PfSR1 controls alternative splicing and steady‐state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs

Abstract

SummaryPlasmodium 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 PfSR1 as a bona fide Ser/Arg-rich (SR) protein that shuttles between the nucleus and cytoplasm and regulates AS in Plasmodium falciparum. Here we show that PfSR1 is localized adjacent to the Nuclear Pore Complex (NPC) clusters in the nucleus of early stage parasites. To identify the endogenous RNA targets of PfSR1, we adapted an inducible overexpression system for tagged PfSR1 and performed RNA immunoprecipitation followed by microarray analysis (RIPchip) to recover and identify the endogenous RNA targets that bind PfSR1. Bioinformatic analysis of these RNAs revealed common sequence motifs potentially recognized by PfSR1. RNA-EMSAs show that PfSR1 preferentially binds RNA molecules containing these motifs. Interestingly, we find that PfSR1 not only regulates AS but also the steady-state levels of mRNAs containing these motifs in vivo.

Translational regulation in blood stages of the malaria parasite Plasmodium spp.: systems‐wide studies pave the way

“…135 Indeed, it was recently shown that PfSR1 binds to 64 transcripts via two purine-rich RNA motifs, similar to its human counterpart SRSF1, and that PfSR1 overexpression resulted in the early detection of gametocyte-specific intron-less transcripts. 136 However, the molecular basis of PfSR1-mediated post-transcriptional regulation is not known. Also, it remains to be seen whether the other splicing factors encoded by the parasite genome perform similar post-transcriptional functions, as has been observed for several mammalian SR proteins.…”

Alternative Splicing in Apicomplexan Parasites

“…Phosphorylation of this putative splicing factor increased RNA binding by 80%, although this protein was not recognized by the aforementioned MAb104 (86). Similarly, PfSR1 was later shown to shuttle between cytoplasm and nucleus, adjacent to nuclear pore complexes (87, 88). The authors further demonstrated that the RS domain was necessary for nuclear localization (87).…”

malERA: An updated research agenda for basic science and enabling technologies in malaria elimination and eradication

“…Notable advances in asexual biology over the past 5 years include improvements in functional genomics, such as more robust RNA sequencing methods [ 130 – 132 ], a deeper understanding of transcription factors such as activator protein 2 (ap2) transcription factors [ 133 ] or alternative RNA splicing [ 134 ], and whole genome sequencing and genotyping of both field isolates and evolved cultures (see Table 1 ). Due to its rapidly decreasing cost and increasing accuracy, sequencing has accelerated our understanding of the mechanisms and modes of action of current and new antimalarials through drug-resistant parasite selection in vitro (reviewed in [ 135 ]) as well as population genetics of the parasite in vivo [ 62 , 136 ].…”