Gianluca Prezza        email
Helmholtz Institute for RNA-based Infection Research

Supervisor:
Jun. Prof. Dr. Alexander Westermann (Würzburg)
Promotion Committee:
Jun. Prof. Dr. Alexander Westermann (Würzburg)
Prof. Dr. Chase Beisel (Würzburg)
Dr. Martin Fraunholz (Würzburg)

Identification and functional characterization of in-vivo-relevant sRNAs in Bacteroides thetaiotaomicron


Bacteroides thetaiotaomicron (B. thetaiotaomicron) is one of the dominant members of the intestinal bacterial consortium in healthy human beings. As an obligate anaerobe, this Gram-negative bacterium resides in the large bowel, where it can contribute the lion's share of the total bacterial biomass. B. thetaiotaomicron serves its host with multiple functions, ranging from the degradation of complex carbohydrates that cannot be catabolized solely by the arsenal of host enzymes, to the maturation of its host's immune system early during development, and, by occupying niches otherwise vacant for pathogenic bacteria, B. thetaiotaomicron provides colonization resistance against enteric infections. The combination of its biological/medical significance, the relative ease of cultivating it under laboratory conditions, and the fact that many strains are genetically tractable, render B. thetaiotaomicron the model organism for microbiota research. Noteworthy, however, while the Bacteroides' proteome and metabolome are subjects of intense research in numerous laboratories around the globe, little is known about the RNA biology of this important microbiota member.

The goal of my project is to identify B. thetaiotaomicron sRNAs that contribute to the interaction of this commensal with human host cells, and to reveal their mechanisms of action. To do this, I will first employ high-throughput approaches (a CRISPRi screen and dual RNA-seq) to identify sRNA candidates that are required for and/or are differentially expressed upon colonization of a 3D host model. I will then follow up promising candidates to identify their target mRNAs and ultimately their role in host colonization. Finally, I will identify RNA-binding proteins that are required for sRNA-target mRNA interactions in B. thetaiotaomicron.

This project will result in the first global picture of the colonization-relevant sRNAs of a member of the human microbiota and will therefore allow for a better understanding of the molecular mechanisms that underlie host-microbiota interactions.