RNA Structure in Transcription Elongation, Termination, and Antitermination

Abstract

INTRODUCTION
The past 25 years have brought us to an unprecedented level of appreciation and understanding of transcriptional mechanisms for controlling gene expression. Major efforts focused initially on promoters, but the importance of events after the initiation step of transcription was underscored by early paradigms from bacteriophage λ for both termination and antitermination of transcription. These included the bacterial termination factor rho, and the phage-encoded proteins N and Q, whose action antagonized it. By the late 1970s, the phenomenon of attenuation in bacterial biosynthetic operons showed clearly that elongation of transcription could be modulated in other surprising ways. During the subsequent decade, mechanistic studies illuminated many functional details in bacterial systems and were extended into eukaryotic systems. Through the 1980s, plausible models incorporated these observations and made clear the greater complexity that lay below the surface. This arose in part from the inherent dichotomy of elongation versus termination: Once under way, RNA polymerase grasps the template very securely to synthesize long RNA molecules rapidly and without error or premature arrest, yet it must stop and release with high efficiency at the designated end. Our glimpse of this conundrum encompasses the genetic commas, semicolons, colons, and periods of transcriptional punctuation, emphasizing the role of RNA in the context of new developments that challenge previous dogma. Only a few representative systems from the literature are described, as space constraints limit a more exhaustive treatment and, to be arbitrarily fair, citation of literature prior to 1992.

Definitions and Concepts
Any discussion of transcriptional...