Using cryo-electron microscopy, researchers have captured freeze-frames of the changing shape of transcription factor IID, a huge molecule and one of the body’s key molecular machines, as It locks onto DNA and loads the machinery for reading the genetic code. The research was done by University of California, Berkeley scientists and posted online this week in advance of print publication in Science.
Transcription factor IID transcribes genes into RNA that will later be used to make proteins. It is made up of more than a dozen distinct proteins that home in on a promoter and tests the sequence to make sure that it has landed on the right spot. Once this confirmation has occurred, it opens up to recruit dozens of other proteins that create mRNA based on the complementary DNA sequence. This then makes its way to the nucleus where it is translated into proteins.
High-resolution structural information is needed to fully understand how TFIID translates the operating instructions into the genome and how this process can go awry, but this has been difficult to achieve thus far. Cryo-EM, the only method that can image large, floppy structures, involves imaging millions of copies of a molecule in every imaginable orientation and combining images. Because TFIID has many moving parts as it binds to DNA, averaging all the frozen positions produces a blurred image.
Now, as a result of more than two years of intensive work by the team, the structure of transcription factor IID has been captured in higher-resolution than ever before. These images are a result of improved detectors developed by the team and improving computer algorithms. The team was able to define five distinct structures of the TFIID molecule.
Knowledge of these structures could help drug designers create solutions that target TFIID to tweak a disease-causing gene. "These structures give you the potential for rationally designing small molecules that will disturb the normal function, because now we don't have just a single structure, we have many structures, which is even more powerful because we can target the motion that we are seeing right now," said Eva Nogales, a UC Berkeley professor of molecular and cell biology and a faculty scientist at Lawrence Berkeley National Laboratory.
Image: The transcription factor IID complex locks onto DNA, checks it's in the right place and then recruits other proteins to start transcribing DNA into RNA. New advances in cryo-EM allowed researchers to define five distinct conformations of TFIID as it locks and loads, providing new targets for drug development. Image courtesy of: Eva Nogales lab, UC Berkeley.