Secondary Structures of rRNAs from All Three Domains of Life

Abstract

Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision).

The RNA Base-Pairing Problem and Base-Pairing Solutions

“…Thompson and Hearst combined the in solution psoralen crosslinking, 2D gel purification, photoreversal and enzymatic sequencing to discover 13 basepaired regions in the E. coli 16S rRNA (Figure 1G) (Thompson and Hearst, 1983). While most of the duplexes from crosslinking are consistent with the evolutionary model built by Noller and Woese and the crystal structure model (Noller and Woese, 1981; Petrov et al, 2014), a few of them could be artifacts of in vitro folding (see review by (Sergiev et al, 2001; Whirl-Carrillo et al, 2002)). Nevertheless, these heroic efforts demonstrated the possibility of using psoralen to study complex RNAs.…”

Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development

“…Asterisks indicate the 28S rRNA regions that interact with 5.8S rRNA. (B) The putative secondary structures for maternal-and somatic-type 5.8S rRNA and their interactions with the equivalent 28S rRNAs are shown (Petrov et al 2014). The region that undergoes the conformational switch and interacts with ribosome-dissociating factors is highlighted in light green (Graifer et al 2005).…”

“…The 18S conserved "sticky regions" (four major regions that are in ESs 3S, 6S, 7S, 12S, and two minor in front of the ESs 3S and 6S) were adapted from Pánek et al (2013). Zebrafish rRNAs secondary structures and structural domains were modeled after the 3D ribosome structure of Homo sapiens (http://apollo.chemistry.gatech.edu/RibosomeGallery) (Petrov et al 2014).…”

The Ribosome Challenge to the RNA World

“…Each structure is experimentally determined by X-ray diffraction or Cryo-EM. This figure is reproduced from Petrov et al 2014b (Petrov et al 2013(Petrov et al , 2014a from four species of varying complexity. rRNA domains are indicated by color.…”