Secondary structure and domain architecture of the 23S and 5S rRNAs
Journal
Nucleic Acids Research
Journal Volume
41
Journal Issue
15
Pages
7522 - 7535
Date Issued
2013
Author(s)
Petrov, Anton S.
Bernier, Chad R.
Hershkovits, Eli
Xue, Yuzhen
Waterbury, Chris C.
Stepanov, Victor G.
Gaucher, Eric A.
Grover, Martha A.
Harvey, Stephen C.
Hud, Nicholas V.
Wartell, Roger M.
Fox, George E.
Williams, Loren Dean
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).
SDGs
Type
journal article