COMPLEXES OF N-ANTITERMINATION PROTEIN OF PHAGE-LAMBDA WITH SPECIFIC AND NONSPECIFIC RNA TARGET SITES ON THE NASCENT TRANSCRIPT

The mechanisms that control N protein dependent antitermination in pha ge lambda have counterparts in many eukaryotic systems, including spec ific regulatory interactions of the antitermination protein with the n ascent RNA transcript. Here we describe the specific and nonspecific R NA binding modes of antitermination protein N. These modes differ mark edly in RNA binding affinity and in structure. N protein, either free in solution or as a complex with nonspecific RNA, lacks observable sec ondary and tertiary structure and binds RNA sequences indiscriminately with a dissociation constant (K-d) of similar to 10(-6) M. In contras t N becomes partially folded with at least 16-18 amino acids of ordere d alpha-helical structure and binds much more tightly (K-d congruent t o 10(-9) M) on forming a highly specific 1:1 complex with its cognate boxB RNA hairpin. These observations and others are used to help defin e a bipartite model of N-dependent antitermination in which these spec ific and nonspecific interactions control the binding of N to the nasc ent transcript, Finally the role of RNA looping in delivering the boun d N to the transcription complex and determining the stability (and th us the terminator specificity) of the resulting antitermination intera ction of N with the RNA polymerase is considered in quantitative terms .