Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme
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Rebecca A. Tinsley
Abstract
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.
©2007 by Walter de Gruyter Berlin New York
Articles in the same Issue
- 25 years of catalytic RNA: looking younger than ever!
- On the occasion of the 25th anniversary of the discovery of catalytic RNA
- An overview of the RNA world – for now
- Group II introns: structure, folding and splicing mechanism
- Expression of protein-coding genes embedded in ribosomal DNA
- Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs
- The spliceosome: a ribozyme at heart?
- A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes
- Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme
- A 2′-methyl or 2′-methylene group at G+1 in precursor tRNA interferes with Mg2+ binding at the enzyme-substrate interface in E-S complexes of E. coli RNase P
- Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism
- Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof
- RNA self-processing towards changed topology and sequence oligomerization
- Plasminogen-dependent internalization of soluble melanotransferrin involves the low-density lipoprotein receptor-related protein and annexin II
- Could the effect of modeled microgravity on osteogenic differentiation of human mesenchymal stem cells be reversed by regulation of signaling pathways?
Articles in the same Issue
- 25 years of catalytic RNA: looking younger than ever!
- On the occasion of the 25th anniversary of the discovery of catalytic RNA
- An overview of the RNA world – for now
- Group II introns: structure, folding and splicing mechanism
- Expression of protein-coding genes embedded in ribosomal DNA
- Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs
- The spliceosome: a ribozyme at heart?
- A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes
- Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme
- A 2′-methyl or 2′-methylene group at G+1 in precursor tRNA interferes with Mg2+ binding at the enzyme-substrate interface in E-S complexes of E. coli RNase P
- Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism
- Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof
- RNA self-processing towards changed topology and sequence oligomerization
- Plasminogen-dependent internalization of soluble melanotransferrin involves the low-density lipoprotein receptor-related protein and annexin II
- Could the effect of modeled microgravity on osteogenic differentiation of human mesenchymal stem cells be reversed by regulation of signaling pathways?
