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The amazing world of bacterial structured RNAs.

Westhof E - Genome Biol. (2010)

Bottom Line: The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, Strasbourg, France. E.Westhof@ibmc-cnrs.unistra.fr

ABSTRACT
The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions.

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Related in: MedlinePlus

RNA secondary structures. Double lines between nucleotides indicate a strong Watson-Crick interaction between C and G; single lines indicate a weaker interaction between A and U. Nucleotides are colored as follows: blue, involved in Watson-Crick pairs; yellow, unpaired; red, involved in non-Watson-Crick pairs; green, the bulging G. The non-Watson-Crick pairs are named after the edges forming the H-bonded pairs and are indicated by: circle, Watson-Crick edge; square, Hoogsteen edge; triangle, Sugar edge. These symbols are blank when the two nucleotides approach in the trans orientation and dark when they approach in the cis orientation. Each panel shows the sequence with only Watson-Crick pairing on the left, the secondary structure with non-Watson-Crick pairing in the middle and the resulting three-dimensional structure on the right. (a) A G-bulged or loop E module completes a hairpin structure by forming non-Watson-Crick pairs within an internal loop. The sequential order of the usually observed set of non-Watson-Crick pairs is maintained, thereby defining a module. The structure of the G-bulged module shown is from helix H11 of the 23S rRNA of Escherichia coli (Protein DataBank (PDB) code 2AW4) [10]. (b) A G-bulged module organizes a three-way junction, leading to a rough co-axiality between two helical stems. The structure of the G-bulged module shown is the one at the junction of helices H16-H21-H22 from the 23S rRNA of Escherichia coli (PDB code 2AW4) [10]. Drawings courtesy of Jose Almeida Cruz.
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Figure 1: RNA secondary structures. Double lines between nucleotides indicate a strong Watson-Crick interaction between C and G; single lines indicate a weaker interaction between A and U. Nucleotides are colored as follows: blue, involved in Watson-Crick pairs; yellow, unpaired; red, involved in non-Watson-Crick pairs; green, the bulging G. The non-Watson-Crick pairs are named after the edges forming the H-bonded pairs and are indicated by: circle, Watson-Crick edge; square, Hoogsteen edge; triangle, Sugar edge. These symbols are blank when the two nucleotides approach in the trans orientation and dark when they approach in the cis orientation. Each panel shows the sequence with only Watson-Crick pairing on the left, the secondary structure with non-Watson-Crick pairing in the middle and the resulting three-dimensional structure on the right. (a) A G-bulged or loop E module completes a hairpin structure by forming non-Watson-Crick pairs within an internal loop. The sequential order of the usually observed set of non-Watson-Crick pairs is maintained, thereby defining a module. The structure of the G-bulged module shown is from helix H11 of the 23S rRNA of Escherichia coli (Protein DataBank (PDB) code 2AW4) [10]. (b) A G-bulged module organizes a three-way junction, leading to a rough co-axiality between two helical stems. The structure of the G-bulged module shown is the one at the junction of helices H16-H21-H22 from the 23S rRNA of Escherichia coli (PDB code 2AW4) [10]. Drawings courtesy of Jose Almeida Cruz.

Mentions: Such RNA architectures are maintained by a multitude of intramolecular contacts, with a resulting network of interactions dominated by non-Watson-Crick pairs. It has been observed that the non-Watson-Crick pairs organize themselves in RNA modules that are crucial for maintaining the three-dimensional structure. In RNA modules, various types of non-Watson-Crick pairs form a set that occurs in a conserved sequential order because of strong constraints due to chemical linkages and base-base stacking. Among those modules, a prominent one is the G-bulged module (Figure 1; also called the sarcin/ricin or loop E module because it occurs in the sarcin/ricin hairpin of the 23S rRNA and in the loop E of the eukaryotic 5S rRNA). In the example shown in Figure 1a, an internal loop of the secondary structure forms a set of non-Watson-Crick pairs typical of G-bulged modules with stacking of the bases and a compact helicoidal fold. RNA modules also organize multiple junctions of helices. In Figure 1b, the single strands joining the helices interact with each other, forming a G-bulged module and a three-way junction with a clear orientation of the helices. In addition, most RNA modules are adapted for binding to other elements or regions, contributing further to the overall architecture. For example, G-bulged modules contribute to RNA function either by RNA-RNA interactions or by RNA-protein contacts. In such instances, the set of non-Watson-Crick base pairs is maintained and the module binds as a whole to either RNA or protein [9].


The amazing world of bacterial structured RNAs.

Westhof E - Genome Biol. (2010)

RNA secondary structures. Double lines between nucleotides indicate a strong Watson-Crick interaction between C and G; single lines indicate a weaker interaction between A and U. Nucleotides are colored as follows: blue, involved in Watson-Crick pairs; yellow, unpaired; red, involved in non-Watson-Crick pairs; green, the bulging G. The non-Watson-Crick pairs are named after the edges forming the H-bonded pairs and are indicated by: circle, Watson-Crick edge; square, Hoogsteen edge; triangle, Sugar edge. These symbols are blank when the two nucleotides approach in the trans orientation and dark when they approach in the cis orientation. Each panel shows the sequence with only Watson-Crick pairing on the left, the secondary structure with non-Watson-Crick pairing in the middle and the resulting three-dimensional structure on the right. (a) A G-bulged or loop E module completes a hairpin structure by forming non-Watson-Crick pairs within an internal loop. The sequential order of the usually observed set of non-Watson-Crick pairs is maintained, thereby defining a module. The structure of the G-bulged module shown is from helix H11 of the 23S rRNA of Escherichia coli (Protein DataBank (PDB) code 2AW4) [10]. (b) A G-bulged module organizes a three-way junction, leading to a rough co-axiality between two helical stems. The structure of the G-bulged module shown is the one at the junction of helices H16-H21-H22 from the 23S rRNA of Escherichia coli (PDB code 2AW4) [10]. Drawings courtesy of Jose Almeida Cruz.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2864558&req=5

Figure 1: RNA secondary structures. Double lines between nucleotides indicate a strong Watson-Crick interaction between C and G; single lines indicate a weaker interaction between A and U. Nucleotides are colored as follows: blue, involved in Watson-Crick pairs; yellow, unpaired; red, involved in non-Watson-Crick pairs; green, the bulging G. The non-Watson-Crick pairs are named after the edges forming the H-bonded pairs and are indicated by: circle, Watson-Crick edge; square, Hoogsteen edge; triangle, Sugar edge. These symbols are blank when the two nucleotides approach in the trans orientation and dark when they approach in the cis orientation. Each panel shows the sequence with only Watson-Crick pairing on the left, the secondary structure with non-Watson-Crick pairing in the middle and the resulting three-dimensional structure on the right. (a) A G-bulged or loop E module completes a hairpin structure by forming non-Watson-Crick pairs within an internal loop. The sequential order of the usually observed set of non-Watson-Crick pairs is maintained, thereby defining a module. The structure of the G-bulged module shown is from helix H11 of the 23S rRNA of Escherichia coli (Protein DataBank (PDB) code 2AW4) [10]. (b) A G-bulged module organizes a three-way junction, leading to a rough co-axiality between two helical stems. The structure of the G-bulged module shown is the one at the junction of helices H16-H21-H22 from the 23S rRNA of Escherichia coli (PDB code 2AW4) [10]. Drawings courtesy of Jose Almeida Cruz.
Mentions: Such RNA architectures are maintained by a multitude of intramolecular contacts, with a resulting network of interactions dominated by non-Watson-Crick pairs. It has been observed that the non-Watson-Crick pairs organize themselves in RNA modules that are crucial for maintaining the three-dimensional structure. In RNA modules, various types of non-Watson-Crick pairs form a set that occurs in a conserved sequential order because of strong constraints due to chemical linkages and base-base stacking. Among those modules, a prominent one is the G-bulged module (Figure 1; also called the sarcin/ricin or loop E module because it occurs in the sarcin/ricin hairpin of the 23S rRNA and in the loop E of the eukaryotic 5S rRNA). In the example shown in Figure 1a, an internal loop of the secondary structure forms a set of non-Watson-Crick pairs typical of G-bulged modules with stacking of the bases and a compact helicoidal fold. RNA modules also organize multiple junctions of helices. In Figure 1b, the single strands joining the helices interact with each other, forming a G-bulged module and a three-way junction with a clear orientation of the helices. In addition, most RNA modules are adapted for binding to other elements or regions, contributing further to the overall architecture. For example, G-bulged modules contribute to RNA function either by RNA-RNA interactions or by RNA-protein contacts. In such instances, the set of non-Watson-Crick base pairs is maintained and the module binds as a whole to either RNA or protein [9].

Bottom Line: The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, Strasbourg, France. E.Westhof@ibmc-cnrs.unistra.fr

ABSTRACT
The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions.

Show MeSH
Related in: MedlinePlus