New Method for Discovering Antibiotics from Bacteria

Numerous natural products produced by microorganisms can be utilized as active ingredients to treat illnesses like cancer and infections. Although the microbes' genes contain the blueprints for these molecules, they frequently do not function in a lab setting.

A group of scientists at the Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) has created a novel genetic technique that uses a naturally occurring bacterial mechanism to transfer genetic material and create new active ingredients. The group's findings were published in the journal Science.

Bacteria are remarkably capable of exchanging genetic material with one another, unlike humans. The spread of genes that make bacteria resistant to antibiotics is a well-known example with far-reaching effects. Their rapid adaptation to various environmental conditions is made possible by this gene transfer, which also plays a significant role in the spread of antibiotic resistance.

This natural principle has now been used by researchers at the German Center for Infection Research (DZIF) and the HIPS to isolate and amplify biosynthetic gene clusters, which are the genetic blueprints for new bioactive natural products from bacteria.

Thanks to their novel method, known as " ACTIMOT, " it is feasible to either directly produce the natural products encoded in the gene clusters in the native bacterium or transfer them into more appropriate microbial production strains to produce the new molecules there. The Helmholtz Centre for Infection Research (HZI) operates the HIPS in partnership with Saarland University.

CRISPR-Cas9 technology sometimes referred to as “gene scissors,” ACTIMOT, or “Advanced Cas9-mediaTed In vivo MObilization and mulTiplication of BGCs,” enables precise modifications to bacteria's genetic material.

Biosynthetic gene clusters are extracted from the genome using ACTIMOT and inserted into a mobile genetic unit, which is subsequently multiplied by the bacterium itself because these gene clusters are frequently less active in a lab setting.

All of these actions are carried out by taking advantage of the molecular mechanism that permits bacteria to pass resistance genes to one another. The production of the encoded natural products is often made possible by the amplification of the gene clusters on these so-called plasmids.

If this fails, the encoded natural products can be readily produced by transferring the generated plasmids into a different production strain. The authors of the current study effectively illustrate both strategies.

Many biosynthetic gene clusters remain suppressed under laboratory conditions for various reasons, and current efforts to reveal the natural products they encode only address a limited number of them. Our approach mimics the natural bacterial gene transfer process to directly liberate and amplify entire biosynthetic gene clusters within the native bacterial cell, granting access to previously hidden natural products. Using this technology, we can access the biosynthetic potential of bacteria much faster and easier, as compared to existing methods.”

Chengzhang Fu, Junior Research Group Leader and Study Last Author, Helmholtz Institute for Pharmaceutical Research Saarland

The group has previously shown that ACTIMOT can result in novel discoveries: 39 new natural products from four previously unidentified natural product classes were found by the researchers during the study. The team is now confident that ACTIMOT can greatly speed up the process of finding new drug candidates.

Microorganisms offer us incredible potential for the production of new chemical matter that we can use, among other things, to develop urgently needed active ingredients. So far, large parts of this microbial treasure remain hidden from us. ACTIMOT will help us to further exploit the biosynthetic potential of bacteria and thus significantly advance the development of new active agents.”

Rolf Müller, Head of Department and Scientific Director, Helmholtz Institute for Pharmaceutical Research Saarland

Rolf Müller is also the Coordinator of the “New Antibiotics” research area at the DZIF, who also took a leading role in the study.

Streptomyces bacteria have been used with ACTIMOT in the current investigation. However, the authors already plan to extend the protocol to additional bacterial species with a high potential for producing unidentified natural products.

Beyond this, ACTIMOT has potential for use in several other fields, such as the large-scale manufacturing of valuable natural products, the investigation of unidentified gene pathways, and the determination of where to begin optimizing natural products.