Sendai virus RNA polymerase scanning for mRNA start sites at gene junctions

Abstract

Mini-genomes expressing two reporter genes and a variable gene junction were used to study Sendai virus RNA polymerase (RdRp) scanning for the mRNA start signal of the downstream gene ( gs 2). We found that RdRp could scan the template efficiently as long as the initiating uridylate of gs 2 (3′ U CCCnnUUUC) was preceded by the conserved intergenic region (3′ GAA) and the last 3 uridylates of the upstream gene end signal ( ge 1; 3′ AUUCUU UUU ). The end of the leader sequence (3′ CUAAAA, which precedes gs 1) could also be used for gene2 expression, but this sequence was considerably less efficient. Increasing the distance between ge 1 and gs 2 (up to 200 nt) led to the progressive loss of gene2 expression, in which half of gene2 expression was lost for each 70 nucleotides of intervening sequence. Beyond 200 nt, gene2 expression was lost more slowly. Our results suggest that there may be two populations of RdRp that scan at gene junctions, which can be distinguished by the efficiency with which they can scan the genome template for gs .