvcK is similar to that observed with strains mutated in genes involved in peptidoglycan synthesis or encoding proteins of the cytoskeleton. The major component of cytoskeleton, MreB, an actin-like protein, together with other proteins, forms a helical structure at the cell membrane that participates in the organization and positioning of the enzymes of peptidoglycan synthesis and maturation. We showed that YvcK is organized as a helical like pattern localized near the inner surface of the membrane, independently of the presence of MreB. Surprisingly and despite that these two proteins do not harbour any similarity of sequence or structure, an overproduction of YvcK restored a normal morphology in an mreB mutant strain and vice versa. Furthermore, as already observed for the mreB mutant, in a yvcK mutant strain, the penicillin-binding protein PBP1 is delocalized and deletion of its gene restores growth of a yvcK mutant on gluconate medium. All these results suggest that YvcK is not only involved in the synthesis of cell wall from gluconeogenic carbon sources but also plays a role in cell morphogenesis. In addition, we have shown that similarily to its Mycobacterium tuberculosis homolog, YvcK is phosphorylated in vitro. We have characterized the phosphorylation of YvcK by the protein kinase PrkC and we identified the Thr 304 as the single phosphorylation site. Furthermore, this phosphorylation appears to play an important role in the complementation of the mreB mutant and repositioning of PBP1.

Glucose allocation is an important cellular process that is misregulated in the interrelated diseases obesity, diabetes and cancer. Cells have evolved critical mechanisms for regulating glucose allocation, one of which is sensory protein kinases. PAS kinase is a key sensory protein kinase that regulates glucose allocation in yeast, mice and man; and is a novel therapeutic target for the treatment of metabolic diseases such as obesity, diabetes and cancer. Despite its importance, the molecular mechanisms of PAS kinase function are largely unknown. Through large-scale protein-interaction studies, we have identified 93 novel binding partners for PAS kinase which help to expand its role in glucose allocation as well as suggest novel roles for PAS kinase including mitochondrial metabolism, cell growth/division, protein modification, stress tolerance, and gene/protein expression. From a subset of these binding partners, we identified 5 in vitro substrates of PAS kinase namely Mot3, Utr1, Zds1, Cbf1 and Pbp1. Additionally, we have further characterized Pbp1 and Cbf1 as PAS kinase substrates through both in vitro and in vivo evidence as well as phenotypic analysis. Evidence is provided for the PAS kinase-dependent phosphorylation and activation of Pbp1, which in turn inhibits cell proliferation through the sequestration of TORC1. In contract, PAS kinase-dependent phosphorylation of Cbf1 inhibits its activity, decreasing cellular respiration. This work elucidates novel molecular mechanisms behind PAS kinase function in both mitochondrial and cell growth pathways in eukaryotic cells, increasing our understanding of the regulation of central metabolism.

Pbp1 is a component of glucose deprivation induced stress granules and is involved in P-body-dependent granule assembly. We have recently shown that Pbp1 plays an important role in the interplay between three sensory protein kinases in yeast: AMP-regulated kinase (Snf1 in yeast), PAS kinase 1 (Psk1 in yeast), and the target of rapamycin complex 1 (TORC1), to regulate glucose allocation during nutrient depletion. This signaling cascade occurs through the SNF1-dependent phosphorylation and activation of Psk1, which phosphorylates and activates poly(A)- binding protein binding protein 1 (Pbp1), which then inhibits TORC1 through sequestration at stress granules. In this study we further characterized the regulation of Pbp1 by PAS kinase through the characterization of the role of the Psk1 homolog (Psk2) in Pbp1 regulation, and the identification of functional Pbp1 binding partners. Human ataxin-2 (ATXN2) is the homolog of yeast Pbp1 and has been shown to play an important role in the development of several ataxias. In this study we have also provided the evidence that human ataxin-2 can complement Pbp1 in yeast, and that human PAS kinase can phosphorylate human ataxin-2. Further characterizing this interplay between PAS kinase and Pbp1/ATXN2 aid in understanding pathways required for proper glucose allocation during nutrient depletion, including reducing cell growth and proliferation when energy is low. In addition, it yields valuable insights into the role of ataxin-2 in the development of devastating ataxias.

Ataxin-2 is an RNA-binding protein that is involved in many crucial cellular processes such as R-loop regulation, mRNA stability, TOR signaling regulation, and stress granule formation. Ataxin-2 is highly conserved, found in organisms ranging from Saccharomyces cerevisiae to Caenorhabditis elegans and Homo sapiens. Recently, ataxin-2 has been linked to the neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). ALS is a fatal disease that causes loss of motor neurons. In addition to ataxin-2 interacting with known ALS risk factor proteins, research into the relationship between ataxin-2 and ALS shows that polyglutamine expansions in ataxin-2 are gain-of-function mutations that lead to overactivity of ataxin-2 and probable neurodegeneration. In fact, targeting ataxin-2 using gene silencing techniques dramatically slows the progression of ALS in both mice and man.The Grose laboratory has characterized a serine-threonine kinase, PAS kinase as upstream kinase and putative activator of ataxin-2. We hypothesize that knockdown of PAS kinase could, therefore, have similar effects to directly downregulating ataxin-2 and its cellular functions. Characterization of Ataxin-2 has revealed that its gain or loss of function lead to distinct cellular phenotypes. One study concluded that lowering ataxin-2 levels reduced the size and number of stress granules in mammalian cells, which was observed through microscopy. Another study found that activation and overexpression of ataxin-2 lead to reduced mTOR levels because of its sequestration to stress granules. Lastly, preliminary data obtained by the Grose laboratory suggests that yeast deficient in Pbp1 (the yeast homologue of ataxin-2) have altered cell cycles.This project describes the cellular readouts used to determine if PAS kinase downregulation confers the same cellular phenotypes as ataxin-2 downregulation. First, we found that PAS kinase does influence ataxin-2 abundance in mammalian cells. Using yeast as a model, we found that Pbp1 influences the cell cycle through its binding partners, causing a reduction in the percentage of cells in the G2 phase compared to the G1 phase. PAS kinase conferred an opposite change, most likely due to the activity of other PAS kinase substrates. Additionally, we found that Pbp1 deficiency is synthetically lethal when in conjunction with deficiency of any one of its cell cycle-related binding partners. The cellular changes cause by Pbp1 deficiency highlight not only the importance of ataxin-2 in the cell, but also the importance of understanding the effects of downregulation of ataxin-2.

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.