Alternative conformations of the ColE1 replication primer modulate its interaction with RNA I.
Replication of the ColE1 plasmid is regulated by the interaction of its primer RNA with a small countertranscript (RNA I) that acts as a repressor of functional primer formation. The interaction is dependent on the specific conformations of the complementary RNA molecules. Early in its synthesis, primer adopts an "anti-RNA I" configuration. As transcription proceeds, it is preempted by formation of an alternative domain designated stem-loop IV. This conformational transition has a significant effect on the rate of association of RNA I with the primer in vitro. Nascent primer in the "anti-RNA I" conformation (135 nucleotides) interacts with RNA I 6-fold faster than primer in the stem-loop IV conformation (241 nucleotides), and 35-fold faster than a 567 nucleotide primer precursor. We propose that a conformation-dependent "window of susceptibility" of primer to RNA I exists during primer transcription, and that altered conformations play a role in modulating the rate of functional primer formation.
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D003086:Bacteriocin Plasmids; D001483:Base Sequence; D004261:DNA Replication; D004926:Escherichia coli / Q000235:genetics; D007700:Kinetics; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial / Q000235:genetics*; D014158:Transcription, Genetic
D012329:RNA, Bacterial