In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum

Abstract

Background: Malaria is the most important parasitic disease in the world with approximately two million people dying every year, mostly due to Plasmodium falciparum infection. During its complex life cycle in the Anopheles vector and human host, the parasite requires the coordinated and modulated expression of diverse sets of genes involved in epigenetic, transcriptional and post-transcriptional regulation. However, despite the availability of the complete sequence of the Plasmodium falciparum genome, we are still quite ignorant about Plasmodium mechanisms of transcriptional gene regulation. This is due to the poor prediction of nuclear proteins, cognate DNA motifs and structures involved in transcription.

Results: A comprehensive directory of proteins reported to be potentially involved in Plasmodium transcriptional machinery was built from all in silico reports and databanks. The transcription-associated proteins were clustered in three main sets of factors: general transcription factors, chromatin-related proteins (structuring, remodelling and histone modifying enzymes), and specific transcription factors. Only a few of these factors have been molecularly analysed. Furthermore, from transcriptome and proteome data we modelled expression patterns of transcripts and corresponding proteins during the intra-erythrocytic cycle. Finally, an interactome of these proteins based either on in silico or on 2-yeast-hybrid experimental approaches is discussed.

Conclusion: This is the first attempt to build a comprehensive directory of potential transcription-associated proteins in Plasmodium. In addition, all complete transcriptome, proteome and interactome raw data were re-analysed, compared and discussed for a better comprehension of the complex biological processes of Plasmodium falciparum transcriptional regulation during the erythrocytic development.

Figure 1

Comparison of the De Risi's and Winzeler's TAP transcriptome data. A phaseogram of De Risi data (centre) was created for every super class of TAPs (I to IV). Winzeler's transcriptome data from two synchronized 3D7 cultures (sorbitol and temperature) were compared gene by gene to De Risi's data (left). The colorimetric representation of De Risi's data is from green to red and Winzeler's blue-yellow (low to high) in line with the different stages of the IDC (ER and LR: early and late rings; ET and LT: early and late trophozoites; ES and LS: early and late schizonts; M: merozoites, G: gametocytes; S: sporozoites). To the right to the phaseogram, the first lane represents the classes and subclasses of TAPs, followed by accession number, and if appropriate the corresponding protein complex and finally the functional annotation.

Figure 2

Genomic localization of the TAP over the different chromosomes. The chromosomes are numbered on the left and centromeres are indicated in grey. The colours of the lines correspond to the different classes of TAPs: red, general transcription factors; orange, chromatin-related factors; green, specific transcription factors and blue, TAP partners and the * indicates the six clusters. The triangles above the lines are: red for histones; blue for Myb and green for HMGB.

Figure 3

Comparison of transcriptome and proteome data issued from Winzeler's, Florens' and Lasonder's reports. Winzeler's transcriptome data, obtained from two different culture synchronizations (see Figure 1), was ordered according to the I-IV class of TAPs and compared to the proteome data obtained from A, B, C and D reports (from left to right) [29-32]. The colorimetric representation of the transcriptome is as in figure 1. The colorimetric representation for the proteome is black-blue for low, orange-red for high as indicated on top of figure. Grey represents absence of detection. Details for each TAP are as in the previous figures.

Figure 4

Potential interactions observed by in silico and yeast two hybrid approach between the GTF and ApiAP2. TAP candidates eliciting interactions from in silico [53] and Y2D data [54] were extracted from PlasmoDB and only the proteins for which an interaction was inferred are presented. The two networks were merged and graphically represented using Cytoscape 2.6 http://www.cytoscape.org. Red circle stands for general transcription factors, yellow for chromatin-related proteins, green for specific transcription factors and blue for partners. Grey lines represent the in silico interactions and pink lines those proposed by the two-hybrid experiment. A. Interaction network for the preinitiation complexe. B. Interaction network for the ApiAP2 TF. For the complete interaction network see Additional file 5.