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Scientists snap first 3-D pictures of the "heart" of the transcription machine
09 Dec 1999

drawing of the transcription machine

A drawing of the transcription machine. Scientific American image
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Berkeley scientists have obtained the first good picture of a major chunk of the machinery that turns genes on and off.

With the help of electron microscopy and a relatively new technique called single particle image analysis, the researchers reconstructed a three-dimensional picture of the heart of the machine -- the part that binds to DNA and starts the process of gene transcription.

The picture shows for the first time how the proteins are arranged, and gives clues to the inner workings of the machinery that transcribes genes -- the complex of proteins that latches onto and copies DNA into an RNA blueprint for building proteins.

"For now, this is very basic, very fundamental research that helps us understand how the machine works," said team leader Eva Nogales, an assistant professor of molecular and cell biology at UC Berkeley and a scientist at the Lawrence Berkeley National Laboratory. "But it has implications for the treatment of disease, since essentially treatment comes down to modifying the behavior of proteins. One way to do that is to regulate transcription, which is why proteins involved in transcription are a major target for drug development."

The results will appear in the Dec. 10 issue of the journal Science.

How it works

The entire machine that transcribes a gene is composed of perhaps 50 proteins, including RNA polymerase, the enzyme that converts DNA code into RNA code. A crew of transcription factors grabs hold of the DNA just above the gene at a site called the core promoter, while associated activators bind to enhancer regions farther upstream of the gene to rev up transcription.

Working as a tightly knit machine, these proteins transcribe a single gene into messenger RNA. The messenger RNA wends its way out of the nucleus to the factories that produce proteins, where it serves as a blueprint for production of a specific protein.

The new detail is of the proteins forming the very large complex that binds DNA.

"We've never had a picture of this entire complex, and it tells us a lot about how this huge molecular machine works," said Robert Tjian, professor of molecular and cell biology and an author of the paper. The vast majority of work reconstructing the cell's transcription machinery has been done by Tjian and his colleagues at UC Berkeley over the past two decades. Both Tjian and Nogales are part of UC Berkeley's Health Sciences Initiative, a research effort that draws scientists from both the physical and biological sciences into the search for solutions to today's major health problems.

Tjian and Nogales admit that the picture now revealed is the first step in a long-term project to determine the three-dimensional arrangement of all the proteins in the machine, in enough detail to see the individual amino acids that make up each protein.

"The resolution we have now is good enough for learning about how things happen in the cell, but drug design comes with atomic modeling at a much finer resolution -- about 10 times better than we have now," Nogales said.

Nogales now is at work sharpening this picture of the complex. She and postdoctoral fellow Frank Andel III could not use standard X-ray crystallography to determine the structure of these proteins because the complex is about 10 times too big and the quantities they can obtain from the nucleus about a thousand times too small for that technique.

Postdoctoral fellows Andreas G. Ladurner and Carla Inouye from Tjian's lab also are authors on the paper.

Source: Robert Sanders, Public Affairs


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Transcription Factor TFIID website

Berkeley's Health Sciences Initiative

Berkeley Molecular & Cell Biology

Nogales Lab


Science Magazine