Atomic force microscopy reveals DNA bending during group II intron ribonucleoprotein particle integration into double-stranded DNA
| Autor: | Wolfgang Frey, James W. Noah, Alan M. Lambowitz, Soyeun Park, Jacob T Whitt, Jiri Perutka |
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| Rok vydání: | 2006 |
| Předmět: |
DNA
Bacterial Base pair Macromolecular Substances Biology Microscopy Atomic Force Biochemistry Models Biological Article chemistry.chemical_compound Bacterial Proteins Complementary DNA Escherichia coli Binding Sites Base Sequence Escherichia coli Proteins Ribonucleoprotein particle Intron RNA Group II intron Molecular biology Reverse transcriptase Introns Cell biology Lactococcus lactis chemistry Ribonucleoproteins Mutation Nucleic Acid Conformation DNA Protein Binding |
| Zdroj: | Biochemistry. 45(41) |
| ISSN: | 0006-2960 |
| Popis: | The mobile Lactococcus lactis Ll.LtrB group II intron integrates into DNA target sites by a mechanism in which the intron RNA reverse splices into one DNA strand, while the intron-encoded protein uses a C-terminal DNA endonuclease domain to cleave the opposite strand and then uses the cleaved 3’ end to prime reverse transcription of the inserted intron RNA. These reactions are mediated by an RNP particle that contains the intron-encoded protein and the excised intron lariat RNA, with both the protein and base pairing of the intron RNA used to recognize DNA target sequences. Here, computational analysis indicates that Escherichia coli DNA target sequences that support Ll.LtrB integration have greater predicted bendability than do random Escherichia coli genomic sequences, and atomic force microscopy shows that target DNA is bent during the reaction with Ll.LtrB RNPs. Time-course and mutational analyses show that DNA bending occurs after reverse splicing and requires subsequent interactions between the intron-encoded protein and the 3’-exon, which lead to two progressively larger bend angles. Our results suggest a model in which RNPs bend the target DNA by maintaining initial contacts with the 5’ exon, while engaging in subsequent 3’-exon interactions that successively position the scissile phosphate for bottom-strand cleavage at the DNA endonuclease active site and then reposition the 3’ end of the cleaved bottom strand at the reverse transcriptase active site for initiation of cDNA synthesis. Our findings indicate that bendability of the DNA target site is a significant factor for Ll.LtrB RNP integration. |
| Databáze: | OpenAIRE |
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