Structural basis for binding of the plasmid ColIb-P9 antisense Inc RNA to its target RNA with the 5'-rUUGGCG-3' motif in the loop sequence
| Autor: | Katsura Asano, Shigeyuki Yokoyama, Kiyoshi Mizobuchi, Tatsuya Niimi |
|---|---|
| Rok vydání: | 1998 |
| Předmět: |
DNA Replication
Base pair Molecular Sequence Data Bacteriocin Plasmids Computational biology Biology Biochemistry Nucleic acid thermodynamics Plasmid Bacterial Proteins RNA Antisense RNA Messenger Molecular Biology Genetics Messenger RNA Base Sequence DNA replication RNA Nucleic Acid Hybridization Hydrogen Bonding Cell Biology Gene Expression Regulation Bacterial Stem-loop DNA-Binding Proteins RNA Bacterial Nucleic Acid Conformation Pseudoknot |
| Zdroj: | The Journal of biological chemistry. 273(19) |
| ISSN: | 0021-9258 |
| Popis: | The sequence 5'-rUUGGCG-3' is conserved within the loop regions of antisense RNAs or their targets involved in replication of various prokaryotic plasmids. In IncIalpha plasmid ColIb-P9, the partially base paired 21-nucleotide loop of a stem-loop called structure I within RepZ mRNA contains this hexanucleotide sequence, and comprises the target site for the antisense Inc RNA. In this report, we find that the base pairing interaction at the 5'-rGGC-3' sequence in the hexanucleotide motif is important for interaction between Inc RNA and structure I. In addition, the 21-base loop domain of structure I is folded tighter than predicted, with the hexanucleotide sequence at the top. The second U residue in the sequence is favored for Inc RNA binding in a base-specific manner. On the other hand, the upper domain of the Inc RNA stem-loop is loosely structured, and maintaining the loop sequence single-stranded is important for the intermolecular interaction. Based on these results, we propose that a structural feature in the loop I domain, conferred probably by the conserved 5'-rUUGGCG-3' sequence, favors binding to a complementary, single-stranded RNA. This model also explains how the RepZ mRNA pseudoknot, described in the accompanying paper (Asano, K., and Mizobuchi, K. (1998) J. Biol. Chem. 273, 11815-11825) is formed specifically with structure I. A possible conformation adopted by the 5'-rUUGGCG-3' loop sequence is discussed. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|