Curiosity-driven experiment helps unravel antibiotic-resistance mystery

An international collaboration has achieved an important breakthrough in understanding the genetic mechanisms that allow bacteria to build resistance to drugs.

Bacteria have multiple defense mechanisms they can use to build resistance to antibiotics, one of the major problems facing public health globally.

One of these mechanisms involves plasmids, small DNA molecules in bacterial cells, which have their own independent genome and carry antibiotic resistance.

If we can work out the roles plasmids play inside bacteria, then we can use the information to develop a new generation of therapeutics that can target drug resistant infections.

John Innes Center researchers and partners used a model plasmid called RK2 that is used globally to study clinically relevant plasmids that transmit antimicrobial resistance.

The study, “KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid,” is published in Nature Microbiology.

Their initial focus was a molecule called KorB which is essential for plasmids to survive within their bacterial hosts. This DNA-binding protein was previously known to have played a role in controlling gene expression but how this happens was unclear.

To figure this out, they teamed up with leading experts from Madrid, New York and Birmingham, UK..

Using advanced microscopy and protein crystallography techniques, the research team discovered that KorB interacts with another molecule called KorA. This KorB-KorA regulatory system shuts down bacterial gene expression, KorB acting as a DNA sliding clamp and KorA as a lock which holds KorB in place.

Together, this complex shuts off gene expression to keep the plasmid safe within its bacterial host.

This newly discovered mechanism offers a fresh insight into long-range gene silencing in bacteria. This is the phenomenon by which regulatory elements such as the KorB-KorA complex can interact with distant target genes, in this case switching them off so that the plasmid can survive in the bacterial host.

First author of the study Dr. Thomas McLean, a postdoctoral researcher at the John Innes Center, says the discovery is a triumph of curiosity-driven science. “Originally, this project set out to focus on KorB. Then a lucky ‘Friday afternoon’ experiment, which was done purely out of curiosity, brought our focus onto the ability for KorA to clamp KorB in the right place at the right time.

“This was a huge breakthrough that drastically changed the direction of the project. Our study provides a new paradigm for bacterial long-range gene regulation and offers a target for novel therapeutics to destabilize plasmids in their host and re-sensitize them to antibiotics.”

The study solves a decades-long conundrum in the field, of how the critical protein KorB controls when genes are switched on and off in the multi-drug-resistant plasmid RK2 in bacteria.

The research is being expanded to include more clinically relevant plasmids and to probe further into the KorB-KorA mechanism to see how it disassembles at the correct time.