Albany 2013: Book of Abstracts

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Conversation 18
June 11-15 2013
©Adenine Press (2012)

Secondary Structure and Domain Architecture of the 23S and 5S rRNAs

We report a de novo re-determination of the secondary structure (2° structure) and domain architecture of the 23S and 5S rRNAs. We used published three-dimensional structures, determined by x-ray diffraction, as input. We assigned nucleotides to helices by accepted molecular interaction and geometric criteria. The result is a significant revision of the 2° structure (Figure 1). The most important change is in the heart of the 23S rRNA, which is represented by an extended single-stranded region in the traditional 2° structure. Three-dimensional structures reveal this portion of the rRNA to be compact and double-helical. Twenty-one tertiary interactions in the traditional 2° structure are converted to secondary interactions in the revised 2° structure. The 5S rRNA is shifted and rotated to reflect its correct location and molecular interactions with the 23S rRNA. The revised 2° structure shows a clear and direct relationship with the three-dimensional structure. We have mapped various structural, functional and phylogenetic data onto the revised 2° structure and onto the traditional 2° structure to compare their utilities. The mapping is performed by the in house RiboVision webserver (available at http://apollo.chemistry.gatech.edu/RiboVision), which is intended for rapid retrieval, analysis, filtering, and display of a variety of ribosomal data. The revised 2° structure of the 23S rRNA shows architectural similarity with the 2° structure of the 16S rRNA, which was not previously apparent.

The revision of the 23S rRNA 2° structures compels a reconsideration of the domain architecture. We partitioned the 23S rRNA into domains using networking analysis of molecular interactions, calculations of 2D folding propensities, sphericity and compactness. We conclude that the best domain model for the 23S rRNA contains seven domains, not six as previously assumed. A newly proposed central domain (Domain 0) forms the essential core of the 23S rRNA, to which other six domains are rooted. The revised 2° structure and domain architecture of E. coli is generalizable to rRNAs of other species extending to all three major domains of the tree of life. We provide editable images of secondary structures with various data mapped on them (http://apollo.chemistry.gatech.edu/RibosomeGallery).


Figure 1. The revised secondary structure and domain architecture of the 23S and 5S rRNAs of E. coli. This secondary structure accurately represents all helices, and contains seven domains (Domain 0, orange; Domain I, purple; Domain II, blue; Domain III, magenta; Domain IV, yellow; Domain V, pink; Domain VI, green). In the conventional secondary structure the central single-stranded region is partitioned between multiple domains, whereas in the revised secondary structure, that same rRNA is helical and is fully within Domain 0. The 5S rRNA is light green and is placed in the proximity of Domain II to reflect its position in three dimensions and its interactions with the 23S rRNA.

This work was supported by the NASA Astrobiology Institute (NNA09DA78A).

Anton S. Petrov 1
Chad R. Bernier1
Eli Hershkovits1
Yuzhen Xue2
Chris C. Waterbury1
Chiaolong Hsiao1
Victor G. Stepanov3
Eric A. Gaucher4
Martha A. Grover2
Stephen C. Harvey1, 4
Nicholas V. Hud1
Roger M. Wartell4
George E. Fox3
Loren Dean Williams1

Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332
1School of Chemistry and Biochemistry, Georgia Institute of Technology
2School of Chemical and Biomolecular Engineering, Georgia Institute of Technology
3Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204
4School of Biology, Georgia Institute of Technology.

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