La transformation génétique naturelle est un mode de transfert horizontal de gènes chez les bactéries, qui contribue au maintien et à l'évolution de leurs génomes. C’est un mécanisme clé pour l’adaptation des bactéries, qui pourrait être responsable de la transmission des résistances aux antibiotiques observée en clinique chez certaines espèces pathogènes (S. pneumoniae, H. pylori,…). La transformation naturelle s’effectue par l’internalisation d’ADN exogène à travers la membrane, puis par sa prise en charge jusqu’à son intégration dans le chromosome bactérien par recombinaison homologue. Le processus de prise en charge fait intervenir la protéine DprA, très conservée dans le monde bactérien, impliquée dans la protection de l’ADN entrant contre les nucléases, et dans le recrutement de la recombinase universelle RecA sur l’ADNsb. DprA joue donc un rôle majeur et a récemment été décrite comme étant impliquée dans d’autres aspects de la transformation génétique naturelle, comme la fermeture de la compétence via une interaction directe avec le régulateur de réponse ComE, ou la levée de la barrière du système de restriction-modification afin de faciliter la transformation. Chez H. pylori, DprA est en opéron avec DprB, suggérant l’implication de ces 2 protéines dans une même voie et une interaction directe entre elles. DprA apparaît donc comme étant au cœur d’un véritable réseau d’interaction, protéique et nucléique. / The natural genetic transformation is a mode of horizontal gene transfer that contributes to the maintenance and to the evolution of the genomes in bacteria. It is a key mechanism for their adaptation which could be responsible for the transmission of antibiotic resistances observed clinically for some pathogenic species (S. pneumoniae, H. pylori...). Natural transformation is performed by internalizing exogenous DNA followed by its processing and its integration into the bacterial chromosome by homologous recombination. The DNA processing involves the highly conserved DprA protein for the protection of the incoming DNA against nucleases and the recruitment of the universal recombinase RecA on ssDNA. DprA plays a key role and has recently been suggested to be involved in other aspects of the natural genetic transformation, such as the shut-off of the competence via a direct interaction with the response regulator ComE, or removal of the restriction-modification barrier system in order to facilitate the processing. In H. pylori, the dprA gene is in operon with dprB, whose function is unknown, suggesting their involvement in the same pathway and their likely direct interaction. DprA appears to be central in protein/nucleic acid interactions network.

Afin de se répliquer et de se propager efficacement, les virus ont développé de multiples stratégies leur permettant d’échapper au système de défense innée : le système IFN de type I. Ce travail de thèse a alors consisté à étudier les interactions entre protéines virales et protéines de ce système de défense afin de mieux comprendre les mécanismes de subversion virale et d’identifier d’éventuelles cibles cellulaires thérapeutiques. La reconstruction d’un réseau d’interactions entre ces protéines nous a permis d’identifier des stratégies différentielles de subversion pour 4 familles virales et de montrer un ciblage massif et significatif des protéines du système IFN de type I par les virus. Les protéines en interaction directe avec ces protéines sont également fortement touchées par les virus et sont de potentiels modulateurs du système IFN de type I. Parmi ces modulateurs, le processus biologique sur-représenté est le transport nucléocytoplasmique et la protéine KPNA1 impliquée dans ce processus a retenu notre attention. L’étude fonctionnelle de l’interaction entre la protéine KPNA1 et la protéine NS3 du VHC a montré que la protéine NS3 associée à son cofacteur NS4A inhibe partiellement la réponse IFN de type I en empêchant l’import nucléaire de STAT1. Ce phénotype pourrait résulter de la dégradation de KPNA1 par NS3/4A. Par ailleurs, l’identification de nouveaux inter-acteurs de la protéine NS1 du virus influenza par criblage double-hybride levure a révélé la protéine induite par les IFN de type I, ADAR1, comme partenaire de la protéine NS1 de multiples souches virales et nous avons montré qu'ADAR1 est un facteur pro-viral dont la fonction editing est activée par NS1 / To replicate and propagate efficiently, viruses have developed multiple strategies allowing them to escape the innatedefense system: the type I IFN system, This work of thesis then consisted in studying the interactions between viralproteins and proteins of this defence system in order to understand better the mechanisms of viral subversion andidentifY possible therapeutic cellular tatgets. The reconstruction of a network of interacting proteins involved in the typeI IFN system allowed us to identifY differentiai subversion strategies for 4 viral families and to show a massive andsignificant targeting of proteins of the type I IFN system by viruses. Proteins directly interacting with the type Iinterferon system network are also strongly targeted by viruses and are potential modulators of the type I IFN system.Among these modulators, the most tatgeted function conesponds to the transport of NLS-bearing substrates to thenucleus and the KPNAI protein involved in this process held our attention. The functional study of the interactionbetween KPNA1 and NS3 protein of the HCV showed that NS3 protein associated with its cofactor NS4A inhibitsprutially the type I IFN response by preventing the nuclear translocation of ST A Tl. This phenotype could result fromthe degradation of KPNAI by NS3/4A. Besides, the identification of new cellular prutners ofNS 1 prote in of influenzavirus by yeast two-hybrid screens revealed ADARI, an interferon-stimulated prote in, as partner of NS 1 of ali testedvirus strains and we showed that ADARI is an essential host factor for viral replication and its editing function isactivated by NS 1 protein

Phosphorylierung modulieren. Obwohl heute bereits Tausende von Phosphorylierungsstellen annotiert sind, sind entsprechende funktionelle Informationen begrenzt. Dies ist zum Teil darauf zurückzuführen, dass es keine Hochdurchsatzmethoden zur Erforschung der Funktion einer Phosphorylierungsstelle gibt. Um dieser Herausforderung zu begegnen, habe ich eine auf Shotgun-Proteomik basierende Strategie zur Messung der RNA-Bindungsaktivität von RBPs und ihren phosphorylierten Proteoformen entwickelt, die 'quantitative RNA-Interactome Capture (qRIC)' genannt wird. QRIC quantifiziert die Pull-Down-Effizienz von RBPs, die mit Oligo(dT)-Magnetbeads isoliert werden. Diese Effizienz korreliert mit der Anzahl der RNA-Bindungsstellen und der Spezifität der Motivbindung, und spiegelt so die RNA-Bindung in vivo wieder. In einer Gegenüberstellung der Pull-Down-Effizienz verschiedener Proteoformen in unbehandelten Zellen, habe ich qRIC als unvoreingenommenes Screening von regulatorischen Phosphorylierungsstellen in RBPs eingesetzt. Für jede einzelne Phosphorylierungsstelle wurde ein Delta-Effizienzwert berechnet, der den Einfluss auf die RNA-Bindung in vivo reflektiert. Die Effizienzunterschiede spiegelten das erwartete Verhalten von RBPs während der Phasentrennung von membranlosen Organellen und die Ladungsabstoßung zwischen Phosphorylierungsstellen und Nukleotiden bei physiologischem pH-Wert wider. Mithilfe des Delta-Effizienzwertes identifizierte ich mehrere bereits bekannte regulatorische Phosphorylierungsstellen in SF3B1, UPF1 und ELAVL1, sowie neue, bisher unbekannte und möglicherweise regulatorische Phosphorylierungsstellen in SERBP1, LARP1 und RBM20. Phosphomimetische Mutationsvarianten dieser Phosphorylierungsstellen wurden analysiert, um den molekularen Einfluss auf die Regulation der RBP-Funktion zu untersuchen. Es konnte gezeigt werden, dass die Phosphorylierung bestimmter Stellen im Spleißregulator RBM20 dessen nukleo-zytoplasmatische Lokalisierung, die Assoziation mit zytosolischen RNA-Granula und die Spleißfunktion beeinflusst. Diese Erkenntnisse könnten sich beispielsweise auf die Entwicklung neuer Behandlungsmethoden für Patienten mit dysfunktionalen RBM20-Mutationen auswirken, die zu dilatativer Kardiomyopathie führen. QRIC kann als Hochdurchsatzverfahren dazu beitragen, unser Wissen über die Regulierung von Protein-RNA-Interaktionen durch Phosphorylierung zu erweitern. / Post-transcriptional regulation of gene expression is fundamental in health and disease. RNA-binding proteins (RBPs) directly bind and govern the fate of RNAs in cells. At the same time, cell signaling cascades control RBP functions by modulating their physicochemical properties through post-translational modifications, like phosphorylation. Although thousands of phosphorylation sites have been annotated, functional information is limited. This, in part, is due to the lack of high-throughput methods that measure function. To tackle this challenge I developed a shotgun proteomics-based strategy for measuring the RNA-binding activity of RBPs and their phosphorylated proteoforms, named quantitative RNA-interactome capture (qRIC). In qRIC, pull-down efficiency of RBPs isolation with oligo(dT) magnetic beads is quantified in cells at steady state and correlates with the number of RNA-binding sites and motif binding specificity, reflecting a link to RNA-binding in vivo. By contrasting pull-down efficiency of different proteoforms in the cells, I applied qRIC as an unbiased screening of regulatory phosphorylation sites in RBPs affecting pull-down efficiency. A delta efficiency score was calculated for each individual phosphorylation site to denote its influence on RNA-binding in vivo. Efficiency differences globally reflected the expected behavior of RBPs during phase separation of membraneless organelles and charge repulsion between phosphorylation sites and nucleotides in physiological pH. Using the delta efficiency score, I identified several previously known regulatory phosphorylation sites in SF3B1, UPF1 and ELAVL1, plus novel candidate regulatory sites in SERBP1, LARP1 and RBM20. Phosphomimetic mutant variants of these sites were analysed to investigate the molecular mechanism of regulation. Importantly, I show that phosphorylation of candidate sites in the splicing regulator RBM20 affects its nucleo-cytoplasmic localization, association with cytosolic RNA granules, and splicing function. These findings could have implications for the development of novel treatments based on kinase activity for patients with dysfunctional RBM20 mutations leading to congenital dilated cardiomyopathy. I anticipate that qRIC, as a high throughput approach, will help to expand our knowledge about the regulation of protein-RNA interactions and their regulation by phosphorylation.

Endocytosis is both an ancient and a diverse feature of the eukaryotic cell. Studying how it evolved can provide insight into the nature of the last common eukaryotic ancestor, and the diversification of eukaryotes into the known extant lineages. In this thesis, I present two studies on the evolution of endocytosis. In the first part of the thesis I report results from a large-scale, phylogenetic and comparative genomic study of clathrin-mediated endocytosis (CME). The CME pathway has been studied to a great level of detail in yeast to mammal model organisms. Several protein families have now been identified as part of the complex set of protein-protein and protein-lipid interactions which mediate endocytosis. To investigate how such complexity evolved, first, I defined the modular nature of the CME interactome (CME-I) by literature review, and then I carried out a systematic phylogenetic and protein domain architecture analysis of the proteins involved. These data were used to construct a model of the evolution of the CME-I network, and to map the expansion of the network's complexity to the eukaryotic tree of life. In the second part of the thesis, I present results from evolutionary and functional studies of the eisosome, a protein complex which has been proposed to regulate the spatial distribution of endocytosis in S. cerevisiae. The phylogeny of eisosomes components Pil1 and Lsp1 reported here, suggests that eisosomes are likely to have originated at the base of the fungi, and then diversified significantly via multiple gene duplications. I thus studied the localisation and function of Pil1 and Lsp1 homologues in Magnaporthe oryzae to investigate the role of eisosomes in filamentous fungi. Results suggests that eisosomes are linked with septal formation and integrity in M. oryzae, and that the septal specific Pil2 paralogue was lost in budding yeasts. Together, the data presented in this thesis describe the evolutionary history of a complex biological system, but also highlights the problem of asymmetry in the understanding of endocytic diversity in the eukaryotes.

La découverte récente de nouveaux gènes, de mécanismes d’épissage alternatif et d’interactions entre les protéines du métabolisme intracellulaire de la Cbl suggère que de nouvelles interactions protéiques peuvent prendre part aux mécanismes de régulation de ce métabolisme. Nos données confirment, dans les cellules humaines des HepG2 et des fibroblastes de patients CblC et cblG, diverses interactions qui ont été jusqu'à présent que décrites in vitro ou chez les bactéries : MS avec méthionine synthase réductase (MSR), MS avec MMACHC et MMACHC avec MMADHC. Nos données révèlent également de nouvelles interactions : MMADHC avec MS, MMADHC avec MSR, MSR avec MMACHC et MS avec les isoformes de MAT. De plus, l'absence de MS ou MMACHC perturbe les interactions impliquant les autres partenaires protéiques de l'interactome MS. En conclusion, cette étude suggère que les différentes étapes du métabolisme intracellulaire de Cbl pourraient se produire dans un grand complexe multiprotéique composé d'au moins de MS, MSR, MMACHC, MMADHC et les isoformes de MAT, et qui contribuerait à protéger la Cbl du milieu cytoplasmique / The recent discovery of new genes, alternative splicing and protein-protein interactions between intracellular processing of vitamin B12 or cobalamin (Cbl) highlights the importance of an MS interactome. The goal of this PhD project is to further characterize the interactions of MS with other potential partners in a so-called MS interactome. Our data confirm for the first time in human cells (HepG2 cells and fibroblasts from cblC and cblG patients) various interactions that were so far only described in vitro or in bacteria: MS with methionine synthase reductase (MSR), MS with MMACHC, and MMACHC with MMADHC. Our data also reveal novel interactions: MMADHC with MTR, MMADHC with MSR, MSR with MMACHC and MS with MAT isoforms. Moreover, our data show that the absence of MS or MMACHC disturbs the interactions involving the other members of the MS interactome. In summary, this study suggests that different steps of the intracellular processing of Cbl could occur in a large multiprotein complex composed of at least MS, MSR, MMACHC, MMADHC and MAT isoforms that would contribute to protect the rare and highly reactive Cbl from the cytoplasmic milieu

Senescent cells interact with the surrounding microenvironment achieving both pro- oncogenic and tumour-suppressive outcomes. In addition to autocrine and paracrine signalling mediated by factors of the senescence-associated secretory phenotype (SASP), we have recently identified that NOTCH1 can drive a unique form of senescence in adjacent cells via juxtacrine signalling. Here, we show that NOTCH1 signalling confers a dramatic impact on chromatin structure during senescence. RAS-induced senescent (RIS) fibroblasts often develop chromatin structures called senescence-associated heterochromatic foci (SAHF). We find that NOTCH1 inhibits SAHF formation at least partially through transcriptional repression of a critical structural component, high-mobility group A (HMGA). Using ATAC-sequencing (assay for transposase accessible chromatin) we demonstrate that nucleosome positioning is substantially altered in RIS and that this re-distribution is also antagonised by NOTCH1, resulting in a distinct chromatin landscape. Importantly, normal or cancer cells that express the NOTCH ligand jagged-1 can drive similar chromatin structural changes in adjacent cells in a cell-cell contact dependent manner. In addition, using a highly optimised chromatin immunoprecipitation (ChIP-seq) protocol and the proximity ligation assay ‘Hi-C’, we demonstrate that HMGA proteins are directly involved in the formation of long-range interactions in RIS cells that may underpin SAHF formation. These ChIP-seq data have also allowed us to identify a unique HMGA1 binding profile, potentially suggesting a novel role for HMGA1 in gene regulation. Together, our data indicate that NOTCH signalling, both cell-autonomously and non-cell-autonomously, can repress HMGA1, a multi-faceted protein that regulates nucleosome positioning (1D structure), SAHF formation (3D structure) and potentially mRNA abundance.

Src homology 3 (SH3) domains are one family of the peptide recognition modules (PRMs), which bind peptides rich in proline or positively charged residues in the target proteins, and play important assembly or regulatory functions in dynamic eukaryotic cellular processes, especially in signal transduction and endocytosis. SH3 domains are conserved from yeast to human, and improper SH3 domain mediated protein-protein interaction (PPI) leads to defects in cellular function and may even result in disease states. Since commonly used large-scale PPI mapping strategies employed full-length proteins or random protein fragments as screening probes and did not identify the particular PPIs mediated by the SH3 domains, I employed a combined experimental and computational strategy to address this problem. I used yeast two-hybrid (Y2H) as my major experimental tool, as well as individual SH3 domains as baits, to map SH3 domain mediated PPI networks, “SH3 domain interactomes”. One of my important contributions has been the improvement for Y2H technology. First, I generated a pair of Y2H host strains that improved the efficiency of high-throughput Y2H screening and validated their usage. These strains were employed in my own research and also were adopted by other researchers in their large-scale PPI network mapping projects. Second, in collaboration with Nicolas Thierry-Mieg, I developed a novel smart-pooling method, Shifted Transversal Design (STD) pooling, and validated its application in large-scale Y2H. STD pooling was proven to be superior among currently available methods for obtaining large-scale PPI maps with higher coverage, high sensitivity and high specificity. I mapped the SH3 domain interactomes for both budding yeast Saccharomyces cerevisiae and nematode worm Caenorhabditis elegans, which contain 27 and 84 SH3 domains, respectively. Comparison of these two SH3 interactomes revealed that the role of the SH3 domain is conserved at a functional but not a structural level, playing a major role in the assembly of an endocytosis network from yeast to worm. Moreover, the worm SH3 domains are additionally involved in metazoan-specific functions such as neurogenesis and vulval development. These results provide valuable insights for our understanding of two important evolutionary processes from single cellular eukaryotes to animals: the functional expansion of the SH3 domains into new cellular modules, as well as the conservation and evolution of some cellular modules at the molecular level, particularly the endocytosis module.

Protein complexes are critical to virtually every biological process performed by living organisms. The cellular “interactome”, or set of physical protein-protein interactions, is of particular interest, but no comprehensive study of human multi-protein complexes has yet been reported. In this Thesis, I describe the development of a novel high-throughput profiling method, which I term Fractionomic Profiling-Mass Spectrometry (or FP-MS), in which biochemical fractionation using non-denaturing high performance liquid chromatography (HPLC), as an alternative to affinity purification (e.g. TAP tagging) or immuno-precipitation, is coupled with tandem mass spectrometry-based protein identification for the global detection of stably-associated protein complexes in mammalian cells or tissues. Using a cell culture model system, I document proof-of-principle experiments confirming the suitability of this method for monitoring large numbers of soluble, stable protein complexes from either crude protein extracts or enriched sub-cellular compartments. Next, I document how, using orthogonal functional genomics information generated in collaboration with computational biology groups as filters, we applied FP-MS co-fractionation profiling to construct a high-quality map of 622 predicted unique soluble human protein complexes that could be biochemically enriched from HeLa and HEK293 nuclear and cytoplasmic extracts. Our network is enriched in assemblies consisting of human disease-linked proteins and contains hundreds of putative new components and novel complexes, many of which are broadly evolutionarily conserved. This study revealed unexpected biological associations, such as the GNL3, FTSJ3, and MKI67IP factors involved in 60S ribosome assembly. It is my expectation that this first systematic, experimentally-derived atlas of putative human protein complexes will constitute a starting point for more in depth, hypothesis-driven functional investigations of basic human molecular and cellular biology. I also note that my generic FP-MS screening approach can, and is currently, being applied by other members of the Emili laboratory to examine the global interactomes of other mammalian cell lines, tissues, sub-cellular compartments, and diverse model organisms, which should expand our understanding of proteome adaptations and association networks associated with cell physiology, animal development and molecular evolution.

Advances in protein topology mapping methods are urgently needed to complement the wealth of interactome data that is presently being generated at a rapid pace. Chemical crosslinking followed by mass spectrometry (MS) has evolved over the last decade as an attractive method for protein topology and interface mapping, and holds great promise as a counterpart to modern interactome studies in the field of proteomics. Furthermore, stabilization of proteins and protein complexes with crosslinking offers many advantages over high-resolution structural mapping methods, including the ability to study protein topologies in vivo. The reliance on direct detection of crosslinked peptides, however, continues to pose challenges to protein topology and interface mapping with chemical crosslinking plus MS. The present body of work aimed to develop a novel generic methodology that utilizes chemical crosslinking, cyanogen bromide (CNBr) cleavage and MS for the low-resolution mapping of protein topologies and interfaces. Through such low-resolution mapping of crosslinked regions, this novel strategy overcomes limitations associated with the direct detection of crosslinked peptides. Following optimization of various steps, the present method was validated with the bacterial DNA-directed RNA polymerase core complex and was subsequently applied to probe the tetrameric assembly of yeast Skp1p-Cdc4p heterodimers. Further improvements were made through the enrichment of crosslinked CNBr-cleaved protein fragments prior to their identification via MS. Two enrichment strategies were developed which depended upon the conjugation of tags to CNBr-cleaved peptide C-termini followed by either tandem affinity purification or tandem reversed-phase HPLC purification. These strategies were successfully applied for the efficient purification of disulfide-linked peptides from peptide mixtures. It is expected that the potential to achieve sensitive mapping of topologies and interfaces of multi-subunit protein complexes in vivo, in combination with further enhancements to permit studies on complex protein samples, will extend the utility of this method to complement large-scale interactome studies.

Src homology 3 (SH3) domains are one family of the peptide recognition modules (PRMs), which bind peptides rich in proline or positively charged residues in the target proteins, and play important assembly or regulatory functions in dynamic eukaryotic cellular processes, especially in signal transduction and endocytosis. SH3 domains are conserved from yeast to human, and improper SH3 domain mediated protein-protein interaction (PPI) leads to defects in cellular function and may even result in disease states. Since commonly used large-scale PPI mapping strategies employed full-length proteins or random protein fragments as screening probes and did not identify the particular PPIs mediated by the SH3 domains, I employed a combined experimental and computational strategy to address this problem. I used yeast two-hybrid (Y2H) as my major experimental tool, as well as individual SH3 domains as baits, to map SH3 domain mediated PPI networks, “SH3 domain interactomes”. One of my important contributions has been the improvement for Y2H technology. First, I generated a pair of Y2H host strains that improved the efficiency of high-throughput Y2H screening and validated their usage. These strains were employed in my own research and also were adopted by other researchers in their large-scale PPI network mapping projects. Second, in collaboration with Nicolas Thierry-Mieg, I developed a novel smart-pooling method, Shifted Transversal Design (STD) pooling, and validated its application in large-scale Y2H. STD pooling was proven to be superior among currently available methods for obtaining large-scale PPI maps with higher coverage, high sensitivity and high specificity. I mapped the SH3 domain interactomes for both budding yeast Saccharomyces cerevisiae and nematode worm Caenorhabditis elegans, which contain 27 and 84 SH3 domains, respectively. Comparison of these two SH3 interactomes revealed that the role of the SH3 domain is conserved at a functional but not a structural level, playing a major role in the assembly of an endocytosis network from yeast to worm. Moreover, the worm SH3 domains are additionally involved in metazoan-specific functions such as neurogenesis and vulval development. These results provide valuable insights for our understanding of two important evolutionary processes from single cellular eukaryotes to animals: the functional expansion of the SH3 domains into new cellular modules, as well as the conservation and evolution of some cellular modules at the molecular level, particularly the endocytosis module.