Unraveling the 'DEAD-box' helicases of Plasmodium falciparum

Abstract

The causative agent for the most fatal form of malaria, Plasmodium falciparum, has developed insecticide and drug resistance with time. Therefore combating this disease is becoming increasingly difficult and this calls for finding alternate ways to control malaria. One of the feasible ways could be to find out inhibitors/drugs specific for the indispensable enzymes of malaria parasite such as helicases. These helicases, which contain intrinsic nucleic acid-dependent ATPase activity, are capable of enzymatically unwinding energetically stable duplex nucleic acids into single-stranded templates and are required for all the nucleic acid transactions. Most of the helicases contain a set of nine extremely conserved amino acid sequences, which are called 'helicase motifs'. Due to the presence of the DEAD (Asp-Glu-Ala-Asp) in one of the conserved motifs, this family is also known as the 'DEAD-box' family. In this review, using bioinformatic approach, we describe the 'DEAD-box' helicases of malaria parasite P. falciparum. An in depth analysis shows that the parasite contains 22 full-length genes, some of which are homologues of well-characterized helicases of this family from other organisms. Recently we have cloned and characterized the first member of this family, which is a homologue of p68 and is expressed during the schizont stage of the development of the parasite [Pradhan, A., Chauhan, V.S., Tuteja, R., 2005a. A novel 'DEAD-box' DNA helicase from Plasmodium falciparum is homologous to p68. Mol. Biochem. Parasitol. 140, 55-60.; Pradhan A., Chauhan V.S., Tuteja R., 2005b. Plasmodium falciparum DNA helicase 60 is a schizont stage specific, bipolar and dual helicase stimulated by PKC phosphorylation. Mol. Biochem. Parasitol. 144, 133-141.]. It will be really interesting to clone and characterize other members of the 'DEAD-box' family and understand their role in the replication and transmission of the parasite. These detailed studies may help to identify a parasite-specific enzyme, which could be a potential drug target to treat malaria. The various steps at which this probable drug can act are also discussed.

Fig. 1

Distribution of amino acids at various positions in a. ‘Q motif; b. ‘Motif I’ and c. ‘Motif VI’ of ‘DEAD-box’ helicases of Plasmodium falciparum. In panel ‘a’ the variation in occurrence of amino acid upstream of ‘Q motif’ has also been shown. The numbers in parenthesis indicate the frequency of occurrence of each amino acid at respective position. The amino acids without any number means that they have occurred only once. Single letter code for amino acids has been used.

Fig. 2

Schematic diagram showing the various conserved motifs of members of ‘DEAD-box’ helicases of Plasmodium falciparum. Open boxes represent the conserved helicase motifs and the amino acid sequence of each motif of each member is written by the single letter code inside the box. Labels above the boxes in number 1 (Q, I, Ia etc.) are the names assigned to these motifs. The number between the motif and above the arrow is the number of amino acids separating the various motifs.

Fig. 2

Schematic diagram showing the various conserved motifs of members of ‘DEAD-box’ helicases of Plasmodium falciparum. Open boxes represent the conserved helicase motifs and the amino acid sequence of each motif of each member is written by the single letter code inside the box. Labels above the boxes in number 1 (Q, I, Ia etc.) are the names assigned to these motifs. The number between the motif and above the arrow is the number of amino acids separating the various motifs.

Fig. 3

Crystal structure of eIF-4A homologue (PF14_0655) of Plasmodium falciparum based on the solved structure of eIF-4A of yeast (Saccharomyces cerevisiae). The structural model of eIF-4A homologue of P. falciparum (PF14_0655) with ID no. Q8IKFO was retrieved from the modbase database (www.modbase.compbio.ucsf.edu). This shows ∼ 61% sequence identity with its template, which is yeast eIF-4A (1fuuB) and was retrieved from the RCSB protein databank (www.pdb.org). The conserved helicase motifs of both of these proteins are indicated in different colors 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). The colors used for various motifs are: Q motif — pink; motif I — yellow; motif Ia — orange; motif Ib — lime; motif II — red; motif III — white; motif V — mauve and motif VI — green.