The Structural Basis of Transcription
Life as we know it depends on turning on and off the proper genes at the correct time. This process of gene expression starts when an RNA message is copied from DNA. Scientists have long known that an enzyme called RNA polymerase II plays the central role in this delicate transcription process. But the exact mechanism by which RNA polymerase II selects specific nucleotides and catalyzes the reaction that incorporates them into a growing RNA strand has not been well understood.
In a new study published in the December 1, 2006 issue of Cell, researchers performed x-ray studies at SSRL Beamlines 11-1 and 9-2 and the Advanced Light Source at Berkeley to investigate the molecular structure of this enzyme in action. The studies revealed that a structural element of the enzyme, called the trigger loop, is involved in both nucleotide recognition and catalysis.
To ensure the accuracy of the transcription process, RNA polymerase II must distinguish between ribonucleotides (nucleotides that make up RNA) and deoxyribonucleotides (nucleotides that make up DNA) in the cell. It also must distinguish between different types of ribonucleotides and add to the RNA strand the one that is complimentary to the deoxyribonucleotide in the DNA template. When such a "correct" ribonucleotide is present, it fits together with an extensive network consisting of the trigger loop, a structural element known as the bridge helix, and other nearby polymerase residues, which all fit together like pieces of a puzzle. Additionally, when the correct ribonucleotide is present, interactions between the puzzle pieces cause the trigger loop to then swing into position beneath the nucleotide and seal off the active site. This move puts the ribonucleotide into the right position to be added to the growing RNA strand, and the interaction between the side chain of the trigger loop and the nucleotide phosphate initiates the catalytic reaction.
The trigger loop's role in both selection and catalysis ensures the accuracy of the transcription process, without which cells would transcribe inefficiently, becoming unhealthy or dying. This finding promises to inform future efforts to manipulate the transcription process for therapeutic and other purposes.