Ataxin-1 is the protein affected in Spinocerebellar Ataxia Type 1 (SCA1) polyglutamine neurodegenerative disease. The biological function of ataxin-1 is unknown. By using live cell fluorescence microscopy and cultured human HeLa cells, we have shown that ataxin-1 nuclear inclusions (ataxin-1 NIs) are unique subnuclear sites of ataxin-1 function that do not resemble typical ataxin-1 polyglutamine nuclear aggregates or neuronal intranuclear inclusions (NIIs). Ataxin-1 NIs form independent of polyglutamine expansion in ataxin-1, and we found that ataxin-1 NIs are capable of recruiting the mRNA export factor TAP /NXF1. We propose that ataxin-1 NIs may be more accurately termed ataxin-1 nuclear bodies (ataxin-1 NBs) and suggest that ataxin-1 NBs play a role in mRNA processing and transport. We discovered that the serine to alanine mutation at position 776 of ataxin-1 (S776), known to inhibit spinocerebellar ataxia type 1 (SCA1) pathogenesis, plays a critical role in the frequency and size of ataxin-1 NBs. We found that polyglutamine expansion was not essential for ataxin-1 NB formation, and that serine 776 may be important in turnover regulation of polyglutamine expanded ataxin-1. In addition, we found that serine 776 does not significantly affect nuclear localization of ataxin-1, and that the ataxin-1 associated protein, 14-3-3 zeta, does not have a role in the nucleo-cytoplasmic transport of ataxin-1. These findings reveal that the serine 776-mediated 14-3-3 zeta co-localization with ataxin-1 is likely not important to SCA1 pathogenesis, but that the role of serine phosphorylation of ataxin-1 does have an effect on the formation of ataxin-1 NBs, thereby implicating ataxin-1 NB formation as important for understanding SCA1 disease. / Thesis / Master of Science (MSc)

Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology and Toxicology Student: Martin Svoreň Supervisor: PharmDr. Martina Čečková, Ph.D. Specialized supervisor: PD Dr. Bernd Evert Title of diploma thesis: Analysis of genomic regions bound and regulated by Ataxin-3 Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease, is a dominantly inherited neurodegenerative disease. In SCA3, the disease protein ataxin-3 (ATXN3) contains an abnormally long polyglutamine (polyQ) tract encoded by CAG repeat expansion. ATXN3 binds DNA and interacts with transcriptional regulators pointing toward a direct role of ATXN3 in transcription. It is conceivable that mutant ATXN3 triggers multiple, interconnected pathogenic cascades leading to neurotoxicity, however, the principal molecular pathomechanism remains elusive. Here, PCR analyses of 16 ATXN3-bound genomic regions recently identified by next generation sequencing of immunoprecipitated ATXN3-bound chromatin fragments confirmed enriched binding of ATXN3 to 5 genomic regions next to genes encoding CCAAT/enhancer binding protein delta (CEBPD), period circadian clock-2 (PER2), phosphatase and tensin homolog (PTEN), serine protease inhibitor family F2 (SERPINF2) and thrombospondin-1 (THBS1). To investigate putative...

Supplementary Information Video attached / <p> Machado-Joseph disease (MJD), also known as Spinocerebellar ataxia type 3 (SCA3) is one of nine poly glutamine neurodegenerative diseases caused by an expansion of CAG DNA triplets in the genes resulting in an expanded poly glutamine tract in the expressed proteins. These proteins are unrelated in function yet all manifest as specific neurological diseases. The Truant lab and others have previously shown that six of the nine polyglutamine proteins display nucleocytoplasmic shuttling capabilities and that this shuttling is affected by polyglutamine expansion. It is believed that deciphering the mechanism of nucleocytoplasmic transport may be important in understanding the normal function of these proteins, which in turn may lead to a better understanding of the pathogenesis of disease. Studies that looked at the subcellular localization of the MJD/SCA3 protein, ataxin-3, have shown that the normal protein is variably distributed between the nucleus and the cytoplasm, whereas mutant ataxin-3 is localized primarily in the nucleus. Using fluorescent protein technology and fluorescence microscopy, this thesis project attempts to analyze the nucleocytoplasmic shuttling capabilities of ataxin-3 and to evaluate the potential mechanisms that govern its translocation into and out of the nucleus. </p> <p> It was revealed that ataxin-3 is able to shuttle into and out of the nucleus and that the shuttling dynamics are dependent on the length of the poly glutamine tract. As well, two putative, CRMl dependent nuclear export signals and a putative, importin-a/~1 dependent, classical, nuclear localization signal were tested and shown to be nonfunctional as transport signals. It was then discovered that ataxin-3 is marginally leptomycin B (an inhibitor ofCRMl dependent nuclear export) sensitive in NIH3T3 and MCF7 cells, more sensitive to the drug in STHdhQ71Q7 cells and even more so in HEK 293 cells. This suggests that an exogenous factor mediates the nuclear import of ataxin-3 through the CRMl pathway. Subsequently, four known binding partners, hHDACl, hHDAC2, hHDAC6 and hHRAD23b, were tested for their potential ability to shuttle ataxin-3. It was concluded that although hHDAC6 had the greatest effect on ataxin-3 subcellular localization, we believe that it does not mediate its nuclear import or export. Future studies would involve an investigation as to how and why different polyglutamine lengths affect the nucleocytoplasmic shuttling of ataxin-3 and to identify the factor(s) that cause ataxin-3 to be more sensitive to LMB treatments in HEK 293 cells. </p> / Thesis / Master of Science (MSc)

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.

Les expansions du codon CAG (polyQ) sont impliquées dans neuf maladies neurodégénératives. Notre groupe a démontré que, lors de la traduction de la protéine ataxine-3 (Atx3) mutée qui est impliquée dans l’ataxie spinocérébelleuse de type 3 (SCA3), un changement du cadre de lecture vers un cadre décalé -1 (GCA) se produit. La traduction dans ce nouveau cadre de lecture entraine la production de polyalanine et ceci amplifierait la toxicité des polyQ. Le changement de cadre de lecture (ccl) ribosomique peut se produire des virus aux mammifères mais peu de choses sont connues sur son impact chez l’humain. Afin d’étudier ce phénomène dans la protéine Atx3 avec expansion de polyQ, nous avons établi un modèle de Drosophile transgénique et testé si c’était l’ARNm ou la protéine mutée qui était toxique. Nous avons aussi employé un essai de toeprinting (TP) afin d’identifier l’emplacement précis où les ribosomes changent de cadre de lecture sur l’ARNm. Nos résultats indiquent que la toxicité est due à la présence de polyalanines faisant suite au ccl et que l’ARNm en soi n’est pas la cause directe de la toxicité. De plus, nous avons observé que les ribosomes s’arrêtent au 48ième codon glutamine et que cet arrêt est spécifique aux polyQ. L’arrêt des ribosomes a d’ailleurs aussi été observé dans d’autres maladies avec expansions de polyQ. Puisque ces maladies ont des caractéristiques communes, un blocage de ce ccl pourrait atténuer les symptômes des patients SCA3 et d’autres maladies à expansions de polyQ / Coding CAG repeat disorders have been associated with nine neurodegenerative disorders. Our group has previously shown that during the translation of mutant ataxine-3 (Atx3), the protein involved in Spinocerebellar Ataxia type 3 (SCA3), a ribosomal frameshift occurs and leads to the reading of a GCA frame rather than a CAG frame. This new reading frame causes the production of polyalanine in the polyglutamine peptide which increases its toxicity. Ribosomal frameshifts are known to occur in all organisms but little is known about this phenomenon in human. To study ribosomal frameshift along the ATXN3 transcript, we generated a transgenic Drosophila model in which we looked at the toxicity of the mRNA. Also, we developed a toeprinting assay to precisely evaluate where the change of reading frame occurs along the mRNA. Our results suggest that the toxicity observed in our Drosophila model results from the production of polyalanine and not from the presence of the mRNA per se. Moreover, the change in reading frame seems to occur at the 48th CAG codon and this pausing of the ribosome also occurs in other polyQ tracts. Because CAG repeat disorders share many characteristics, an alteration of the frameshift could alleviate symptoms of SCA3 patients as well as of many other diseases with coding CAG repeats.

Les expansions du codon CAG (polyQ) sont impliquées dans neuf maladies neurodégénératives. Notre groupe a démontré que, lors de la traduction de la protéine ataxine-3 (Atx3) mutée qui est impliquée dans l’ataxie spinocérébelleuse de type 3 (SCA3), un changement du cadre de lecture vers un cadre décalé -1 (GCA) se produit. La traduction dans ce nouveau cadre de lecture entraine la production de polyalanine et ceci amplifierait la toxicité des polyQ. Le changement de cadre de lecture (ccl) ribosomique peut se produire des virus aux mammifères mais peu de choses sont connues sur son impact chez l’humain. Afin d’étudier ce phénomène dans la protéine Atx3 avec expansion de polyQ, nous avons établi un modèle de Drosophile transgénique et testé si c’était l’ARNm ou la protéine mutée qui était toxique. Nous avons aussi employé un essai de toeprinting (TP) afin d’identifier l’emplacement précis où les ribosomes changent de cadre de lecture sur l’ARNm. Nos résultats indiquent que la toxicité est due à la présence de polyalanines faisant suite au ccl et que l’ARNm en soi n’est pas la cause directe de la toxicité. De plus, nous avons observé que les ribosomes s’arrêtent au 48ième codon glutamine et que cet arrêt est spécifique aux polyQ. L’arrêt des ribosomes a d’ailleurs aussi été observé dans d’autres maladies avec expansions de polyQ. Puisque ces maladies ont des caractéristiques communes, un blocage de ce ccl pourrait atténuer les symptômes des patients SCA3 et d’autres maladies à expansions de polyQ / Coding CAG repeat disorders have been associated with nine neurodegenerative disorders. Our group has previously shown that during the translation of mutant ataxine-3 (Atx3), the protein involved in Spinocerebellar Ataxia type 3 (SCA3), a ribosomal frameshift occurs and leads to the reading of a GCA frame rather than a CAG frame. This new reading frame causes the production of polyalanine in the polyglutamine peptide which increases its toxicity. Ribosomal frameshifts are known to occur in all organisms but little is known about this phenomenon in human. To study ribosomal frameshift along the ATXN3 transcript, we generated a transgenic Drosophila model in which we looked at the toxicity of the mRNA. Also, we developed a toeprinting assay to precisely evaluate where the change of reading frame occurs along the mRNA. Our results suggest that the toxicity observed in our Drosophila model results from the production of polyalanine and not from the presence of the mRNA per se. Moreover, the change in reading frame seems to occur at the 48th CAG codon and this pausing of the ribosome also occurs in other polyQ tracts. Because CAG repeat disorders share many characteristics, an alteration of the frameshift could alleviate symptoms of SCA3 patients as well as of many other diseases with coding CAG repeats.

To identify the risk factors being associated with aetiology of amyotrophic lateral sclerosis (ALS), a series of systematic reviews based on existing observational epidemiological studies identified through searching of bibliographic databases were conducted. Associations between ALS and a number of genetic and environmental risk factors were examined using meta-analysis. Specifically we found that previous exposure to lead, pesticides, solvents, experience of trauma and electric shock were associated with relative increased risks of developing ALS of 86% [odds ratio (OR) =1.86, 95% CI: 1.39-2.48], 57% (OR=1.57,95% CI: 1.19-2.08), 47% (OR=1.47, 95%CI: 1.13-1.80), 64% (OR=1.64; 95%CI: 1.36-1.98), and 2.27% (OR=3.27, 95%CI:1.87-5.73) respectively, compared to their corresponding controls. The presence of intermediate CAG repeat expansion in the ATXN2 gene was associated with a 4.4 -fold increase in the risk of ALS (OR=4.44, 95%CI: 2.91-6.76). However, the attributable risk associated with each identified risk factor was estimated to be less than 5% of all ALS cases. These results confirm that ALS is a rare multifactorial degenerative condition of motor-neurons.

To identify the risk factors being associated with aetiology of amyotrophic lateral sclerosis (ALS), a series of systematic reviews based on existing observational epidemiological studies identified through searching of bibliographic databases were conducted. Associations between ALS and a number of genetic and environmental risk factors were examined using meta-analysis. Specifically we found that previous exposure to lead, pesticides, solvents, experience of trauma and electric shock were associated with relative increased risks of developing ALS of 86% [odds ratio (OR) =1.86, 95% CI: 1.39-2.48], 57% (OR=1.57,95% CI: 1.19-2.08), 47% (OR=1.47, 95%CI: 1.13-1.80), 64% (OR=1.64; 95%CI: 1.36-1.98), and 2.27% (OR=3.27, 95%CI:1.87-5.73) respectively, compared to their corresponding controls. The presence of intermediate CAG repeat expansion in the ATXN2 gene was associated with a 4.4 -fold increase in the risk of ALS (OR=4.44, 95%CI: 2.91-6.76). However, the attributable risk associated with each identified risk factor was estimated to be less than 5% of all ALS cases. These results confirm that ALS is a rare multifactorial degenerative condition of motor-neurons.

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.