Philip TATHAM – 17/12/2025

PhD defense :

Mechanistic diversity and catalytic innovations in radical SAM enzymes : Discovery and characterization of two novel reactions

For more than two decades, the superfamily of S-adenosyl-L-methionine radical (radical SAM) enzymes has continued to astonish by the breadth and sophistication of the transformations it catalyzes. Ubiquitous across all domains of life, these enzymes harness radical chemistry to remodel, functionalize, or assemble a wide variety of biomolecules, including secondary metabolites, nucleic acids, proteins, and ribosomally derived peptides. Despite twenty years of intensive research, their architectural diversity and mechanistic versatility remain largely unexplored

In this context, we investigated two singular representatives that embody complementary facets of radical biochemistry. The first enzyme is characterized by a bimodular organization associating two distinct functional domains. This unprecedented architecture enables the combination of two paradoxical successive radical reactions, ultimately installing original post-translational modifications on a RiPP peptide.

By integrating spectroscopy, structural biology, and biochemical approaches, we sought to capture and characterize reaction intermediates, thereby providing a comprehensive view of the enzyme’s mechanism. These studies shed new light on the role of oxygen in radical SAM catalysis and revealed an unsuspected reactivity.
 
The second enzyme investigated in this work, PylB, is involved in the biosynthesis of the twenty-second proteogenic amino acid, pyrrolysine. We demonstrated that, despite its minimalist architecture, this enzyme catalyzes an unprecedented intramolecular rearrangement of lysine, relying on an original mechanism of radical economy: the 5′-deoxyadenosyl radical generated at the onset of the reaction is recycled throughout catalysis. Unexpectedly, we further showed that this enzyme can reutilize its product as a substrate, thereby conferring complete reversibility to the reaction, as demonstrated by isotopic labeling experiments and spectroscopic analyses.
 
Beyond their biochemical, structural, and spectroscopic characterization, the study of these two enzymatic systems provides new insights into the functional and catalytic evolution of radical SAM enzymes. It highlights the remarkable richness of this emerging superfamily of biocatalysts and opens unprecedented avenues for exploring their extraordinary diversity.

Jury members:

  • Nicolas ROUHIER, Professor, University of Lorraine – Reviewer & Examiner
  • Pierre CROZET, Associate professor (HDR), Sorbonne University – Reviewer & Examiner
  • Alessandra CARBONE, Professor, Sorbonne University – Examiner
  • Benoît D’AUTRÉAUX, Research Director, INSERM (University Paris-Saclay) – Examiner
  • Frédéric AVENIER, Professor, University Paris-Saclay – Examiner
  • Sylvie LAUTRU, Research Director, CNRS (University Paris-Saclay) – Examiner

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