The tertiary structure of group II introns: implications for biological function and evolution

Abstract

Group II introns are some of the largest ribozymes in nature, and they are a major source of information about RNA assembly and tertiary structural organization. These introns are of biological significance because they are self-splicing mobile elements that have migrated into diverse genomes and played a major role in the genomic organization and metabolism of most life forms. The tertiary structure of group II introns has been the subject of many phylogenetic, genetic, biochemical and biophysical investigations, all of which are consistent with the recent crystal structure of an intact group IIC intron from the alkaliphilic eubacterium Oceanobacillus iheyensis. The crystal structure reveals that catalytic intron domain V is enfolded within the other intronic domains through an elaborate network of diverse tertiary interactions. Within the folded core, DV adopts an activated conformation that readily binds catalytic metal ions and positions them in a manner appropriate for reaction with nucleic acid targets. The tertiary structure of the group II intron reveals new information on motifs for RNA architectural organization, mechanisms of group II intron catalysis, and the evolutionary relationships among RNA processing systems. Guided by the structure and the wealth of previous genetic and biochemical work, it is now possible to deduce the probable location of DVI and the site of additional domains that contribute to the function of the highly derived group IIB and IIA introns.

Keywords::

• RNA splicing
• transposition
• ribozyme
• enzymology
• crystallography

Acknowledgements

I thank Kevin Keating for stimulating discussions on the probable location of derived domains, for critical reading of the manuscript and for assistance with the preparation of figures. I also thank Olga Fedorova and Amelia Johnson for assistance with figures and editing of the manuscript. I thank Philip Perlman and Marlene Belfort for stimulating discussions and suggestions.

Declaration of interest

I am an Investigator with the Howard Hughes Medical Institute, which supported this work. This work was also supported by a generous grant from the National Institutes of Health (GM50313). The author report no conflicts of interest. The author alone is responsible for the content and writing of the paper.

Editor: Marvin Wickens