PMID:15895996
| Citation |
Wong, T, Sosnick, TR and Pan, T (2005) Mechanistic insights on the folding of a large ribozyme during transcription. Biochemistry 44:7535-42 |
|---|---|
| Abstract |
RNA folding during transcription resembles folding in a cellular environment. We previously investigated the folding of a large ribozyme derived from a bacterial RNase P RNA during its transcription by the Escherichia coli RNA polymerase and the effect of the elongation factor NusA. We found that transcriptional pausing at a specific site induced by NusA significantly altered the folding pathway. In this work, we compare folding during transcription by the E. coli RNA polymerase of circularly permuted variants and site-specific mutants of the RNase P ribozyme to elucidate the molecular mechanism of transcriptional pausing and RNA folding. The effect of NusA-induced pausing depends on the order of RNA synthesis and only affects local folding of the RNA. Pausing likely prevents a misfolded structure between the 5' strand of a helix and its adjacent junction located in the specificity domain and a region known to bind single-stranded RNA located in the catalytic domain. These results lead to a structural model on how transcriptional pausing affects folding of RNase P RNA. Structural rearrangements of a nascent RNA transcript enhanced by transcriptional pausing may be a general feature of RNA folding during transcription. |
| Links |
PubMed Online version:10.1021/bi047560l |
| Keywords |
Base Sequence; Catalysis; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/genetics; Molecular Sequence Data; Mutagenesis, Site-Directed; Mutation; Nucleic Acid Conformation; Nucleic Acid Hybridization; Peptide Elongation Factors/chemistry; RNA, Catalytic/chemistry; RNA, Catalytic/genetics; Ribonuclease P/chemistry; Ribonuclease P/genetics; Transcription Factors/chemistry; Transcription, Genetic |
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