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P f SR 1 controls alternative splicing and steady‐state RNA levels in P lasmodium falciparum through preferential recognition of specific RNA motifs
Author(s) -
Eshar Shiri,
Altenhofen Lindsey,
Rabner Alona,
Ross Phil,
Fastman Yair,
MandelGutfreund Yael,
Karni Rotem,
Llinás Manuel,
Dzikowski Ron
Publication year - 2015
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/mmi.13007
Subject(s) - biology , rna , rna splicing , rna binding protein , rna recognition motif , proteome , microbiology and biotechnology , alternative splicing , plasmodium falciparum , immunoprecipitation , messenger rna , genetics , gene , malaria , immunology
Summary P lasmodium species have evolved complex biology to adapt to different hosts and changing environments throughout their life cycle. Remarkably, these adaptations are achieved by a relatively small genome. One way by which the parasite expands its proteome is through alternative splicing ( AS ). We recently identified P f SR 1 as a bona fide S er/ A rg‐rich ( SR ) protein that shuttles between the nucleus and cytoplasm and regulates AS in P lasmodium falciparum . Here we show that P f SR 1 is localized adjacent to the N uclear P ore C omplex ( NPC ) clusters in the nucleus of early stage parasites. To identify the endogenous RNA targets of P f SR 1, we adapted an inducible overexpression system for tagged P f SR 1 and performed RNA immunoprecipitation followed by microarray analysis ( RIP ‐chip) to recover and identify the endogenous RNA targets that bind P f SR 1. Bioinformatic analysis of these RNAs revealed common sequence motifs potentially recognized by P f SR 1. RNA ‐ EMSA s show that P f SR 1 preferentially binds RNA molecules containing these motifs. Interestingly, we find that P f SR 1 not only regulates AS but also the steady‐state levels of m RNA s containing these motifs in vivo .