2025/08/07 by Thi Ngan Giang Nguyen, Md Mostafa Kamal, Chien‐Ling Lin +1 · 1 voice
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Protist diversity and phylogeny #Microbial Community Ecology and Physiology #RNA modifications and cancer
paper · pdf · doi:10.1101/2025.08.05.668791
openalex publication_date 2025/08/07 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Abstract The integration of symbionts into host cells during endosymbiosis significantly alters gene expression and cell physiology. Though alternative splicing facilitates cellular adaptation through rapid modulation of gene expression and protein isoform diversity, its regulatory role during endosymbiosis remains poorly understood. Paramecium bursaria , which harbors hundreds of Chlorella variabilis algae within its cytoplasm, offers a powerful model to study splicing during endosymbiosis, especially given its exceptionally short introns (median ∼24 nt). Using time-course RNA sequencing of symbiotic and aposymbiotic cells, we found that splicing, especially of 5’ proximal introns, enhances gene expression. Moreover, we identified 883 genes with differentially spliced introns, particularly enriched in transmembrane transporters essential for establishing nutrient exchange between a host cell and algal symbionts. Splicing regulation correlated with expression changes in conserved spliceosome components, implicating that these factors act as splicing enhancers or repressors during symbiosis. By exploring intron orthology across ciliates, we found that conserved introns exhibited more efficient splicing, characterized by lower GC content and uniform length, suggesting that intron evolution favors features that optimize expression. Our study reveals how splicing contributes to host adaptation during endosymbiosis and highlights the evolutionary dynamics of short introns in eukaryotes. Key points Paramecium retains conserved core spliceosome genes but employs unique splicing regulation. Alternative splicing regulates metabolism during endosymbiosis, especially for transporter genes. Older introns evolve toward ∼24 nt length and low GC for efficient splicing and expression.