Le chromosome circulaire de la bactérie Escherichia coli est composé de quatre macrodomaines et deux régions non structurées. Cette organisation influence la ségrégation des chromatides sœurs et la mobilité de l’ADN chromosomique. La structuration de la région terminus (Ter) en macrodomaine est lié à l’interaction de la protéine MatP avec la séquence cible de 13 pb (sic) appelée matS répétée 23 fois dans ce domaine de 800 kb. Le travail réalisé durant ma thèse a permis l’identification et la caractérisation d’un système site-spécifique qui restreint à la région Ter un effet associé à la protéine MatP qui contraint la mobilité de l’ADN et retarde la ségrégation de loci après réplication. Deux séquences spécifiques de 12 pb localisées dans les macrodomaines Right et Left sont requises et suffisantes pour arrêter la propagation du processus de contrainte sur le reste du chromosome. Les changements de propriétés de l’ADN ne sont pas dus à la présence d’un procédé agissant en trans mais probablement à un effet agissant en cis à longue distance et partant des sites matS. De manière remarquable, ces changements de propriétés sont régulés au cours du cycle cellulaire et ne sont présents seulement quand le macrodomaine Ter est associé à la machinerie de division au centre de la cellule. L’insulation de la région Ter requière une protéine nouvellement identifiée comme encrée à la membrane que nous avons nommé TidP et qui a été conservé avec la protéine MatP au cours de l’évolution. Nos résultats indiquent que deux systèmes d’organisation spécifiques sont requis pour l’organisation du macrodomaine Ter au cours du cycle cellulaire. Un second aspect de mon travail a été la caractérisation des mécanismes de contraintes affectant les macrodomaines Right et Left. Nous avons montré, en étudiant le comportement de grands cercles d’ADN excisés, que les propriétés de ces macrodomaines sont conservées dans un contexte extra-chromosomique. Ces résultats suggèrent l’implication d’éléments associés à la molécule d’ADN dans ces macrodomaines et responsable de leur organisation. / The organization of the Escherichia coli chromosome into a ring composed of four macrodomains and two less-structured region influences the segregation of sister chromatids and the mobility of chromosomal DNA. The structuring of the terminus region (Ter) into a macrodomain relies on the interaction of the protein MatP with a 13 bp target called matS repeated 23 times in the 800-kb long domain. The work performed during my Ph. D. allowed the identification and characterization of a site-specific system that restricts to the Ter region an effect associated to MatP that constrains DNA mobility and delays loci segregation. Two specific 12 bp sequences located in the flanking Left and Right macrodomains are required and sufficient to impede the spreading of the constraining process to the rest of the chromosome. The change of DNA properties does not rely on the presence of a trans-acting process but rather involves a cis-effect acting at a long distance from matS sites. Remarkably, the constraining process is regulated during the cell cycle and occurs only when the Ter MD is associated with the division machinery at mid-cell. Insulation of the Ter region requires a newly identified membrane-anchored protein designated TidP conserved with MatP through evolution. Our results indicate that 2 specific organizational systems are required for the management of the Ter region during the cell cycle. A second aspect of my work, consisted in the characterization of constraining mechanisms affecting the Right and Left macrodomains. I have shown, using excisions of large chromosomal rings, that their macrodomain properties were conserved in an extrachromosomal context, suggesting that a chromatin like structuring was involved in their organization.

<p dir="ltr">Ubiquitination and ADP-ribosylation are reversible post-translational modifications involved in various cellular activities. Pathogens like <i>Legionella pneumophila</i> and <i>Chromobacterium violaceum</i> target host ubiquitin system via modifications involving ADP-ribosylation. Specifically, <i>Legionella pneumophila</i> mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. On the other hand, <i>Chromobacterium violaceum</i> effector CteC ADP-ribosylates threonine 66 of ubiquitin and causes overall blocking of host ubiquitin signaling. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. In the current study, a proteome-wide screening of ubiquitin interactors in the <i>Legionella</i> secreted proteome was performed, which led to the <i>Legionella</i> macrodomain effector MavL as a regulator of the SidE-mediated ubiquitination pathway by reversing the ubiquitin arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by modified ubiquitin. Crystal structure of ADP-ribose-bound MavL was determined, providing structural insights into substrate recognition and catalytic mechanism. Further bioinformatical analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes uniquely selective for mono-ADP-ribosylated arginine residue. The arginine-specific macrodomains are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in <i>Drosophila melanogaster</i>. Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. The crystal structure of NAD⁺-bound CteC was also determined, which provided insights into its ADP-ribosylation activity and its ubiquitin specificity. Collectively, the studies described here provide biochemical and structural characterizations and mechanistic insights into bacterial effectors associated with ubiquitin ADP-ribosylation.</p>

Gene expression pathways exhibit many “twists and turns,” with theoretically numerous ways in which the pathways can be regulated by both negative and positive feedback mechanisms. A key step in gene expression is RNA maturation (RNA processing), which in the bacterial cell can be accomplished through RNA binding and enzymatic cleavages. The well-characterized bacterial protein Ribonuclease III (RNase III), is a conserved, double-stranded(ds)-specific ribonuclease. In the gram-negative bacterium Escherichia coli, RNase III catalytic activity is subject to both positive and negative regulation. A recent study has indicated that an E. coli protein, YmdB, may negatively regulate RNase III catalytic activity. It has been proposed that YmdB inhibition of RNase III may be part of an adaptive, post-transcriptional physiological response to cellular stress. In E. coli, the model organism in this study, YmdB protein is encoded by the single ymdB gene, and has a predicted molecular mass of ~18.8 kDa. YmdB has been classified as a macrodomain protein, as it exhibits a characteristic fold that specifically provides an ADP-ribose (ADPR) binding site. While YmdB can bind ADPR with good affinity, there may be additional ligands for the binding site. Thus, YmdB protein may interact with other components in the cell, which in turn could modulate the interaction of YmdB with RNase III. In previous research conducted within the Nicholson laboratory at Temple University, affinity-purified Escherchia coli(Ec) YmdB and Aquifex aeolicus (Aa) YmdB were found to exhibit ribonucleolytic activity. This observation initiated the long-term goal of learning how YmdB regulates RNase III, and how the ribonucleolytic activity of YmdB may be involved in this process. The specific goal of this thesis project was to further characterize the ribonucleolytic activity of Ec-YmdB through site-specific mutational analysis. Mutations were introduced into a proposed adenine-binding pocket previously identified by crystallography and by molecular modeling. The adenine-binding pocket is a region within the macrodomain fold where ADP-ribose could bind. The mutations were examined for their effect on Ec-YmdB cleavage of a model RNA, R1.1. The results of this study will contribute to the development of a model describing how the ribonucleolytic activity of YmdB is regulated. / Biology