Bulged-out nucleotides protect an antisense RNA from RNase III cleavage
(1995) In Nucleic Acids Research 23(4). p.571-579- Abstract
Bulged-out nucleotides or internal loops are present in the stem-loop structures of several antisense RNAs. We have used the antisense/target RNA system (CopA/CopT) that controls the copy number of plasmid R1 to examine the possible biological function of bulged-out nucleotides. Two regions within the major stem-loop of the antisense RNA, CopA, carry bulged-out nucleotides. Base pairing in either one or both of these regions of the stem was restored by site-specific mutagenesis and in one case a new internal loop was introduced. The set of mutant and wild-type CopA variants was characterized structurally in vitro. The results reported here indicate a possible function of the bulges: their presence protects CopA RNA from being a... (More)
Bulged-out nucleotides or internal loops are present in the stem-loop structures of several antisense RNAs. We have used the antisense/target RNA system (CopA/CopT) that controls the copy number of plasmid R1 to examine the possible biological function of bulged-out nucleotides. Two regions within the major stem-loop of the antisense RNA, CopA, carry bulged-out nucleotides. Base pairing in either one or both of these regions of the stem was restored by site-specific mutagenesis and in one case a new internal loop was introduced. The set of mutant and wild-type CopA variants was characterized structurally in vitro. The results reported here indicate a possible function of the bulges: their presence protects CopA RNA from being a substrate for the double-strand-specific enzyme RNase III. In vitro cleavage rates were drastically increased when either the lower or both bulges were absent. This is paralleled by a similar, but not identical, effect of the bulges on metabolic stability of the CopA RNAs in vivo. The degradation pathways of wild-type and mutant CopA in various strain backgrounds are discussed. In the accompanying paper, we address the significance of bulges in CopA for binding to the target RNA in vitro and for its inhibitory efficiency in vivo.
(Less)
- author
- Hjalt, Tord Å. H. LU and Wagner, E. Gerhart H.
- publishing date
- 1995-02-25
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Bacterial Proteins/metabolism, Base Sequence, Endoribonucleases/metabolism, Escherichia coli/enzymology, Escherichia coli Proteins, Half-Life, Molecular Sequence Data, Mutagenesis, Site-Directed, Nucleic Acid Conformation, R Factors/genetics, RNA, Antisense/chemistry, RNA, Bacterial/chemistry, Ribonuclease III, Rifampin/pharmacology, Transcription, Genetic/drug effects
- in
- Nucleic Acids Research
- volume
- 23
- issue
- 4
- pages
- 9 pages
- publisher
- Oxford University Press
- external identifiers
-
- pmid:7534906
- scopus:0028919939
- ISSN
- 0305-1048
- DOI
- 10.1093/nar/23.4.571
- language
- English
- LU publication?
- no
- id
- bf693b55-951c-46fc-9de0-3264d9ebb9ab
- date added to LUP
- 2023-11-16 11:37:31
- date last changed
- 2024-02-13 02:55:34
@article{bf693b55-951c-46fc-9de0-3264d9ebb9ab,
abstract = {{<p>Bulged-out nucleotides or internal loops are present in the stem-loop structures of several antisense RNAs. We have used the antisense/target RNA system (CopA/CopT) that controls the copy number of plasmid R1 to examine the possible biological function of bulged-out nucleotides. Two regions within the major stem-loop of the antisense RNA, CopA, carry bulged-out nucleotides. Base pairing in either one or both of these regions of the stem was restored by site-specific mutagenesis and in one case a new internal loop was introduced. The set of mutant and wild-type CopA variants was characterized structurally in vitro. The results reported here indicate a possible function of the bulges: their presence protects CopA RNA from being a substrate for the double-strand-specific enzyme RNase III. In vitro cleavage rates were drastically increased when either the lower or both bulges were absent. This is paralleled by a similar, but not identical, effect of the bulges on metabolic stability of the CopA RNAs in vivo. The degradation pathways of wild-type and mutant CopA in various strain backgrounds are discussed. In the accompanying paper, we address the significance of bulges in CopA for binding to the target RNA in vitro and for its inhibitory efficiency in vivo.</p>}},
author = {{Hjalt, Tord Å. H. and Wagner, E. Gerhart H.}},
issn = {{0305-1048}},
keywords = {{Bacterial Proteins/metabolism; Base Sequence; Endoribonucleases/metabolism; Escherichia coli/enzymology; Escherichia coli Proteins; Half-Life; Molecular Sequence Data; Mutagenesis, Site-Directed; Nucleic Acid Conformation; R Factors/genetics; RNA, Antisense/chemistry; RNA, Bacterial/chemistry; Ribonuclease III; Rifampin/pharmacology; Transcription, Genetic/drug effects}},
language = {{eng}},
month = {{02}},
number = {{4}},
pages = {{571--579}},
publisher = {{Oxford University Press}},
series = {{Nucleic Acids Research}},
title = {{Bulged-out nucleotides protect an antisense RNA from RNase III cleavage}},
url = {{http://dx.doi.org/10.1093/nar/23.4.571}},
doi = {{10.1093/nar/23.4.571}},
volume = {{23}},
year = {{1995}},
}