DNA Replication Restart in Archaea

International audienceOne fundamental challenge of cells is to accurately copy their genetic material for cell prolif‐eration. This task is performed by core machineries considered conserved in all three domainsof life: bacteria, archaea and eukaryotes..

Identification of a novel gene encoding a flavin-dependent tRNA:m(5)U methyltransferase in bacteria—evolutionary implications

Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA:m(5)U-54 MTase). In all Eukarya and many Gram-negative Bacteria, the methyl donor for this reaction is S-adenosyl-l-methionine (S-AdoMet), while in several Gram-positive Bacteria, the source of carbon is N(5), N(10)-methylenetetrahydrofolate (CH(2)H(4)folate). We have identified the gene for Bacillus subtilis tRNA:m(5)U-54 MTase. The encoded recombinant protein contains tightly bound flavin and is active in Escherichia coli mutant lacking m(5)U-54 in tRNAs and in vitro using T7 tRNA transcript as substrate. This gene is currently annotated gid in Genome Data Banks and it is here renamed trmFO. TrmFO (Gid) orthologs have also been identified in many other bacterial genomes and comparison of their amino acid sequences reveals that they are phylogenetically distinct from either ThyA or ThyX class of thymidylate synthases, which catalyze folate-dependent formation of deoxyribothymine monophosphate, the universal DNA precursor

Transcriptional Activation and Cell Cycle Block Are the Keys for 5-Fluorouracil Induced Up-Regulation of Human Thymidylate Synthase Expression

International audienceBackground: 5-fluorouracil, a commonly used chemotherapeutic agent, up-regulates expression of human thymidylate synthase (hTS). Several different regulatory mechanisms have been proposed to mediate this up-regulation in distinct cell lines, but their specific contributions in a single cell line have not been investigated to date. We have established the relative contributions of these previously proposed regulatory mechanisms in the ovarian cancer cell line 2008 and the corresponding cisplatin-resistant and 5-FU cross-resistant-subline C13*. Methodology/Principal Findings: Using RNA polymerase II inhibitor DRB treated cell cultures, we showed that 70-80% of up-regulation of hTS results from transcriptional activation of TYMS mRNA. Moreover, we report that 5-FU compromises the cell cycle by blocking the 2008 and C13* cell lines in the S phase. As previous work has established that TYMS mRNA is synthesized in the S and G 1 phase and hTS is localized in the nuclei during S and G 2-M phase, the observed cell cycle changes are also expected to affect the intracellular regulation of hTS. Our data also suggest that the inhibition of the catalytic activity of hTS and the up-regulation of the hTS protein level are not causally linked, as the inactivated ternary complex, formed by hTS, deoxyuridine monophosphate and methylenetetrahydrofolate, was detected already 3 hours after 5-FU exposure, whereas substantial increase in global TS levels was detected only after 24 hours. Conclusions/Significance: Altogether, our data indicate that constitutive TYMS mRNA transcription, cell cycle-induced hTS regulation and hTS enzyme stability are the three key mechanisms responsible for 5-fluorouracil induced up-regulation of human thymidylate synthase expression in the two ovarian cancer cell lines studied. As these three independent regulatory phenomena occur in a precise order, our work provides a feasible rationale for earlier observed synergistic combinations of 5-FU with other drugs and may suggest novel therapeutic strategies. Cop. 2012 Ligabue et al

Advances and challenges in drug design against tuberculosis: application of in silico approaches

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A study of membrane-bound cytochromes c participating in photosynthesis and respiration in Rhodobacter

Rhodobacter capsulatus contains several c-type cytochromes. Two of them, the periplasmic cyt c\sb2 and the membrane bound cyt c\sb{y}, are capable of connecting the cyt bc\sb1 complex to the photochemical reaction center and the cyt c oxidase, and hence supporting photosynthetic and aerobic respiratory growth. The detailed functional and physico-chemical properties of cyt c\sb2 have been extensively characterized previously; however, much less was known about the corresponding properties of cyt c\sb{y} prior to this work. Therefore, topology analyses and the purification of R. capsulatus cyt c\sb{y} were undertaken. The results indicate that the amino-terminal signal sequence-like domain of cyt c\sb{y} is sufficient to attach cyt c\sb{y} to the membrane. Moreover, it was shown that the physico-chemical properties of cytochromes c\sb2 and c\sb{y} closely resemble each other, suggesting that their different electron transfer properties are likely due to the differences in their cellular localization (i.e. periplasm vs. cytoplasmic membrane). Consequently, it was demonstrated that, presumably due to the relative immobility of cyt c\sb{y} in the membrane, cyt c\sb{y} is capable of supporting multiple turnovers of the photosynthetic electron transfer chain more efficiently than cyt c\sb2. Unexpectedly, a c-type cytochrome homologous to R. capsularus cyt c\sb{y} was discovered also in R. sphaeroides. This cytochrome was found to be unable to support photosynthetic growth, but yet it is fully functional in respiration. The function of this cyt c was further investigated by constructing chimera between R. capsulatus and R. sphaeroides cytochromes c\sb{y}. These findings raise an intriguing issue with regard to the evolution of various electron carriers participating in respiratory electron transfer

Dual role for cytochrome cbb3 oxidase in clinically relevant proteobacteria?

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Caractérisation par des études génétiques et biochimiques d'une nouvelle thymidylate synthase, ThyX

Les thymidylate synthases sont des enzymes catalysant la transméthylation du dUMP en dTMP, précurseur essentiel à la synthèse de l'ADN. Si la thymidylate synthase A est étudiée depuis près de 50 ans, la thymidylate synthase X, elle, a été découverte il y a peu dans notre laboratoire. Ces deux familles d'enzymes ne sont pas homologues, elles ne présentent aucune similarité ni de séquence ni de structure. La caractérisation de cette nouvelle enzyme par l'utilisation de techniques génétiques et biochimiques a permis de montrer que la thymidylate synthase X est essentielle chez Rhodobacter capsulatus en absence de thymidine dans le milieu de culture. D'autre part, la réalisation de mutations ponctuelles dans le gène thyX de Helicobacter pylori capable de complémenter une souche ?thyA d'Escherichia coli, nous a permis de localiser le site actif de l'enzyme, à l'interphase de 3 sous-unités de l'homotétramère et de proposer une fonction pour quelques résidus. L'étude in silico de la répartition des gènes thyA et thyX dans les génomes entièrement séquencés a mise en évidence qu'une majorité d'hyperthermophiles possède le gène thyX et que la quasi totalité des eucaryotes étudiés possède thyA.La présence de thyX dans le génome de nombreux organismes incapables d'incorporer de la thymidine et pathogènes pour l'Homme, fait de la thymidylate synthase X une cible idéale pour le développement de nouveaux médicaments. Par ailleurs, la vision que nous avions de l'évolution des acides nucléiques se complique: le passage du monde ADN-U au monde ADN-T doit prendre en compte l'invention de deux familles non homologues de thymidylate synthases.Thymidylate synthase catalyzes the methylation of dUMP to dTMP, an essential precursor required for DNA synthesis. Although thymidylate synthase A has been studied for nearly 50 years, thymidylate synthase X was only recently discovered in our laboratory. No sequence nor structural similarity exists between two different thymidylate synthases families. Characterization of this novel enzyme using genetic and biochemical approaches demonstrated that thymidylate synthase X is essential for the growth of Rhodobacter capsulatus in absence of thymidine. Construction of site specific mutations in Helicobacter pylori thyX gene, which is capable of restoring wild-type phenotype for Escherichia coli deltathyA strain, revealed function for several amino acid residues and permitted the location of the ThyX active site at the interphase of three sub-units of the homotetrameric ThyX complex. In silico studies of the distribution of thyA and thyX genes in the entirely sequenced genomes highlighted that a majority of hyperthermophiles have thyX gene and that practically all of the studied eucaryotes possess thyA gene. The presence of thyX gene in the genome of many human pathogenic organisms unable to incorporate exogenous thymidine makes thymidylate synthase X an ideal target for the development of new drugs. In addition, the discovery of ThyX has complicated our understanding of evolution of DNA itself, since invention of two different families of thymidylate synthases indicates that transition between U-DNA (DNA with uracil) and "current" T-DNA (DNA with thymidine) took place twice.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Etude de la réplication de l'ADN chez l'archaea halophile Haloferax volcanii.

J'ai étudié, durant mon travail de thèse, la réplication de l'ADN chez l'archaea halophile Haloferax volcanii. Le premier objectif de ma thèse était de mettre en place l'utilisation des outils génétiques disponibles chez H. volcanii, dont la méthode de délétion de gène par intégration/excision de plasmide (pop-in/pop-out), pour un usage routinier au laboratoire. L'annotation partielle des gènes impliqués dans les mécanismes de réplication et réparation de l'ADN a permis d'identifier 16 protéines Initiator Cdc6/Orc1 putatives. L'utilisation des outils génétiques, combinée à une analyse des biais de représentation des nucléotides, nous ont permis d'identifier cinq origines de réplication. Le chromosome majeur possède au moins deux origines de réplication tandis qu'une autre est retrouvée sur les deux épisomes pHV1 et pHV4. L'activité in vivo de ces origines a pu être confirmée par cartographie des sites d'initiation de la réplication (RIP mapping) et par gel bidimensionnels d'ADN. L'étude des peptides interagissant avec PCNA nous a permis d'identifier que RnaseH interagit avec PCNA pour former un complexe inactif. Nos analyses génétiques chez H. volcanii ont permis d'illustrer l'implication dans les processus de réparation de l'ADN des protéines Fen1 et de manière surprenante de RNAseH I et RnaseHII. Ces analyses ont montré que Fen1 intervient aussi dans la réplication de l'ADN. J'ai pu confirmer que les fragments d'Okazaki font moins de 200 bases et portent une amorce ARN synthétisée par la primase de type eucaryote PriS/L qui est essentielle chez H. volcanii. En revanche, la primase de type bactérienne putative DnaG peut être inactivée, mais son rôle reste à caractériser. Mes travaux ont démontré qu'avec ses multiples réplicons et des outils génétiques efficaces permettant la caractérisation des gènes, H. volcanii est un modèle novateur et pertinent pour l'étude de la réplication de l'ADN chez les archaea.During my doctoral work, I have studied DNA replication in the halophilic archaeon Haloferax volcanii. The first aim of this study was to establish the use of available genetic tools for H. volcanii, including the pop-in/pop-out gene deletion system, for routine work at the laboratory. A partial annotation of the genes implicated in DNA replication and repair allowed the identification of 16 putative Initiator Cdc6/Orc1. The use of genetics combined with nucleotide skews analyses allowed the identification of five replication origins. The main chromosome carries at least two replication origins whereas another origin is used to replicate both pHV1 and pHV4. The in vivo activity of these origins could be confirmed by replication initiation point mapping and DNA two-dimensional gels. The study of PCNA interacting peptides revealed that archaeal RNAseH interacts with PCNA to form an inactive complex. Genetic analyses with H. volcanii revealed the implication in DNA repair of Fen1 and surprisingly RnaseHI and RnaseHII. These studies also showed that Fen1 is required for DNA replication. I confirmed that H. volcanii Okazaki fragments are less than 200 bases long and carry an RNA primer synthesized by the essential PriS/L eukaryotic-like primase. On the other hand, the putative bacterial-like primase DnaG can be deleted and its role remains to be characterized. My studies have demonstrated that with its multi-replicon structure and efficient genetic tools for gene characterization, H. volcanii is a novel and pertinent model for the study of archaeal DNA replication.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF