title: A bioinformatic survey of RNA-binding proteins in Plasmodium.
abstract: BACKGROUND
  The malaria parasites in the genus Plasmodium have a very complicated life cycle involving an invertebrate vector and a vertebrate host. RNA-binding proteins (RBPs) are critical factors involved in every aspect of the development of these parasites. However, very few RBPs have been functionally characterized to date in the human parasite Plasmodium falciparum.
  
  
  METHODS
  Using different bioinformatic methods and tools we searched P. falciparum genome to list and annotate RBPs. A representative 3D models for each of the RBD domain identified in P. falciparum was created using I-TESSAR and SWISS-MODEL. Microarray and RNAseq data analysis pertaining PfRBPs was performed using MeV software. Finally, Cytoscape was used to create protein-protein interaction network for CITH-Dozi and Caf1-CCR4-Not complexes.
  
  
  RESULTS
  We report the identification of 189 putative RBP genes belonging to 13 different families in Plasmodium, which comprise 3.5% of all annotated genes. Almost 90% (169/189) of these genes belong to six prominent RBP classes, namely RNA recognition motifs, DEAD/H-box RNA helicases, K homology, Zinc finger, Puf and Alba gene families. Interestingly, almost all of the identified RNA-binding helicases and KH genes have cognate homologs in model species, suggesting their evolutionary conservation. Exploration of the existing P. falciparum blood-stage transcriptomes revealed that most RBPs have peak mRNA expression levels early during the intraerythrocytic development cycle, which taper off in later stages. Nearly 27% of RBPs have elevated expression in gametocytes, while 47 and 24% have elevated mRNA expression in ookinete and asexual stages. Comparative interactome analyses using human and Plasmodium protein-protein interaction datasets suggest extensive conservation of the PfCITH/PfDOZI and PfCaf1-CCR4-NOT complexes.
  
  
  CONCLUSIONS
  The Plasmodium parasites possess a large number of putative RBPs belonging to most of RBP families identified so far, suggesting the presence of extensive post-transcriptional regulation in these parasites. Taken together, in silico identification of these putative RBPs provides a foundation for future functional studies aimed at defining a unique network of post-transcriptional regulation in P. falciparum.
authors.affiliation: Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA.
authors.forename: B P Niranjan
authors.initials: BP
authors.lastname: Reddy
authors.affiliation: Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA.
authors.forename: Sony
authors.initials: S
authors.lastname: Shrestha
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, W223 Millennium Science Complex, University Park, PA, 16802, USA.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Hart
authors.affiliation: Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Liang
authors.affiliation: Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Kemirembe
authors.affiliation: Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA. Luc2@psu.edu.
authors.forename: Liwang
authors.initials: L
authors.lastname: Cui
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, W223 Millennium Science Complex, University Park, PA, 16802, USA. Scott.Lindner@psu.edu.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Lindner
mesh_terms: D019295:Computational Biology; D010961:Plasmodium / Q000235:genetics*; D015800:Protozoan Proteins / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics*
chemical_list: D015800:Protozoan Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins