Volume 388, Issue 7

Group II introns are large autocatalytic RNAs found in organellar genomes of plants and lower eukaryotes, as well as in some bacterial genomes. Interestingly, these ribozymes share characteristic traits with both spliceosomal introns and non-LTR retrotransposons and may have a common evolutionary ancestor. Furthermore, group II intron features such as structure, folding and catalytic mechanism differ considerably from those of other large ribozymes, making group II introns an attractive model system to gain novel insights into RNA biology and biochemistry. This review explores recent advances in the structural and mechanistic characterization of group II intron architecture and self-splicing.

Ribosomal DNA (rDNA) is a specialised chromosomal location that is dedicated to high-level transcription of ribosomal RNA genes. Interestingly, rDNAs are frequently interrupted by parasitic elements, some of which carry protein genes. These are non-LTR retrotransposons and group II introns that encode reverse transcriptase-like genes, and group I introns and archaeal introns that encode homing endonuclease genes (HEGs). Although rDNA-embedded protein genes are widespread in nuclei, organelles and bacteria, there is surprisingly little information available on how these genes are expressed. Exceptions include a handful of HEGs from group I introns. Recent studies have revealed unusual and essential roles of group I and group I-like ribozymes in the endogenous expression of HEGs. Here we discuss general aspects of rDNA-embedded protein genes and focus on HEG expression from group I introns in the nucleolus.

The major enzymatic activity of the ribosome is the catalysis of peptide bond formation. The active site – the peptidyl transferase center – is composed of ribosomal RNA (rRNA), and interactions between rRNA and the reactants, peptidyl-tRNA and aminoacyl-tRNA, are crucial for the reaction to proceed rapidly and efficiently. Here, we describe the influence of rRNA interactions with cytidine residues in A-site substrate analogs (C-puromycin or CC-puromycin), mimicking C74 and C75 of tRNA on the reaction. Base-pairing of C75 with G2553 of 23S rRNA accelerates peptide bond formation, presumably by stabilizing the peptidyl transferase center in its productive conformation. When C74 is also present in the substrate analog, the reaction is slowed down considerably, indicating a slow step in substrate binding to the active site, which limits the reaction rate. The tRNA-rRNA interactions lead to a robust reaction that is insensitive to pH changes or base substitutions in 23S rRNA at the active site of the ribosome.

The spliceosome, the multi-megadalton molecular machine that performs splicing, consists of over 200 different proteins and five small nuclear RNAs (snRNAs). Extensive mechanistic and structural similarities to self-splicing group II introns, large ribozymes found in prokaryotes and lower eukaryotes that catalyze an identical reaction, strongly suggest that the spliceosomal RNAs are in fact the catalytic components of the spliceosome. Of the five spliceosomal RNAs, U2 and U6 are the only ones that are absolutely required for both steps of splicing. These two snRNAs form an elaborate base-paired complex that might in fact constitute the active site of the spliceosome.

A novel chemo-genetic approach for the analysis of general acid-base catalysis by nucleobases in ribozymes is reviewed. This involves substitution of a C-nucleoside with imidazole in place of a natural nucleobase. The Varkud satellite ribozyme in which the nucleobase at the critical 756 position has been replaced by imidazole is active in both cleavage and ligation reactions. Similarly, a modified hairpin ribozyme with the nucleobase at position 8 substituted by imidazole is active in cleavage and ligation reactions. Although the rates are lower than those of the natural ribozymes, they are significantly greater than other variants at these positions. The dependence of the hairpin ribozyme reaction rates on pH has been studied. Both cleavage and ligation reactions display a bell-shaped pH dependence, consistent with general acid-base catalysis involving the nucleotide at position 8.

The HDV ribozyme is an RNA enzyme from the human pathogenic hepatitis delta virus (HDV) that has recently also been identified in the human genome. It folds into a compact, nested double-pseudoknot. We examined here the functional relevance of the capping loop L4 and the helical crossover J1/2, which tightly interlace the two helical stacks of the ribozyme. Peripheral structural elements such as these are present in cis -acting, but not trans -acting ribozymes, which may explain the order-of-magnitude decrease in cleavage activity observed in trans -acting ribozymes with promise in gene therapy applications. Comparison of a systematic set of cis - and trans -acting HDV ribozymes shows that the absence of either L4 or J1/2 significantly and independently impacts catalytic activity. Using terbium(III) footprinting and affinity studies, as well as distance measurements based on time-resolved fluorescence resonance energy transfer, we find that J1/2 is most important for conferring structural properties similar to those of the cis -acting ribozyme. Our results are consistent with a model in which removal of either a helical crossover or surprisingly a capping loop induces greater dynamics and expansion of the catalytic core at long range, impacting local and global folding, as well as catalytic function.

We analyzed processing of precursor tRNAs carrying a single 2′-deoxy, 2′-OCH 3 , or locked nucleic acid (LNA) modification at G+1 by Escherichia coli RNase P RNA in the absence and presence of its protein cofactor. The extra methyl or methylene group caused a substrate binding defect, which was rescued at higher divalent metal ion (M 2+ ) concentrations (more efficiently with Mn 2+ than Mg 2+ ), and had a minor effect on cleavage chemistry at saturating M 2+ concentrations. The 2′-OCH 3 and LNA modification at G+1 resulted in higher metal ion cooperativity for substrate binding to RNase P RNA without affecting cleavage site selection. This indicates disruption of an M 2+ binding site in enzyme-substrate complexes, which is compensated for by occupation of alternative M 2+ binding sites of lower affinity. The 2′-deoxy modification at G+1 caused at most a two-fold decrease in the cleavage rate; this mild defect relative to 2′-OCH 3 and LNA at G+1 indicates that the defect caused by the latter two is steric in nature. We propose that the 2′-hydroxyl at G+1 in the substrate is in the immediate vicinity of the M 2+ cluster at the phosphates of A67 to U69 in helix P4 of E. coli RNase P RNA.

The hammerhead ribozyme is a small, intensively studied catalytic RNA, and has been used as a prototype for understanding how RNA catalysis works. In 2003, the importance of a set of tertiary contacts that appear in natural sequences of the hammerhead RNA was finally understood. The presence of these contact regions in stems I and II in ‘full-length hammerhead ribozymes’ is accompanied by an up to 1000-fold catalytic rate enhancement, indicating a profound structural effect upon the active site. Although the new structure resolved most of what appeared to be irreconcilable differences with mechanistic studies in solution, it did so in a way that is simultaneously reconcilable with earlier crystallographic mechanistic studies, within the limits imposed by the truncated sequence of the minimal hammerhead. Here we present an analysis of the correspondence between the full-length and minimal hammerhead crystal structures, using adiabatic morphing calculations that for the first time test the hypothesis that the minimal hammerhead structure occasionally visits the active conformation, both in solution and in the crystalline state in a sterically allowed manner, and argue that this is the simplest hypothesis that consistently explains all of the experimental observations.

The hammerhead ribozyme is a small RNA endonuclease found in sub-viral plant pathogens, in transcripts from certain animal satellite DNAs and encoded at distinct loci of Arabidopsis thaliana . Kinetic analyses of tertiary stabilised ribozymes from peach latent mosaic viroid (PLMVd), Schistosoma mansoni and A. thaliana revealed a ten-fold difference in cleavage rates. Core nucleotide variations affected cleavage reactions least in the A. thaliana ribozyme, and most in the S. mansoni ribozyme. The reverse ligation reaction was catalysed efficiently by the PLMVd and A. thaliana ribozymes. The different behaviour of the individual hammerhead ribozymes is discussed in terms of structure and function.

Reversible chemistry, allowing for chain-forming as well as chain-breaking steps, is important for biological self-organization. In this context, ribozymes, catalyzing both RNA cleavage and ligation, may have significantly contributed to extending the sequence space and length of RNA molecules in early life forms. Here we present an engineered RNA that self-processes by passing through a number of cleavage and ligation steps. Intermolecular reactions compete with intramolecular reactions, resulting in a variety of products. Our results demonstrate that RNA can undergo self-oligomerization, which may have been important for extending the RNA genome size in RNA world scenarios.

We investigated the effect of plasminogen (Plg) on the internalization of recombinant soluble melanotransferrin (sMTf) using U87 human glioblastoma cells and murine embryonic fibroblasts (MEF) deficient in the low-density lipoprotein receptor-related protein (LRP). Using biospecific interaction analysis, both Glu- and Lys-Plg were shown to interact with immobilized sMTf. The binding of sMTf at the cell surface increased in the presence of both forms of Plg in control and in LRP-deficient MEF cells, whereas the uptake was strongly stimulated only by Lys-Plg in control MEF and U87 cells. In addition, in the presence of Lys-Plg, the internalization of sMTf was a saturable process, sensitive to temperature and dependent on the integrity of lysine residues. The addition of the receptor-associated protein, lactoferrin and aprotinin, as well as a monoclonal antibody (mAb) directed against LRP, inhibited the Lys-Plg-dependent uptake of sMTf. These results suggest an important role for LRP in this process. In addition, using binding and uptake assays in the presence of anti-annexin II mAb, we showed that annexin II might be responsible for the initial binding of sMTf in the presence of Plg. Our results suggest a Plg-mediated internalization mechanism for the clearance of sMTf via annexin II and LRP.

Microgravity (MG) results in a reduction in bone formation. Bone formation involves osteogenic differentiation from mesenchymal stem cells (hMSCs) in bone marrow. We modeled MG to determine its effects on osteogenesis of hMSCs and used activators or inhibitors of signaling factors to regulate osteogenic differentiation. Under osteogenic induction, MG reduced osteogenic differentiation of hMSCs and decreased the expression of osteoblast gene markers. The expression of Runx2 was also inhibited, whereas the expression of PPARγ2 increased. MG also decreased phosphorylation of ERK, but increased phosphorylation of p38MAPK. SB203580, a p38MAPK inhibitor, was able to inhibit the phosphorylation of p38MAPK, but did not reduce the expression of PPARγ2. Bone morphogenetic protein (BMP) increased the expression of Runx2. Fibroblast growth factor 2 (FGF2) increased the phosphorylation of ERK, but did not significantly increase the expression of osteoblast gene markers. The combination of BMP, FGF2 and SB203580 significantly reversed the effect of MG on osteogenic differentiation of hMSCs. Our results suggest that modeled MG inhibits the osteogenic differentiation and increases the adipogenic differentiation of hMSCs through different signaling pathways. Therefore, the effect of MG on the differentiation of hMSCs could be reversed by the mediation of signaling pathways.