The role of Staphylococcus aureus RNA-binding proteins in regulating host adaptive responses

Supervisors: Sander Granneman, Ross Fitzgerald

Project Description:

Methicillin-resistant S. aureus (MRSA) is causing major health-care problems world-wide and is becoming increasingly difficult to treat with current antibiotics. S. aureus is one of the most successful human and livestock pathogens and a common cause of skin infections and respiratory diseases that can be life threatening. This emphasizes the importance of developing alternative therapeutic approaches to combat infections. S. aureus is such an effective pathogen because it can very rapidly adapt to environmental insults, such as alteration in host temperature and attack by the immune system. This enables it not only to survive in hostile conditions, but also to persist within the host. To achieve such rapid adaptation, S. aureus remodels its transcriptome within minutes of stress imposition. Transcription factors were thought to be mainly responsible for directing this process, however, post-transcriptional regulators, such as RNA-binding proteins (RBPs), are now recognized as key players in controlling adaptive responses by modulating mRNA translation and/or degradation rates. Although several RBPs have been discovered in S. aureus and shown to be important for pathogenicity, the majority have unknown functions. This underscores the need for a thorough characterization of these molecules.

The project:
Although RBPs are believed to play a fundamental role in regulating gene expression during host adaptive responses, it remains unclear which RBPs are the key players in this process and how they control rapid gene expression remodelling. Using novel proteomic approaches, we have uncovered a large number of novel S. aureus RBPs, including several metabolic enzymes. Our current working model is that S. aureus metabolic RBPs function as novel post-transcriptional regulators that directly couple expression of virulence genes to changes in nutrient availability. To test this hypothesis, the student will functionally characterize several novel metabolic RBPs with an emphasis on understanding their role in survival in a nutrient deprived host environment, such as the blood stream. The project will utilize a number of highly multidisciplinary approaches: In Ross Fitzgerald’s group, the student will become adept in molecular Microbiology by applying a broad spectrum of phenotypical assays as well as learning about infection models to assess the role of these RBPs in bacterial pathogenicity (1). In Dr. Granneman’s group the student will learn state-of-the-art biochemical approaches for identifying novel RBPs and their RNA targets (2,3). The student will also receive training in bioinformatics to mine the massive next generation sequencing and mass-spectrometry datasets.

Our vision is that a detailed characterization of S. aureus RBPs involved in post-transcriptional regulatory systems may uncover new avenues for improving treatment of infections and/or reveal new targets for antimicrobial drug development.

1)    Wilson, G. J. et al. A novel core genome-encoded superantigen contributes to lethality of community-associated MRSA necrotizing pneumonia. PLoS Pathog 7, e1002271 (2011).
2)    van Nues, R. et al. Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress. Nat Commun 8, 12 (2017).
3)    Urdaneta, E. et al. Purification of Cross-linked RNA-protein Complexes by Phenol-Toluol Extraction. bioRxiv. DOI:

If you wish to apply for this project, please go to this link.