Genetic Blueprint Drawn for Natural Antibiotic

Antibiotic-resistant infections loom as one of health care’s growing problems, with the potential to undo some of the stunning progress society has made in combating infectious disease. The most useful antibiotics target vital processes common to all bacteria, allowing them to fight a range of bacterial infections. Penicillin, for instance, interferes with the formation of the bacterial cell wall, without which the organism cannot live. Unfortunately, there are only a few known targets that have such a broad impact.

One compound that has attracted attention is moenomycin, a molecular weapon produced by certain bacteria. This substance ruins the cell wall of pathogenic bacteria, but in a different way than penicillin does. In its natural form, it is not useful in humans as a drug, though scientists in several labs have been working on ways to create a similar compound that could be used clinically.

Reporting in the March 26 Chemistry and Biology, the lab of Suzanne Walker, HMS professor of microbiology and molecular genetics, details the bacterial genetic pathway used to produce moenomycin. With this set of instructions, scientists may be able to tweak the pathway to formulate similar molecules that can be used as drugs.

The dense structure of the bacterial cell wall, made of long sugar chains stitched together with peptides, surrounds bacterial cells like a protective coat of chain mail. But while penicillin and its related compounds target the stitching together of carbohydrate strands, moenomycin blocks the formation of the strands in the first place, by striking a group of enzymes that assemble them. “It’s the only known inhibitor of these important enzymes,” Walker said. “It’s the only thing we have to go on as a blueprint if we want to make better drugs” that mimic this action.

Moenomycin is produced by Streptomyces ghanaensis, a microbe that lives in the soil. Postdoctoral fellow Bohdan Ostash developed some genetic tools to manipulate S. ghanaensis. He was able to isolate a small gene cluster responsible for part of the pathway that yields the compound, but the cluster turned out not to contain all the genes necessary for manufacturing the entire product. The team decided that the most direct approach, in this case, was to sequence the entire genome of the organism and find the missing pathway elements within its genetic code. They worked with Bruce Birren, director of the Microbial Sequencing Center at the Broad Institute, to do the sequencing.

Enough was known about moenomycin to predict what the necessary genes might look like. By searching the sequence, the scientists identified another, larger gene cluster that met all of the criteria. Ostash then went back to the lab to confirm that this larger cluster is the one needed to produce the antibiotic. As a final proof, the team was able to transfer the gene cluster into a different organism and make it produce moenomycin derivatives. Because this organism has a faster growth rate, it produces the product more efficiently.

With the blueprint for moenomycin in hand, Walker’s lab can now start to manipulate the machinery to produce similar molecules that might serve as better drugs. Walker said that the first step is to see how far the machinery can be pared down. Her team believes they need eight or nine genes to make the essential components of the molecule, a surprisingly small number for such a large product. Next, they can begin to alter the properties of the molecule to create a simpler product that retains the action of the antibiotic.

Having microorganisms produce the drug themselves is the fastest way to quickly make fragments of the drug to see what the minimal structural portion is that retains full activity. Finding new drugs will also become easier with the availability of the crystal structure of the class of enzyme that moenomycin targets, published recently by Walker’s group and that of Natalie Strynadka at the University of British Columbia.

Walker said that the gene cluster her team uncovered is interesting from a more fundamental standpoint, because it is small yet assembles a complex product. This cluster seems to work by pasting together components that are already present in the cell, rather than creating them from scratch. Walker said that moenomycin assembly involves “a very small number of tailoring reactions, and the subunits come from cellular metabolite pools.” Organisms like streptomycetes often produce so-called secondary metabolites during late phases in their growth—these are not the primary products needed to grow, but a host of chemicals that often have antibacterial or other useful properties. Moenomycin production, Walker said, may provide some insight into how the cell transitions from a stage of growth to a stage of antibiotic production.

Walker believes that research into antibiotics and other natural products could be advanced by efforts to sequence genomes of soil microorganisms, which the NIH currently does not fund. “The majority of natural products that are antibiotics or antitumor agents come from soil microbes,” Walker said. This study shows that the genetic code can offer some surprising clues that can’t be uncovered with traditional approaches. Previous sequencing efforts have focused on pathogens, but Walker believes these “little natural-product factories” have much to offer medicine, as well.