title: Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes.
abstract: BACKGROUND
  To date, only a few transcription factors have been identified in the genome of the parasite Plasmodium falciparum, the causative agent of malaria. Moreover, no detailed molecular analysis of its basal transcription machinery, which is otherwise well-conserved in the crown group of eukaryotes, has yet been reported. In this study, we have used a combination of sensitive sequence analysis methods to predict the existence of several parasite encoded general transcription factors associated with RNA polymerase II.
  
  
  RESULTS
  Several orthologs of general transcription factors associated with RNA polymerase II can be predicted among the hypothetical proteins of the P. falciparum genome using the two-dimensional Hydrophobic Cluster Analysis (HCA) together with profile-based search methods (PSI-BLAST). These predicted orthologous genes encoding putative transcription factors include the large subunit of TFIIA and two candidates for its small subunit, the TFIIE beta-subunit, which would associate with the previously known TFIIE alpha-subunit, the TFIIF beta-subunit, as well as the p62/TFB1 subunit of the TFIIH core. Within TFIID, the putative orthologs of TAF1, TAF2, TAF7 and TAF10 were also predicted. However, no candidates for TAFs with classical histone fold domain (HFD) were found, suggesting an unusual architecture of TFIID complex of RNA polymerase II in the parasite.
  
  
  CONCLUSIONS
  Taken together, these results suggest that more general transcription factors may be present in the P. falciparum proteome than initially thought. The prediction of these orthologous general transcription factors opens the way for further studies dealing with transcriptional regulation in P. falciparum. These alternative and sensitive sequence analysis methods can help to identify candidates for other transcriptional regulatory factors in P. falciparum. They will also facilitate the prediction of biological functions for several orphan proteins from other apicomplexan parasites such as Toxoplasma gondii, Cryptosporidium parvum and Eimeria.
authors.affiliation: Centre National de la Recherche Scientifique CNRS UMR7590, Universités Paris 6 et Paris 7, Département de Biologie Structurale, IMPMC, 75252 Paris Cedex 05, France. Isabelle.Callebaut@impmc.jussieu.fr
authors.forename: Isabelle
authors.initials: I
authors.lastname: Callebaut
authors.forename: Karine
authors.initials: K
authors.lastname: Prat
authors.forename: Edwige
authors.initials: E
authors.lastname: Meurice
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Mornon
authors.forename: Stanislas
authors.initials: S
authors.lastname: Tomavo
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D016000:Cluster Analysis; D017124:Conserved Sequence; D030562:Databases, Protein; D016678:Genome; D006801:Humans; D008954:Models, Biological; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010963:Plasmodium falciparum / Q000201:enzymology*; D017434:Protein Structure, Tertiary; D012313:RNA / Q000378:metabolism; D012319:RNA Polymerase II / Q000235:genetics* / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D035561:Transcription Factor TFIIA / Q000235:genetics; D035362:Transcription Factor TFIID / Q000235:genetics; D051758:Transcription Factor TFIIH / Q000235:genetics; D035165:Transcription Factors, General / Q000235:genetics* / Q000502:physiology; D019473:Transcription Factors, TFII / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D035561:Transcription Factor TFIIA; D035362:Transcription Factor TFIID; D035165:Transcription Factors, General; D019473:Transcription Factors, TFII; D051758:Transcription Factor TFIIH; D012313:RNA; D012319:RNA Polymerase II; C056604:transcription factor TFIIF