Structure of a bacterial RNA polymerase holoenzyme open promoter complex
Open Access
- 8 September 2015
- journal article
- research article
- Published by eLife Sciences Publications, Ltd in eLife
Abstract
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the −10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the −10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation.Keywords
Funding Information
- National Center for Research Resources (NCRR) (1S10RR027037, RR-15301)
- National Institute of Biomedical Imaging and Bioengineering (NIBIB) (P30-EB-009998)
- The Rockefeller University (Merck Postdoctoral Fellowship)
- National Institute of General Medical Sciences (NIGMS) (F32 GM103170)
- National Institute of General Medical Sciences (NIGMS) (R01 GM038660)
- National Institute of General Medical Sciences (NIGMS) (R01 GM053759)
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