Researchers led by Professor Karl-Peter Hopfner, Director of the Gene Center Munich at LMU, have recently shed light on the TATA-box binding protein (TBP) displacement process by Mot1 enzyme. In the intricate world of gene regulation, various proteins bind to DNA to activate or suppress gene expression. One of these key regulatory proteins is the TATA-box binding protein, or TBP, which initiates the process of DNA reading by binding to a specific DNA sequence.
However, incorrectly bound TBPs need to be removed from the DNA to maintain the proper functioning of the cellular machinery. To perform this crucial task, a specialized enzyme called Mot1 is employed, which belongs to the Swi2/Snf2 remodeler family that uses ATP energy to break protein-DNA bonds.
For their work, the scientists used cryogenic electron microscopy to generate detailed 3D structural models of the remodeling reaction at various stages. These snapshots allowed them to visualize the intricate structural details of the TBP displacement process.
In the TBP displacement process, Mot1 grips the DNA strand close to the TBP protein and twists and bends it to displace TBP. This process prevents TBP from rebinding to the DNA, and the displaced TBP is then recycled. Interestingly, the researchers discovered that Mot1 uses a motor that is common to all Swi2/Snf2 remodeler family members but deploys it differently to achieve different functions. In the case of Mot1, the motor completely detaches proteins from the DNA.
The team hopes these findings apply to other complex Swi2/Snf2 molecular machines that play a role in essential cellular processes, such as carcinogenesis and neuronal development. The Swi2/Snf2 family transcription regulator Modifier of Transcription 1 (Mot1) uses ATP to disassociate and reallocate the TATA box-binding protein (TBP) from and between promoters.
The researchers determined the cryogenic electron microscopy structures that capture different states of the remodeling reaction to reveal how Mot1 removes TBP from TATA box DNA. They discovered that the motor grips DNA in the presence of ATP and swings back after ATP hydrolysis, dislodging TBP and moving it to a thermodynamically less stable position on the DNA strand. A chaperone element then traps the displaced TBP, blocking its DNA binding site.
These findings, published in Nature Structural & Molecular Biology, reveal the varied workings of the Swi2/Snf2 remodeler family and how they can remodel protein-DNA complexes through DNA bending without processive DNA tracking. They also provide mechanical similarities to RNA gripping DEAD box helicases and RIG-I-like immune sensors. The study's results may give more insight into molecular machines that can be harnessed to tackle complex diseases like cancer and neurodegeneration.