Host adaptation of Plasmodium falciparum translational control

Malaria, caused by the intracellular protozoan parasite Plasmodium falciparum, continues to be a significant global health challenge. One of the major difficulties in combating the disease is the parasite's ability to constantly respond and adapt to changes in its human host environment. Alterations in host environment are tightly linked to disease progression in the intraerythrocytic development cycle (IDC), which is why the parasite has developed unique metabolic adaptation strategies. However, it remains unclear how the parasites sense such changes and regulate protein synthesis, particularly given its lack of the canonical TOR pathway. Thus, understanding how the parasite controls its translation under conditions of limited nutrient availability is crucial for gaining deeper insights into host-parasite interactions and adaptation, which may ultimately aid the development of more effective antimalarial therapies.

Notably, P. falciparum can serve as a unique model system for studying translational control as it presents the extremely AT-rich genome, skewed codon and amino acid (AA) usage, but a non-redundant set of tRNA genes. These features raise important questions regarding the ways in which the parasite offsets its codon usage bias to maintain efficient translation, and whether these evolutionary outcomes are neutral or represent adaptive strategies of the parasite to its host.

Therefore, this thesis explores how P. falciparum adapts to the human host environment through the lens of tRNA regulation, focusing on tRNA expression dynamics, aminoacylation and tRNA modifications. In Project I and II, by optimizing the tRNA sequencing protocol, we systematically explored the tRNA profiles in P. falciparum across various developmental stages and under different stress stimuli. In Project III, using multi-omics analysis, we elucidated a novel feature of host metabolic adaptation which underlies translational control.

We provide evidence that the biased AA usage in the P. falciparum genome is adaptive to host hemoglobin (HB), the primary internal source of AAs. Notably, we show that highly expressed transcripts have a lower requirement and hence dependency on AAs that are scarce or entirely absent, such as Isoleucine (Ile), which cannot be obtained through HB digestion and must be acquired from the external host environment.

Through comprehensive tRNA profiling in P. falciparum, we discovered a discordance between anticodon and codon pools. Specifically, tRNA responsible for decoding AAs that are scarce in HB exhibit lower expression levels, suggesting varied decoding efficiency for different AAs. Interestingly, genes associated with lipid synthesis and proliferation have adapted to incorporate a high level of HB- rare AAs such as Ile in their encoded proteins. This adaptation enables the parasite to regulate its proliferation by selectively repressing the protein synthesis of these genes during the periods of nutrient scarcity. Furthermore, by exposing parasites to AA deprivation, we revealed a non-canonical stress sensing mechanism facilitated by the regulation of Ile-tRNA aminoacylation . This, in turn, triggers selective ribosome stalling on Ile-rich transcripts, thereby selectively regulating the translation of these genes. Remarkably, this mechanism is unique as it is independent of kinase-mediated signaling cascades, enabling a decentralized resource allocation that is directly governed by the availability and need for nutrients.

By analyzing other metabolically relevant pathways, we suggest that the adaptative strategies used by P. falciparum may have evolved similarly in other intracellular parasites. Our study provides insights that metabolic constrains play an essential role in shaping the protein primary sequence and amino acid composition, challenging the prevailing view that functional constrains are the primary evolutionary drivers. This perspective offers new insights into protein and genome evolution, in particular, it may serve as an interesting model to explore the role of mutation bias in adaptive evolution.

This thesis presents three related projects:

Project I: We optimized tRNA sequencing techniques to provide a comprehensive view of the tRNA profiling in P. falciparum, focusing on tRNA abundance, aminoacylation levels as well as a variety of nucleotide modifications.

Project II: We explored tRNA modifications during stage transitions and under different stress conditions.

Project III: By employing multi-omics analysis, we uncovered a novel layer of metabolic adaptation in P. falciparum characterized by its highly biased AA usage in its proteome and is coupled to a regulated tRNA expression program.

List of scientific papers

I. Qian Li, Leonie Vetter, Ylva Veith, Elena Christ, Ákos Végvári, Cagla Sahin, Ulf Ribacke, Mats Wahlgren, Johan Ankarklev, Ola Larsson, Sherwin Chun-Leung Chan. tRNA regulation and amino acid usage bias reflect a coordinated metabolic adaptation in Plasmodium falciparum (iScience). https://doi.org/10.1016/j.isci.2024.111167

II. Qian Li, Ylva Veith, Elena Christ, Mats Wahlgren, Johan Ankarklev, Ola Larsson, Sherwin Chun-Leung Chan. tRNA base methylation identification and quantification in Plasmodium falciparum. [Manuscript]