Mechanism Of Sigma-Dependent Pausing In Regulation Of The Bacteriophage Lambda Late Gene Operon

Abstract

The movement of RNA polymerase (RNAP) along a DNA template is punctuated by frequent pauses during which the elongation complex persists at a single position for an extended period of time. Such pausing events have been shown to function in the regulation of gene expression at the level of transcription. A prototypical example of regulatory pausing is provided by the lambdoid phage late gene operon, in which a DNA-encoded [sigma]70-dependent pause element halts transcription to facilitate incorporation of the antiterminator Q into the paused elongation complex. Upon binding, Q triggers rapid escape of the now terminator-resistant elongation complex from the pause site. The [sigma]70-dependent pause element consists of a hexameric "-10-like sequence", which functions by capturing RNAP through contacts with the [sigma]70 subunit, and a "translocation pause element" (TPE), a pause-inducing element that underlies transcription pausing in E. coli. Here, we show that the TPE contributes to [sigma]70-dependent pausing by limiting the rate at which paused complexes attempt to escape the pause and we identify a novel sub-element that contributes to TPE function. Furthermore, we use a functional analogy to show that Q drives escape from the [sigma]70-dependent pause in a process that is mechanistically related to escape from a promoter during transcription initiation.