title: Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction.
abstract: BACKGROUND
  Subtelomeric RIFIN genes constitute the most abundant multigene family in Plasmodium falciparum. RIFIN products are targets for the human immune response and contribute to the antigenic variability of the parasite. They are transmembrane proteins grouped into two sub-families (RIF_A and RIF_B). Although recent data show that RIF_A and RIF_B have different sub-cellular localisations and possibly different functions, the same structural organisation has been proposed for members of the two sub-families. Despite recent advances, our knowledge of the regulation of RIFIN gene expression is still poor and the biological role of the protein products remain obscure.
  
  
  RESULTS
  Comparative studies on RIFINs in three clones of P. falciparum (3D7, HB3 and Dd2) by Multidimensional scaling (MDS) showed that gene sequences evolve differently in the 5'upstream, coding, and 3'downstream regions, and suggested a possible role of highly conserved 3' downstream sequences. Despite the expected polymorphism, we found that the overall structure of RIFIN repertoires is conserved among clones suggesting a balance between genetic drift and homogenisation mechanisms which guarantees emergence of novel variants but preserves the functionality of genes. Protein sequences from a bona fide set of 3D7 RIFINs were submitted to predictors of secondary structure elements. In contrast with the previously proposed structural organisation, no signal peptide and only one transmembrane helix were predicted for the majority of RIF_As. Finally, we developed a strategy to obtain a reliable 3D-model for RIF_As. We generated 265 possible structures from 53 non-redundant sequences, from which clustering and quality assessments selected two models as the most representative for putative RIFIN protein structures.
  
  
  CONCLUSIONS
  First, comparative analyses of RIFIN repertoires in different clones of P. falciparum provide insights on evolutionary mechanisms shaping the multigene family. Secondly, we found that members of the two sub-families RIF_As and RIF_Bs have different structural organization in accordance with recent experimental results. Finally, representative models for RIF_As have an "Armadillo-like" fold which is known to promote protein-protein interactions in diverse contexts.
authors.affiliation: Dipartimento di Malattie Infettive, Parassitarie ed Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Roma, Italy. ebultrini@yahoo.com
authors.forename: Emanuele
authors.initials: E
authors.lastname: Bultrini
authors.forename: Kevin
authors.initials: K
authors.lastname: Brick
authors.forename: Srayanta
authors.initials: S
authors.lastname: Mukherjee
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.forename: Francesco
authors.initials: F
authors.lastname: Silvestrini
authors.forename: Pietro
authors.initials: P
authors.lastname: Alano
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Pizzi
mesh_terms: D000818:Animals; D000940:Antigenic Variation; D055028:Comparative Genomic Hybridization; D016054:DNA, Protozoan / Q000235:genetics; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D018503:Genome, Protozoan; D023281:Genomics; D008565:Membrane Proteins / Q000235:genetics*; D008958:Models, Molecular; D005810:Multigene Family; D010963:Plasmodium falciparum / Q000235:genetics*; D017433:Protein Structure, Secondary; D015800:Protozoan Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D016054:DNA, Protozoan; D008565:Membrane Proteins; D015800:Protozoan Proteins; C534665:RIFIN protein, Plasmodium falciparum