A team of Rutgers CCB researchers led by Richard H. Ebright and Eddy Arnold has determined the three-dimensional structure of the transcription initiation complex, the key intermediate in the process by which cells read out genetic information in DNA.
In a paper published in Science, the Rutgers CCB scientists show how the molecular machine responsible for transcription initiation--a protein complex that consists of the enzyme RNA polymerase and the initiation factor δ- recognizes a specific site on DNA preceding a gene, binds to DNA, unwinds the DNA helix, and pre-organizes the unwound DNA to enable subsequent reactions.
"Determining the structure of a functional, specific transcription initiation complex has been a goal of researchers for three decades," said Ebright, a professor in Rutgers CCB and a laboratory director at the Waksman Institute of Microbiology at Rutgers.
The structure determined by the Rutgers CCB researchers is the structure of a transcription initiation complex from a bacterium. The structure provides a foundation for understanding bacterial transcription initiation and transcriptional regulation and provides a starting point for developing new antibacterial agents that function by inhibiting bacterial transcription. Because the transcription machineries in bacteria and higher organisms are structurally and mechanistically related, the structure also provides a framework for understanding transcription and transcriptional regulation in higher organisms, including humans.
The structure defines the interactions that RNA polymerase and δ make with the DNA site for transcription initiation, known as the "promoter." In particular, the structure defines interactions with a segment of the promoter that RNA polymerase and δ unwind to form single-stranded DNA (the "transcription bubble") and specific DNA sequences that RNA polymerase and δ recognize and bind to within this segment of the promoter (the "-10 element," the "discriminator element," and a new DNA sequence identified in this work, the "core recognition element").
The structure shows that a first part of δ recognizes the -10 element through contacts with single-stranded DNA that entail the unstacking and insertion of DNA bases of the -10 element into pockets. A second part of δ recognizes the discriminator element through contacts with single-stranded DNA that entail the unstacking and insertion of a DNA base of the discriminator element into a pocket. A third part of δ contacts the other strand of DNA and pre-organizes it to serve as the template for RNA synthesis. Finally, RNA polymerase recognizes the core recognition element through contacts with single-stranded DNA, unstacking and inserting a DNA base into a pocket.
Zhang, Y., Feng, Y., Chatterjee, S., Tuske, S., Ho, M., Arnold, E., and Ebright, RH. (2012); Structural basis of transcription initiation, Science 338, 1076-1080.