A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum

Abstract

Background: Plasmodium parasites are causative agents of malaria which affects >500 million people and claims approximately 2 million lives annually. The completion of Plasmodium genome sequencing and availability of PlasmoDB database has provided a platform for systematic study of parasite genome. Aminoacyl-tRNA synthetases (aaRSs) are pivotal enzymes for protein translation and other vital cellular processes. We report an extensive analysis of the Plasmodium falciparum genome to identify and classify aaRSs in this organism.

Results: Using various computational and bioinformatics tools, we have identified 37 aaRSs in P. falciparum. Our key observations are: (i) fraction of proteome dedicated to aaRSs in P. falciparum is very high compared to many other organisms; (ii) 23 out of 37 Pf-aaRS sequences contain signal peptides possibly directing them to different cellular organelles; (iii) expression profiles of Pf-aaRSs vary considerably at various life cycle stages of the parasite; (iv) several PfaaRSs posses very unusual domain architectures; (v) phylogenetic analyses reveal evolutionary relatedness of several parasite aaRSs to bacterial and plants aaRSs; (vi) three dimensional structural modelling has provided insights which could be exploited in inhibitor discovery against parasite aaRSs.

Conclusion: We have identified 37 Pf-aaRSs based on our bioinformatics analysis. Our data reveal several unique attributes in this protein family. We have annotated all 37 Pf-aaRSs based on predicted localization, phylogenetics, domain architectures and their overall protein expression profiles. The sets of distinct features elaborated in this work will provide a platform for experimental dissection of this family of enzymes, possibly for the discovery of novel drugs against malaria.

Figure 1

(a) Predictied number of aaRSs present in Plasmodium falciparum (Pf), Rattus norvegicus (Rn), Saccharomyces cerevisiae (Sc), Drosophila melanogaster (Dm), Homo sapiens (Hs), Oryza sativa (Os), Dictyostelium discoidium (Dd), Mycobacterium tuberculosis (Mtb), Escherichia coli (Ec), and Methanocalclococcus jannaschii (Mj). (b) Diagram representing fraction of proteome (in percentage) dedicated to the aaRS proteins in various organisms.

Figure 2

Bar graph showing number of different aaRSs in Plasmodium falciparum and Homo sapiens. The number of alanyl- and threonyl- tRNA synthetases is higher in humans whereas P. falciparum seems richer in phe tRNA synthetases.

Figure 3

(a) Percentage predicted distribution of Pf-aaRSs in different organelles within the parasite. (b) A schematic of all Pf-aaRSs and their predicted cellular localization. Detailed information regarding gene IDs can be found in additional file 1. Pf-aaRSs predicted to be common between apicoplast & mitochondria, mitochondria & nucleus and apicoplast & nucleus are marked with diamond, triangle and square shapes respectively.

Figure 4

Diagrammatic representation of Pf-aaRS protein expression which are specifically expressed in different life stages of the parasite based on mass spectrometry data [82].

Figure 5

Representation of unusual domain architectures in Pf-aaRSs and related proteins. A generic aaRS is also shown on top. Domain name abbreviations are YB, Ybak associating domain; TS-II, class II tRNA synthetase; AC, anticodon binding site; ED, editing domain; GST, glutathione-Stransferase C-terminal region; RBD, S4 RNA binding domain; TS, tRNA synthetase core domain; STK, serine-threonine kinase; FTS, phenylalanine-tRNA synthetase; PTS, prolinetRNA synthetase; VTS, valine-tRNA synthetase; MTS, methionine-tRNA synthetase; YTS, tyrosine-tRNA synthetase; ETS, glutamate-tRNA synthetase.

Figure 6

(a) Evolutionary tree was constructed using the PHYML based on maximum likelihood method. P. falciparum TyrRSs (PlasmoDB id -MAL8p1.125 and PF11_0181) are labeled as green triangles. One of the TryRSs (MAL8p1.125) is evolutionarily closer to H. sapiens whereas the other TyrRS (PF11_0181) is closer to E. coli. Total of 102 species were considered for the evolutionary analysis and were taken from three domains of life. (b) List of Pf-aaRS sequences evolutionarily closer to their E. coli and A. Thaliana counterparts.

Figure 7

Left and right panels of the figure represent sequence and structural comparison of bacterial type Plasmodium TyrRS (PF11_0181) with human mitochondrial TyrRS (2PID) and the cytosolic Plasmodium TyrRS (Mal8p1.125) with human cytosolic TyrRS (1N3L). a) A structure-based sequence alignment of the catalytic domain of Plasmodium TyrRSs with human TyrRSs. Insertions in Pf and human sequences are colored in light blue and orange respectively. Class I synthetase conserved motifs are colored red. Residues involved in tRNA recognition and catalysis are indicated in green (same residues in Pf and Hs) and violet & boxed (different in Pf and Hs). The secondary structural elements are shown above the sequence alignments. Conserved residues are indicated by asterisk below the sequence alignment. (b) Superposition of Pf-TyrRS and Hs-TyrRS depicting the structural differences. Pf-Tyr is colored grey and Hs-TyrRS is colored tan. Insertions in Pf-TyrRSs are highlighted in blue whereas Hs-TyrRS insertions are in orange. Motif 1 in Pf (PF11_0181 - HLGN and Mal8p1.125 - HIAQ) and Hs (2PID - HVGH and 1N3L - HVAY) TyrRSs has been encircled red whereas Motif 2 in Pf (PF11_0181 - KLGKS and Mal8p1.125 - KMSKS) and Hs (2PID - KYSKS and 1N3L - KMSSS) is encircled green. (c) Snapshot of the active sites of Pf and Hs TyrRSs (superimposed) structures. Non-conserved active site residues colored violet are encircled.