STRUCTURAL AND FUNCTIONAL-PROPERTIES OF THE SEGMENTS OF LAMBDA-CRO MESSENGER-RNA THAT INTERACT WITH TRANSCRIPTION TERMINATION FACTOR RHO

Termination of transcription at tR1, the Rho-dependent terminator between genes cro and cII of bacteriophage λ, is dependent upon the structure of segments near the 3′ end of the nascent cro gene transcript and on contacts between Rho protein and a 3′ proximal segment called rut. The characteristics of the structure of cro RNA in the region from residue 220 to residue 355 in free, isolated RNA and in the presence of Rho or NusA proteins were analyzed by measuring relative rates of reactivity of individual nucleotides with chemicals and enzymes of defined specificities. The results indicate that the rut segments are single-stranded and become blocked to the action of the various probes in the presence of Rho factor. They also show that this region contains two stem-loop structures; one involves the boxB sequence of nutR, the other precedes the tR1 subsite II end points. The results provide direct evidence for a primary binding contact between Rho protein and the rut segment of cro RNA and demonstrate that this binding contact remains stable when the cro RNA is serving as a cofactor for ATP hydrolysis, an observation that is consistent with a mechanism in which Rho maintains contact with the rut region while it makes additional interactions with RNA that are coupled to ATP hydrolysis. © 1990.