A bioinformatic survey of RNA-binding proteins in Plasmodium

BMC Genomics

Research Article

Scott E. Lindner¹  Kevin J. Hart¹  BP Niranjan Reddy²  Karen Kemirembe²  Sony Shrestha²  Xiaoying Liang²  Liwang Cui² 

[1] Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, W223 Millennium Science Complex, 16802, University Park, PA, USA;Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, 16802, University Park, PA, USA;

关键词: RNA-binding proteins (RBPs);    Post transcriptional regulation (PTR);    Pre-mRNA splicing;    Ribosome biogenesis;    mRNA processing;    Stress granules;    Malaria;    Plasmodium;   

DOI  :  10.1186/s12864-015-2092-1

 received in 2015-04-18, accepted in 2015-10-15,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe 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.MethodsUsing 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.ResultsWe 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Reddy et al. 2015