Limits...
Secondary structure and domain architecture of the 23S and 5S rRNAs.

Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD - Nucleic Acids Res. (2013)

Bottom Line: We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness.The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed.Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.

ABSTRACT
We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery).

Show MeSH
The 2° structures and domain architectures of the 23S and 5S rRNAs of E. coli. (a) The traditional 2° structurephylo, which is sheared into two fragments, and contains a central single-stranded region and six domains (Domain I, purple; Domain II, blue; Domain III, magenta; Domain IV, yellow; Domain V, pink; Domain VI, green), and (b) 2° structure3D, which accurately represents all helices, and contains seven domains (Domain 0 in orange; Domains I-VI are colored as in panel 1a). In 2° structurephylo, the central single-stranded region is partitioned between multiple domains, whereas in 2° structure3D, that same rRNA is double-helical and is fully contained within Domain 0. The 5S rRNA is light green and is placed in the proximity of Domain II in 2° structure3D to reflect its position in three dimensions and its interactions with the 23S rRNA.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3753638&req=5

gkt513-F1: The 2° structures and domain architectures of the 23S and 5S rRNAs of E. coli. (a) The traditional 2° structurephylo, which is sheared into two fragments, and contains a central single-stranded region and six domains (Domain I, purple; Domain II, blue; Domain III, magenta; Domain IV, yellow; Domain V, pink; Domain VI, green), and (b) 2° structure3D, which accurately represents all helices, and contains seven domains (Domain 0 in orange; Domains I-VI are colored as in panel 1a). In 2° structurephylo, the central single-stranded region is partitioned between multiple domains, whereas in 2° structure3D, that same rRNA is double-helical and is fully contained within Domain 0. The 5S rRNA is light green and is placed in the proximity of Domain II in 2° structure3D to reflect its position in three dimensions and its interactions with the 23S rRNA.

Mentions: The ribosome, a macromolecular assembly of ribosomal RNAs (rRNAs) and ribosomal proteins (rProteins), synthesizes coded proteins in every cell of every organism. The ribosome comprises of large and small subunits that catalyze peptide bond formation (LSU) and decode mRNA (SSU). A key advance in understanding the ribosome was the determination of rRNA secondary structures (2° structures) by Brimacombe (1), Branlant (2) and Noller and Gutell (3). Noller and Gutell outlined the broadly appropriated ‘canonical’ 2° structure of the bacterial 23S rRNA (Figure 1a). Hundreds of 2° structures of rRNAs from a wide variety of organisms and organelles are available (3–10).Figure 1.


Secondary structure and domain architecture of the 23S and 5S rRNAs.

Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD - Nucleic Acids Res. (2013)

The 2° structures and domain architectures of the 23S and 5S rRNAs of E. coli. (a) The traditional 2° structurephylo, which is sheared into two fragments, and contains a central single-stranded region and six domains (Domain I, purple; Domain II, blue; Domain III, magenta; Domain IV, yellow; Domain V, pink; Domain VI, green), and (b) 2° structure3D, which accurately represents all helices, and contains seven domains (Domain 0 in orange; Domains I-VI are colored as in panel 1a). In 2° structurephylo, the central single-stranded region is partitioned between multiple domains, whereas in 2° structure3D, that same rRNA is double-helical and is fully contained within Domain 0. The 5S rRNA is light green and is placed in the proximity of Domain II in 2° structure3D to reflect its position in three dimensions and its interactions with the 23S rRNA.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3753638&req=5

gkt513-F1: The 2° structures and domain architectures of the 23S and 5S rRNAs of E. coli. (a) The traditional 2° structurephylo, which is sheared into two fragments, and contains a central single-stranded region and six domains (Domain I, purple; Domain II, blue; Domain III, magenta; Domain IV, yellow; Domain V, pink; Domain VI, green), and (b) 2° structure3D, which accurately represents all helices, and contains seven domains (Domain 0 in orange; Domains I-VI are colored as in panel 1a). In 2° structurephylo, the central single-stranded region is partitioned between multiple domains, whereas in 2° structure3D, that same rRNA is double-helical and is fully contained within Domain 0. The 5S rRNA is light green and is placed in the proximity of Domain II in 2° structure3D to reflect its position in three dimensions and its interactions with the 23S rRNA.
Mentions: The ribosome, a macromolecular assembly of ribosomal RNAs (rRNAs) and ribosomal proteins (rProteins), synthesizes coded proteins in every cell of every organism. The ribosome comprises of large and small subunits that catalyze peptide bond formation (LSU) and decode mRNA (SSU). A key advance in understanding the ribosome was the determination of rRNA secondary structures (2° structures) by Brimacombe (1), Branlant (2) and Noller and Gutell (3). Noller and Gutell outlined the broadly appropriated ‘canonical’ 2° structure of the bacterial 23S rRNA (Figure 1a). Hundreds of 2° structures of rRNAs from a wide variety of organisms and organelles are available (3–10).Figure 1.

Bottom Line: We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness.The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed.Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.

ABSTRACT
We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery).

Show MeSH