Charpentier Research Projects

Regulatory small RNAs and RNases

In addition to CRISPR-associated RNAs, bacteria encode several other small RNAs (sRNAs) that play critical regulatory roles in important biological pathways. We have identified a number of putative cis-acting sRNAs (e.g., riboswitches) and trans-acting sRNAs in the human pathogen Streptococcus pyogenes. We address the question of how selected sRNAs integrate into the general regulatory network controlling pathogenesis and related mechanisms in this pathogen. We aim to understand the regulation of sRNA expression by ribonucleases, analyze the biological functions of sRNAs, identify their interaction partners, and determine their modes of action at the molecular and cellular levels.

CRISPR-Cas Adaptive Immunity

To protect themselves from the attack by invading alien genomes (in particular phages and plasmids), bacteria and archaea have evolved an RNA-guided adaptive immune system, called CRISPR-Cas (clustered, regularly interspaced short palindromic repeats–CRISPR-associated proteins). The system uses ribonucleoprotein complexes composed of short CRISPR RNAs (crRNAs) and Cas protein(s) to silence invading nucleic acid sequences in a sequence-specific manner. We are interested in deciphering the molecular mechanisms involved in the adaptation, expression and interference phases of the bacterial immune system. We are also focusing on the molecular details of the recently discovered tracrRNA:crRNA-Cas9 genome editing mechanism/technology as well as of recently identified CRISPR-Cas systems.

Toxin-Antitoxin Systems

Toxin-antitoxin (TA) systems consist of a stable toxin that causes growth arrest or cell death by inhibiting essential cellular processes and a labile antitoxin, which counteracts the toxin. Initially, TA systems were described as a stabilization element of plasmids, but these two gene modules are also ubiquitous in prokaryotic genomes. When encoded on the genome, they often function as a regulatory switch that converts bacteria into persisters, a dormant state that is associated with increased antibiotic tolerance. We have recently identified several putative TA loci in the Gram-positive human pathogen Streptococcus pyogenes in a bioinformatics search. We aim to characterize these loci, elucidate the molecular mechanisms of these TA systems, and unravel their biological roles, including the triggers for activation of the toxins and their significance for persister cell formation.

Bacterial and Vesicular Interactions with Host Innate Immunity

Bacteria must sense and respond to their environment in order to adapt to the ever-changing environment. We are interested in one mechanism allowing bacteria to respond to host immune-mediated stress conditions via export of defined protein, lipid and nucleic acid laden extracellular membrane-derived vesicles (MVs). MVs act in multiple ways to exert a decisive impact on host-pathogen interactions during infection by pathogenic bacteria. We employ an array of molecular and cellular techniques to understand the formation of MVs and their roles during infection and immunity to fully comprehend the impact of MVs on bacterial virulence and the host immune response and to possibly harness the identified mechanisms into potentially novel anti-infective principles.

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