Project Details
Projekt
Identification and characterization of small proteins in Staphylococcus aureus
Applicants
Professorin Dr. Susanne Engelmann; Dr. Stephan Fuchs
Subject Area
Metabolism, Biochemistry and Genetics of Microorganisms
General Genetics and Functional Genome Biology
General Genetics and Functional Genome Biology
Term
from 2020 to 2024
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 453220503
Small proteins play diverse and essential roles in bacterial physiology and virulence. In Staphylococcus aureus, delta-hemolysin with only 26 amino acids (aa) and phenol-soluble modulins (20 - 40 aa) induce membrane disorders up to lysis of various human blood cells. Due to their intrinsically limited sequence information and their tendency to be species-specific, small proteins are extremely difficult to predict and experimentally detect. This explains why this group of proteins is still clearly underrepresented in current studies. In a recent study, we optimized our analytical strategies for the mass spectrometric detection of proteins with not more than 100 aa (SP100) and were able to identify 185 SP100 in S. aureus Newman. Of these 69 were not covered by the annotation used (NC_009641.1; 07/06/2013). Using Ribosome profiling, translational activity for 139 of the corresponding small reading frames (sORFs) has been successfully proven. In this project we aim at (i) an improved global detection of sORFs and their products in S. aureus using a supervised learning model and optimized mass spectrometric methods and (ii) a functional characterization of selected small proteins already identified in our previous work. For an improved empirical and evidence-based annotation of sORFs in S. aureus we will apply both machine learning (based on random forest) and experimental methods (MS-based detection of labeled N-terminal peptides). Furthermore, our proteogenomics analysis pipeline Pepper (open-source; https://gitlab.com/s.fuchs/pepper) will be further developed to process and integrate multi-omics results (MS, RNASeq, RiboSeq). A special focus will be on the proportion of small proteins in the membrane proteome. Selected SP100 candidates, whose existence has been demonstrated in our current work, will be functionally characterized by studying gene expression of (complemented) deletion mutants under different membrane stress inducing conditions.
DFG Programme
Priority Programmes
