Scientists provide new insight on how gene expression is controlled

Photo of Robert Landick
Professor Robert Landick.

New research on transcriptional pausing, which helps control gene expression in cells, will aid in the understanding of the enzyme RNA polymerase — a key player in the process and an important drug target.

Researchers have provided this new insight on the mechanism underlying the control of gene expression in all living organisms in a study published today (Jan. 8) in eLife.

The findings could ultimately improve the understanding of how certain antibacterial drugs work against the enzyme RNA polymerase (RNAP) in treating conditions such as Clostridium difficile infections and tuberculosis.

In order for genes to be ultimately expressed as the proteins and other molecules organisms need, two steps have to occur. Transcription is the first, where RNAP reads the information in a strand on DNA, which is then copied into a new molecule of messenger RNA (mRNA). In the second stage, the molecule then moves on to be processed or translated into proteins.

Although introductory biology students everywhere learn about the process of transcription, the process is far from fully understood. In fact, to help control gene expression levels, transcriptional pausing by RNAP can occur between the two stages, providing a kind of ‘roadblock’ where transcription may be terminated or modulated by the cell if need be.

Illustrtion of the pause process and molecular structure.
An illustration of the transcriptional pause process, which helps to control gene expression in cells. Image courtesy of Robert Landick.

Biochemistry professor and senior author Robert Landick and his team of researchers have revealed the elemental mechanism behind this pausing for the first time.

“A sequence that causes pausing of RNAPs in all organisms, from bacteria to mammals, halts the enzyme in a paused state from which longer-lived pauses can arise,” says Landick, who is also affiliated with the Department of Bacteriology. “As the fundamental mechanism of this elemental pause is not well defined, we decided to explore this using a variety of biochemical and biophysical approaches.”

The team’s analyses first revealed that the elemental pause process involves several biological players, which together create a barrier to prevent escape from paused states. The process also causes a modest conformational shift that makes RNAP ‘stumble’ in feeding DNA into its reaction center, temporarily stopping it from making RNA.

“We also found that transcriptional pausing makes RNAP loosen its grip and backtrack on the DNA while paused,” says Landick. “Together, these results provide a framework to understand how the process is controlled by certain conditions and regulators within cells.”

He adds that these insights could aid future efforts to design synthetic genes, for example to direct the pausing behavior of RNAP in a way that yields desired outputs from genes. It could also help the understanding of how certain drugs, known as RNAP inhibitors, target the enzyme.

“For now, we would like to try and generate structures of paused transcription complexes obtained at a series of time intervals,” Landick concludes. “This would allow us to see exactly how parts of the enzyme move as it enters and leaves the paused state.”

This research was funded by the National Institutes of Health Grant R01 GM38660.

Story adapted from a press release by Emily Packer for eLife.