[Show abstract][Hide abstract] ABSTRACT: Tetraloop-receptor interactions are prevalent structural units in RNAs, and include the GAAA/11-nt and GNRA-minor groove interactions. In this study, we have compiled a set of 78 nonredundant loop-helix interactions from X-ray crystal structures, and examined them for the extent of their sequence and structural variation. Of the 78 interactions in the set, only four were classical GAAA/11-nt motifs, while over half (48) were GNRA-minor groove interactions. The GNRA-minor groove interactions were not a homogeneous set, but were divided into five subclasses. The most predominant subclass is characterized by two triple base pair interactions in the minor groove, flanked by two ribose zipper contacts. This geometry may be considered the "standard" GNRA-minor groove interaction, while the other four subclasses are alternative ways to form interfaces between a minor groove and tetraloop. The remaining 26 structures in the set of 78 have loops interacting with mostly idiosyncratic receptors. Among the entire set, a number of sequence-structure correlations can be identified, which may be used as initial hypotheses in predicting three-dimensional structures from primary sequences. Conversely, other sequence patterns are not predictive; for example, GAAA loop sequences and GG/CC receptors bind to each other with three distinct geometries. Finally, we observe an example of structural evolution in group II introns, in which loop-receptor motifs are substituted for each other while maintaining the larger three-dimensional geometry. Overall, the study gives a more complete view of RNA loop-helix interactions that exist in nature.
[Show abstract][Hide abstract] ABSTRACT: Group II introns are a major class of ribozymes found in bacteria, mitochondria, and plastids. Many introns contain reverse transcriptase open reading frames (ORFs) that confer mobility to the introns and allow them to persist as selfish DNAs. Here, we report an updated compilation of group II introns in Eubacteria and Archaea comprising 234 introns. One new phylogenetic class is identified, as well as several specialized lineages. In addition, we undertake a detailed search for ORF-less group II introns in bacterial genomes in order to find undiscovered introns that either entirely lack an ORF or encode a novel ORF. Unlike organellar group II introns, we find only a handful of ORF-less introns in bacteria, suggesting that if a substantial number exist, they must be divergent from known introns. Together, these results highlight the retroelement character of bacterial group II introns, and suggest that their long-term survival is dependent upon retromobility.
[Show abstract][Hide abstract] ABSTRACT: Group II introns are self-splicing ribozymes believed to be the ancestors of spliceosomal introns. Many group II introns encode reverse transcriptases that promote both RNA splicing and intron mobility to new genomic sites. Here we used a circular permutation and crosslinking method to establish 16 intramolecular distance relationships within the mobile Lactococcus lactis Ll.LtrB-DeltaORF intron. Using these new constraints together with 13 established tertiary interactions and eight published crosslinks, we modeled a complete three-dimensional structure of the intron. We also used the circular permutation strategy to map RNA-protein interaction sites through fluorescence quenching and crosslinking assays. Our model provides a comprehensive structural framework for understanding the function of group II ribozymes, their natural structural variations, and the mechanisms by which the intron-encoded protein promotes RNA splicing and intron mobility. The model also suggests an arrangement of active site elements that may be conserved in the spliceosome.
[Show abstract][Hide abstract] ABSTRACT: This chapter discusses the progress and techniques of RNA structure and modeling. To understand the structure of RNA, it is necessary to first understand some of the unique biochemical properties associated with RNA and its structural elements. These properties directly lead to the formation of structural elements and motifs in tertiary structures. These include not only basic structure elements like helices, loops, bulges, and junctions but also less common elements like ribose zipper and tetraloop-receptor that contribute to the difficulty of tertiary structure prediction. The study of RNA structure started later than protein structure research, people followed the path of protein studies for experience and methods, such as crystallography and molecular dynamic simulation. A group of RNA molecules that have been used for structural studies are the ribozymes. A ribozyme is an RNA molecule that has the ability to catalyze a reaction. The characterization of RNA structure and structural dynamics is greatly enhanced by the application of chemical and enzymatic probes of RNA structure in solution. These probes enable to study RNA structures in conditions that are physiologically relevant and to investigate their interactions with partner molecules and to detect enzymatic active sites.
No preview · Article · Feb 2008 · Progress in Nucleic Acid Research and Molecular Biology