Designed enzyme rescues live bacteria

It’s hard to get proteins designed from scratch, called de novo proteins, to catalyze reactions nearly as efficiently as native enzymes do. Although de novo-designed proteins have shown off their catalytic prowess in lab glassware, getting them to catalyze reactions at levels that can affect the biology of living organisms hasn’t been easy.

Michael H. Hecht and coworkers at Princeton University have done so by designing a de novo protein that sustains living bacteria genetically modified to require its catalytic activity (Nat. Chem. Biol. 2018, DOI: 10.1038/nchembio.2550). The work could lead to other de novo enzymes that perform useful biological roles in cells.

F. Akif Tezcan’s group at the University of California, San Diego, previously mutated a natural redox protein to perform β-lactamase activity in bacteria. And Hecht’s group showed earlier that a de novo protein could sustain living bacteria lacking an essential gene, but most likely worked by nonenzymatic means. The new study shows that de novo proteins can perform essential catalytic roles in cells.

Hecht’s group started with a de novo four-helix protein called Syn-IF. When expressed in Escherichia coli mutated to remove ferric enterobactin esterase, Syn-IF allowed the microbes to survive under low-iron conditions. The natural esterase’s activity also helps bacteria thrive in low-iron environments. But Syn-IF showed no detectable enzymatic activity. The researchers next mutated it and screened for mutants that could sustain low-iron bacteria better than Syn-IF did. The result was Syn-F4, which catalyzed the same reaction as the natural esterase.

The new study “is significant and exciting,” says Ivan V. Korendovych of Syracuse University, not only because Syn-F4 works in bacteria but also because it has a simple four-helix structure, raising the possibility of designing comparably simple proteins that catalyze other reactions in live organisms.

Syn-F4 “not only replaced the function of a naturally evolved enzyme but, remarkably, used a completely different sequence, structure, and mechanism to do so,” adds Burckhard Seelig of the University of Minnesota. “The ability to create non-natural enzymes that function in a living organism is crucial to realize the hopes of synthetic biology.”