Proteogenomic-assisted exploration of the molecular mechanisms underlying Salmonella infection

In recent years, high-throughput techniques such as next-generation sequencing allowed us to study complex biological processes at a comprehensive, genome-wide scale. Such techniques became a
platform for the development of novel, more specialized tools. A
paragon example of this is the ribosome profiling technique that
enabled the global measurement of protein synthesis, translation, by
sequencing of ribosome-protected messenger RNA fragments. The
advent of such technologies allowed us to shed light on the highly
underappreciated complexity of genomes.
In this project, we build upon the newly gained knowledge on
genome structures and further explore the translatome of Salmonella
to answer the most principal mechanistic questions about the
bacterial infection process. For this, we will combine state-of-the-art
proteomics and genomic technologies to obtain a comprehensive
view of Salmonella as well as host response mechanisms upon host
cell infection. With newly developed, ribosome profiling-based
strategies we will further explore the previously understudied diversity
of the bacterial genome thereby highlighting unknown translation
products implicated in the infection process. By providing a truly
functional annotation of the Salmonella genome, we set off to deepen
our understanding of the infection process, highlight (new) effectors
and virulence factors overall providing a solid foundation for the
development of novel diagnostic tools and antimicrobial treatments.