A greater understanding of the fundamental mechanisms of regulation in pathogens is critical to generate new findings in basic science and possibly translate them into novel biotechnological and biomedical applications (e.g. genome editing tools, anti-infective strategies). A successful example of the application of our basic research in biotechnology and medicine is our recent discovery of an RNA-guided DNA cleavage mechanism that has been harnessed as an RNA programmable genome engineering technology and that stems from our analysis of the adaptive immune CRISPR-Cas9 system in bacterial pathogens.
Our laboratory investigates fundamental mechanisms of regulation in processes of infection and immunity with a focus on Gram-positive bacterial pathogens. We are interested in understanding how RNAs and proteins coordinate to modulate gene expression at the transcriptional, post-transcriptional and post-translational level. We study regulatory RNAs and proteins in various biological pathways such as horizontal gene transfer, adaptation to stress, physiology, persistence, virulence, infection and immunity. In particular, we do research on interference systems in the defense against genetic elements (CRISPR-Cas), small regulatory RNAs that interfere with pathogenic processes, protein quality control that regulates bacterial adaptation, physiology and virulence, and the mechanisms of bacterial recognition by immune cells.
We employ a combination of -omics, genetic, molecular, biochemical, physiological and cell infection approaches to identify new molecules and decipher their origins, functions and modes of action at the molecular and cellular level. A pathogen mostly studied in the laboratory is Streptococcus pyogenes also called Group A streptococcus that can cause highly aggressive invasive infections such as toxic shock and necrotizing diseases. In the past years, we have also investigated the genetics and biology of Listeria monocytogenes, Staphylococcus aureus and Streptococcus pneumoniae.
CRISPR-Cas: RNA-mediated interference in immunity
To protect themselves from 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 and understanding the molecular details of the recently discovered Cas9-tracrRNA:crRNA genome editing tool as well as novel systems.
Regulatory small RNAs
In addition to the CRISPR-associated RNAs, bacteria encode multiple other small RNAs (sRNAs) that play critical regulatory functions in major 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 are addressing the question of how selected sRNAs integrate into the general regulatory network controlling pathogenesis and related mechanisms in this pathogen. We want to understand the regulation of sRNA expression by ribonucleases, analyze the biological functions of sRNAs, identify their interacting partners and determine their modes of action at the molecular and cellular level.
Regulatory protein quality control
During infection, bacterial pathogens face a wide variety of adverse and fluctuating conditions within the human host and have evolved multiple strategies to mount appropriate responses. In bacteria, Clp (Caseinolytic proteins)/HSP100 (heat-shock proteins) proteins are important components of the bacterial stress response, influencing adaptation, survival or virulence. We have identified substrates of the Clp proteolytic machinery in human Gram-positive pathogenic bacteria. We are now investigating the mechanisms of substrate targeting and degradation on a molecular, cellular and physiological level. In this context, we are also interested in understanding the regulation of the Clp response by phosphorylation.
Regulation by RNAs and proteins in innate immunity
Initial recognition of pathogens by the innate immune system constitutes the key step in defence against infectious microorganisms. Inappropriate recognition may result in insufficient immune responses, but an over-activation of the immune system may be equally deleterious. Innate immune cells respond to Streptococcus pyogenes infection by producing pro-inflammatory cytokines through the involvement of the adaptor molecule MyD88 or STING/TBK1 depending on the nature of the pathogen-associated molecular pattern (PAMP) recognized (DNA or RNA). We are interested in investigating RNA- and protein-mediated mechanisms involved in the response of immune cells to S. pyogenes infection.