Abstract
Hatchet RNAs are members of a novel self-cleaving ribozyme class that was recently discovered by using a bioinformatics search strategy. The consensus sequence and secondary structure of this class includes 13 highly conserved and numerous other modestly conserved nucleotides interspersed among bulges linking four base-paired substructures. A representative hatchet ribozyme from a metagenomic source requires divalent ions such as Mg2+ to promote RNA strand scission with a maximum rate constant of ∼4 min−1. As with all other small self-cleaving ribozymes discovered to date, hatchet ribozymes employ a general mechanism for catalysis involving the nucleophilic attack of a ribose 2′-oxygen atom on an adjacent phosphorus center. Kinetic characteristics of the reaction demonstrate that members of this ribozyme class have an essential requirement for divalent metal ions and that they might have a complex active site that employs multiple catalytic strategies to accelerate RNA cleavage by internal phosphoester transfer.
Highlights
Self-cleaving ribozymes that function by internal phosphoester transfer are the most diverse of the various classes of RNA enzymes found in nature (Ferré-D’Amaré and Scott 2010)
Given the novel consensus sequence and structure of hatchet RNAs, and given the distinctive kinetic features of the representatives examined in this study, it is clear that they constitute a novel self-cleaving ribozyme class
As more genomes are sequenced, and as additional correlations are made between certain gene types and self-cleaving ribozymes, it is likely that the total number of distinct ribozyme classes will continue to increase
Summary
Self-cleaving ribozymes that function by internal phosphoester transfer are the most diverse of the various classes of RNA enzymes found in nature (Ferré-D’Amaré and Scott 2010) They comprise nine of the 14 different ribozyme classes that have been discovered to date. A bioinformatics pipeline that employed comparative sequence and structural analysis algorithms was used to search for novel structured RNAs in a collection of noncoding regions near genes commonly associated with known self-cleaving ribozymes. One of these newly found ribozymes, called hatchet, was shown to undergo site-specific self-cleavage in the presence of Mg2+ ions (Weinberg et al 2015). Our findings suggest that the active site formed by this ribozyme class might be complex, and some representatives might be capable of promoting high-speed RNA cleavage
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