Chemical Tagging of Protein Lipoylation

Expanding the Scope of Genetically Encoded Lysine PTMs with Lactylation, β-Hydroxybutyrylation and Lipoylation

Post-translational modifications (PTMs) occurring on lysine residues, especially diverse forms of acylations, have seen rapid growth over the past two decades. Among them, lactylation and β-hydroxybutyrylation of lysine side-chains are newly identified histone marks and their implications in physiology and diseases have aroused broad research interest. Meanwhile, lysine lipoylation is highly conserved in diverse organisms and well known for the pivotal role in central metabolic pathways, and recent findings in the proteomic profiling of protein lipoylation have nonetheless suggested a pressing need for an extensive investigation. For both basic and applied research, it is highly necessary to prepare PTM-bearing proteins particularly in a site-specific manner. Herein, we use genetic code expansion to site-specifically generate these lysine PTMs, including lactylation, β-hydroxybutyrylation and lipoylation in proteins in E. coli and mammalian cells. Notably using strategies including activity-based selection, screening and rational design, unique pyrrolysyl-tRNA synthetase variants were successfully evolved for each of the three non-canonical amino acids and enable efficient production of recombinant proteins, thus holding promise to benefit relevant studies. Through encoding these ncAAs, we examined the deacylase activities of mammalian sirtuins to these modifications, and importantly unfold lipoamidase activity of several sirtuins.

Functionalised Cofactor Mimics for Interactome Discovery and Beyond

Cofactors are required for almost half of all enzyme reactions, but their functions and binding partners are not fully understood even after decades of research. Functionalised cofactor mimics that bind in place of the unmodified cofactor can provide answers, as well as expand the scope of cofactor activity. Through chemical proteomics approaches such as activity-based protein profiling, the interactome and localisation of the native cofactor in its physiological environment can be deciphered and previously uncharacterised proteins annotated. Furthermore, cofactors that supply functional groups to substrate biomolecules can be hijacked by mimics to site-specifically label targets and unravel the complex biology of post-translational protein modification. The diverse activity of cofactors has inspired the design of mimics for use as inhibitors, antibiotic therapeutics, and chemo- and biosensors, and cofactor conjugates have enabled the generation of novel enzymes and artificial DNAzymes.