Structural variation and uniformity among tetraloop-receptor interactions and other loop-helix interactions in RNA crystal structures.

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.

Group II introns in eubacteria and archaea: ORF-less introns and new varieties.

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.

A three-dimensional model of a group II intron RNA and its interaction with the intron-encoded reverse transcriptase.

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.

deltaEF1 represses BMP-2-induced differentiation of C2C12 myoblasts into the osteoblast lineage.

Osteoblasts, derived from pluripotent mesenchymal precursor cells, acquire their differentiated phenotypes under the control of a series of regulatory factors, the best known of which is BMP-2. Our recent preliminary studies suggest that expression of deltaEF1, a member of the zinc finger-homeodomain transcription factor family, is significantly down-regulated as human mesenchymal stem cells (MSCs) are subjected to osteoblastic differentiation in the presence of BMP-2. Here we demonstrate that overexpression of deltaEF1 in murine pre-myoblast C2C12 cells resulted in a decrease in the mRNA levels of early osteoblast marker genes induced by BMP-2 including osterix and collagen type I. This inhibitory effect was further confirmed by decreased alkaline phosphatase (ALP) activities. Neither of the zinc finger clusters of deltaEF1 is necessary for its repressive effect on BMP-2-induced osteoblastic differentiation of C2C12 cells. Immunoprecipitation results indicated that deltaEF1 did not physically associate with Smads proteins, suggesting that the inhibitory effect of deltaEF1 may be Smad-independent. deltaEF1 overexpression in C2C12 cells resulted in down-regulation of activating protein-1 (AP-1) activities promoted by BMP-2. Moreover, deltaEF1 exhibited transrepression on murine osteocalcin gene which effect is partially mediated through diminishing of AP-1 signaling. These results suggest that deltaEF1 acts as a potent inhibitor of BMP-2-induced osteogenesis in vitro, in part, by differentially regulating the AP-1 signaling pathway.