Genome-wide identification and analysis of RNA secondary structures in response to glucose in Plasmodium falciparum

Food intake has a significant effect on systemic physiology. The growth, development and transmission of malaria-causing Plasmodium parasites rely on carbohydrate utilization, and parasites must rapidly adapt to fluctuating host glucose concentrations throughout their life cycle. However, the precise process by which Plasmodium parasites quickly react and adapt to glucose stress, in general, remains elusive. The goal of this investigation was to determine whether glucose starvation affects the RNA secondary structure of parasites. In this study, we applied different short-term glucose stresses on parasites to determine the effect of host-derived glucose nutrients on the dynamics of parasite development and RNA secondary structures. We found that the S-type rRNA expression level in the low glucose-treated group was higher than that in the 2 mg/mL control group. The RNA-seq results indicated that glucose significantly affects the expression of genes involved in RNA-related processes, antigenic variation, transport processes, stimulus response, and DNA-related activities. Metabolomics studies also revealed that several types of sugar compounds exhibit a decrease in metabolic activity when subjected to a reduction in glucose supply. Via analysis of three glucose conditions, we identified the RNA secondary structures of more than 2,721 transcripts throughout the intraerythrocytic trophozoite stage. We discovered a positive correlation between mRNA structural flexibility (icSHAPE scores) and transcript abundance (RPKM values), demonstrating a direct association between RNA structural openness and steady-state mRNA levels. Our results revealed structural alterations in the entire transcriptome, including glucose transporters, metabolic enzymes, and the erythrocyte invasion protein family. These genes were mainly enriched in response to stimuli or preferential biological processes. The total number of genes with changes in icSHAPE scores in the UTRs was significantly greater for the 3′ UTRs than the 5′ UTRs. Furthermore, by comparing icSHAPE reactivity profiles across glucose conditions, we identified candidate cis-acting RNA motifs predominantly located within UTRs, whose structural flexibility changed rapidly in response to glucose fluctuation. We term these glucose-responsive RNA motifs, as they constitute promising regulatory elements for future research into post-transcriptional glucose sensing mechanisms. Our findings clarify glucose stress-triggered remodeling of in vivo RNA secondary structure during the P. falciparum intraerythrocytic stage, reveal the functional relevance of structural dynamics in parasite environmental adaptation, and lay a foundational resource for future nutrient stress and post-transcriptional regulatory research. These findings show that glucose, the primary carbon source for parasite survival, modulates RNA secondary structural dynamics via nutrient-sensing cascades to modulate parasite proliferation and adaptive development, which offers clues for developing novel antimalarial therapies.