Mitochondrial proteins and complexes in Leishmania and Trypanosoma involved in U-insertion/deletion RNA editing

Abstract

A number of mitochondrial proteins have been identified in Leishmania sp. and Trypanosoma brucei that may be involved in U-insertion/deletion RNA editing. Only a few of these have yet been characterized sufficiently to be able to assign functional names for the proteins in both species, and most have been denoted by a variety of species-specific and laboratory-specific operational names, leading to a terminology confusion both within and outside of this field. In this review, we summarize the present status of our knowledge of the orthologous and unique putative editing proteins in both species and the functional motifs identified by sequence analysis and by experimentation. An online Supplemental sequence database (http://164.67.60.200/proteins/protsmini1.asp) is also provided as a research resource.

FIGURE 1.

L-complex proteins with protein- and nucleic acid-binding motifs. The locations of the tryptic peptide sequences used for the L. major gene identifications are indicated by triangles in this and the following figures. All motif identifications in this and the following figures were performed using SMART (http://smart.embl-heidelberg.de/) and PFAM (http://www.sanger.ac.uk/Software/Pfam/index.shtml). The e-values are indicated in parentheses. Mitochondrial target signals were identified by MitoProt (http://www.mips.biochem.mpg.de/cgi-bin/proj/medgen/mitofilter), SMART, or SignalP (http://www.cbs.dtu.dk/services/SignalP/). The probabilities from MitoProt are given above the figure. Note that the motifs in LC-10 and LC-7b were identified by similarity with the SSB motif in LC-11. All sequences were obtained from the GeneDB Leishmania major and Trypanosoma brucei databases.

FIGURE 2.

L-complex proteins with RNase III motifs. Note that the motif in LC-8 was identified by similarity with the RNase III motif in LC-6a. The L. major homologs to the T. brucei MP90 and MP67 were identified by database mining.

FIGURE 3.

L-complex proteins with nuclease motifs. The LC-3 protein identified by mass spectrometry lacks most of the Exo_endo_phos motif present in MP99, but otherwise is very similar.

FIGURE 4.

The L. major L-complex RET2 3′-TUTase. The homolog in T. brucei was identified by database searching (Aphasizhev et al. 2002) and has been characterized experimentally (Ernst et al. 2003).

FIGURE 5.

The L-complex REL1 and REL2 RNA ligases. Five conserved ligase motifs (McManus et al. 2001) are indicated as is the location of the lysine residues that covalently bind AMP. These motifs can be recognized by multiple alignments with known ligase enzymes.

FIGURE 6.

Multiple alignments of portions of selected genes to illustrate the five conserved motifs in REL1 and RELL2 characteristic of DNA and RNA ligases (Shuman and Schwer 1995; Odell et al. 2000; McManus et al. 2001). (T3) Bacteriophage T3; (T7) bacteriophage T7; (Vac) Vaccinia virus; (At) Arabidopsis thaliana; (Mj) Methanocaldococcus jannaschii; (Cj) Campylobacter jejuni; (Sc) Saccharomyces cerevisiae; (Hu) human; (Ec) E. coli; (Ae) Aquifex aeolicus; (Mg) Mycoplasma genitalium; (T4) bacteriophage T4; (ChlV) Chlorella virus; (Tb) T. brucei; (Ce) Caenorhabditis elegans; (Lt) L. tarentolae; (Lm) L. major; (*) αPO₄-binding residues; ($) metal-binding residues; (@) ribose O-binding residue; (#) residue binding to Arg; (&) adenine-binding residue.

FIGURE 7.

MRP-complex proteins. The L. major MRP RNA-binding proteins and the three associated proteins (AP1, AP2, AP3) identified by double affinity isolation (Aphasizhev et al. 2003b) are indicated.

FIGURE 8.

RET1 proteins. The L. major and T. brucei RET1 TUTases are shown (Aphasizhev et al. 2002).

FIGURE 9.

Several proteins that may be involved in RNA editing. The L. major orthologs of the RNA-binding proteins, RBP16 and RGGm, and the putative helicase, mHel61, are shown. The T. brucei REAP-1 is shown because there is no ortholog of this protein in the L. major database.

FIGURE 10.

Diagrammatic model for higher-order organization of editing complexes. The L-complex is shown as a dimer, for which the evidence is suggestive, and the three complexes are shown as interacting via RNA. The gRNA and mRNA indicated are the most likely candidates, but the existence of other RNA species has not been ruled out. The gRNA structure shown is taken from the model of Hermann et al. (1997).