Identification and characterization of a transcription pause site in rotavirus

In rotavirus, transcription of the 11 double-stranded RNA genome segments occurs within the structurally intact subviral particle, and nascent transcripts are released through channels penetrating the two capsid layers at the icosahedral vertices. To gain insight into the early molecular events in transcription, we used high-resolution polyacrylamide gel electrophoresis to investigate the length distribution of transcription products at various times following initiation. We observed that, in the subviral particle under normal conditions, transcript initiation and capping are followed by a momentary pause in elongation after the addition of 6 to 7 nucleotides. In the absence of the capping reaction cofactor S-adenosylmethionine, conditions under which the rate of nucleotide incorporation is reduced, we observe a significant decrease in the ratio of paused to full length transcripts. We propose that this pause site may represent the point at which specific molecular events take place to facilitate processive elongation. Furthermore, our results indicate that the presence of specific ligands on the viral surface, such as VP7 in the mature virion, inhibits polymerase function. From the perspective of the viral replication cycle, this inhibition may serve to ensure that transcription occurs with greatest efficiency only after the virus has entered the cytoplasm and assumed the form of a double layered particle.