Deutsche Forschungsgemeinschaft [SFB960 project A3 to S.D., R.R. and M.T. and SFB960 project A7 to D.G]; National Institutes of Health Academic Research Enhancement Award [R15 GM083306 to M.B.]. Funding for open access charge: Deutsche Forschungsgemeinschaft.
Nucleic Acids Research
Genetic transcription, Transcription factors, RNA polymerases
Transcription initiation by archaeal RNA polymerase (RNAP) and eukaryotic RNAP II requires the general transcription factor (TF) B/ IIB. Structural analyses of eukaryotic transcription initiation complexes locate the B-reader domain of TFIIB in close proximity to the active site of RNAP II. Here, we present the first crosslinking mapping data that describe the dynamic transitions of an archaeal TFB to provide evidence for structural rearrangements within the transcription complex during transition from initiation to early elongation phase of transcription. Using a highly specific UV-inducible crosslinking system based on the unnatural amino acid para-benzoyl-phenylalanine allowed us to analyze contacts of the Pyrococcus furiosus TFB B-reader domain with site-specific radiolabeled DNA templates in preinitiation and initially transcribing complexes. Crosslink reactions at different initiation steps demonstrate interactions of TFB with DNA at registers +6 to +14, and reduced contacts at +15, with structural transitions of the B-reader domain detected at register +10. Our data suggest that the B-reader domain of TFB interacts with nascent RNA at register +6 and +8 and it is displaced from the transcribed-strand during the transition from +9 to +10, followed by the collapse of the transcription bubble and release of TFB from register +15 onwards.
Dexl, S., Reichelt, R., Kraatz, K., Schulz, S., Grohmann, D., Bartlett, M., and Thomm, M. (2018). Nucleic Acids Research, Volume 46, Issue 19, 1 January 1753, Pages 10066–10081.