Biologists at the Washington University in St. Louis are using comparative metabologenomics to try to uncover what may be “silencing” Streptomyces (the bacteria responsible for the first bacterial antibiotics to treat tuberculosis back in the 1940s) and preventing it from producing desirable compounds encoded by its genes.

“We examined genetic differences across the genomes of Streptomyces while at the same time looking at antibiotic outputs,” said Joshua Blodgett, assistant professor of biology in Arts & Sciences, the corresponding author of a research article (“A comparative metabologenomic approach reveals mechanistic insights into Streptomyces antibiotic crypticity”) published in PNAS. “This study highlights comparative metabologenomics as a powerful approach to expose the features that differentiate strong antibiotic producers from weaker ones.”

Blodgett’s team, including recent PhD graduate Yunci Qi and postdoctoral research associate Keshav Nepal, PhD, compared a group of antibiotic-producing strains of Streptomyces and other nonproducing or poor-producing strains to reveal genomic differences that could affect drug production.

The researchers found a few key differences between the strains. Notably, the good producers of polycyclic tetramate macrolactam (PTM) antibiotics seemed to benefit from griseorhodin production, which the researchers did not anticipate and originally had tried to eliminate.

But a handful of nucleotides matter, too. Metabologenomics revealed that the presence or absence of two to three nucleotides can tune the switches that drive PTM antibiotic production. This type of fine control previously had been found in certain bacteria that cause disease, but largely had been overlooked in bacteria that produce drugs.

Streptomyces genomes harbor numerous, biosynthetic gene clusters (BGCs) encoding for drug-like compounds. While some of these BGCs readily yield expected products, many do not. Biosynthetic crypticity represents a significant hurdle to drug discovery, and the biological mechanisms that underpin it remain poorly understood. Polycyclic tetramate macrolactam (PTM) antibiotic production is widespread within the Streptomyces genus, and examples of active and cryptic PTM BGCs are known,” write the investigators.

“To reveal further insights into the causes of biosynthetic crypticity, we employed a PTM-targeted comparative metabologenomics approach to analyze a panel of S. griseus clade strains that included both poor and robust PTM producers. By comparing the genomes and PTM production profiles of these strains, we systematically mapped the PTM promoter architecture within the group, revealed that these promoters are directly activated via the global regulator AdpA, and discovered that small promoter insertion–deletion lesions (indels) differentiate weaker PTM producers from stronger ones.

“We also revealed an unexpected link between robust PTM expression and griseorhodin pigment coproduction, with weaker S. griseus–clade PTM producers being unable to produce the latter compound. This study highlights promoter indels and biosynthetic interactions as important, genetically encoded factors that impact BGC outputs, providing mechanistic insights that will undoubtedly extend to other Streptomyces BGCs.

“We highlight comparative metabologenomics as a powerful approach to expose genomic features that differentiate strong, antibiotic producers from weaker ones. This should prove useful for rational discovery efforts and is orthogonal to current engineering and molecular signaling approaches now standard in the field.”

“Our work highlights the problem of silent gene clusters and the need to understand them for next-generation drug discovery,” Blodgett said. “Comparative metabologenomics is a generally adoptable strategy, and we hope that others might use it to examine their own strains and drug pathways.”