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No description available.

POLQ is a unique multifunctional replication and repair gene that encodes a multidomain protein with a N-terminal superfamily 2 helicase and a C-terminal A-family polymerase. Although the function of the polymerase domain has been investigated, little is understood regarding the helicase domain. Multiple studies have reported that polymerase θ-helicase (Polθ-helicase) is unable to unwind DNA. However, it exhibits ATPase activity that is stimulated by single-stranded DNA, which presents a biochemical conundrum. In contrast to previous reports, we demonstrate that Polθ-helicase (residues 1– 894) efficiently unwinds DNA with 3'–5' polarity, including DNA with 3' or 5' overhangs, blunt- ended DNA, and replication forks. Polθ-helicase also efficiently unwinds RNA-DNA hybrids and exhibits a preference for unwinding the lagging strand at replication forks, similar to related HELQ helicase. Finally, we find that Polθ-helicase can facilitate strand displacement synthesis by Polθ-polymerase, suggesting a plausible function for the helicase domain. Taken together, these findings indicate nucleic acid unwinding as a relevant activity for Pol theta in replication repair. DNA polymerase theta is a unique polymerase-helicase fusion protein that promotes microhomology-mediated end-joining of DNA double-strand breaks. How full-length human DNA polymerase theta performs microhomology-mediated end-joining and is regulated by the helicase and disordered central domain remains unknown. We find that the helicase upregulates DNA polymerase theta microhomology-mediated end-joining activity in an ATPase-independent manner. Using single-particle microscopy, we find that DNA polymerase theta forms large multimeric complexes that promote DNA accumulation and end-joining. We further find that the disordered central domain regulates DNA polymerase theta multimerization and governs its DNA substrate requirements for end-joining. In summary, these studies identify major regulatory functions for the helicase and central domains in DNA end-joining and the structural organization of DNA polymerase theta. / Biomedical Sciences

<p> Sigma S (RpoS), encoded by rpoS, is a subunit of RNA polymerase holoenzyme that controls the expression of many genes in stationary phase of various gram negative bacteria. Escherichia coli expresses these genes to withstand environmental stress and nutrient starvation. Several naturally occurring mutant alleles of the gene have been reported and indicate key differences from laboratory strains. We sought to explore the role of natural alleles of the rpoS gene (from non- K12 strains) and thus the sigma subunit relative to the K12 allele. To study the effect of the rpoS polymorphism on gene expression ofRpoS regulon members, rpoS alleles from ECOR- 21, ECOR-28, ECOR-37 and ECOR-40 as well as MG1655 were cloned into the same background, MG1655 ΔrpoS:cat osmY-lacZ. Sequence analysis showed rpoS alleles from all the natural strains tested were different from MG1655 and each other. The strain with rpoS allele from ECOR-28 had increased expression of osmY and katE similar to MG1655. In contrast, rpoS allele from ECOR- 37 showed low expression of osmYbut not as low as ECOR-21 and ECOR-40 which had expression similar to the rpoS mutant. Not surprisingly, recombinant strains with rpoS alleles from ECOR-21, ECOR-37 and ECOR-40 showed no expression of katE (HPII). These suggest that RpoS in ECOR-28 has high activity similar to wildtype K12 strain while RpoS in ECOR-21, ECOR-37 and ECOR-40 has very low or no activity. We conclude that natural E. coli strains have polymorphism in their rpoS ORF which cause variation in the regulatory activities of RpoS on its regulon. </p> / Thesis / Master of Science (MSc)

Rotavirus (RV) is a viral pathogen that causes severe, watery diarrhea and vomiting in the young of humans and other animals. RV infections result in over 200,000 pediatric deaths around the world each year, especially in developing nations. Within the infected host cell, RV forms inclusion bodies, called viroplasms, where many stages of viral replication occur. The RV polymerase, known as VP1, must localize to viroplasms during infection where it replicates the virus' RNA genome. The work described in this dissertation focused on identifying region(s) of VP1 essential for its viroplasmic localization and its function as a polymerase. We found that a single amino acid change in a region of the polymerase called the N-terminal domain negatively impacted its capacity to localize to viroplasms during infection as well as its enzymatic activity in a test tube. Follow up studies using VP1 proteins from divergent strains and a mutant containing only the N-terminal domain of VP1 provided more insight into polymerase localization determinants. In total, our work suggests that the VP1 N-terminal domain plays an important role in localizing the polymerase to viroplasms via interactions with other viral proteins and supporting its function as a polymerase. / Ph. D.

<p>Translesion synthesis is a fundamental biological process that enables DNA replication across lesion sites to ensure timely duplication of genetic information at the cost of replication fidelity, and it is implicated in development of cancer drug resistance after chemotherapy. The eukaryotic Y-family polymerase Rev1 is an essential scaffolding protein in translesion synthesis. Its C-terminal domain (CTD), which interacts with translesion polymerase &#950; through the Rev7 subunit and with polymerases &#954;, &#953; and &#951; in vertebrates through the Rev1-interacting region (RIR), is absolutely required for function. </p><p>In chapter 1, the solution structures of the mouse Rev1 CTD and its complex with the Pol &#954; RIR are reported, revealing an atypical four-helix bundle. Yeast two-hybrid assays were used to identify a Rev7-binding surface centered at the &#945;2-&#945;3 loop and N-terminal half of &#945;3 of the Rev1 CTD. Binding of the mouse Pol &#954; RIR to the Rev1 CTD induces folding of the disordered RIR peptide into a three-turn &#945;-helix, with the helix stabilized by an N-terminal cap. RIR-binding also induces folding of a disordered N-terminal loop of the Rev1 CTD into a &#946;-hairpin that projects over the shallow &#945;1-&#945;2 surface and creates a deep hydrophobic cavity to interact with the essential FF residues juxtaposed on the same side of the RIR helix. The combined structural and biochemical studies reveal two distinct surfaces of the Rev1 CTD that separately mediate the assembly of extension and insertion translesion polymerase complexes.</p><p>The multifaceted abilities of the Rev1 CTD are further explicated in chapter 2 where the purification and structure determination of a quaternary translesion polymerase complex consisting of the Rev1 CTD, the heterodimeric Pol &#950; complex, and the Pol &#954; RIR is reported. Yeast two-hybrid assays were employed to identify important interface residues of the translesion polymerase complex. The structural elucidation of such a quaternary translesion polymerase complex encompassing both insertion and extension polymerases bridged by the Rev1 CTD provides the first molecular explanation of the essential scaffolding function of Rev1 and highlights the Rev1 CTD as a promising target for developing novel cancer therapeutics to suppress translesion synthesis. Our studies support the notion that vertebrate insertion and extension polymerases could structurally cooperate within a mega translesion polymerase complex (translesionsome) nucleated by Rev1 to achieve efficient lesion bypass without incurring an additional switching mechanism.</p><p>Chapter 3 explores the ubiquitin-binding capacity of the FAAP20 UBZ in an effort to begin understanding its requirement for recruitment of the Fanconi anemia complex to interstrand DNA crosslink sites and for interaction with the translesion synthesis machinery through recognition of monoubiquitinated Rev1. FAAP20 is an integral component of the Fanconi anemia core complex that mediates the repair of DNA interstrand crosslinks. Although the UBZ-ubiquitin interaction is thought to be exclusively encapsulated within the &#946;&#946;&#945; module of UBZ, it is revealed that the FAAP20-ubiquitin interaction extends beyond such a canonical zinc-finger motif. Instead, ubiquitin-binding by FAAP20 is accompanied by transforming a disordered tail C-terminal to the UBZ of FAAP20 into a rigid, extended &#946;-loop that latches onto the complex interface of the FAAP20 UBZ and ubiquitin, with the invariant C-terminal tryptophan emanating toward I44Ub for enhanced binding specificity and affinity. Substitution of the C-terminal tryptophan with alanine in FAAP20 not only abolishes FAAP20-ubiquitin binding in vitro, but also causes profound cellular hypersensitivity to DNA interstrand crosslink lesions in vivo, highlighting the indispensable role of the C-terminal tail of FAAP20, beyond the compact zinc finger module, toward ubiquitin recognition and Fanconi anemia complex-mediated DNA interstrand crosslink repair.</p><p>Having structurally elucidated the molecular basis of the essential scaffolding function of the Rev1 CTD, the search for small molecule inhibitors of the Rev1-Rev7 interaction has been initiated toward the goal of developing novel adjuvants to DNA targeting chemotherapeutics. Screening efforts have led to the discovery of a lead compound, JH-RE-06*NaOH, that specifically targets the Rev7-binding hydrophobic pocket of the Rev1 CTD with low micromolar affinity, effectively inhibiting the Rev1-Rev7 interaction in an in vitro ELISA assay developed for high-throughput screening of small molecule libraries. With the potential for positive outcomes in future in vivo assays, we hope to develop JH-RE-06*NaOH into the first potent inhibitor of translesion synthesis in cancer patients being treated with DNA-targetng chemotherapeutics to aid in sensitization and prevention of chemoresistance development in malignancies.</p> / Dissertation

En réponse à son environnement composé de signaux endogènes et exogènes, une cellule doit pouvoir adapter son transcriptome, et cela à travers une modulation fine de l'expression de ses gènes. Les mécanismes permettant une telle adaptation reposent sur de multiples paramètres, entre autre l'organisation du génome, que ce soit au niveau de sa séquence primaire ou de son organisation au sein de la chromatine qui est un support pour l'intégration de nombreuses informations (structurelles et épigénétiques). De plus, l'organisation tridimensionnelle du noyau cellulaire apporte des contraintes physiques et fonctionnelles qui contribuent également à ces régulations. Afin de comprendre comment toutes ces informations peuvent être intégrées lorsqu'un signal régule la transcription d'un ensemble de gènes colinéaires («cluster» de gènes), nos études se sont focalisées sur la description et dissection des mécanismes impliqués dans la régulation coordonnées de gènes œstrogéno-dépendant par le récepteur aux œstrogènes (ER) et ses facteurs pionniers (FOXA1, FOXA2 et GATAs) dans des cellules cancéreuses d'origine mammaire. Dans ce cadre, nous nous sommes plus particulièrement intéressés au cluster TFF, situé sur le bras long du chromosome 21, incluant le gène modèle TFF1, en utilisant des techniques d'analyse à grande échelle (ChIP-chip, ChIP-seq, 4C et analyses transcriptomiques). / A given cell has to be able to adapt its fate and homeostasis in response to endogenous and exogenous signals. This adaptation occurs through finely tuned regulations of genes' expressions leading to the variation of their transcriptomes. Multiple parameters have to be integrated in order to provide such mechanisms of regulation. First, the primary sequence of the genome and its organization into chromatin are major regulatory components that harbor genetic, structural and epigenetic information. Second, the three-dimensional organization of the genome into the nucleus brings both physical and functional constraints that also contribute towards these regulatory processes. Here, we engaged a work aiming to understand and dissect how these several levels of information are integrated during the transcriptional regulation of colinear genes (cluster of genes) by the same signal. We took as a model the coordinated regulation of the estrogen-sensitive TFF cluster driven by the estrogen receptor (ER) and its pioneering factors (FOXA1, FOXA2 and GATAs) in mammary cancer cells. This cluster is located within the long arm of the chromosome 21, and contains the gene model termed TFF1. We used large-scale methods (ChIP-chip, ChIP-seq, 4C and microarray transcriptomic analyses) to decipher these dynamic mechanisms.

Transcription of the ribosomal genes accounts for the majority of transcription in the cell due to the constant high demand for ribosomes. The number of proteins synthesized correlates with an effective ribosomal biogenesis, which is regulated by cell growth and proliferation. In the work presented in this thesis, we have investigated the ribosomal RNA genes 45S and 5S rRNA, which are transcribed by RNA Pol I and RNA Pol III, respectively. The focus of this work is the chromatin remodelling complex B-WICH, which is composed of WSTF, the ATPase SNF2h and NM1. We have studied in particular its role in ribosomal gene transcription. We showed in Study I that B-WICH is required to set the stage at rRNA gene promoters by remodelling the chromatin into an open, transcriptionally active configuration. This results in the binding of histone acetyl transferases to the genes and subsequent histone acetylation, which is needed for ribosomal gene activation. Study II investigated the role of B-WICH in transcription mediated by RNA polymerase III. We showed that B-WICH is essential to create an accessible chromatin atmosphere at 5S rRNA genes, which is compatible with the results obtained in Study 1. In this case, however, B-WICH operates as a licensing factor for c-Myc and the Myc/Max/Mxd network. Study III confirmed the importance and the function of the B-WICH complex as an activator of ribosomal genes. We demonstrated that B-WICH is important for the remodelling of the rDNA chromatin into an active, competent state in response to extracellular stimuli, and that the association of the B-WICH complex to the rRNA gene promoter is regulated by proliferative and metabolic changes in cells. The work presented in this thesis has confirmed that the B-WICH complex is an important regulator and activator of Pol I and Pol III transcription. We conclude that B-WICH is essential for remodelling the rDNA chromatin into a transcriptionally active state, as required for efficient ribosomal gene transcription. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.</p><p> </p>

Die Organtransplantation stellt ein therapeutisches Verfahren für Patienten mit irreversibel geschädigten Organen dar. Doch weist dieses Behandlungskonzept weiterhin einen wesentlichen Nachteil auf: noch immer wird der langfristige Erfolg der Therapie zu oft durch die so genannte Transplantatabstoßung gefährdet. Hierbei handelt sich um eine vom Organtransplantat ausgelöste Immunantwort, die zu dessen Zerstörung führt. Die derzeit einzige Möglichkeit eine Abstoßung zu verhindern, ist die Unterdrückung des Immunsystems mit so genannten Immunsuppressiva. Auch wenn diese erstmals in den 60er Jahren des 20. Jahrhunderts erfolgreich eingesetzten Medikamente ständig verbessert werden, bleiben die von ihnen ausgelösten Nebenwirkungen weiterhin ein ernstzunehmendes Problem. Sie unterdrücken die gesamte körpereigene Abwehr, was zum Schutz der Organtransplantate vor Abstoßung gewünscht ist, doch fördern sie hierdurch die Entstehung von Tumoren und Infektionen. Bei der Transplantatabstoßung handelt es sich um eine von CD4+ T-Lymphozyten ausgelöste Immunantwort. Diese Lymphozyten werden von allogenen Peptiden, die von Spender-MHC-Molekülen stammen, über den indirekten Weg der Alloantigenerkennung aktiviert. An der Transplantatabstoßung ist zwar eine Vielzahl von Alloantigenen beteiligt, doch ist es möglich, Peptidantigene zu identifizieren, die einen nachweisbaren Effekt auf die Transplantatabstoßung ausüben. So wurde in der eigenen Arbeitsgruppe die für die Abstoßung allogener Organtransplantate beteiligten MHC (RT1u)-Peptidantigene charakterisiert. Insbesondere die Bedeutung des aus 19 Aminosäuren bestehenden allogenen Peptids P1 für die Alloimmunantwort wurde intensiv untersucht. So weisen P1-spezifische T-Lymphozyten ein ausgeprägtes Th1-Cytokin-Muster auf und beschleunigen die Abstoßung von Wistar-Furth-Organtransplantaten in Lewis-Ratten. Das Ziel dieser Arbeit war die Charakterisierung des T-Zellrezeptor Vb-Repertoires P1-spezifischer T-Lymphozyten mit der Methode des PCR-ELISA. In einem ersten Schritt wurden Thymozyten und T-Lymphozyten unterschiedlicher Lymphknotenstationen untersucht. Thymozyten exprimierten alle 22 TCR Vb-Elemente und einzig TCR Vb14 war überrepräsentiert. Die T-Lymphozyten der cervikalen, mesenterialen, iliakalen und poplitealen Lymphknoten zeigten ebenfalls eine charakteristische Überexpression bestimmter TCR Vb-Elemente. So exprimierten cervikale T-Lymphozyten bevorzugt die TCR Vb-Elemente 2, 6, 8.3 und 16, mesenteriale T-Lymphozyten die TCR Vb-Elemente 2, 4, und 8.1, illiakale T-Lymphozyten die TCR Vb-Elemente 2 und 6 und popliteale T-Lymphozyten die TCR Vb-Elemente 2, 4 und 9. Die Immunisierung mit dem nicht-immunogenen Kontrollpeptid (Autoantigen) Ac führte zu einer leichten Veränderung des T-Zellrezeptor-Repertoires, bei der die TCR Vb-Elemente 14 und 16 überexprimiert waren. Das Adjuvant TiterMax beeinflusste kaum das TCR Vb-Repertoire. Die Immunisierung mit dem allogenen Peptid P1 führte zu einer eindeutigen Beeinflussung des T-Zellrezeptor-Repertoires. Popliteale T-Lymphozyten, die 7 Tage nach Immunisierung analysiert wurden, zeigten ein Repertoire, bei dem die TCR Vb-Elemente 15, 16, 17 und 20 überexprimiert waren. Dieses Repertoire war am Tag 3 nach Immunisierung noch nicht so ausgebildet. Wurden die antigenspezifischen T-Lymphozyten nach ihrer Isolierung mit P1 in vitro restimuliert, so waren in diesem T-Zellrezeptor-Repertoire die TCR Vb-Elemente 8.3, 15, 16 und 20 überexprimiert. Zum Vergleich: in naiven T-Lymphozyten waren die Vb-Elemente 2, 4 und 9 überexprimiert. Damit war es zu einer deutlichen Verschiebung im T-Zellrezeptor-Repertoire antigenspezifischer T-Lymphozyten gekommen, die auf das Peptidantigen P1 zurückzuführen ist. Mit der Methode des PCR-ELISA wurde das T-Zellrezeptor-Repertoire antigenspezifischer T-Lymphozyten bestimmt. Hiermit sind wesentliche Voraussetzungen geschaffen worden, um T-Zellklone zu etablieren und ihre Bedeutung für die Transplantatabstoßung genauer zu untersuchen. / Organ transplantation is an important medical therapy for patients with irreversibly damaged organs. However, this therapeutic intervention has a great disadvantage because the long-term success of organ allografts is still too often endangered by the so called allograft rejection, an immune response directed to the allograft and leading to its destruction. The major approach for the prevention and management of allograft rejection is to suppress the immune system with immunosuppressive agents. These agents were introduced into transplantation medicine in the 1960s and since that time they have been continually improved. However, their side effects remain a seriousness problem because the suppression of the immune defence inhibits the allograft rejection on the one hand but causes infections and increases tumour incidence on the other hand. The allograft rejection is mediated by CD4+ T lymphocytes and the responsible antigens recognized by them are allogenic peptides processed from donor MHC molecules. Although a large number of allgenenic peptides are involved in allograft rejection, it is possible to identify certain peptide antigens involved in allograft rejection. In our group allogeneic peptides from MHC class I molecules from Wistar Furth rats were investigated. The significance of the allogeneic peptide P1, consisting of 19 amino acids, in inducing allograft rejection was analysed in detail. P1-specific T lymphocytes demonstrated a Th1-cytokine dominated profile and accelerated the rejection of allografts in Lewis rats donated by Wistar Furth rats. The aim of this study was to characterise the T cell receptor (TCR) Vb repertoire of P1-specific T lymphocytes with the PCR-ELISA technique. First, thymocytes and T lymphocytes from different lymph nodes were analysed. Thymocytes expressed all 22 TCR Vb elements and only TCR Vb14 was overrepresented. The T lymphocytes of cervical, mesenteric, iliacal und popliteal lymph nodes also demonstrated a certain repertoire of overrepresented TCR Vb elements. In cervical T lymphocytes the expression levels of the TCR Vb elements 2, 6, 8.3 and 16 were increased; in mesenteric T lymphocytes the TCR Vb elements 2, 4 and 8.1; in illiacal T lymphocytes the TCR Vb elements 2 and 6; and in popliteal T lymphocytes the TCR Vb elements 2, 4 and 9. The immunisation with the autoantigen Ac led to a small variation of the TCR Vb repertoire and the TCR Vb elements 14 and 16 were overrepresented. The adjuvant TiterMax did not influence the TCR Vb repertoire. In contrast, the immunisation with the allogeneic peptide P1 clearly influenced the T cell receptor repertoire. Popliteal T lymphocytes analysed 7 days after immunisation demonstrated a TCR Vb repertoire where the TCR Vb elements 15, 16, 17 und 20 were overrepresented. On day 3 after immunisation this repertoire was not yet clearly developed. In P1-specific T lymphocytes restimulated in vitro the expression levels of the TCR Vb elements 8.3, 15, 16 and 20 were increased. In comparison, in naïve T lymphocytes the TCR Vb elements 2, 4 and 9 were overrepresented. These results underline that the immunisation with peptide P1 induces a characteristic TCR Vb repertoire. The TCR Vb repertoire of P1-specific T lymphocytes was analysed with the PCR-ELISA technique. The determination of the T cell receptor repertoire is a prerequisite to establish T cell clones and to analyse their involvement in allograft rejection.

Cells have lesion bypass DNA polymerases (DNAPs), often in the Y-Family, which synthesize passed DNA damage. One class of Y-Family DNAPs includes hDNAP k, EcDNAP IV and SsDbh, which insert accurately opposite N2-dG adducts, including BP-N2-dG formed from benzo[a]pyrene (BP). Another class includes hDNAP h, EcDNAP V and SsDpo4, which insert accurately opposite UV-damage. For correct Watson-Crick pairing between BP-N2-dG and dCTP, the BP moiety must be in the minor groove. On the minor groove side of the active site, k/IV/Dbh-class DNAPs have large openings that accommodate the BP moiety. Primer extension assays with purified proteins show that DNAP IV correctly inserts dCTP opposite BP more than 10-fold faster than it mis-inserts dATP, dGTP, or dTTP. In contrast, h/V/Dpo4-class DNAPs have small active site openings, which cannot accommodate BP and lead to a distorted structure and increased mutagenesis; e.g., Dpo4 has dGTP and dATP insertion rates that are 10-fold greater than those of dCTP. The opening in Dpo4 is plugged and bulky, whereas DNAP IV has a relatively spacious cavity. Consistent with this model, mutants of Dpo4 with a larger opening insert up to 10-fold more accurately opposite BP-N2-dG. Near the active site, Dpo4 has a single non-covalent bridge (NCB) between the little finger domain and the thumb-palm-fingers domain. DNAP IV and Dbh have a second, distal NCB that is 8 angstroms away from the active site towards the 3' end of the template DNA. Dpo4 becomes nearly 5-fold more accurate when mutated to carry a distal NCB, suggesting that NCB's also help control mutagenesis. Lastly, the active site of Dpo4 has a cavity in the major groove side, which may allow base flipping and dGTP insertion opposite -BP, while k/IV/Dbh-type polymerases do not. When this cavity is plugged in Dpo4 by mutagenesis or the introduction of an N-clasp motif, dGTP rates increase by nearly 20-fold. In conclusion, this data suggests that three structural regions contribute to accurate dCTP insertion opposite BP-N2-dG by k/IV/Dbh-class DNAPs: a large opening on the minor groove side near the active site, a cavity on the major groove side, and the number of non-covalent bridges between the little finger domain and the thumb-palm-fingers domain.