Structure of TraR bound to RNA polymerase obtained using cryo-electron microscopy. Chen et al. (CC BY 4.0)
Cells need to make proteins in order to survive. To make a protein, a cell first needs to take the information from a gene coded in its DNA and copy it into a template made of a different molecule called RNA via a process called transcription. Not all genes are transcribed or expressed at the same time or the same rate, because a cell needs different proteins depending on its environment. The molecules that regulate when each gene is transcribed are called transcription factors.
When the bacterium Escherichia coli is starved for the building blocks it needs to make proteins, it changes the expression of almost one quarter of its genes within 5 minutes. This broad response requires two transcription factors, ppGpp and DksA. Unlike most transcription factors, these two molecules bind directly to the enzyme responsible for transcribing DNA into RNA, the RNA polymerase, but they do not bind to DNA.
Another transcription factor called TraR can mimic the combined effects of ppGpp and DksA on transcription, changing the conformation of RNA polymerase in the same way. Now, Chen et al. have used a high-resolution imaging technique called cryo-electron microscopy to reveal the details of how the structure of RNA polymerase changes in response to TraR binding, and by analogy, in response to ppGpp and DksA.
The experiments showed that TraR interacts with regions of RNA polymerase that move when the protein binds DNA. These interactions can either help or hinder the start of transcription depending on which DNA sequence the RNA polymerase binds. Using the structures obtained via cryo-electron microscopy as guides, Chen et al. mutated each of the mobile parts of RNA polymerase individually to determine which interactions with TraR were necessary to change gene expression.
These results shed light on a fundamental process in all living cells, the initiation of transcription, and how it changes in response to the cell's nutritional environment. This may help explain how different cells regulate gene expression and may also lead to the development of new antibiotics.
