First detailed structure of a transcription initiation complex

October 18, 2012 § Leave a comment

Overall structure of the transcription initiation complex. Image provided by Richard Ebright.

The first high-resolution structure of a functional transcription initiation complex is now ready for viewing, announced researchers in the latest issue of Science. In their paper, a team led by Richard Ebright and Eddy Arnold at Rutgers University showed the three-dimensional structure in detail of this key machinery in the DNA-to-RNA process.

Transcription is process by which an RNA copy is made of the genetic code in DNA. The complex that kicks off this process is called the transcription initiation complex. The machinery consists of a set of proteins that includes RNA polymerase and at least one general transcription factor. This machine preps the DNA for transcription by correctly picking out the proper site (called a promoter), binding to it and then unwinding it. “Determining the structure of a functional, specific transcription initiation complex has been a goal of researchers for three decades,” said Ebright, who is also an investigator of the Howard Hughes Medical Institute, in a press release.

Ebright and colleagues determined the structure of the complex by studying protein crystals at 2.9 and 3.0 Å resolution made from the bacterium Thermus thermophilus. The complexes contained RNA polymerase, the general transcription factor called sigma, a single-stranded  DNA segment corresponding to the unwound transcription bubble of the promoter, and the downstream double-stranded DNA.

The investigators worked out the details of the interactions RNA polymerase and sigma have with the site of the gene promoter. The structure showed that a part of the sigma factor recognized the -10 element through contacts with single-stranded DNA. The recognition involved unstacking and inserting DNA bases of the -10 element into pockets in the sigma factor. Another part of the factor recognized the discriminator element via contacts in the single-stranded DNA through a similar mechanism of unstacking and insertion. A third part of sigma factor made contact with the other strand of DNA and organized it so it could serve as the template for RNA synthesis.

Besides showing how RNA polymerase and sigma recognized and bound to known parts of the DNA, such as the -10 element (also known as the Pribnow box) and the discriminator element, Ebright and colleagues discovered a new DNA sequence element that they call the core recognition element. This element is a section of the DNA with which the main part of the RNA polymerase interacts  in the transcription bubble at nontemplate-strand positions -4 to +2.

The structure described in Science is a starting point for developing new antibacterial agents that work by inhibiting bacterial transcription, says Ebright. Because the transcription machineries in bacteria and higher organisms are similar, this structure also can help us understand transcription and transcriptional regulation in other organisms.

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