RNA-binding domain proteins in Kinetoplastids: a comparative analysis

Abstract

RNA-binding proteins are important in many aspects of RNA processing, function, and destruction. One class of such proteins contains the RNA recognition motif (RRM), which consists of about 90 amino acid residues, including the canonical RNP1 octapeptide: (K/R)G(F/Y)(G/A)FVX(F/Y). We used a variety of homology searches to classify all of the RRM proteins of the three kinetoplastids Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major. All three organisms have similar sets of RRM-containing protein orthologues, suggesting common posttranscriptional processing and regulatory pathways. Of the 75 RRM proteins identified in T. brucei, only 13 had clear homologues in other eukaryotes, although 8 more could be given putative functional assignments. A comparison with the 18 RRM proteins of the obligate intracellular parasite Encephalitozoon cuniculi revealed just 3 RRM proteins which appear to be conserved at the primary sequence level throughout eukaryotic evolution: poly(A) binding protein, the rRNA-processing protein MRD1, and the nuclear cap binding protein.

FIG. 1.

Comparison of RRM proteins in Encephalitozoon cuniculi, Trypanosoma brucei, Saccharomyces cerevisiae, Plasmodium falciparum, Schizosaccharomyces pombe, Caenorhabditis elegans, and Brachydanio rerio. The proteins were classified into groups according to the number of RRMs.

FIG. 2.

Phylogenetic tree of the T. brucei RNA-binding-domain proteins. Alignments of the 75 sequences from T. brucei were performed with the ClustalW algorithm using the DNAStar package, and the radial tree was plotted with TreeView software.

FIG. 3.

Domain structures of T. brucei proteins found mainly in the lower half of Fig. 2. Locus numbers are in the left column, and protein names are on the right. Different domains are specific colors as shown on the adjacent blocks; the strongest RNA-binding-domain matches are black, and the weakest are light gray. Proteins encoded by adjacent genes are bracketed.

FIG. 4.

Domain structures of T. brucei proteins found mainly in the upper half of Fig. 2. The key is as for Fig. 3. DRBD17 did not fit and so is shown broken into two portions.