Petra Van Damme - PROPHECY

Petra Van Damme

Description of the PI

Petra Van Damme was born in Ghent, Belgium, in 1978. She received a degree in Biochemistry from Ghent University, Belgium, in 2001 and a PhD from the same university in 2008, at the Department of Biomolecular Medicine, where she is currently a full-time research professor.
Her original research focused on the development of a repertoire of proteome-analytical methods for the identification and characterization of proteins by the isolation of proteome-representative peptides, including amino- and carboxy-terminal peptides. Since the isolation of N-termini inherently led to the discovery and further analysis of protein N-termini and their specific modifications, her research focus later diverged from the study of proteolysis to the study of protein N-terminal protein modifications (e.g. protein N-terminal acetylation) and the application of proteogenomics strategies (including ribosome profiling) to map translation initiation landscapes in bacteria and eukaryotes. Her recent discoveries relate to the existence of N-terminal proteoforms (i.e. N-terminal protein variants raised upon alternative translation initiation) and improving the annotation of genomes. Here, combining state of the art proteomics technologies with ribosome profiling, an unprecedented view of actively translated regions of several genomes was gained that, to this point, remained relatively unexplored due to limitations of currently employed strategies. Currently she is holder of an ERC starting grant (PROPHECY), to conduct research in the field of bacterial infection biology. She has published over 80 journal papers.

Description of the project

My group will aim at bettering our understanding of bacterial infection biology. While deep sequencing has enabled the study of gene expression at the transcript level in both bacterial pathogen and host simultaneously, the depth of sequencing has so far proven to be unsatisfactory in case of the bacterial pathogen. Moreover, the study of bacterial proteome changes upon infection remains highly unexplored because of the higher proteome complexity of the host cell compared to the pathogen. These challenges clearly stress the need for novel strategies based on complementary proteogenomics approaches enabling translation control studies in bacterial pathogens in a host context.
Since my recent findings revealed translation of numerous previously unidentified (small) open reading frames and expression of alternative N-terminal proteoforms when studying bacterial translation, my group will explore the repertoire of bacterial proteoforms employed to establish a successful interaction with its host cell. For this, we will develop and apply a complementary cutting-edge riboproteogenomic toolset which will enable, for the first time, targeted systematic genome- and proteome-wide surveys of bacterial transcriptional and translational activity during actual host cell infection. By exploiting this proteogenomics toolset in combination with molecular biology, genetics, cell biological and cell physiological approaches, we strive to obtain answers to intriguing fundamental questions of host/pathogen interactions. Overall, the identification of new pathogen virulence factors will contribute to the development of innovative therapeutics and diagnostics for multiple models of infectious diseases.