Structural insight into process of gene regulation

In the cell nucleus, numerous proteins bind to the DNA molecule in order to regulate the activity of certain genes. One such is the TATA-box binding protein (TBP), which binds to a specific DNA sequence and constitutes an initial signal for the reading of DNA. Incorrectly bound TBP is removed from the DNA by a special enzyme called Mot1 and ‘recycled.’ This enzyme belongs to a large family of molecular machines, the so-called Swi2/Snf2 remodelers, which use the energy from ATP to break protein-DNA bonds.

Scientists led by Professor Karl-Peter Hopfner, Director of the Gene Center Munich at LMU, have now worked out a detailed account of this heretofore imprecisely understood displacement process. Using cryogenic electron microscopy, the researchers generated various ‘snapshots’ of the remodeling reaction. This allowed them to visualize structural details of the TBP displacement process in 3D structural models. In one or more passes, Mot1 grips DNA situated close to TBP and bends and twists it until the TBP is displaced while also preventing any rebinding to the DNA.

This process shows the varied workings of the Swi2/Snf2 remodeler family: all members have the same motor, but use it differently, whether it is to repackage DNA or – as in the case of Mot1 – to completely detach proteins from DNA. In the future, the researchers want to apply the acquired knowledge also to more complex Swi2/Snf2 molecular machines, which play a role in processes such as carcinogenesis or the development of neurons.

Stephan Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP: Structural basis for TBP displacement from TATA box DNA by the Swi2/Snf2 ATPase Mot1. Nature Structural & Molecular Biology 2023