Functional and structural characterization of a putative discontinuous group I intron


Students: Matthew Knowe, Brooklyn Fillinger


Enzymes are Nature’s catalysts: they accelerate chemical reactions by several orders of magnitude, allowing even inherently slow reactions to proceed with the speed needed to sustain life. One of the challenges of bio-related research is to understand the power of enzymes.


Until a few years ago, we believed that ribozymes (enzymes made entirely of RNA) were formed by stretches of contiguous nucleotides that adopt complex three-dimensional structures in the cellular environment; however, recent work on the hammerhead ribozyme [1] showed that ‘discontinuous’ ribozymes, in which two RNA regions distant in sequence recombine in-vivo to form an active ribozyme, are also present in Nature.




In this project, we are investigating a putative discontinuous group I intron. Catalytic introns are particular ribozymes that excise themselves from the surrounding RNA. This ‘cut and paste’ process (splicing) allows, for example, formation of sequences that meaningfully encode for proteins. Dr S. O. Rogers (one of our collaborators) recently reported the existence of a minimal group I intron (the ‘PaSSU intron’, shown above) that lacks structural elements conserved in larger group I introns [2,3]. This intron splices when long flanking regions (exons) are present, but not when these exons are minimal. It is therefore possible that regions outside the intron assist the splicing process. We are measuring the reaction kinetics of introns with progressively removed flanking regions, and using structural probes to determine whether the removal of these flanking regions cause changes to the intron’s three-dimensional structure.


[1] Martick, M., Horan, L. H., Noller, H.F., and Scott, W.G.  (2008). A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA.  Nature 454, 899

[2] Harris, L., and Rogers, S.O. (2008). Splicing and evolution of an unusually small group I intron. Curr. Genet. 54, 213.


[3] Harris, L., and Rogers, S.O. (2011). Evolution of small putative group I introns in the SSU rRNA gene locus of Phialophora species.  BMC Res. Notes 4, 258.




Proposed secondary structure of the PaSSU intron. Lower-case letters represent exon regions.