PolyA tracks and poly-lysine repeats are the Achilles heel ofPlasmodium falciparum

Abstract

Plasmodium falciparum, the causative agent of human malaria, is an apicomplexan parasite with a complex, multi-host life cycle. Sixty percent of transcripts from its extreme AT-rich (81%) genome possess coding polyadenosine (polyA) runs, distinguishing the parasite from its hosts and other sequenced organisms. Recent studies indicate that transcripts with polyA runs encoding poly-lysine are hot spots for ribosome stalling and frameshifting, eliciting mRNA surveillance pathways and attenuating protein synthesis in the majority of prokaryotic and eukaryotic organisms. Here, we show that the P. falciparum translational machinery is paradigm-breaking. Using bioinformatic and biochemical approaches, we demonstrate that both endogenous genes and reporter sequences containing long polyA runs are efficiently and accurately transcribed and translated in P. falciparum cells. Translation of polyA tracks in the parasite does not elicit any response from mRNA surveillance pathways usually seen in host human cells or organisms with similar AT content. The translation efficiency and accuracy of the parasite protein synthesis machinery reveals a unique role of ribosomes in the evolution and adaptation of P. falciparum to an AU-rich transcriptome and polybasic amino sequences. Finally, we show that the ability of P. falciparum to synthesize long poly-lysine repeats has given this parasite a unique protein exportome and an advantage in infectivity that can be suppressed by addition of exogenous poly-basic polymers.

Adaptation of Translational Machinery in Malaria Parasites to Accommodate Translation of Poly-Adenosine Stretches Throughout Its Life Cycle

“…Surprisingly, the higher AT-content of the P. falciparum genome cannot be fully explained by increased AT-richness in intergenic regions, but rather by contributions of AT-richness in both coding 76.22% (Table 1) and non-coding genome 90% (Gardner et al, 2002a). Overall, gene organization patterns in P. falciparum are not influenced by the AT-bias (Glöckner, 2000; Szafranski et al, 2005; Djuranovic et al, 2018). However, what distinguishes Plasmodium species from other AT-rich organisms is distribution of consecutive adenosine nucleotides resulting in unusually high percentage of polyA track genes (Table 2).…”

“…The genomes of P. falciparum and related Plasmodium species have apparently evolved independently to reach extreme AT-bias (Table 2). Interestingly, while the two groups of Plasmodium species can be separated based on their AT-genomic content (median of 75% versus a median of 55% AT-richness), both groups accommodate a considerable amount of polyA tracks within the coding regions (Djuranovic et al, 2018).…”

“…Additionally, NO and other RNS species may be important factors in the soluble heme-hemozoin equilibration (Ostera et al, 2011). Interestingly, another erythrocytic parasite from Apicomplexa phylum, Babesia microti , does not degrade hemoglobin and has a considerably less AT-rich genome (61.02%) and polyA tracks (2.17% of genes with polyA tracks) compared to P. falciparum (Cornillot et al, 2012; Djuranovic et al, 2018). Although Plasmodium spp.…”

“…However, long-read, single molecule, real-time sequencing allowed for complete telomere-to-telomere de novo assembly of the P. falciparum genome thereby overcoming the problems associated with next generation sequencing of AT-rich genomes (Vembar et al, 2016b). The consequence of AT-richness is the presence of extended tracts of As, Ts, and TAs in introns and intergenic regions (Glöckner, 2000; Szafranski et al, 2005) as well as unusually high number of genes containing coding polyadenosine (polyA) repeats compared to the other species (Habich, 2016; Djuranovic et al, 2018). Repetitions of 12 or more adenosine nucleotides in gene coding sequences, so-called polyA tracks, were recently found to act as negative gene regulation motifs at the level of mRNA translation in all tested organisms (Arthur et al, 2015; Koutmou et al, 2015).…”

“…However, Plasmodium species represent an exception to this rule. The percentage of polyA carrying transcripts in the genome exceeds 60% for most Plasmodium spp., including P. falciparum (64%) (Djuranovic et al, 2018). The pervasive ribosomal stalling and frameshifting found on polyA tracks in other eukaryotes (Arthur et al, 2015; Koutmou et al, 2015; Tournu et al, 2019) would make it almost impossible for the majority of Plasmodium proteins to be efficiently and correctly synthesized.…”