Ancient Antibiotic Resurrected

Paleomycin

Researchers have, for the first time, reconstructed the appearance of the “ancestor” of a prevalent class of antibiotics—the ancient form of all glycopeptide antibiotics produced by primordial bacteria. Furthermore, they successfully revived this ancestral antibiotic, named Paleomycin, by introducing the corresponding genes into a modern bacterium. Subsequently, this bacterium produced the ancient Paleomycin, proving its potency as an original therapeutic agent.

Antibiotics are indispensable in modern medicine. However, their origin lies in the evolutionary arms race among microbes: millions of years ago, bacteria and fungi produced antibiotic molecules to fend off rivals and foes. Many contemporary antibiotic classes trace their roots back to molds or soil bacteria.

Thousands of antibiotic compounds have been isolated from natural sources, and many more remain undiscovered, showcasing their immense structural diversity,” explains Mathias Hansen from Monash University in Australia and his colleagues. “Yet, we have limited knowledge of the molecular mechanisms behind the evolution of these natural products.

Genealogical Tree of Glycopeptide Antibiotics Reconstructed

vancomycin or teicomycin
Modern glycopeptide antibiotics such as vancomycin or teicomycin have a similar basic structure, but differ in their complexity. Image: Hansen et al./ Nature Communications, CC-by 4.0.

Hansen and his team have now been able to trace the evolution of one of these ancient defense molecules. They reconstructed the development of Glycopeptide Antibiotics (GPA), a class of drugs that includes common antibiotics such as Vancomycin and Teicoplanin. These molecules share a core of several ring-shaped peptides and enzymes that attack the cell wall of target bacteria. The instructions for building these structures are encoded in multiple biosynthetic gene clusters (BGC).

In their journey to the ancestor of Glycopeptide Antibiotics, the researchers compared the gene clusters of 29 different variants of these drugs. “Our main goal was to understand the gene losses and gains and the chronological sequence of evolutionary events in the history of BGC evolution,” they explained. Based on these comparative analyses, the team constructed a phylogenetic tree of GPA structures.

The Original Form Was Surprisingly Complex

Paleomycin: This is what the reconstructed original form of the glycopeptide antibiotics looks like.
Paleomycin: This is what the reconstructed original form of the glycopeptide antibiotics looks like. Image: Hansen et al./ Nature Communications, CC-by 4.0.

The antibiotic phylogenetic tree revealed that all Glycopeptide Antibiotics actually trace back to a common ancestral form—a molecule that was “invented” by an ancient bacterium long ago. This primal antibiotic was named Paleomycin by the researchers. Through mutations, recombinations, and horizontal gene exchanges between different bacteria, all currently known forms of Glycopeptide Antibiotics gradually evolved from Paleomycin.

Surprisingly, however, this evolution did not follow the expected path from a simple basic molecule to increasingly complex structures. Instead, it occurred in the reverse direction. “Our results show that the ancestor named Paleomycin already had a complex, tetracyclic core consisting of seven peptides with ring-shaped attachments,” reported Hansen and his colleagues. Thus, the primal form of antibiotics resembled the modern, relatively complex Teicoplanin more than the Vancomycin, which is constructed from only three central peptides.

Accordingly, bacteria simplified rather than expanded the structure of their defense molecules—presumably to conserve chemical resources and energy. “These are substances with a complex chemical structure that cost the bacterium a lot of energy. Simplifying while maintaining function could offer an evolutionary advantage,” explained senior author Nadine Ziemert from the University of Tübingen.

Bacteria Bring Paleomycin Back to Life

The researchers aimed to assess the effectiveness of the primary antibiotic, Paleomycin. To achieve this, they chose to resurrect Paleomycin by introducing its biosynthetic gene clusters into Amycolatopsis japonicum, a bacterium naturally producing the glycopeptide antibiotic Ristomycin. Consequently, this genetically modified strain commenced the production of Paleomycin instead of its own GPA version.

Creating such an ancient molecule was described as a thrilling experience, akin to reviving a dinosaur or a woolly mammoth, according to Ziemert. Subsequent tests confirmed the reconstructed Paleomycin’s antibiotic efficacy. In cell cultures of the test bacterium Bacillus subtilis, clear zones in the bacterial lawn appeared shortly, indicating Paleomycin’s bactericidal activity.

The research team posits that their journey back to the origin of glycopeptide antibiotics yields valuable insights not only into the evolution of these agents but also for the development of new synthetic variants. Ziemert explains that this temporal exploration provides a foundation for advancing this crucial antibiotic class using technical methods.

Source: (Nature Comunications, 2023; doi: 10.1038/s41467-023-43451-4)