Abstract
BackgroundRNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular biology. Here we report the identification of a divergent RNA ligase 2 (DpRNL) from Diplonema papillatum (Diplonemea), a member of the kinetoplastids’ sister group.MethodsWe identified DpRNL with methods based on sensitive hidden Markov Model. Then, using homology modeling and molecular dynamics simulations, we established a three dimensional structure model of DpRNL complexed with ATP and Mg2+.ResultsThe 3D model of Diplonema was compared with available crystal structures from Trypanosoma brucei, bacteriophage T4, and two archaeans. Interaction of DpRNL with ATP is predicted to involve double π-stacking, which has not been reported before in RNA ligases. This particular contact would shift the orientation of ATP and have considerable consequences on the interaction network of amino acids in the catalytic pocket. We postulate that certain canonical amino acids assume different functional roles in DpRNL compared to structurally homologous residues in other RNA ligases 2, a reassignment indicative of constructive neutral evolution. Finally, both structure comparison and phylogenetic analysis show that DpRNL is not specifically related to RNA ligases from trypanosomes, suggesting a unique adaptation of the latter for RNA editing, after the split of diplonemids and kinetoplastids.ConclusionHomology modeling and molecular dynamics simulations strongly suggest that DpRNL is an RNA ligase 2. The predicted innovative reshaping of DpRNL’s catalytic pocket is worthwhile to be tested experimentally.Electronic supplementary materialThe online version of this article (doi:10.1186/s12900-015-0046-0) contains supplementary material, which is available to authorized users.
Highlights
RNA ligases 2 are scarce and scattered across the tree of life
Hidden Markov model (HMM)-based detection of a divergent RNA ligase 2 in Diplonema In general, proteins of D. papillatum display a low level of sequence similarity with homologs of other taxa, and are difficult to identify with tools based on sequence similarity such as BLAST [26]
We employed more sensitive methods based on Hidden Markov Models (HMMs)
Summary
RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular biology. RNA ligase from phage T4, the work horse of molecular biology research, is the best known member of a large protein family encompassing RNA and DNA ligation enzymes [1]. RNA ligase 1 enzymes are mainly present in viruses, mammals and fungi [8]. This enzyme class is typically involved in defense as exemplified by its founding member, the phage T4 RNL1, which is deployed in the counter-attack against antiviral strategies of bacteria [9], but is involved in tRNA intron splicing [10] and in Moreira et al BMC Structural Biology (2015) 15:20 the unconventional splicing initiating the unfolded protein response of the endoplasmatic reticulum. The biological role of RNA ligases 2 is unknown, except for the members of kinetoplastids [12]
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