PhD project

Supervisor: Ivan Ahel

Poly(ADP-ribose) polymerases (PARPs) are the major family of enzymes that synthesize an abundant posttranslational protein modification called ADP-ribosylation. Through their ability to modify different target proteins and to respond to variety of stimuli, PARPs control genome stability, cell differentiation, metabolism and immune responses. Inherited defects in the protein components of the pathways regulated by PARPs often cause disease in humans such as cancer, immunodeficiencies, neurodegeneration and developmental syndromes. In recent years it has become apparent that using specific drugs to inhibit or modulate protein ADP-ribosylation can be very effective in disease treatment (for example breast, ovarian, pancreatic and prostate cancer). Thus, furthering our knowledge of the protein factors and pathways regulated by PARPs provides a basis for the development of new therapies.

PARP1 is the most active PARP enzyme in human cells and it is critical for the regulation of nuclear processes such as DNA damage repair, transcription, maintenance of chromatin structure, replication and mitosis. In our laboratory we recently identified a previously uncharacterised protein as an interactor of PARP1. We have called this chromatin factor HPF1 (for histone PARylation factor 1) and showed that HPF1 allows PARP1 to specifically ADP-ribosylate serine residues in histones and many other proteins important for the maintenance of genome stability. Additionally, we uncovered that ARH3 enzyme act as a specific hydrolase that reverses serine ADP-ribosylation in cells. The aim of the PhD project will be to elucidate the exact molecular and physiological functions of HPF1, ARH3 and their target proteins in regulation of genome stability, which will also cover the newly identified interplay between ADP-ribosylation and ubiquitylation signalling. Our laboratory uses a large variety of techniques that will enable us to efficiently study the relevant processes on different levels (protein biochemistry, cell biology and Drosophila melanogaster genetic model, bioinformatics and structural biology), and it will possible to tailor the experimental approach according to the student’s experience and preferences.

Keywords:

• PARP, ubiquitylation, DNA damage repair, chromatin, PARP, Biochemistry, Cancer / Oncology, Cell Biology / Development, Genetics, Molecular Biology, Structural Biology

Publications:

• Suskiewicz, M.J., Zobel, F., Ogden, T.E., Fontana, P., Ariza, A., Yang, J., Zhu, K., Bracken, L., Hawthorne, W.J., Ahel, D., Neuhaus, D., and Ahel, I. (2020) HPF1 completes the PARP active site for DNA-damage induced ADP-ribosylation. Nature 579, 598-602.
• Prokhorova, E., Zobel, F., Smith, R., Zentout, S., Gibbs-Seymour, I., Schützenhofer, K., Peters, A., Groslambert, J., Zorzini, V., Agnew, T., Brognard, J., Nielsen, M.L., Ahel, D., Huet, S., Suskiewicz, M.J., and  Ahel, I. (2021) Serine-linked PARP1 auto-modification controls PARP inhibitor response. Nature Commun 12, 4055.
• Zhu, K., Suskiewicz, M.J., Hloušek-Kasun, A., Meudal, H., Mikoč, A., Aucagne, A., Ahel, D., and Ahel, I. (2022) DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on protein substrates. Science Advances 8, eadd4253.
• Bilokapic, S., Suskiewicz, M.J., Ahel, I., and Halic, M. (2020) Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin. Nature 585, 609-613.
• Fontana, P., Bonfiglio, J.J., Palazzo, .L, Bartlett, E., Matic, I., and Ahel, I. (2017) Serine ADP-ribosylation reversal by the hydrolase ARH3. Elife 6. pii: e28533.
• Fontana, P., Buch-Larsen, S.C., Suyari, O., Smith, R., Suskiewicz, M.J., Schützenhofer, K., Ariza, A., Rack, J.G.M., Nielsen, M.L., and Ahel, I. (2023) Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling. Nat Commun 14, 3200.