Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages

Abstract

The characterization of the transcriptome and proteome of Plasmodium falciparum has been a tremendous resource for the understanding of the molecular physiology of this parasite. However, the translational dynamics that link steady-state mRNA with protein levels are not well understood. In this study, we bridge this disconnect by measuring genome-wide translation using ribosome profiling, through five stages of the P. falciparum blood phase developmental cycle. Our findings show that transcription and translation are tightly coupled, with overt translational control occurring for less than 10% of the transcriptome. Translationally regulated genes are predominantly associated with merozoite egress functions. We systematically define mRNA 5′ leader sequences, and 3′ UTRs, as well as antisense transcripts, along with ribosome occupancy for each, and establish that accumulation of ribosomes on 5′ leaders is a common transcript feature. This work represents the highest resolution and broadest portrait of gene expression and translation to date for this medically important parasite.DOI: http://dx.doi.org/10.7554/eLife.04106.001

Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum

“…These in fact appear to be widespread and may influence translation efficiency or enrich the pools of proteins (de Klerk and Hoen, 2015). Interestingly, initial comparison of our TSS map with the recently published profile of ribosome occupancy during the IDC of P. falciparum (Caro et al, 2014) suggests that a dynamic change in TSS usage may be accompanied by a switch between translation initiation sites (Figure S4H). Additionally, it further argues for the likely co-existence of transcript isoforms that are differentially translated (Figure S4I).…”

“…The concomitant expression of several isoforms with varying 5′ UTRs may have important regulatory consequences (Davuluri et al, 2008), notably by influencing transcript stability or translation efficiency (de Klerk and Hoen, 2015). Interestingly, recent ribosome and polysome profiling studies in P. falciparum have reported enrichment for ribosomes along the 5′ UTR of numerous transcripts (Bunnik et al, 2013; Caro et al, 2014), including those lacking AUGs (Caro et al, 2014). This suggests the existence of upstream open reading frames (uORFs) that are actively translated from non-cognate initiation codons (Ingolia, 2014) and may affect the efficiency of translation of the full-length transcript.…”

The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis

“…Profiling has proven to be increasingly valuable in studies of the translation process, for example, in the discovery of novel open reading frames (ORFs), the determination of elongation rates, the identification of sites of ribosome pausing and in the study of protein folding (for review, see Morris 2009;Weiss and Atkins 2011;Michel and Baranov 2013;Ingolia 2014;Jackson and Standart 2015). It also has broad application in the analysis of global gene expression and has been exploited in studies of infectious diseases (Stern-Ginossar et al 2012, 2015Liu et al 2013;Arias et al 2014;Caro et al 2014;Jensen et al 2014;Muzzey et al 2014;Vasquez et al 2014;Yang et al 2015), cell growth, differentiation and development Huang et al 2013;Lee et al 2013;Stadler and Fire, 2013;Stumpf et al 2013;Subramaniam et al 2013;Baudin-Baillieu et al 2014;Brubaker et al 2014;Duncan and Mata 2014;Gonzalez et al 2014;Hendriks et al 2014;Katz et al 2014;Kronja et al 2014;Schrader et al 2014;Vaidyanathan et al 2014;de Klerk et al 2015), apoptosis (Wiita et al 2013), mitochondrial gene expression and disease (Rooijers et al 2013;Williams et al 2014), cell stress (Gerashenko et al 2012;Labunskyy et al 2014;Zid and O'Shea 2014;Sidrauski et al 2015), cell toxicity …”

Illuminating Parasite Protein Production by Ribosome Profiling

“…While ribosome profiling has been utilized in a number of model organisms and human cells (for example, [7–9]), the approach has only recently seen application in infectious disease biology. Key examples include probing the effects of viral infection on host cells [10], investigating the mechanism of macrolide inhibition [11], and describing developmental regulation of protein production in the protozoan parasites Trypanosoma brucei [12,13], Trypanosoma cruzi [14], and Plasmodium falciparum [15]. Additionally it has been employed in gene discovery in T. brucei [16] and viruses [3,17].…”

“…In T. brucei , animal-derived [12] and cultured BF [13] have been compared to PCF; while in T. cruzi , dividing epimastigotes have been compared to non-dividing metacyclic trypomastigotes (both are cultured insect stages) [14]. In P. falciparum , the entire asexual erythrocytic cycle (from ring forms that arise shortly after invasion of red blood cells through to merozoites shortly after egress, Figure 3B) has been examined [15]. …”