Proteins help to regulate almost every process in the body, and come in various forms, sizes and purposes. Cells contain thousands of different proteins, but not every protein is needed at all times. To create new proteins, the information on a gene first needs to be transcribed into RNA (template molecules of the DNA) in a process known as transcription. A complex machinery inside the cell then uses the copy as a template to assemble the protein.

So-called transcription factors (also proteins) can switch the copying process on or off by binding to the start point of a gene. They can act alone or in complex with other proteins. The transcription factor called ASCIZ, for example, helps to regulate the production of a protein called LC8. LC8 attaches to more than 100 different proteins and plays an important role in many cell processes. Therefore, fine-tuning its production is essential.

The shape of a protein is critical to its purpose. Like most proteins, transcription factors are made up of chains of amino acids that fold into a specific three-dimensional (3D) structurewith a region that recognizes and binds to a specific DNA sequence. But many transcription factors also contain flexible, ‘disordered’ regions that do not fold into a rigid 3D shape. These may help to control the activity of genes, but their exact role is unclear.

ASCIZ contains an exceptionally long, disordered region that has multiple positions for binding LC8 along its chain. Previous research has shown that ASCIZ binds to the LC8 gene and increases transcription to produce more LC8 proteins. Once the protein levels are high enough, LC8 is thought to bind to the disordered region of ASCIZ and switch off transcription. Human ASCIZ proteins have 11 binding sites for LC8 molecules, while fruit flies have seven. Until now it was not clear why so many different binding sites exist.

To address this question, Clark et al. combined biophysical, structural and molecular biology techniques to analyze proteins from humans and fruit flies and to test their role in human cells. This revealed that LC8 and ASCIZ form a dynamic mixture of complexes, instead of a single fully-occupied complex. As the number of LC8 molecules bound to ASCIZ increased, the rate of transcription dropped. However, all of the binding sites were rarely fully occupied. Instead, three to four attached LC8 molecules seemed to be sufficient to ensure that LC8 levels remain balanced. When the number of LC8 molecules exceeded this value, the attachment rate for additional LC8 slowed down. So, even when there was an excess of LC8, most of the human ASCIZ binding sites were only partially filled. This way, the production of LC8 proteins was slowed, rather than fully shut down. As a result, the cells were able to fine-tune the transcription rate of LC8 and maintain a stable and balanced pool of these proteins.

This work suggests that disordered regions on transcription factors could help to keep cellular systems steady in the face of changing conditions. In the future, the combination of methods used here could reveal new information about other proteins with disordered regions.

eLife 2018;7:e36258 DOI: 10.7554/eLife.36258

The full paper is available here.