Identification and bioinformatics characterization of translation initiation complex eIF4F components and poly(A)-binding protein from Plasmodium falciparum

Abstract

Protein synthesis in eukaryotes initiates with binding of the multisubunit translation initiation complex eIF4F.  This complex contains eIF4E, eIF4A and eIF4G.  eIF4E directly interacts with the cap structure, eIF4A is an RNA helicase and eIF4G acts as a scaffold for the complex.  eIF4G contains the binding sites for both the subunits i.e. eIF4A and eIF4E and it also interacts with poly(A)-binding protein (PABP).  In present study we have identified and characterized the main components of the eIF4F complex i.e. eIF4E, eIF4A and eIF4G and PABP from Plasmodium falciparum.  Molecular modeling of PfeIF4E, PfeIF4G and PfPABP confirms that they contain all the characteristic conserved structural features.  We have annotated some of the genes of P. falciparum and as a result these studies demonstrate that the components of translation initiation complex are highly conserved.  Therefore these studies will contribute to understand the basic biology and components of translation complex in P. falciparum.

Acknowledgements

The author thanks Moaz Ahmad and Arun Pradhan for help in preparation of figures. The work in R.T. laboratory is supported by Department of Science and Technology grant. Infra-structural support from the Department of Biotechnology, Government of India is gratefully acknowledged.

Figures and Tables

Figure 1 (A) Comparison of amino acid sequences of P. falciparum eIF-4E protein (PlasmoDB No. PFC0635c; GenBank accession No. EF043517) with other eIF-4E from Plasmodium berghei (XP_674865), Theileria annulata (CAI74251), Cryptosporidium parvum (CAD98650), Pisum sativum (ABG35118), Saccharomyces cerevisiae (NP_014502) and Homo sapiens (P06730). The accession numbers of the aligned sequences are written in brackets. (B) Phylogenetic guide tree using Clustal W program based on the multiple alignment. A value of 0.1 corresponds to a difference of 10% between two sequences.

Figure 2 (A) Amino acid alignment of P. falciparum eIF4E (PlasmoDB No. PFC0635c, GenBank accession number EF043517) and human eIF4E (GenBank accession number P06730). The amino acids responsible for 7-methyl GDP-binding and eIF4G binding are marked by red and blue asterisk respectively. (B) A three-dimensional model for PfeIF4E was created as described in text, which was based on the crystal structure of human eIF4E.16 The structures have been displayed using molecular visualization program for displaying, animating and analyzing large biomolecule systems using 3-dimensional graphics and built-in scripting (VMD software www.ks.uiuc.edu). (i) Super imposed image of the structure of human (green) and P. falciparum (red) eIF4E The amino acids responsible for the binding of eIF4G in (ii) human and (iii) P. falciparum eIF4E have been marked and are shown in yellow in the models.

Figure 3 (A) Comparison of amino acid sequences of P. falciparum eIF-4G protein (PlasmoDB No. MAL13P1.63) with other eIF4G from Plasmodium yoelii (XP_727991), Schizosaccharomyces pombe (Q10475), Oryza sativa (AAO72569) and Homo sapiens (AF104913). The accession numbers of the aligned sequences are written in brackets. (B) Phylogenetic guide tree using Clustal W program based on the multiple alignment. A value of 0.1 corresponds to a difference of 10% between two sequences.

Figure 4 (A) Comparison of amino acid sequence (from amino acid 888-1125) of P. falciparum eIF4G protein (PlasmoDB no. MAL13P1.63) with eIF4G (from amino acid 712-944) of H. sapiens (GenBank accession number AF104913). (B) Three-dimensional models for (i) human eIF4G and (ii) P. falciparum eIF4G were created as described in text. The structures have been displayed using the same program as described in legend to Figure 1B. This model has been built by using only the phylogenetically conserved middle domain i.e., amino acid 888 to amino acid 1125 in PfeIF4G. A super-imposed image is shown in (iii).

Figure 5 (A) Comparison of amino acid sequences of P. falciparum PABP protein (PlasmoDB No. PFL1170w; GenBank accession No. EF116593) with other PABP from Plasmodium berghei (XP_677383), Theileria annulata (CAI73150), Cryptosporidium parvum (CAD98589), Schizosaccharomyces pombe (AAA35320), Oryza sativa (XP_481529) and Homo sapiens (CAI12298). The accession numbers of the aligned sequences are written in brackets. (B) Phylogenetic guide tree using Clustal W program based on the multiple alignment. A value of 0.1 corresponds to a difference of 10% between two sequences.

Figure 6 (A) Comparison of amino acid sequence of P. falciparum (PlasmoDB no. PFL1170w, GenBank accession number EF116593) and human PABP (GenBank accession number CAI 12298). The RNA recognition motifs (RRM) 1–2, 3 and 4 have been highlighted with green, blue and orange color respectively. (b) Three-dimensional models for human PABP and various fragments of PfPABP were created as described in text. The structures have been displayed using the same program as described in legend to Figure 1B. (B) (i)–(iii) Show the modeled structure of human (in yellow) and PfPABP (in green from amino acid 1–180), PfPABP (in blue from amino acid 1–264) and PfPABP (in orange from amino acid 1–531) respectively.

Figure 7 (A) Schematic diagram showing the interaction of various components (eIF4E, eIF4G and PABP) with the N-terminal, Middle and C-terminal domains of eIF4G. (B) Schematic diagram of translation initiation complex in P. falciparum. The name and PlasmoDB number of each component is written.