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Obe, D.

Publications and source records attributed to Obe, D..

2 recordsLinked to original sources

Comparative genomic insights into the action of suicide Thi4 thiazole synthases

Suicide thiazole synthases (Thi4) are mononuclear metal enzymes that form the thiazole moiety of thiamin from NAD+, glycine, and a sulfur atom that is stripped from an active-site cysteine residue, causing enzyme inactivation. Comparative genomic analysis indicates that prokaryotic Thi4 genes often cluster on the chromosomal regions encoding ThiS, ThiF, and other proteins that can produce, relay, or use persulfide or thiocarboxylate sulfur. This genomic evidence suggests that certain suicide Thi4s might use a persulfide or thiocarboxylate as sulfur donor instead of the active-site cysteine - i.e., that they can operate in a non-suicide mode - and that a metal cofactor reservoir supports Thi4 function. To explore these possibilities, we performed proof-of-concept experiments using Escherichia coli as a heterologous platform. A representative bacterial Thi4 that clustered with thiS and thiF complemented an E. coli {Delta}thiG (thiazole auxotroph) single mutant better than a {Delta}thiG {Delta}thiF {Delta}thiS triple mutant, consistent with predicted interactions with the host sulfide transfer chain. Collectively, this evidence indicates that suicide Thi4s may not necessarily operate suicidally and highlights genomic and structural clues that warrant deeper biochemical investigation.

biochemistry↗

Harnessing Mass Spectrometry-Based Proteomics for Continuous Directed Evolution

Continuous directed evolution is a powerful Synthetic Biology tool to engineer proteins with desired functions in vivo. Mimicking natural evolution, it involves repeated cycles of high-frequency mutagenesis, selection, and replication within platform cells, where the function of the target gene is tightly linked to the host cells fitness. However, cells might escape the selection pressure due to the inherent flexibility of their metabolism, which allows for adaptation. Whole-proteome analysis as well as targeted proteomics offer valuable insights into global and specific cellular changes. They can identify modifications in the target protein and its interactors to help understand its evolution and network integration. Using the continuous evolution of the Arabidopsis methionine synthases AtMS1 and AtMS2 as an example, we demonstrate how mass spectrometry-based proteomics can be applied in CDE, propose specific checkpoints for its integration and illustrate its role in informed decision making.

synthetic biology↗