Using innovative methods, EMBL scientists have uncovered key interactions between molecular machines, opening new avenues for drug development. For the first time, researchers have captured a real-time molecular movie showing how two important cellular processes, transcription and translation, interact in bacteria.

Using single-molecule multicolor fluorescence microscopy, the Duss group at the EMBL Laboratory in Heidelberg produced a movie showing the interaction of bacterial RNA polymerase (marked with pink spheres) and ribosomes (marked with green spheres) on the same mRNA molecule (white line between spheres). Photo credit: Isabel RomeroCalvo/EMBL

In all living organisms, DNA contains the code that defines the structure and function of cells. An enzyme called RNA polymerase deciphers this code and converts it into RNA, a molecule very similar to DNA. This process of converting the code of life from DNA to RNA is called transcription. Next, a molecular machine called a ribosome uses the information encoded in RNA to build proteins -- molecules that perform most of the cell's basic functions. This process is called translation.

This video summarizes how we currently understand how transcription and translation are physically and functionally coupled to each other. Using multicolor single-molecule fluorescence microscopy, we simultaneously tracked transcriptional and translational elongation and the coupling between RNA polymerase and ribosomes. We see how individual ribosomes slow down after collision with RNA polymerase, and how they activate RNA polymerase through long-range physical coupling. Image source: EMBL

"In bacterial cells, transcription and translation take place in the same cellular compartment," explains Olivier Duss, group leader at EMBL Heidelberg and senior author of the new study. "In human cells, transcription occurs in the nucleus, which is where the DNA is stored and is separated from the rest of the cell by a membrane. The transcribed RNA is then transported outside the nucleus and translated into protein, which occurs entirely in the cytoplasm (the area of ​​the cell surrounding the nucleus). Bacterial cells have a much simpler cellular structure and do not have a nucleus, so not only can transcription and translation occur simultaneously in the same place."

Scientists had previously described transcription and translation as a single process, but had less understanding of how the two interact. This is partly because these studies rely on techniques such as cryo-electron microscopy, which requires frozen samples and therefore can only provide a snapshot of the process.

Advanced tools for capturing molecular interactions

The Duce research group uses single-molecule techniques, structural biology and biochemistry to understand how large molecular machines involved in important cellular functions cooperate with each other.

To study how translation and transcription work together, a team co-led by research scientist Nusrat Qureshi artificially recreated the cellular environment required for these processes. In this way, they could closely track the dynamics of each pair-by-pair interaction of ribosomes and RNA polymerase using a technique called single-molecule multicolor fluorescence microscopy.

Simply put, this technique works by tagging RNA polymerase and ribosomes with small chemicals that act like proximity sensors. When these two molecules interact, they emit signals that can be picked up by a fluorescence microscope. When they stop interacting, the signal disappears.

In this way, the scientists captured several minutes of dynamic interactions between RNA polymerase and ribosomes. For the first time ever, they could observe the processes of transcription and translation simultaneously through a microscope.

"I'm very excited that we can finally observe the entire process," Duce said. "We can put these snapshots into action, which gives us a better understanding of how the two machines work together. Putting it all together, we can start to see emerging behaviors that wouldn't have been predicted otherwise."

One of the emerging behaviors that scientists have discovered is that RNA polymerase and ribosomes can communicate through a relatively long stretch of circular RNA, even when they are far apart.

In this case, the two molecular machines are like a pair of climbers tethered by a long rope. The ropes are loose enough to prevent collisions, but tight enough for each climber to help the other if needed.

The team also observed that transcription is more efficient when translation occurs simultaneously. In other words, when an active RNA polymerase is followed by an ongoing ribosome on the same RNA molecule, its productivity is higher.

"It's wonderful to be able to observe how these processes work together. Anyone who works in a team knows the importance of collaboration," Duce said. "If everyone tries to do it alone, efficiency is greatly reduced. The cell's molecular machinery seems to know this, too."

Impact on antibiotic development

While this study focused on isolated molecules in artificial settings, the Duce research team is now preparing to extend their understanding of this process to living cells. As part of a recent European Community Research Council comprehensive grant, they also plan to include more cellular processes in their research to see whether "climbing" coordination involves more than just two partners.

At a time when antibiotic resistance is a major health concern, revealing how bacteria's basic cellular machinery works paves the way for the development of new ways to fight bacterial pathogens. It is possible for researchers to go beyond standard antibiotics and prevent resistance problems by cooperatively targeting two cellular machines instead of just one.

"This work is a great example of the importance of basic research from a broader perspective," Duss said. "Basic research helps us understand how biology works, which then translates into new discoveries such as new drugs, advanced treatments and better opportunities."

The new research is published in the journal Nature.

Compiled from /ScitechDaily

DOI:10.1038/s41586-024-08308-w