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).
Highlights
The ribosome, a macromolecular assembly of ribosomal RNAs and ribosomal proteins, synthesizes coded proteins in every cell of every organism
The most significant discrepancy is in the heart of the 23S ribosomal RNAs (rRNAs), which is represented by extended single-strands in the traditional 2 structure (Figure 1a)
We provide highresolution editable versions of both 2 structure3D and 2 structurephylo mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution and partitioning of rRNA into helices and domains
Summary
The ribosome, a macromolecular assembly of ribosomal RNAs (rRNAs) and ribosomal proteins (rProteins), synthesizes coded proteins in every cell of every organism. 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]. RNA 2 structures, with symbolic representations of base pairs, double-helices, loops, bulges and singlestrands, provide frameworks for understanding structure, folding and function and for organizing a wide variety of information. A second key advance in understanding the ribosome was the determination of high-resolution 3D structures [10,11,12,13,14,15,16,17,18] from all three primary domains of the tree of life; Bacteria, Archaea and Eukaryota.
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