Cultured bacteria make hypermodified peptides

Polytheonamides are extensively modified peptides produced by bacteria in the microbiomes of marine sponges. These pore-forming peptides are toxic to cells, which makes them intriguing as possible cancer drugs. A major problem is that the bacteria that make the peptides can’t be cultured.

Now, Jörn Piel of the Swiss Federal Institute of Technology (ETH), Zurich, and coworkers have identified a cluster of enzymes in another bacterium that produces similarly hypermodified peptides (Nat. Chem. 2019, DOI: 10.1038/s41557-019-0323-9). And unlike the bacteria from the marine sponge, Microvirgula aerodenitrificans can be grown in cell culture.

M. aerodenitrificans produces its own class of modified peptides called aeronamides. The peptides are ribosomally synthesized with leader and core portions. The enzyme cluster recognizes the leader portion and modifies the core. The modifications include iterative epimerization to introduce 21 d-amino acids, methylation of various carbon and nitrogen atoms in the peptide, and dehydration. After the modifications are done, an enzyme cleaves the core from the leader. In addition to making its own peptides, the bacterium can make hypermodified peptides using DNA sequences from other organisms.

The yield isn’t very good at this point, however. After growing the bacteria for 2 days in a 5 L cell culture, the researchers were able to isolate only about 600 µg of the peptide aeronamide A. “We’re working on improving promoter systems and trying a different plasmid so that we can up the production of the peptide,” says Agneya Bhushan, a graduate student in Piel’s lab who did much of the work.

The researchers “have a way to go before they are able to robustly produce material,” says Bradley S. Moore, a natural products expert at the University of California San Diego. “But given the significant structural complexity, that result is quite remarkable and a tremendous first step that gave them insight into the potent bioactivity” of aeronamide A.

The researchers are now trying to engineer other core sequences that can be similarly modified, and they plan to screen such peptides against pharmaceutical targets.