Leontis N B, Stombaugh J, Westhof E
Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules Article de journal
Dans: Biochimie, vol. 84, no. 9, p. 961-973, 2002, ISBN: 12458088, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial/*chemistry/genetics RNA, Base Pairing Base Sequence Catalytic Domain Conserved Sequence Databases, Factual Models, Molecular *Nucleic Acid Conformation RNA, Non-P.H.S. Support, P.H.S., Ribosomal/*chemistry/genetics Sequence Alignment Support, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules},
author = {N B Leontis and J Stombaugh and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12458088},
isbn = {12458088},
year = {2002},
date = {2002-01-01},
journal = {Biochimie},
volume = {84},
number = {9},
pages = {961-973},
abstract = {The traditional way to infer RNA secondary structure involves an iterative process of alignment and evaluation of covariation statistics between all positions possibly involved in basepairing. Watson-Crick basepairs typically show covariations that score well when examples of two or more possible basepairs occur. This is not necessarily the case for non-Watson-Crick basepairing geometries. For example, for sheared (trans Hoogsteen/Sugar edge) pairs, one base is highly conserved (always A or mostly A with some C or U), while the other can vary (G or A and sometimes C and U as well). RNA motifs consist of ordered, stacked arrays of non-Watson-Crick basepairs that in the secondary structure representation form hairpin or internal loops, multi-stem junctions, and even pseudoknots. Although RNA motifs occur recurrently and contribute in a modular fashion to RNA architecture, it is usually not apparent which bases interact and whether it is by edge-to-edge H-bonding or solely by stacking interactions. Using a modular sequence-analysis approach, recurrent motifs related to the sarcin-ricin loop of 23S RNA and to loop E from 5S RNA were predicted in universally conserved regions of the large ribosomal RNAs (16S- and 23S-like) before the publication of high-resolution, atomic-level structures of representative examples of 16S and 23S rRNA molecules in their native contexts. This provides the opportunity to evaluate the predictive power of motif-level sequence analysis, with the goal of automating the process for predicting RNA motifs in genomic sequences. The process of inferring structure from sequence by constructing accurate alignments is a circular one. The crucial link that allows a productive iteration of motif modeling and realignment is the comparison of the sequence variations for each putative pair with the corresponding isostericity matrix to determine which basepairs are consistent both with the sequence and the geometrical data.},
note = {0300-9084
Journal Article},
keywords = {Bacterial/*chemistry/genetics RNA, Base Pairing Base Sequence Catalytic Domain Conserved Sequence Databases, Factual Models, Molecular *Nucleic Acid Conformation RNA, Non-P.H.S. Support, P.H.S., Ribosomal/*chemistry/genetics Sequence Alignment Support, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Moine H, Nurse K, Ehresmann B, Ehresmann C, Ofengand J
Conformational analysis of Escherichia coli 30S ribosomes containing the single-base mutations G530U, U1498G, G1401C, and C1501G and the double-base mutation G1401C/C1501G Article de journal
Dans: Biochemistry, vol. 36, no. 44, p. 13700-13709, 1997, ISBN: 9354641, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemical synthesis/*chemistry/genetics Ribosomes/chemistry/genetics Structure-Activity Relationship Support, Bacterial/*chemistry/genetics RNA, Base Sequence Cytosine Nucleotides/genetics Deoxyuridine Escherichia coli/genetics Guanine Nucleotides/genetics Molecular Sequence Data *Mutagenesis, Non-U.S. Gov't, Ribosomal, Site-Directed *Nucleic Acid Conformation RNA, Unité ARN
@article{,
title = {Conformational analysis of Escherichia coli 30S ribosomes containing the single-base mutations G530U, U1498G, G1401C, and C1501G and the double-base mutation G1401C/C1501G},
author = {H Moine and K Nurse and B Ehresmann and C Ehresmann and J Ofengand},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9354641},
isbn = {9354641},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry},
volume = {36},
number = {44},
pages = {13700-13709},
abstract = {Biochemical and genetic studies have pointed out the importance of several sites in 16S ribosomal RNA of Escherichia coli in the decoding process. These sites consist of the core of the decoding center (1400/1500 region) and two other segments (530 and 1050/1200 regions). To detect a possible structural link between these functionally related regions, we analyzed their sensitivity to conformational changes induced by mutations which are located in each of these regions and are known to affect the decoding process. The conformations of five segments of 16S rRNA (1-106, 406-569, 780-978, 997-1247, and 1334-1519) were analyzed by chemical probing of 30S ribosomes containing the following mutations: G530U, U1498G, G1401C, C1501G, and G1401C/C1501G. Ribosomes reconstituted with natural wild-type 16S RNA showed only minor conformational differences with respect to ribosomes isolated from cells. When 16S RNA made in vitro replaced natural 16S RNA, a slightly looser conformation of the central core region was found. Mutant ribosomes made by reconstitution with mutant 16S RNA made in vitro showed conformational effects which were in all cases localized to the region of secondary structure surrounding the site of mutation. Although the core of the decoding center (1400/1500 region) and the two other sites (530 and 1050/1200 regions) participating in the decoding function have been functionally linked, our data indicate that they are structurally independent. They also provide evidence for an unusual structure of the 1400/1500 decoding center, possibly involving noncanonical interactions. Furthermore, the absence of any conformational effect induced by the G530U mutation except at the site of mutation itself points to its direct, as opposed to indirect, involvement in the decoding function of the ribosome.},
note = {0006-2960
Journal Article},
keywords = {16S/chemical synthesis/*chemistry/genetics Ribosomes/chemistry/genetics Structure-Activity Relationship Support, Bacterial/*chemistry/genetics RNA, Base Sequence Cytosine Nucleotides/genetics Deoxyuridine Escherichia coli/genetics Guanine Nucleotides/genetics Molecular Sequence Data *Mutagenesis, Non-U.S. Gov't, Ribosomal, Site-Directed *Nucleic Acid Conformation RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}