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Ribosomal RNA contains many posttranscriptionally modified nucleosides, particularly in the functional parts of the ribosome. The distribution of these modifications varies from one organism to another. In Bacillus subtilis ,the model organism for Gram-positive bacteria, mass spectrometry experiments revealed the presence of 7-methylguanosine (m7G) at position 2574 of the 23S rRNA, which lies in the A-site of the peptidyl transferase center of the large ribosomal subunit. Testing several m7G methyltransferase candidates allowed to identify the RlmQ enzyme, encoded by the ywbD open reading frame, as the MTase responsible for this modification. The enzyme methylates free RNA and not ribosomal 50S or 70S particles, suggesting that modification occurs in the early steps of ribosome biogenesis., SCOPUS: le.j, info:eu-repo/semantics/published

Human Immunodeficiency Virus type 1 (HIV-1) infection can be managed but not cured by the current combinatory antiretroviral therapy (cART). The replication rate of HIV-1, which is directly correlated to the rate of disease progression to Acquired Immunodeficiency Syndrome (AIDS), is controlled primarily at the transcription level of viral genes, which is not targeted by cART. The arrest of the cART is associated with a rapid viremia rebound due to the persistence of long-term reservoirs of virally infected cells, which cannot be eliminated by cART corresponding to cell types or tissue compartments where virally infected cells are maintained. These reservoirs are heterogeneous and principally composed of CD4+ T cells and myeloid cells, the latter understudied and poorly represented in cure-based efforts. Importantly, each reservoir harbors a unique regulation of HIV-1 gene expression. Even though most transcriptional studies on HIV-1 have only focused on the viral promoter 5’long terminal repeat (5’LTR), our laboratory has previously reported an intragenic cis-regulatory region (IRR), which the complete functional unit forming the HIV-1 IRR is composed, from 5’ to 3’, of three subdomains: the 5103 fragment, the hypersensitive site 7 (HS7), and the 5105 fragment. In this context, further deciphering the specific molecular mechanisms underlying HIV-1 gene expression in all host cell types (including myeloid cells) and from each transcriptional regulatory element (including the IRR) is crucial for a deeper understanding of HIV-1 biology and pathogenesis.In the first part of my PhD thesis, we determined the in vivo epigenetic landscape of the IRR in latent and reactivated conditions and in both T-lymphoid and myeloid-infected cells, representing the two major cellular contexts of HIV-1 infection. We demonstrated that the IRR harbored the characteristic features of an enhancer in these two physiological contexts. Second, we explored the contribution of the intragenic lin, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Bovine Leukemia Virus (BLV) and Human T-Lymphotropic Virus type I (HTLV-1) are two oncogenic retroviruses characterized by viral latency, thereby allowing escape from the host immune surveillance and the development of BLV- and HTLV-1-associated diseases. In this PhD thesis, we demonstrated for the first time the role of the cellular factor UHRF1 (Ubiquitin-like with PHD and RING Finger domains 1) in the transcriptional repression of BLV and HTLV-1. We showed the in vitro binding and in vivo recruitment of UHRF1 to the BLV and HTLV-1 transcriptional promoters located in the viral 5’ Long Terminal Repeat (5’LTR). We demonstrated the repressive role of UHRF1 in BLV and HTLV-1 gene expression in both basal and transactivated conditions using transient transfection assays. Moreover, we showed that UHRF1 epigenetically repressed the HTLV-1 5’LTR using RNA interference and that UHRF1 interacted with the HTLV-1 Tax transactivator. Finally, our results using primary cells from HTLV-1-infected individuals suggested the involvement of UHRF1 in the tumoral development observed in the HTLV-1-infected individuals. In conclusion, this PhD thesis provides a better understanding of BLV and HTLV-1 transcriptional regulations and offers new perspectives for developing innovative therapeutic strategies against BLV and HTLV-1 infections and their associated diseases., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

RelA/SpoT Homologs (RSH) enzymes control the bacterial stringent response through the synthesis and hydrolysis of the alarmone (p)ppGpp. Current biochemical and structural data is not sufficient to correctly understand RSH enzymatic activity as well as their regulation and interaction with molecular partners. This doctoral thesis has demonstrated the implication of Rel ACT domain in the regulation of its enzymatic activity and its interaction with the EIIANtr protein in Caulobacter crescentus. In addition, it has also confirmed the presence of a dedicated (p)ppGpp allosteric binding site in the catalytic domain of Rel in Bacillus subtilis and characterized the regulation of the latter’s activity during potassium starvation, notably by the resolution of the crystallographic structure of Rel complexed with the DarB protein. Through the discovery of these novel results, this thesis deepens the fundamental workings of RSH activity regulation., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Toxin-antitoxin (TA) systems are small genetic modules that are widespread in prokaryotes. While initially discovered on plasmids, which they stabilize, TA systems are also abundantly found on bacterial chromosomes. Their functions are highly debated and have been examined in this thesis. First, we show that TA systems do not seem to play a role in stress response or antibiotic tolerance, as previously reported in the literature. Secondly, our single cell experiments demonstrate that the activation of TA systems promotes cell death in cells when a TA-encoding plasmid is lost, indicating that TA activation leads to death and not to a state of stress tolerance. We therefore conclude that TA systems are addictive genes that promote their own retention and that of the genetic elements that encode them., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Long RSHs are enzymes that synthetize and hydrolyse a secondary messenger molecule, (p)ppGpp. This molecule acts as a global regulator targeting metabolic processes to ensure bacterial survival upon environmental challenges. Because (p)ppGpp is linked with bacterial virulence and resistance to antibiotics, a fundamental understanding of its regulation is key to develop novel antimicrobial treatments. Long RSH have two N-terminal domains, one for hydrolysis of (p)ppGpp (HD-domain) and one for synthesis of (p)ppGpp (SYNTH-domain), and four regulatory domains at the C-terminus that control catalysis by the N-terminal domains. A combination of structure determination and biochemical assays were used to study the long RSHs at the molecular level and determine the bases of the allosteric mechanisms that control the activities of the enzymes. The data demonstrate an allosteric conformational switch between the N-terminal catalytic domains of these enzymes that prevent futile catalytic cycles. Indeed, the data shows binding of substrates to one catalytic domain allosterically inhibits substrate-binding and catalysis by the opposing catalytic domain. Furthermore, feedback activation of (p)ppGpp-synthesis, the molecular basis of which was unknown, in context of amino-acid starvation was studied. The allosteric positive feedback regulation of (p)ppGpp-synthesis was shown to exploit the conformational switch between the two catalytic states to modulate both activities. An allosteric binding-pocket was located at the linker-region between the two catalytic domains at which (p)ppGpp-synthesis is auto-induced allosterically while (p)ppGpp-hydrolysis is inhibited. Lastly, the conformational landscape involved in the regulation of these enzymes was explored using Nanobodies to discover a previously undetected regulatory hotspot. Based on the conformational switch as well, this regulatory hotspot modulates catalytic activity allosterically. The newly discovered hotspot might be impor, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Chromosomal translocations that involve the nucleoporin NUP98 are recurrent in childhood therapy-related acute myeloid leukemias, characterized by disruption of normal hematopoiesis and bone marrow failure. Previous experiments showed that the expression of Nup98 fusion proteins leads to changes in nuclear envelope architecture and HOXA9 overexpression. My work provided new data supporting a mechanical function of RB in the nuclear architecture of NUP98 fusions, disclosing a possible mechanism of action involving the chromatin regulators. Furthermore, new pieces of evidence on HOXA9 regulation mediated by NUP98-related leukemia were revealed, which might be interesting for new target identification for the treatment of HOXA9-overexpressing diseases, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Toutes les cellules de l’organisme relarguent de façon constitutive des nucléotides dans l’espace extracellulaire. Ces nucléotides extracellulaires agissent comme des molécules de signalisation, entre autres, via les récepteurs P2Y (P2YRs) qui sont des récepteurs couplés aux protéines G (GPCRs). Les P2YRs sont exprimés, pour la majorité, de façon ubiquitaire dans l’organisme. L’analyse phénotypique des lignées de souris knockout pour les P2YRs (P2YR-/-) a permis de confirmer l’importance de cette voie de communication dans différents processus physio/pathologiques. Au sein de notre laboratoire, grâce à l’utilisation de souris P2YR-/-, nous étudions depuis quelques années le rôle de ces récepteurs dans la biologie des cellules stromales mésenchymateuses multipotentes (MSCs). Ces cellules se caractérisent par une faible immunogénicité et surtout par la propriété de multipotence, i.e. capacité de se différencier en plusieurs types cellulaires (adipocytes, chondroblastes, ostéoblastes). Cette dernière propriété suscite l’intérêt de la médecine régénérative qui vise à exploiter la multipotence de ces cellules en thérapie cellulaire. Toutefois, leur utilisation à des fins thérapeutiques est encore limitée, notamment parce que les mécanismes régulateurs de ces processus de différenciation sont encore mal compris. Il est donc fondamental de continuer à étudier les voies de signalisation régulant les processus de différenciation de ces cellules pour leurs applications cliniques.Dans ce travail de recherche, nous avons investigué l’implication de la signalisation dépendant des P2YR dans le modèle expérimental des MSCs dérivées du tissu adipeux sous-cutané inguinal (ATMSCs) murin. D’abord, nous avons montré que parmi les 7 sous-types connus de récepteur P2Ys, les ATMSCs expriment le P2Y2R (récepteur à l’ATP et l’UTP) et le P2Y6R (récepteur à l’UDP) et que ces récepteurs sont fonctionnels. Par une approche combinant l’analyse quantitative de leur expression, l’effet de leur act, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

The high conservation of nucleotides of the T-loop, including their chemical identity, are hallmarks of tRNAs from organisms belonging to the three Domains of Life. These structural characteristics allow the T-loop to adopt a peculiar intraloop conformation able to interact specifically with other conserved residues of the D-loop, which ultimately folds the mature tRNA in a unique functional canonical L-shaped architecture. Paradoxically, despite the high conservation of modified nucleotides in the T-loop, enzymes catalyzing their formation depend mostly on the considered organism, attesting for an independent but convergent evolution of the post-transcriptional modification processes. The driving force behind this is the preservation of a native conformation of the tRNA elbow that underlies the various interactions of tRNA molecules with different cellular components., SCOPUS: re.j, info:eu-repo/semantics/published

Human Onchocerciasis is a neglected tropical disease of debilitating consequences caused by the nodule dwelling nematode Onchocerca volvulus. Excretory Secretory Products (ESPs) help the parasite to establishing infection in an immunocompetent host and thus make O. volvulus ESPs potential sources of diagnostic, therapeutic or immunomodulatory markers. Here, a blend of bioinformatics, biochemical, analytical and immunologic methods were employed to identify one such ESP as a GM2 activator protein orthologue. The cDNA of OvGM2AP was detected in most parasite stages and the protein was detected in ESPs of adult males, adult females and L3 stage. Recombinant OvGM2AP was expressed in Sf21 insect cells and was found to be glycosylated at Asn 173 by mass spectrometry analysis. The recombinant OvGM2AP could significantly differentiate infected from non-infected individuals on total IgG ELISA. No improvement in diagnostic indices was observed when IgG sub-classes were used to detect OvGM2AP by ELISA. A drop in IgG titre was observed to correlate with increased rounds of ivermectin administration. However, as observed from alignment of OvGM2AP sequences with other nematode species, recombinant OvGM2AP was found to cross react with sera from patients with other nematode infections such as Loa loa, Mansonella perstans and Brugia malayi. GM2 degradation to GM3 could not be mediated by OvGM2AP in the presence of human β-hexosaminidase A. However, when examined for competitive inhibition with artificial GM2 substrates such as MUG and MUGs, OvGM2AP was found to competitively inhibit the degradation of MUG by β-hexosaminidase A as opposed to the human GM2AP. Due to the genetic intractability of O. volvulus, Caenorhabditis elegans was used as a model to study the function of OvGM2AP. The C. elegans orthologous gene cpp-1 was found to be expressed predominantly in the hypoderm, with a paralogous form confined to specialized hypodermis such as seam cells. CRISPR-CAS9 mediated knock-out, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii., SCOPUS: ar.j, info:eu-repo/semantics/published

M42 aminopeptidases are dinuclear enzymes widely found in prokaryotes but completely absent from eukaryotes. They have been proposed to hydrolyze peptides downstream the proteasome or other related proteolytic complexes. Their description relies mainly on the pioneering work on four M42 aminopeptidases from Pyrococcus horikoshii. Their quaternary structure consists of twelve subunits adopting a tetrahedral-shaped structure. Such a spatial organization allows the compartmentalization of the active sites which are only accessible to unfolded peptides. The dodecamer assembly results from the self-association of dimers under the control of the metal ion cofactors. Both oligomers have been shown to co-exist in vivo and heterododecamers with broadened substrate specificity may even occur. Yet, the molecular determinants behind the dodecamer assembly remain unknown due the lack of a high-resolution structure of a stable dimer. In addition, the bacterial M42 aminopeptidases are still ill-described due to the paucity of structural studies. This work focuses mainly on the characterization of TmPep1050, an M42 aminopeptidase from Thermotoga maritima. As expected, TmPep1050 adopts the genuine tetrahedral-shaped structure with twelve subunits. It also displays a leucyl-aminopeptidase activity requiring Co2+ as a cofactor. In addition to its catalytic function, Co2+ has a role in the enzyme thermostability and oligomerization. The absence of Co2+ provokes the disassembly of active TmPep1050 dodecamers into inactive dimers. The process, however, is reversible since Co2+ triggers the self-association of dimers into dodecamers, as shown by native MS. The main achievement of this work is the determination of the first high-resolution structure of a dimer, allowing to better understand the dimer-dodecamer transition. Several structural motifs involved in oligomerization are displaced or highly flexible in the TmPep1050 dimer structure. Furthermore, a loop bringing two catalytic releva, Option Biologie moléculaire du Doctorat en Sciences, info:eu-repo/semantics/nonPublished

While ammonium is an excellent nitrogen source for microorganisms and plants, it is known as acytotoxic metabolite and for its critical role in acid/base homeostasis in animals. Ammonium transportinside the cells is ensured by proteins of the Mep-Amt-Rh superfamily, which are conserved frombacteria to humans.The main objective of the thesis is to refine the understanding of the regulation of the three ammoniumtransport proteins Mep1, Mep2 and Mep3 from Saccharomyces cerevisiae. The three Mep proteins areregulated by the Npr1 kinase and the conserved TORC1 signaling pathway. While the activity of Mep2is regulated by phosphorylation of the C-terminal 457 serine, the activity of Mep1 and Mep3 is inhibitedby the factor Amu1 / Par32. In the presence of a poor nitrogen source, Npr1 induces phosphorylation ofAmu1 which appears mainly cytosolic and, Mep1 and Mep3 are active. On the other hand, in thepresence of a good nitrogen source, the activity of TORC1 induces the inhibition of Npr1 and thereforethe dephosphorylation of Amu1 which accumulates at the cell surface and inactivates Mep1 and Mep3.In order to further study the regulation of Mep1 / 3, a genetic screen was performed to isolate suppressorsrecovering Mep1-dependent ammonium transport in the absence of Npr1. Several mutations, insertionsand deletions have been identified in the MEP1 and AMU1 genes allowing Mep1 to be activeindependently of Npr1. This work shows that all the point mutations in Mep1 delimit an area at theinterface between the hydrophobic body of Mep1 and the cytosol, and that part of the C-terminus (CTR)is required for optimal activity of Mep1 but appears dispensable for regulation by Amu1 and Npr1. Thegenetic screen also shows that the last 15 amino acids of Amu1 are required to inactivate Mep1. Finally,the isolation of suppressors showing no mutation in MEP1 and AMU1 could reveal new factors involvedin the control of Mep1.The results indicate that Mep1 is inactivated in the presence of glutamine, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

The dimorphic transition from the yeast to the filamentous form of growth allows cells to explore their environment for more suitable niches and is often crucial for the virulence of pathogenic fungi. In contrast to their Mep1/3 paralogues, fungal Mep2-type ammonium transport proteins of the conserved Mep-Amt-Rh family have been assigned an additional receptor role required to trigger the filamentation signal in response to ammonium scarcity. Here, genetic, kinetic, expression and structure-function analyses were used to shed light on the poorly characterized signaling role of Saccharomyces cerevisiae Mep2. We show that Mep2 variants lacking the C-terminal tail conserve the ability to induce filamentation, revealing that signaling can proceed in the absence of exclusive binding of putative partners to the largest cytosolic domain of the protein. Our data support that filamentation signaling requires the conformational changes accompanying substrate translocation through the pore crossing the hydrophobic core of Mep2. pHluorin reporter assays show that the transport activity of Mep2 and of non-signaling Mep1 differently affect yeast cytosolic pH in vivo, and that the unique pore variant Mep2H194E, with apparent uncoupling of transport and signaling functions, acquires increased ability of acidification. Functional characterization in Xenopus oocytes reveals that Mep2 mediates electroneutral substrate translocation while Mep1 performs electrogenic transport. Our findings highlight that the Mep2-dependent filamentation induction is connected to its specific transport mechanism, suggesting a role of pH in signal mediation. We also show that the signaling process is conserved for the Mep2 protein from the human pathogen Candida albicans. Our results allow to propose a model for the sensing function of Mep2 where pH and calcium are key players., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

The M42 aminopeptidases are a family of dinuclear aminopeptidases widely distributed in Prokaryotes. They are potentially associated to the proteasome, achieving complete peptide destruction. Their most peculiar characteristic is their quaternary structure, a tetrahedron-shaped particle made of twelve subunits. The catalytic site of M42 aminopeptidases is defined by seven conserved residues. Five of them are involved in metal ion binding which is important to maintain both the activity and the oligomeric state. The sixth conserved residue, a glutamate, is the catalytic base deprotonating the water molecule during peptide bond hydrolysis. The seventh residue is an aspartate whose function remains poorly understood. This aspartate residue, however, must have a critical role as it is strictly conserved in all MH clan enzymes. It forms some kind of catalytic triad with the histidine residue and the metal ion of the M2 binding site. We assess its role in TmPep1050, an M42 aminopeptidase of Thermotoga maritima, through a mutational approach. Asp-62 was substituted with alanine, asparagine, or glutamate residue. The Asp-62 substitutions completely abolished TmPep1050 activity and impeded dodecamer formation. They also interfered with metal ion binding as only one cobalt ion is bound per subunit instead of two. The structure of Asp62Ala variant was solved at 1.5 Å showing how the substitution has an impact on the active site fold. We propose a structural role for Asp-62, helping to stabilize a crucial loop in the active site and to position correctly the catalytic base and a metal ion ligand of the M1 site., SCOPUS: ar.j, info:eu-repo/semantics/published

The M42 aminopeptidases form functionally active complexes made of 12 subunits. Their assembly process appears to be regulated by their metal ion cofactors triggering a dimer-dodecamer transition. Upon metal ion binding, several structural modifications occur in the active site and at the interaction interface, shaping dimers to promote the self-assembly. To observe such modifications, stable oligomers must be isolated prior to structural study. Reported here is a method that allows the purification of stable dodecamers and dimers of TmPep1050, an M42 aminopeptidase of T. maritima, and their structure determination by X-ray crystallography. Dimers were prepared from dodecamers by removing metal ions with a chelating agent. Without their cofactor, dodecamers became less stable and were fully dissociated upon heating. The oligomeric structures were solved by the straightforward molecular replacement approach. To illustrate the methodology, the structure of a TmPep1050 variant, totally impaired in metal ion binding, is presented showing no further breakdown of dimers to monomers., SCOPUS: ar.j, info:eu-repo/semantics/published

RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes. The lack of complex structures results in poorly understood RNA recognition patterns and methylation reaction mechanisms. On the contrary, many cofactor-bound MTase structures are available, resulting in well-understood protein:cofactor recognition, that can guide the design of bisubstrate analogues that mimic the state at which both the substrate and the cofactor is bound. Such bisubstrate analogues were recently synthesized for proteins monomethylating the N6-atom of adenine (m6A). These proteins include, amongst others, RlmJ in E. coli and METLL3:METT14 and METTL16 in human. As a proof-of-concept, we here test the ability of the bisubstrate analogues to mimic the substrate:cofactor bound state during catalysis by studying their binding to RlmJ using differential scanning fluorimetry, isothermal titration calorimetry and X-ray crystallography. We find that the methylated adenine base binds in the correct pocket, and thus these analogues could potentially be used broadly to study the RNA recognition and catalytic mechanism of m6A MTases. Two bisubstrate analogues bind RlmJ with micro-molar affinity, and could serve as starting scaffolds for inhibitor design against m6A RNA MTases. The same analogues cause changes in the melting temperature of the m1A RNA MTase, TrmK, indicating non-selective protein:compound complex formation. Thus, optimization of these molecular scaffolds for m6A RNA MTase inhibition should aim to increase selectivity, as well as affinity., info:eu-repo/semantics/published

The M42 aminopeptidases are dinuclear aminopeptidases displaying a peculiar tetrahedron-shaped structure with 12 subunits. Their quaternary structure results from the self-assembly of six dimers controlled by their divalent metal ion cofactors. The oligomeric-state transition remains debated despite the structural characterization of several archaeal M42 aminopeptidases. The main bottleneck is the lack of dimer structures, hindering the understanding of structural changes occurring during the oligomerization process. We present the first dimer structure of an M42 aminopeptidase, TmPep1050 of Thermotoga maritima, along with the dodecamer structure. The comparison of both structures has allowed us to describe how the metal ion cofactors modulate the active-site fold and, subsequently, affect the interaction interface between dimers. A mutational study shows that the M1 site strictly controls dodecamer formation. The dodecamer structure of TmPep1050 also reveals that a part of the dimerization domain delimits the catalytic pocket and could participate in substrate binding., SCOPUS: ar.j, info:eu-repo/semantics/published

TTP/Tis11 family of proteins are a major family of AU-rich elements binding proteins (ARE-BPs) that have been shown to play a particularly important role in the control of inflammation and in cancer, mostly by inducing the rapid decay of their target ARE containing mRNAs. TTP/Tis11 proteins levels are tightly controlled and highly affected by environmental cues as well as cell type. In this work, we studied the role of TTP/Tis11 proteins in two different settings where their protein levels might be strongly affected. dTis11 protein was strongly affected by oxygen concentration variation in Drosophila S2 cells and was involved in the control of the metabolic adaptation of S2 cells to those changes. In the other setting, TTP was shown to be involved in the homeostasis of intestinal Treg cells in mice through the control of the mRNA encoding RALDH2, an enzyme of the vitamin A metabolism., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Bacteria occupy an impressive diversity of environments in which complex networks of interactions shape the microbial communities’ relationships. In this context, an arsenal of bacterial nanoweapons have been selected to increase the relative fitness of each player. Some of these interactions depend on molecules diffused in the media whereas others rely on direct cell-to-cell contact. The type VI secretion system (T6SS) is one of those sophisticated ways to interact with neighboring cells. These supramolecular complexes allow Gram-negative bacteria to puncture the outer membrane of a cell in a contact- dependent manner and subsequently release a cocktail of toxins named effectors. Here we characterized RhsC, an effector of the Rhs family encoded in the Xenorhabdus bovienii SS-2004 genome. The carboxy-terminal domain of this Rhs toxin (RhsC-CT) shows a R-S-ExE catalytic motif characteristic of arginine ADP-ribosyltransferases. We demonstrated that this RhsC-CT uses the NAD+ coenzyme to ADP-ribosylate various protein targets in E. coli. The activity of this RhsC-CT toxin is inhibited via direct interaction with its cognate RhsIc immunity protein for which we obtained a structure., Option Biologie moléculaire du Doctorat en Sciences, info:eu-repo/semantics/nonPublished

1-Methyladenosine (m1A) is a modified nucleoside found at positions 9, 14, 22 and 58 of tRNAs, which arises from the transfer of a methyl group onto the N1-atom of adenosine. The yqfN gene of Bacillus subtilis encodes the methyltransferase TrmK (BsTrmK) responsible for the formation of m1A22 in tRNA. Here, we show that BsTrmK displays a broad substrate specificity, and methylates seven out of eight tRNA isoacceptor families of B. subtilis bearing an A22. In addition to a non-Watson-Crick base-pair between the target A22 and a purine at position 13, the formation of m1A22 by BsTrmK requires a full-length tRNA with intact tRNA elbow and anticodon stem. We solved the crystal structure of BsTrmK showing an N-terminal catalytic domain harbouring the typical Rossmann-like fold of Class-I methyltransferases and a C-terminal coiled-coil domain. We used NMR chemical shift mapping to drive the docking of BstRNASer to BsTrmK in complex with its methyl-donor cofactor S-adenosyl-L-methionine (SAM). In this model, validated by methyltransferase activity assays on BsTrmK mutants, both domains of BsTrmK participate in tRNA binding. BsTrmK recognises tRNA with very few structural changes in both partner, the non-Watson-Crick R13-A22 base-pair positioning the A22 N1-atom close to the SAM methyl group., SCOPUS: ar.j, info:eu-repo/semantics/published

HIV-1 infections can be treated but not cured by the current antiretroviral therapy regimens. One of the major barriers to HIV-1 eradication is the persistence of the virus in treated HIV+ individuals under the form of reservoirs. A continuum of molecular mechanisms, at the epigenetic, transcriptional and post-transcriptional levels maintains HIV-1 gene expression silent in its reservoirs. A better understanding of HIV-1 molecular mechanisms of persistence thus allows to devise novel therapeutic approaches to eradicate the virus. In this context, our thesis aimed at characterizing the molecular mechanisms of HIV-1 persistence in its T-lymphoid and myeloid reservoirs. More specifically, we have studied the epigenetic and transcriptional mechanisms of HIV-1 persistence at three different levels. First, we have investigated the DNA methylation-mediated mechanisms underlying the heterogeneity of the DNA methylation inhibitor 5-aza-2’-deoxycytidine potency in the reactivation of HIV-1 gene expression from latently-infected CD4+ T cells. Second, we have studied the contribution of the intragenic binding sites for the cellular PU.1 transcription factor in the specific regulation of HIV-1 gene expression in myeloid lineages. Finally, in a third study, we have designed a new tool to study the transcriptional landscape of HIV-1 in LTRs-suppressed proviruses. Collectively, our work has offered individual insights into the molecular mechanisms underlying the heterogeneity of HIV-1 T-lymphoid and myeloid reservoirs, with the ultimate goal of developing new HIV-1 curative strategies and improving the quality of life of HIV+ individuals., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Les apolipoprotéines L (APOL) forment une famille de protéines conservées chez les mammifères. L’APOL6 murine est principalement exprimée par les adipocytes présents dans le tissu adipeux. Dans un modèle de culture d’adipocytes, l’adipogénèse a causé l’induction de l’expression de l’APOL6. Celle-ci a pu encore être modulée à la hausse par de l’IFNγ, et à la baisse par du TGFβ. Des facteurs élevant la concentration en AMP cyclique ont aussi permis de diminuer l’expression d’APOL6. In vivo, lorsque des souris APOL6 KO ont été nourries par un régime riche en graisses, elles ont pris moins de poids que les souris WT correspondantes. De plus, les adipocytes des souris APOL6 KO obèses étaient plus petits que ceux des contrôles WT. Finalement, la recherche de protéines interagissant avec l’APOL6 par immunoprécipitation a permis de mettre en évidence une majorité de protéines associées au cytosquelette d’actine. En conclusion, l’APOL6 semble être associée au cytosquelette d’actine des adipocytes et permettrait la régulation de la taille de leurs gouttelettes lipidiques., Apolipoproteins L (APOL) are a family of conserved proteins among mammals. Murine APOL6 is mainly expressed by adipocytes in the adipose tissue. In a model of in vitro adipocyte cell culture, adipogenesis induced the expression of APOL6. This expression increased with IFNγ and decreased with TGFβ. Cyclic-AMP elevating agents also decreased the expression of APOL6. In vivo, APOL6 KO mice that were fed with a high fat diet gained less weight than their wild type (WT) counterparts. Furthermore, adipocytes from obese APOL6 KO mice were smaller than those from WT controls. Finally, immunoprecipitation experiments showed that APOL6 probably interacted with actin cytoskeleton proteins within adipocytes. In conclusion, APOL6 is likely associated with the actin cytoskeleton in adipocytes and could be involved in the regulation of the size of lipid droplets., Option Biologie moléculaire du Doctorat en Sciences, info:eu-repo/semantics/nonPublished

RÉSUMÉCsrA est un régulateur post-transcriptionnel contrôlant l’expression et/ou la stabilité des ARNm auxquels il se lie. Il appartient à la famille des régulateurs globaux et contrôle une grande variété de fonctions apparemment non liées. Dans le cas de CsrA, il s’agit principalement de fonctions métaboliques et de fonctions liées aux comportements sociaux des bactéries. Cependant, les limites de la régulation exercée par CsrA sur la physiologie cellulaire sont floues car ses cibles directes semblent abondantes mais difficiles à identifier et, parmi celles-ci, d’autres régulateurs important étendent indirectement l’influence de CsrA.Au cours de cette thèse, nous avons étudié les effets de la délétion du gène csrA à l’échelle de la population bactérienne (1), de la cellule bactérienne (2) et au niveau génétique (3) dans une souche d’Escherichia coli uropathogène. Les infections urinaires font parties des infections bactériennes les plus courantes, présentent un mécanisme de chronicité faisant intervenir la formation de biofilms et E. coli est le principal agent responsable de ces infections. (1) Nous avons montré que l’architecture des biofilms formés par la souche uropathogène d’E. coli était différente de celle décrite pour la souche de laboratoire et que la délétion de csrA affectait fortement cette architecture. (2) Nous avons également montré que le gène csrA n’était pas essentiel mais que sa délétion entraînait un défaut de croissance ainsi qu’une perte d’homéostasie de l’enveloppe. (3) Finalement, nous avons étudié des mutants compensatoires obtenus au travers d’une expérience d’évolution expérimentale partant du mutant ΔcsrA et montré que les différents phénotypes testés étaient restaurés dans ces mutants compensatoires sans qu’aucun changement génétique ne soit identifié.SUMMARYCsrA is a global post-transcriptional regulator controlling the expression/stability of its mRNA targets. It regulates a wide variety of apparently unrelated functions mainly relate, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

CsrA est un régulateur global très conservé au sein des bactéries, qui contrôle la stabilité et/ou l'expression des ARN messagers avec lesquels il interagit. CsrA est impliqué dans de nombreuses voies de régulation, notamment le métabolisme central du carbone ainsi que les comportements sociaux tels que la motilité ou la formation de biofilms. De plus, de récents travaux effectués dans notre laboratoire ont montré une influence de CsrA sur l'homéostasie de l'enveloppe. La régulation de l'expression et de l'activité de CsrA est majoritairement due à des boucles de rétrocontrôle au sein du métabolisme central et de la réponse stringente.L’objectif de notre travail était d’identifier de nouveaux régulateurs de l'expression de csrA. Nous avons tout d'abord étudié la modification de 3 phénotypes influencés par CsrA dans différentes souches mutantes. Cette première approche nous a permis d'identifier les systèmes à deux composants CpxR/A et EnvZ/OmpR comme potentiels régulateurs de l'expression de csrA. Nous nous sommes ensuite attaché à caractériser la régulation de l'expression de csrA par CpxR/A. Nous avons montré que CpxR/A régule positivement la transcription de csrA en milieu riche et en milieu chimiquement défini contenant des acides aminés. Nous avons mis en évidence que le facteur de transcription CpxR se lie sur 2 sites de fixation sur la région promotrice de csrA et régule ainsi l'activité du principal promoteur de csrA., CsrA is a global regulator conserved within the bacterial kingdom. CsrA is a post-transcriptional regulator that interacts with messenger RNAs and controls their expression and/or stability. CsrA is involved in numerous pathways, especially in the central carbon metabolism and the social behaviours, like motility and biofilm formation. Moreover, recent data obtained in our lab indicate the implication of CsrA in the envelope homeostasis. The regulation of the expression of CsrA is mainly due to feedback loops taking place in the central carbon metabolism and stringent response.The objective of our work was to identify new regulators of csrA expression. Firstly, we studied the modification of CsrA-dependent phenotypes in different mutant strains. This approach allowed us to identify the 2 two component systems CpxR/A and EnvZ/OmpR as potential regulators of csrA expression. We focused on the characterisation of the regulation of csrA expression by CpxR/A. We demonstrated that CpxR/A up-regulates csrA transcription both in rich and chemically-defined medium supplemented with amino acids. Furthermore, we showed that the transcription factor CpxR binds the csrA promoter region on 2 binding sites and thus regulates the activity of the main promoter of csrA., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Bacterial toxin-antitoxin (TA) systems are small genetic elements that are composed of a toxic protein and its cognate antidote that is unstable. Type II TA systems are the most common in bacterial genomes. In type II TAs both toxin and antitoxin are proteins that form a complex in which the toxic activity is inhibited. This complex also participates in transcription repression of the operon coding for TA. Even though these systems are abundant in bacterial genomes, their roles remain unclear. TAs encoded on mobile genetic elements contribute to their stability in growing population and favour their horizontal transfer. The function of TAs encoded on chromosomes is less clear and is a subject of intense debates. The predominant hypothesis is that they participate in stress response. The type II toxin are mostly translation inhibitors that target translation at different stages using different enzymatic activities. Some other type II toxins target DNA replication or synthesis of peptidoglycan. This thesis presents a novel toxin, AtaT, that modifies the initiator transfer RNA on the methionine. After the modification acetylated acMet-tRNAfMet fails to interact with initiation factor 2 and therefore is not delivered to the ribosome 30S subunit, which leads to translation inhibition. Crystal structures of AtaT toxin, its antitoxin AtaR and their complex interacting with DNA allow us to visualise the regulation cycle of AtaRT toxin antitoxin system. The link between the synthesis of the toxin, its neutralisation by the antitoxin and their participation in the transcription regulation of ataRT operon is validated both in vitro and in vivo., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

tRNA molecules get heavily modified post-transcriptionally. The N-1 methylation of purines at position 9 of eukaryal and archaeal tRNA is catalyzed by the SPOUT methyltranferase Trm10. Remarkably, while certain Trm10 orthologs are specific for either guanosine or adenosine, others show a dual specificity. Structural and functional studies have been performed on guanosine- and adenosine-specific enzymes. Here we report the structure and biochemical analysis of the dual-specificity enzyme from Thermococcus kodakaraensis (TkTrm10). We report the first crystal structure of a construct of this enzyme, consisting of the N-terminal domain and the catalytic SPOUT domain. Moreover, crystal structures of the SPOUT domain, either in the apo form or bound to S-adenosyl-L-methionine or S-adenosyl-L-homocysteine reveal the conformational plasticity of two active site loops upon substrate binding. Kinetic analysis shows that TkTrm10 has a high affinity for its tRNA substrates, while the enzyme on its own has a very low methyltransferase activity. Mutation of either of two active site aspartate residues (Asp206 and Asp245) to Asn or Ala results in only modest effects on the N-1 methylation reaction, with a small shift toward a preference for m1G formation over m1A formation. Only a double D206A/D245A mutation severely impairs activity. These results are in line with the recent finding that the single active-site aspartate was dispensable for activity in the guanosine-specific Trm10 from yeast, and suggest that also dual-specificity Trm10 orthologs use a noncanonical tRNA methyltransferase mechanism without residues acting as general base catalysts., SCOPUS: ar.j, info:eu-repo/semantics/published

Mitochondrial tRNAs are transcribed as long polycistronic transcripts of precursor tRNAs and undergo posttranscriptional modifications such as endonucleolytic processing and methylation required for their correct structure and function. Among them, 5-end processing and purine 9 N1-methylation of mitochondrial tRNA are catalyzed by two proteinaceous complexes with overlapping subunit composition. The Mg2-dependent RNase P complex for 5-end cleavage comprises the methyltransferase domain– containing protein tRNA methyltransferase 10C, mitochondrial RNase P subunit (TRMT10C/MRPP1), short-chain oxidoreductase hydroxysteroid 17-dehydroge-nase 10 (HSD17B10/MRPP2), and metallonuclease KIAA0391/ MRPP3. An MRPP1–MRPP2 subcomplex also catalyzes the formation of 1-methyladenosine/1-methylguanosine at position 9 using S-adenosyl-L-methionine as methyl donor. However, a lack of structural information has precluded insights into how these complexes methylate and process mitochondrial tRNA. Here, we used a combination of X-ray crystallography, interaction and activity assays, and small angle X-ray scattering (SAXS) to gain structural insight into the two tRNA modification complexes and their components. The MRPP1 N terminus is involved in tRNA binding and monomer–monomer self-interaction, whereas the C-terminal SPOUT fold contains key residues for S-adenosyl-L-methionine binding and N1-methylation., SCOPUS: ar.j, info:eu-repo/semantics/published

Bovine Leukemia Virus (BLV) latency is a viral strategy used to escape from the host immune system and contribute to tumor development. However, the recent discovery of a highly expressed miRNA cluster has suggested that BLV latency is partially true. In our PhD thesis, we studied the epigenetic and transcriptional regulations of this RNA polymerase III (RNAPIII)- dependent miRNA cluster and of a newly discovered RNA polymerase II (RNAPII)-dependent promoter (which drives an active antisense transcription). Moreover, our data suggested a putative collision phenomenon between RNAPII and RNAPIII convergent transcriptions. In the second part of our PhD thesis, we therefore provided new insights into this complex transcriptional network. In the third part of this work, we demonstrated the recruitment of CTCF, a multi-functional transcriptional regulator, along the BLV genome and provided data explaining its putative functions in BLV transcriptional and epigenetic regulations but also in viral-host genome long-range interactions. In conclusion, our PhD thesis provides a better understanding of the transcriptional network regulating BLV gene expression and new ideas to study BLV-induced leukemia development. La latence virale, principale caractéristique de l’infection par le virus de la leucémie bovine (BLV), permet au virus d’échapper au système immunitaire de l’hôte et contribue au développement tumoral. Cependant, la récente découverte d’une région codant pour des miRNAs viraux et activement transcrite par l’ARN polymérase III (RNAPIII), suggère que la latence virale n’est que partiellement vraie. Dans cette thèse, nous avons étudié les régulations transcriptionnelle et épigénétique du promoteur RNAPIII-dépendant contrôlant l’expression des miRNAs du BLV, ainsi que celles d’un nouveau promoteur ARN polymérase II (RNAPII)-dépendant, découvert au cours de notre travail de thèse. Suite à nos données, suggérant de l’interférence transcriptionnelle, nous avons ensuite étudi, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

La vacuole de la levure joue un rôle dans le stockage de nutriments, la dégradation des macromolécules et le recyclage de métabolites. En accord avec ces fonctions, des protéines se trouvant à la membrane vacuolaire catalysent le transport de divers composés à travers la membrane. Ceci permet par exemple à la vacuole d’accumuler un grand stock d’arginine et d’autres acides aminés cationiques ainsi que de mobiliser des acides aminés durant une carence en azote. Par ailleurs, les scientifiques soupçonnent l’existence d’un transporteur de cystéine, essentiel au contrôle redox de la vacuole et à la protéolyse. Afin d’étudier plus en détail le transport d’acides aminés dans la vacuole, nous avons mis au point un protocole d’isolement de vacuoles intactes suivi de tests d’entrée d’acides aminés. Dans un premier temps, cela nous a permis de caractériser pour la première fois un transport de cystéine dans les vacuoles intactes. En combinant des analyses bioinformatiques avec un screening d’une collection de souches mutantes pour une sensibilité à la cystéine ou la cystine (un dimère de cystéine), nous avons pu proposer une liste de gènes candidats codant pour un transporteur de cystéine à la membrane vacuolaire. Dans un deuxième temps, nous avons caractérisé la protéine Ypq2 comme un facilitateur de haute affinité catalysant l’export d’arginine hors de la vacuole en condition de carence en azote. En outre, nous avons identifié un nouveau transporteur, Vat1, nécessaire à l’établissement du stock d’arginine vacuolaire. Nos résultats sont conciliables avec l’existence d’un couplage fonctionnel entre les voies de sortie et d’import d’arginine dans la vacuole., Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Chez les eucaryotes, le complexe kinase TORC1 (Target Of Rapamycin Complex 1) joue un rôle central dans le contrôle de la croissance cellulaire. Il intègre de nombreux signaux et agit en modulant l’état de phosphorylation de différents effecteurs, principalement des protéines impliquées dans des processus anaboliques ou cataboliques. Parmi ces signaux, on distingue notamment les acides aminés. Ces derniers agissent sur TORC1 via l’action de protéines de la famille des GTPases Rag, elles-mêmes régulées par des facteurs GEF et GAP. Des études récentes sur des cellules mammifères ont mis en évidence l’existence de senseurs d'acides aminés, capables de moduler l'activité des facteurs GEF et GAP. Chez la levure, ces senseurs restent toutefois inconnus. Chez la levure, TORC1 contrôle la fonction de plusieurs protéines y compris des transporteurs d'acides aminés de la membrane plasmique, comme la perméase générale des acides aminés, Gap1. C’est via sa branche de signalisation Tap2-PP2A/Npr1 que TORC1 contrôle l'ubiquitylation et le trafic intracellulaire de ces transporteurs, et ceci, en modulant l’activité d’adaptateurs de type α-arrestine de l'ubiquitine-ligase Rsp5.Dans ce travail, nous avons combiné des approches de génétique et de biochimie chez la levure afin d’étudier la régulation de TORC1 et son rôle dans l'endocytose en réponse au substrat de Gap1, la perméase générale des acide aminés, et de Can1, la perméase spécifique de l'arginine.Dans la première et la deuxième partie de ce travail, je décris ma contribution à l'étude qui visait à élucider le mécanisme d'ubiquitylation de Gap1 et de Can1 induite par le transport de leurs substrats. Le modèle déduit de ce travail propose que cette régulation négative n'est pas due à l'accumulation intracellulaire des acides aminés transportés, mais à un changement conformationnel des perméases, couplé à la réaction de transport et qui fait apparaitre un état ouvert vers l'intérieur, entraînant ainsi le remodelage de la queue, The Target of Rapamycin Complex 1 (TORC1) plays a pivotal role in controlling cell growth in probably all eukaryotic organisms. It operates by integrating upstream signals like growth factors and nutrients to modulate by phosphorylation multiple downstream effectors, mostly proteins involved in anabolic or catabolic processes. Among the various signals that impinge on TORC1, nitrogen sources, in particular amino acids are primordial input signals modulating TORC1 activity through the conserved Rag family of GTPases. Recent studies in mammals have shed the light on the existence of various sensor systems of internal amino acids that modulate the activity of the GEF and GAP factors acting on the Rag GTPases. Yet, in yeast the amino acid sensing events acting upstream of the Rag GTPase (named Gtr1 and Gtr2) regulators remain poorly known. Yeast TORC1 controls the function of many proteins including several plasma membrane amino acid transporters, e.g. Gap1, the general amino acid permease. It does so via the Tap2-PP2A/Npr1-signaling branch that controls the ubiquitylation and intracellular trafficking of these proteins through regulation of α-arrestin-type adaptors of the ubiquitin-ligase Rsp5. In this work, we combined yeast genetics and biochemical assays to study TORC1 regulation by amino acids and to illustrate the role of TORC1 in substrate-transport mediated endocytosis of Gap1 and of the arginine specific permease, Can1. In the first and second part of this work, I describe my contribution to the study that aimed at elucidating the mechanism of substrate-transport-mediated ubiquitylation and endocytosis of Gap1 and Can1. The model deduced from this work states that this down-regulation is not due to intracellular accumulation of the transported amino acids, but to substrate-transport-induced conformational transition of the transporters to an inward-facing state, resulting in remodeling of their N-terminal cytoplasmic tail and subsequent exposure of a hidden bin, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

La maladie d’Alzheimer (MA) est un désordre neuro-dégénératif chronique fatal et la forme la plus répandue des démences chez l’adulte qui touchent plus de 28 millions de personnes dans le monde. En absence de traitement pour les démences neurodégénérative dont la maladie d’Alzheimer, le coût de celles-ci est estimé à 1 trillion d’USD en 2018 ce qui représente des enjeux économiques et sociétaux majeurs au niveau national et mondial. La MA est une forme d’amylose qui est caractérisée par l’agrégation du peptide amyloïde beta (Aβ) dans le cerveau des patients. Le facteur de risque génétique principal de la forme tardive (après 65 ans) de cette maladie est l’isoforme E4 de l’apolipoprotéine E (apoE) qui intervient dans le transport et le métabolisme des lipides et interagit avec le peptide Aβ. La modulation de la structure des isoformes d’apoE et de leur interaction avec l’Aβ apparaît comme une cible prometteuse dans la conception rationnelle de thérapies de la maladie. Celle-ci nécessite néanmoins une compréhension approfondie des propriétés structurales et dynamiques des deux partenaires moléculaires. Dans le cadre de cette thèse, nous avons étudié la structure de trois isoformes (E2, E3 et E4) de l’apoE par différentes techniques de biologie structurale et principalement par la réticulation chimique couplée à la spectrométrie de masse (CXMS) quantitative et par la bioinformatique structurale. Ces données complémentées par la spectroscopie infrarouge ont permis de construire des modèles structuraux de l’apoE2, E3 et E4. Nous avons mis en évidence l’interaction des domaines N- et C-terminal et la présence de multiples conformations de l’apoE chez les trois isoformes. Nos données suggèrent un équilibre entre deux principales conformations de l’apoE dont la population relative diffère entre les trois isoformes. Nous proposons les interfaces à cibler dans le cadre de thérapie visant à moduler les propriétés structurales des isoformes de l’apoE.Nous avons également mis en, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

MRPP2 (also known as HSD10/SDR5C1) is a multifunctional protein that harbours both catalytic and non-catalytic functions. The protein belongs to the short-chain dehydrogenase/reductases (SDR) family and is involved in the catabolism of isoleucine in vivo and steroid metabolism in vitro. MRPP2 also moonlights in a complex with the MRPP1 (also known as TRMT10C) protein for N1-methylation of purines at position 9 of mitochondrial tRNA, and in a complex with MRPP1 and MRPP3 (also known as PRORP) proteins for 5′-end processing of mitochondrial precursor tRNA. Inherited mutations in the HSD17B10 gene encoding MRPP2 protein lead to a childhood disorder characterised by progressive neurodegeneration, cardiomyopathy or both. Here we report two patients with novel missense mutations in the HSD17B10 gene (c.34G > C and c.526G > A), resulting in the p.V12L and p.V176M substitutions. Val12 and Val176 are highly conserved residues located at different regions of the MRPP2 structure. Recombinant mutant proteins were expressed and characterised biochemically to investigate their effects towards the functions of MRPP2 and associated complexes in vitro. Both mutant proteins showed significant reduction in the dehydrogenase, methyltransferase and tRNA processing activities compared to wildtype, associated with reduced stability for protein with p.V12L, whereas the protein carrying p.V176M showed impaired kinetics and complex formation. This study therefore identified two distinctive molecular mechanisms to explain the biochemical defects for the novel missense patient mutations., SCOPUS: ar.j, info:eu-repo/semantics/published

Toxin–antitoxin (TA) loci are prevalent in bacterial genomes. They are suggested to play a central role in dormancy and persister states. Under normal growth conditions, TA toxins are neutralized by their cognate antitoxins, and under stress conditions, toxins are freed and inhibit essential cellular processes using a variety of mechanisms. Here we characterize ataR–ataT, a novel TA system, from enterohemorrhagic Escherichia coli. We show that the toxin AtaT is a GNAT family enzyme that transfers an acetyl group from acetyl coenzyme A to the amine group of the methionyl aminoacyl moiety of initiator tRNA. AtaT specifically modifies Met-tRNAfMet, but no other aminoacyl-tRNAs, including the elongator Met-tRNAMet. We demonstrate that once acetylated, AcMet-tRNAfMet fails to interact with initiation factor-2 (IF2), resulting in disruption of the translation initiation complex. This work reveals a new mechanism of translation inhibition and confirms Met-tRNAfMet as a prime target to efficiently block cell growth., SCOPUS: ar.j, info:eu-repo/semantics/published

Purine nucleosides on position 9 of eukaryal and archaeal tRNAs are frequently modified in vivo by the post-transcriptional addition of a methyl group on their N1 atom. The methyltransferase Trm10 is responsible for this modification in both these domains of life. While certain Trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of tRNA, others have a dual specificity. Until now structural information about this enzyme family was only available for the catalytic SPOUT domain of Trm10 proteins that show specificity toward guanosine. Here, we present the first crystal structure of a full length Trm10 orthologue specific for adenosine, revealing next to the catalytic SPOUT domain also N- and C-terminal domains. This structure hence provides crucial insights in the tRNA binding mechanism of this unique monomeric family of SPOUT methyltransferases. Moreover, structural comparison of this adenosine-specific Trm10 orthologue with guanosine-specific Trm10 orthologues suggests that the N1 methylation of adenosine relies on additional catalytic residues., SCOPUS: ar.j, info:eu-repo/semantics/published

La moelle épinière assure la transmission des messages nerveux entre l’encéphale et le reste du corps et assure la coordination des mouvements rythmiques de la locomotion. Elle est constituée d’un grand nombre de types différents d’interneurones et de neurones moteurs, organisés en circuits neuronaux. Les circuits impliqués dans la transmission des informations sensorielles et dans les mouvements des membres sont localisés respectivement dans les parties dorsale et ventrale de la moelle épinière. Les mécanismes moléculaires contrôlant la spécification de ces différents types de neurones dans la moelle épinière restent actuellement mal connus. Au cours de mon travail de thèse, je me suis intéressée à la famille des gènes Prdm (PR Domain containing methyltransferase). Ces gènes sont conservés évolutivement. Ils codent pour des facteurs de transcription jouant des rôles importants dans le développement embryonnaire et sont fréquemment impliqués dans des maladies chez l’Homme. Ces facteurs sont caractérisés par la présence d’un domaine PR semblable au domaine SET trouvé dans des protéines à activité histone méthyltransférase et d’un nombre variable de doigts à zinc. Je me suis focalisée essentiellement sur les gènes Prdm12 et Prdm13, des gènes exprimés de manière précoce et localisés dans le système nerveux en développement et dont la fonction était totalement inconnue. Nos résultats ont montré que l’expression de Prdm12 dans la partie ventrale de la moelle épinière est dépendante de l’acide rétinoïque et du facteur de transcription Pax6 et que Prdm12 est restreint au domaine p1 via l’action répressive des facteurs de transcription Dbx1 et Nkx6 exprimés dans les domaines de progéniteurs adjacents. Prdm12 fonctionne comme déterminant de la destinée des interneurones V1, des interneurones impliqués dans le contrôle des mouvements de la locomotion et essentiels à la survie des neurones moteurs. Prdm12 agirait en réprimant, probablement directement, l’exp, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

La moelle épinière assure la transmission des messages nerveux entre l’encéphale et le reste du corps et assure la coordination des mouvements rythmiques de la locomotion. Elle est constituée d’un grand nombre de types différents d’interneurones et de neurones moteurs, organisés en circuits neuronaux. Les circuits impliqués dans la transmission des informations sensorielles et dans les mouvements des membres sont localisés respectivement dans les parties dorsale et ventrale de la moelle épinière. Les mécanismes moléculaires contrôlant la spécification de ces différents types de neurones dans la moelle épinière restent actuellement mal connus. Au cours de mon travail de thèse, je me suis intéressée à la famille des gènes Prdm (PR Domain containing methyltransferase). Ces gènes sont conservés évolutivement. Ils codent pour des facteurs de transcription jouant des rôles importants dans le développement embryonnaire et sont fréquemment impliqués dans des maladies chez l’Homme. Ces facteurs sont caractérisés par la présence d’un domaine PR semblable au domaine SET trouvé dans des protéines à activité histone méthyltransférase et d’un nombre variable de doigts à zinc. Je me suis focalisée essentiellement sur les gènes Prdm12 et Prdm13, des gènes exprimés de manière précoce et localisés dans le système nerveux en développement et dont la fonction était totalement inconnue. Nos résultats ont montré que l’expression de Prdm12 dans la partie ventrale de la moelle épinière est dépendante de l’acide rétinoïque et du facteur de transcription Pax6 et que Prdm12 est restreint au domaine p1 via l’action répressive des facteurs de transcription Dbx1 et Nkx6 exprimés dans les domaines de progéniteurs adjacents. Prdm12 fonctionne comme déterminant de la destinée des interneurones V1, des interneurones impliqués dans le contrôle des mouvements de la locomotion et essentiels à la survie des neurones moteurs. Prdm12 agirait en réprimant, probablement directement, l’exp, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Le trypanosome sud américain, Trypanosoma cruzi, transmis par un insecte hématophage de type triatome est le protozoaire connus pour causer la maladie de Chagas chez l’Homme. Le cycle de vie de ce parasite alterne à la fois sur le type d’hôte, insecte ou hôte vertébré, et sur la forme :trypomastigote pour la forme quiescente et amastigote et épimastigote pour les formes prolifératives. Concernant la forme, seuls les parasites épimastigotes évoluent et prolifèrent dans le tube digestif des triatomes et possèdent un système endocytaire actif nécessaire à leur besoin énergétique. Toutefois, cette endocytose est restreinte à deux sites membranaires, la poche flagellaire et le cytostome, à partir desquels se créent des cargos endocytaires. Ces cargos endocytaires fusionnent ensuite avec un réseau vésiculaire endosomal qui délivre son contenu dans des réservosomes, compartiments similaires aux lysosomes.Chez le trypanosome africain (Trypanosoma brucei brucei), l’endocytose ne se réalise qu’au niveau de la poche flagellaire. Certaines protéines appartenant à cette voie endocytaire sont modifiées par de longues chaines de résidus poly-N-acétyllactosamine (pNAL) de manière post-traductionnelle. Initialement, il a été proposé que ces résidus puissent agir en tant que signal de tri dans le processus d’endocytose chez ces parasites.En nous basant sur les travaux qui ont été réalisés chez le trypanosome africain, nous nous sommes proposés d’approfondir les connaissances sur la voie endocytaire du trypanosome sud américain (Trypanosoma cruzi) qui est beaucoup moins étudié. Pour ce faire, à l’aide de deux lectines, la tomatolectine et la lectine de Griffonia simplicifolia qui présentent respectivement une affinité pour les résidus pNAL et les résidus N-acétylglucosamine (GlcNAc) en fin de chaine, nous avons pu enrichir et caractériser par LC-MS², 173 glycoprotéines putatives dont plus de 13% sont localisées dans la voie endocytaire. Parmi les protéines identifiées, en plus des nom, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

During translation, the transfer RNAs (tRNAs) play the crucial role of adaptors between the messenger RNA and the amino acids. The tRNAs are first transcribed as pre-tRNAs which are then maturated. During this maturation, several nucleosides are modified by tRNA modification enzymes. These modifications are important for the functions of the tRNAs and for their correct folding. Many of the modifications are methylations of the bases or the ribose. Four families of tRNA methyltransferases are known, among which the SPOUT superfamily. Proteins of this superfamily are characterised by a C-terminal topological knot where the methyl donor is bound. With the exception of the monomeric Trm10, all known SPOUT proteins are dimeric and have an active site composed of residues of both protomers. Interestingly, depending on the organism, the same modification can be catalysed by completely unrelated enzymes. On the other hand, homologous enzymes can have different specificities or/and activities. These differences are well illustrated for the TrmJ and Trm10 enzymes.In the first part of this work we have identified the TrmJ enzyme of Sulfolobus acidocaldarius (the model organism of hyperthermophilic Crenarchaeota) which 2’-O-methylates the nucleoside at position 32 of tRNAs. This protein belongs to the SPOUT superfamily and is homologous to TrmJ of the bacterium Escherichia coli. A comparative study shows that the two enzymes have different specificities for the nature of the nucleoside at position 32 as well as for their tRNA substrates. To try to understand these shifts of specificity at a molecular level we solved the crystal structure of the SPOUT domains of the two TrmJ proteins.In the second part of this work, we have determined the crystal structure of the Trm10 protein of S. acidocaldarius. This is the first structure of a 1-methyladenosine (m1A) specific Trm10 and also the first structure of a full length Trm10 protein. The Trm10 protein of S. acidocaldarius is di, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

African trypanosomes are a major plague in sub-Saharan Africa. They cause sleeping sickness in humans and nagana in cattle. These parasites are transmitted between their mammalian hosts by tsetse flies. They are adapting to their different environments through differentiation processes. These processes involve, amongst other things, the expression of different surface coats. These coats are made of procyclin protein at the insect midgut procyclic stage and of variant surface glycoprotein (VSG) at the mammalian bloodstream stage. At a given time, one VSG is expressed from a single VSG gene out of a repertoire of more than 1500 VSG genes present in the trypanosomes genome. The expressed VSG gene is always located at one of fifteen telomeric polycistronic transcription units called expression sites (ES). The VSG coat is changed regularly in a process called antigenic variation allowing trypanosomes to escape the immune response. The exact mechanism controlling the selection of the active ES is not yet known and controversies have been raised concerning the ES transcription control. Although several molecular factors involved in the ES monoallelic-expression have been identified, none of them seems to be a critical regulator.Thus during my thesis we decided to explore two aspects of ES expression: (A) deciphering the level at which this expression is controlled and (B) fishing for new protein factors controlling this expression.A) It is not even clear at which level the ES transcription control takes place. In particular, there has been debate on whether it is taking place at the transcription initiation or elongation level. Previous experiments generated contradictory conclusions and gave rise to two different models. The first model suggested that transcription initiation takes place in all ESs simultaneously. The second model suggested that transcription is initiated in only two ESs, one being fully active and a second being pre-active. These two models were, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

The 2'-O-methylation of the nucleoside at position 32 of tRNA is found in organisms belonging to the three domains of life. Unrelated enzymes catalyzing this modification in Bacteria (TrmJ) and Eukarya (Trm7) have already been identified, but until now, no information is available for the archaeal enzyme. In this work we have identified the methyltransferase of the archaeon Sulfolobus acidocaldarius responsible for the 2'-O-methylation at position 32. This enzyme is a homolog of the bacterial TrmJ. Remarkably, both enzymes have different specificities for the nature of the nucleoside at position 32. While the four canonical nucleosides are substrates of the Escherichia coli enzyme, the archaeal TrmJ can only methylate the ribose of a cytidine. Moreover, the two enzymes recognize their tRNA substrates in a different way. We have solved the crystal structure of the catalytic domain of both enzymes to gain better understanding of these differences at a molecular level., Journal Article, SCOPUS: ar.j, info:eu-repo/semantics/published

The 2'-O-methylation of the nucleoside at position 32 of tRNA is found in organisms belonging to the three domains of life. Unrelated enzymes catalyzing this modification in Bacteria (TrmJ) and Eukarya (Trm7) have already been identified, but until now, no information is available for the archaeal enzyme. In this work we have identified the methyltransferase of the archaeon Sulfolobus acidocaldarius responsible for the 2'-O-methylation at position 32. This enzyme is a homolog of the bacterial TrmJ. Remarkably, both enzymes have different specificities for the nature of the nucleoside at position 32. While the four canonical nucleosides are substrates of the Escherichia coli enzyme, the archaeal TrmJ can only methylate the ribose of a cytidine. Moreover, the two enzymes recognize their tRNA substrates in a different way. We have solved the crystal structure of the catalytic domain of both enzymes to gain better understanding of these differences at a molecular level., Journal Article, SCOPUS: ar.j, info:eu-repo/semantics/published

Plasma membrane transport proteins play a crucial role in all cells by conferring to the cell surface a selective permeability to a wide range of ions and small molecules. The activity of these transporters is often regulated by controlling their amount at the plasma membrane, via intracellular trafficking. The recent boom in the numbers of crystallized transporters shows that many of them that belong to different functional families with little sequence similarity adopt the same structural fold implying a conserved transport mechanism. These proteins belong to the APC (Amino acid-Polyamine-organoCation) superfamily and their fold is typified by the bacterial leucine transporter LeuT. This LeuT fold is characterized by inverted structural repeats of 5 transmembrane domains that harbor the central substrate-binding site and a pseudo-symmetry axis parallel to the membrane. The yeast Saccharomyces cerevisiae possesses about 16 amino acid permeases (yAAPs) that belong to the APC superfamily and that display various substrate specificity ranges and affinities. Topological, mutational analysis and in silico data indicate that yAAPS adopt the LeuT fold.In this work we combined computational modeling and yeast genetics to study substrate binding by yAAPs and the endocytosis of these transporters in response to substrate transport. In the first part of this work, we analyzed the selective recognition of arginine by the yeast specific arginine permease, Can1. We constructed three-dimensional models of Can1 using as a template the recently resolved structure of AdiC, the bacterial arginine:agmatine antiporter, which is also a member of the APC superfamily. By comparison of the binding pockets of Can1 and Lyp1, the yeast specific lysine permease, we identified key residues that are involved in the recognition of the main and side chains of arginine. We first showed that the network of interactions of arginine in Can1 is similar to that of AdiC, and that the selective reco, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

L’infection par le rétrovirus complexe T-lymphotrope HTLV-1 (Human T-cell Leukemia Virus type 1), premier rétrovirus humain découvert, touche de 10 à 20 millions de personnes à travers le monde dans des régions endémiques et induit des désordres lymphoprolifératifs de cellules T. Seulement 5 % des personnes infectées développent, après une longue phase asymptomatique, une maladie dont une forme agressive et rapidement mortelle de leucémie nommée ATLL (Adult T-cell Leukaemia/Lymphoma).L’infection par le virus HTLV-1 se caractérise par l’absence de virémie due à la latence du virus dans la majorité des cellules infectées suite à la répression transcriptionnelle de l’expression virale in vivo. Cette latence favorise très probablement le développement tumoral en permettant aux cellules infectées d’échapper à la réponse immunitaire médiée par l’hôte infecté. Au cours de ce travail, nous avons tout d’abord identifié deux nouveaux sites de liaison pour le facteur de transcription Sp1, localisés dans la région R du promoteur LTR du HTLV-1. Nous les avons caractérisés physiquement par des expériences de retard de migration sur gel et avons mis en évidence la liaison de Sp1 au niveau de ces deux sites. Nous avons ensuite déterminé l’affinité de Sp1 pour les différents sites du promoteur du HTLV-1 et avons montré que les sites Sp11 (localisé dans la région U3) et Sp15 (localisé dans la région U5) sont les plus forts. Nous avons étudié l’impact de mutations de tous les sites Sp1 du LTRHTLV-1 sur son activité promotrice en conditions basales et transactivées par Tax dans le contexte d’un vecteur rapporteur épisomal. Nous avons mis en évidence que les sites Sp1 de la région R du LTRHTLV-1 agissent comme répresseurs de la transcription du LTR5’ mais n’ont aucun effet sur l’activité promotrice du LTR3’.Dans une seconde partie de notre travail, nous avons étudié l’implication du cofacteur CTIP2 dans la répression transcriptionnelle du HTLV-1 et avons mis en évidence sa capa, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Doctorat en Sciences, info:eu-repo/semantics/nonPublished

The process of specific gene transcription by RNA polymerase II (Pol II) is initiated by thebinding of specific transcription factors to DNA. A global understanding of the mechanisms of genetranscriptional regulation of Saccharomyces cerevisiae goes through the description of the targets andthe behavior of those transcription factors.The GATA factors are specific transcription factors intervening in the regulation of NitrogenCatabolite Repression (NCR)-sensitive genes, a mechanism encompassing the transcriptionalregulations leading to the preferential use of good nitrogen sources of the growth medium of yeast inthe presence of less good nitrogen sources. Those 4 GATA factors involved in NCR comprise 2activators (Gat1 and Gln3) and 2 repressors (Gzf3 and Dal80).Generally speaking, the promoters of genes have always been described like the main place forthe integration of the transcription regulation signals relayed by the general and specific transcriptionfactors and the chromatin remodeling factors. Furthermore, the GATA factors have been described asintegrating the external signals of nitrogen availability thanks to their specific DNA binding toconsensus GATA sequences in the promoter of NCR-sensitive genes. The results presented hereintroduce many nuances to the model, notably implying new proteins but also new regions in theregulation process of the NCR-sensitive gene regulation. Indeed, the first goal of this work is todiscover and understand the mechanisms of NCR-sensitive gene regulation that will explain thevariations in their expression levels in the presence of various nitrogen sources and their dependencytowards the GATA factors.Strikingly, it appeared that GATA factor positioning was not limited to the promoter, butoccurred also in the transcribed region. It seems that the transcription factors may have been drivenby the general transcription machinery (Pol II). The binding of a chromatin remo, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

L’expression des gènes chez les organismes eucaryotes est un processus hautement régulé dans l’espace et dans le temps. Les ARN messagers, premièrement décrits comme simples intermédiaires entre l’ADN et les protéines, s’avèrent être des éléments centraux de la régulation de l’expression génique :les régulations post-transcriptionnelles vont influencer la stabilité, la traductibilité et la localisation des ARN messagers (ARNm). Le contrôle de la dégradation des ARNm est un moyen efficace d’adapter rapidement la production des protéines en fonction des besoins de la cellule. La dégradation des ARNm est un processus actif qui nécessite soit l’élimination de la coiffe en 5’ ou de la queue polyA en 3’, soit un clivage endonucléolytique. Dans la plupart des cas, le messager est premièrement déadénylé, puis décoiffé avant d’être dégradé dans le sens 5’-3’ ou dans le sens 3’-5’. De plus, les ARNm en cours de dégradation sont relocalisés dans des granules cytoplasmiques appelés Processing Bodies où les facteurs de la dégradation sont concentrés. On trouve dans les messagers codant pour des protéines dont la production doit être finement régulée, une variété importante d’éléments régulateurs (éléments cis) le plus souvent au sein de leur région 3’ non traduite. La régulation de la stabilité d’ARNm porteurs d’éléments riches en adénine et uridine (ARE) dans leur région 3’ non traduite (3’UTR) par les protéines capables de reconnaitre et lier ces éléments (ARE-BP) constitue un des exemples les plus documentés de régulations post-transcriptionnelles de l’expression des gène, mais le mécanisme moléculaire de cette régulation est encore mal compris.Nous avons utilisé le messager codant pour le peptide antimicrobien CécropineA1 lié par l’ARE-BP dTIS11 comme modèle pour étudier les régulations post-transcriptionnelles dépendantes des ARE chez la drosophile. Au cours de ce travail, nous avons démontré que le messager CecA1 subit une déadénylation biphasique. En effet, une déadény, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

The nucleo-cytoplasmic compartmentalization enables eukaryotic cells to develop sophisticated post-transcriptional regulations of gene expression. However, managing the exchanges of macromolecules between the two compartments also represents a formidable challenge for the cells. Nucleo-cytoplasmic exchanges rely on specialized soluble carriers and take place at nuclear pore complexes that span the nuclear envelope. Active nucleo-cytoplasmic transport of proteins, in particular, is performed mainly by a family of carriers called karyopherins, which includes about twenty members in mammals. Some of them, called importins, recognize nuclear localization signals (NLSs) in their substrates and convey them into the nucleus. Others, called exportins, recognize nuclear export signals (NESs) in their substrates and bring them back to the cytoplasm. Many RNA-binding proteins (RBPs) shuttle between the nucleus and the cytoplasm, where they can often fulfill different functions. RBPs also frequently localize into specialized microdomains that are not delimited by a membrane but in which specific factors are concentrated. Those include processing bodies and stress granules, which are cytoplasmic foci associated with mRNA decay, storage and translational repression. Post-transcriptional regulations mediated by RBPs can therefore be modulated rapidly and efficiently through changes in the localization of RBPs.The first part of this work focuses on the subcellular localization and nucleo-cytoplasmic transport of the Drosophila RBP dTIS11. Like its mammalian and yeast homologues, dTIS11 binds AU-rich elements in the 3’UTR of its target mRNAs, and stimulates their rapid deadenylation and decay. Here, we have observed that although dTIS11 appears to be located mostly in the cytoplasm, it is constantly shuttling in and out of the nucleus. We show that the export of dTIS11 from the nucleus depends on the CRM1 exportin and is mediated by a hydrophobic NES that encompasses residues, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

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