title: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institut Pasteur, Unité d'Immunologie Moléculaire des Parasites, CNRS URA 2581, 25-28 rue du Dr Roux, 75724, Paris cedex 15, France. bischoff@pasteur.fr
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Bischoff
authors.forename: Catherine
authors.initials: C
authors.lastname: Vaquero
mesh_terms: D002843:Chromatin / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004912:Erythrocytes / Q000469:parasitology; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018503:Genome, Protozoan; D010963:Plasmodium falciparum / Q000235:genetics* / Q000254:growth & development; D020543:Proteome / Q000378:metabolism; D015800:Protozoan Proteins / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D002843:Chromatin; D020543:Proteome; D015800:Protozoan Proteins; D014157:Transcription Factors