Restructuring of an RNA polymerase holoenzyme elongation complex by lambdoid phage Q proteins

^*Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853; and ^‡Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616

Contributed by Jeffrey W. Roberts

Abstract

The structure of an intermediate in the initiation to elongation transition of Escherichia coli RNA polymerase has been visualized through region-specific DNA cleavage by the hydroxyl radical reagent FeBABE. FeBABE was tethered to specific sites of the σ⁷⁰ subunit and incorporated into two specialized paused elongation complexes that obligatorily retain the σ⁷⁰ initiation subunit and are targets for modification by lambdoid phage late gene antiterminators. The FeBABE cleavage pattern reveals structures similar to open complex, except for notable changes to region 3 of σ⁷⁰ that might reflect the presence of stably bound transcript. Binding of the antiterminator protein Q displaces the reactivity of FeBABE conjugated to region 4 of σ⁷⁰, suggesting that σ⁷⁰ subunit rearrangement is a step in conversion of RNAP to the antiterminating form.

Footnotes

↵ † Present address: Howard Hughes Medical Institute, University of California, Molecular and Cell Biology, 401 Barker Hall, Berkeley, CA 94720-3204.
↵ § Present address: Sandia National Laboratories, P.O. Box 969 MS9951, Livermore, CA 94551-0969.
↵ ¶ To whom reprint requests should be addressed. E-mail: jwr7{at}cornell.edu.
This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected on April 27, 1999.
Abbreviations:

RNAP,

RNA polymerase;

ds,

double-stranded;

ss,

single-stranded