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Genes and Development
Vol. 11, No. 17, pp. 2214-2226, September 1, 1997


RESEARCH PAPER
An RNA enhancer in a phage transcriptional antitermination complex functions as a structural switch

Leila Su,1,4 James T. Radek,1,4 Laura A. Labeots,1 Klaas Hallenga,1 Patrick Hermanto,1 Huifen Chen,1 Satoe Nakagawa,1 Ming Zhao,1 Steve Kates,2 and Michael A. Weiss1,3,5

1 Department of Biochemistry and Molecular Biology and Center for Molecular Oncology, The University of Chicago, Chicago, Illinois 60637-5419 USA; 2 PerSeptive Biosystems, Framingham, Massachusetts 01710 USA; 3 Department of Chemistry, The University of Chicago, Chicago, Illinois 60637 USA

Antitermination protein N regulates the transcriptional program of phage lambda  through recognition of RNA enhancer elements. Binding of an arginine-rich peptide to one face of an RNA hairpin organizes the other, which in turn binds to the host antitermination complex. The induced RNA structure mimics a GNRA hairpin, an organizational element of rRNA and ribozymes. The two faces of the RNA, bridged by a sheared GA base pair, exhibit a specific pattern of base stacking and base flipping. This pattern is extended by stacking of an aromatic amino acid side chain with an unpaired adenine at the N-binding surface. Such extended stacking is coupled to induction of a specific internal RNA architecture and is blocked by RNA mutations associated in vivo with loss of transcriptional antitermination activity. Mimicry of a motif of RNA assembly by an RNA-protein complex permits its engagement within the antitermination machinery.

[Key Words: Gene regulation; transcriptional elongation; nut site; RNA structure; RNA polymerase]

GENES & DEVELOPMENT 11:2214-2226 © 1997 by Cold Spring Harbor Laboratory Press ISSN 0890-9369/97 $5.00
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