Direct Modulation of RNA Polymerase Core Functions by Basal Transcription Factors

Abstract

Archaeal RNA polymerases (RNAPs) are recruited to promoters through the joint action of three basal transcription factors: TATA-binding protein, TFB (archaeal homolog of TFIIB), and TFE (archaeal homolog of TFIIE). Our results demonstrate several new insights into the mechanisms of TFB and TFE during the transcription cycle. (i) The N-terminal Zn ribbon of TFB displays a surprising degree of redundancy for the recruitment of RNAP during transcription initiation in the archaeal system. (ii) The B-finger domain of TFB participates in transcription initiation events by stimulating abortive and productive transcription in a recruitment-independent function. TFB thus combines physical recruitment of the RNAP with an active role in influencing the catalytic properties of RNAP during transcription initiation. (iii) TFB mutations are complemented by TFE, thereby demonstrating that both factors act synergistically during transcription initiation. (iv) An additional function of TFE is to dynamically alter the nucleic acid-binding properties of RNAP by stabilizing the initiation complex and destabilizing elongation complexes.

ACKNOWLEDGMENTS

We thank the members of Martin Buck's laboratory for advice regarding heteroduplex promoter variants and for many helpful discussions. We are especially grateful to Ramesh Wigneshweraraj, Peter Brick, Silvia Onesti, Kristine Arnvig, and Mohamed Ouhammouch for valuable comments on the manuscript.

This work was supported by a Wellcome Trust Project grant (grant 068764/Z/02/Z) to R.O.J.W.