A bioinformatic survey of RNA-binding proteins in Plasmodium

• Published in: BMC genomics Vol. 16; no. 887; p. 890
• Main Authors: Reddy, B P Niranjan, Shrestha, Sony, Hart, Kevin J, Liang, Xiaoying, Kemirembe, Karen, Cui, Liwang, Lindner, Scott E
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 02-11-2015; BioMed Central
• Subjects: Analysis; Binding proteins; Chemical properties; Computational Biology; Genetic aspects; Genomics; Plasmodium; Plasmodium - genetics; Protozoan Proteins - genetics; RNA sequencing; RNA, Messenger - genetics; RNA-Binding Proteins - genetics; Surveys; United States
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-015-2092-1

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.
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.
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.
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.