During a recent study led by researchers from Northwestern University, they peered inside a human cell for the first time to look at a multi-subunit machine that is responsible for the regulation of gene expression. The study was published in the journal Science. This marks the first time the human Mediator complex has been visualised in 3D in the human cell. Called the Mediator-bound pre-initiation complex (Med-PIC), the structure is a key player in determining which genes are activated and which are suppressed. The mediator helps position the rest of the complex, RNA polymerase II and the general transcription factors at the beginning of genes that the cell wants to transcribe.
The researchers visualised the complex in high resolution using cryogenic electron microscopy (cryo-EM), enabling them to better understand how it works. As this complex plays a role in many diseases, including cancer, neurodegenerative diseases, HIV and metabolic disorders, researchers new understanding of its structure could potentially be leveraged to treat disease.
Northwestern's Yuan He, senior author of the study said, this machine is so basic to every branch of modern molecular biology in the context of gene expression. Visualising the structure in 3D will help us answer basic biological questions, such as how DNA is copied to RNA.
Ryan Abdella, the paper's co-first author said, seeing this structure allows us to understand how it works. It's like taking apart a common household appliance to see how everything fits together. Now we can understand how the proteins in the complex come together to perform their function.
Famed biochemist Roger Kornberg discovered the Mediator complex in yeast in 1990, a project for which he won the 2006 Nobel Prize in Chemistry. But Mediator comprises daunting 26 subunits, 56 total when combined with the pre-initiation complex, it's taken researchers until now to obtain high-resolution images of the human version.
Yuan He said, it's a technically quite challenging project. These complexes are scarce. It takes hundreds of liters of human cells, which are very hard to grow, to obtain small amounts of the protein complexes. breakthrough came when his team put the sample on a single layer of graphene oxide. By providing this support, the graphene sheet minimised the amount of sample needed for imaging. And compared to the typical support used amorphous carbon graphene improved the signal-to-noise ratio for higher-resolution imaging.
After preparing the sample, the team used cryo-EM, a relatively new technique that won the 2017 Nobel Prize in Chemistry to determine the 3D shape of proteins, which are often thousands of times smaller than the width of a human hair. The technique works by blasting a stream of electrons at a flash-frozen sample to take many 2D images. For this study, his team captured hundreds of thousands of images of the Med-PIC complex. They then used computational methods to reconstruct a 3D image.
Talyzina said, solving this complex was like assembling a puzzle. Some of those subunits were already known from other experiments, but we had no idea how the pieces assembled together or interacted with each other. With our final structure, we were finally able to see this whole complex and understand its organisation.
The resulting image shows the Med-PIC complex as a flat, elongated structure, measuring 45 nanometers in length. The researchers also were surprised to discover that the Mediator moves relative to the rest of the complex, binding to RNA polymerase II at a hinge point.
Abdella concluded, Mediator moves like a pendulum. Next, we want to understand what this flexibility means. We think it might have an impact on the activity of a key enzyme within the complex.