The molecular mechanisms underlying control of antibiotic production by hormones in soil bacteria have been elicited for the first time in a study by scientists at University of Warwick in Coventry, U.K., and at Monash University in Melbourne, Australia.
Reported in the February 3, 2021, edition of Nature, the study's findings could lead to the more efficient and cost-effective production of existing antibiotics and the discovery of new antibiotics in this era of increasing antibiotic resistance.
"Antimicrobial resistance is posing an ever-greater global health threat, but relatively few new antibiotics are making it to market... due to a combination of economic, societal and political factors," study co-leader Greg Challis told BioWorld Science.
Challis is a professor of chemistry at the University of Warwick and a professor of biochemistry and molecular biology at Monash University.
Most clinically useful antibiotics, including aminoglycosides, macrolides and tetracyclines, are derived from molecules produced by soil bacteria, primarily Actinobacteria, which are cultivated in the laboratory to allow their extraction.
However, production of these molecules is frequently switched off in laboratory cultures, making them difficult to isolate.
"Actinobacteria almost certainly produce antibiotics to deter other species of bacteria competing with them for nutrients in the soil," Challis said. But "in laboratory cultures, these other bacteria aren't present, so the Actinobacteria turn off the unneeded antibiotic production to save energy."
The bacteria control antibiotic production using small hormone-like molecules. Challis and his team investigated a specific class of such hormones, the 2-akyl-4-hydroxymethylfuran-3-carboxylic acids (AHFCAs), in the new study to determine its role in controlling production of an antibiotic in the Actinobacterium Streptomyces coelicolor.
"A model organism widely used to study antibiotic production and the mechanisms controlling it, we first discovered AHFCAs as a new class of Actinobacterial hormones in S. coelicolor, so we are following up on our earlier work," explained Challis.
Using X-ray crystallography and single-particle cryo-electron microscopy (cEM), the researchers analyzed the structure of a protein transcription factor bound to a specific region of bacterial DNA, which prevents the bacterium from producing the antibiotic.
They then determined the structure of the transcription factor with a synthesized version of one of the AHFCA hormones bound to it, which revealed how the DNA is released and antibiotic production switched on.
"We urgently need new antibiotics to tackle antibiotic resistance," said study co-leader Chris Corre, an associate professor of synthetic biology in the University of Warwick's Departments of Life Sciences and Chemistry.
"Similar processes are already known to control production of many important molecules, so if we understood the mechanisms controlling their production, we could improve the process, making it more economically viable," said Corre.
Moreover, "although we were only looking at one particular class of hormones, the mechanism we found appears to be [evolutionarily] conserved across all of the different hormone classes in Actinobacteria."
"This indicates that systems recognizing the various different hormone classes in Actinobacteria have a common evolutionary origin," explained Challis, further suggesting that "the mechanism could be exploited to turn on the production of a wide range of antibiotics controlled by several distinct hormone classes."
Indeed, Actinobacteria have a complex development cycle, into which production of antibiotics is integrated, but as mentioned, when grown in pure culture media, they often switch off antibiotic production, confounding their study.
A better understanding of the molecular mechanisms controlling this process could allow the production of new antibiotics not produced in laboratory cultures to be switched off. "We could use such strategies to turn on production of new antibiotics in Actinobacteria, among which we'd hope to find those that could be useful for tackling infections caused by resistant microbes and other diseases," said Corre.
However, the key to the discovery was determining the structure of the complex of the transcription factor bound to the DNA and to overcome challenges with X-ray crystallography.
"Few structures of this type of protein-DNA assemblage have been determined using high resolution X-ray crystallography, due to the difficulty obtaining suitable high quality crystals, which can be challenging and time-consuming," said Challis.
"Using cEM, we have circumvented this challenge, which should make it easier to determine the structures of similar complexes in the future," he noted. "Cryo-EM images biomolecules that have been suspended in vitreous ice, which circumvents the need to obtain high-quality crystals for structure determination."
"By developing a detailed understanding of the mechanisms controlling antibiotic production, we can design rational strategies for turning on the production of antibiotics that aren't normally made in pure laboratory cultures," he said.
"Such antibiotics are likely to have novel structures and hit new targets, or known targets in new ways, which should enable us to develop antibiotics that circumvent mechanisms conferring resistance to currently used antibiotics."