The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of <i>proVWX</i> in <i>E. coli</i>

Nucleoid associated proteins (NAPs) maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-organisation. While this model is supported by in vitro studies, direct in vivo evidence is lacking. Here, we use RT-qPCR and 3C-qPCR to study the transcriptional and architectural profiles of the H-NS (histone-like nucleoid structuring protein)-regulated, osmoresponsive proVWX operon of Escherichia coli at different osmolarities and provide in vivo evidence for transcription regulation by NAP-mediated chromosome re-modelling in bacteria. By consolidating our in vivo investigations with earlier in vitro and in silico studies that provide mechanistic details of how H-NS re-models DNA in response to osmolarity, we report that activation of proVWX in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges upon adaptation to hyperosmolarity represses the operon. Our results also reveal additional structural features associated with changes in proVWX transcript levels such as the decompaction of local chromatin upstream of the operon, highlighting that further complexity underlies the regulation of this model operon. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that chromosome re-modelling may be a typical feature of transcriptional control in bacteria

Lsr2 is an important determinant of intracellular growth and virulence in Mycobacterium abscessus

Mycobacterium abscessus, a pathogen responsible for severe lung infections in cystic fibrosis patients, exhibits either smooth (S) or rough (R) morphotypes. The S-to-R transition correlates with inhibition of the synthesis and/or transport of glycopeptidolipids (GPLs) and is associated with an increase of pathogenicity in animal and human hosts. Lsr2 is a small nucleoid-associated protein highly conserved in mycobacteria, including M. abscessus, and is a functional homologue of the heat-stable nucleoid-structuring protein (H-NS). It is essential in Mycobacterium tuberculosis but not in the non-pathogenic model organism Mycobacterium smegmatis. It acts as a master transcriptional regulator of multiple genes involved in virulence and immunogenicity through binding to AT-rich genomic regions. Previous transcriptomic studies, confirmed here by quantitative PCR, showed increased expression of lsr2 (MAB_0545) in R morphotypes when compared to their S counterparts, suggesting a possible role of this protein in the virulence of the R form. This was addressed by generating lsr2 knock-out mutants in both S (Δlsr2-S) and R (Δlsr2-R) variants, demonstrating that this gene is dispensable for M. abscessus growth. We show that the wild-type S variant, Δlsr2-S and Δlsr2-R strains were more sensitive to H2O2 as compared to the wild-type R variant of M. abscessus. Importantly, virulence of the Lsr2 mutants was considerably diminished in cellular models (macrophage and amoeba) as well as in infected animals (mouse and zebrafish). Collectively, these results emphasize the importance of Lsr2 in M. abscessus virulence

GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae

Motivation Multi-scale modeling of biological systems requires integration of various information about genes and proteins that are connected together in networks. Spatial, temporal and functional information is available; however, it is still a challenge to retrieve and explore this knowledge in an integrated, quick and user-friendly manner. Results We present GEMMER (GEnome-wide tool for Multi-scale Modeling data Extraction and Representation), a web-based data-integration tool that facilitates high quality visualization of physical, regulatory and genetic interactions between proteins/genes in Saccharomyces cerevisiae. GEMMER creates network visualizations that integrate information on function, temporal expression, localization and abundance from various existing databases. GEMMER supports modeling efforts by effortlessly gathering this information and providing convenient export options for images and their underlying data. Availability and implementation GEMMER is freely available at http://gemmer.barberislab.com. Source code, written in Python, JavaScript library D3js, PHP and JSON, is freely available at https://github.com/barberislab/GEMMER.</p

Épigénétique de la spondyloarthrite

International audienceLa spondyloarthrite (SpA) est un rhumatisme inflammatoire chronique d’étiologie inconnue dont la survenue résulte de l’interaction de facteurs de prédisposition environnementaux et génétiques. Malgré des avancées récentes, une large fraction de la prédisposition génétique à la SpA demeure inexpliquée. Plusieurs mécanismes ont été proposés pour expliquer cette part d’héritabilité manquante, tels que l’épigénétique, qui peut jouer un rôle à l’interface entre facteurs génétiques et environnementaux de susceptibilité. L’épigénétique se réfère aux variations de l’expression génique qui n’impliquent aucun changement de la séquence d’ADN. Les mécanismes épigénétiques comprennent principalement la méthylation de l’ADN, les modifications des histones et les ARN non codants. La perturbation de l’un de ces systèmes peut conduire à une altération de l’expression génique susceptible de favoriser le développement de la maladie. Grâce aux récents progrès technologiques, on observe un intérêt croissant pour le domaine de l’épigénétique dans le contexte des maladies complexes comme la SpA. Cependant, les études épigénétiques sont confrontées à des obstacles méthodologiques qui limitent l’interprétation de leurs résultats : petite taille des échantillons, absence de confirmation des résultats, choix inapproprié des témoins, choix inadéquat du type cellulaire/tissulaire. Dans le futur, l’association de l’épigénétique aux autres données « -omiques » permettra de mieux comprendre la pathogénie de la SpA. Ces problématiques doivent être résolues avant d’envisager l’utilisation des marques épigénétiques en routine clinique, en tant que biomarqueurs ou cibles médicamenteuses