Five-layer systems analysis of Leishmania stage differentiation reveals an essential role for protein degradation in parasite development

Vector-borne, protist parasites have evolved complex developmental programs to adapt to very distinct host environments. How these important pathogens transition between insect and mammalian stages is only poorly understood. Here, we investigated stage differentiation in Leishmania donovani , a trypanosomatid parasite with constitutive gene transcription, offering a model to study post-transcriptional regulation. Using a five-layer integrative systems analysis (genome to metabolome), we compared hamster-derived amastigotes and culture-derived promastigotes. Genomic adaptation was excluded as a major driver of differentiation, while differential mRNA turnover emerged as a key mechanism of stage-specific gene expression. Transcriptomic and proteomic comparisons revealed a broad dynamic range of protein abundance changes that correlated poorly with mRNA levels. This discrepancy was linked to (i) altered snoRNA expression and rRNA modifications, indicating stage-specific tuning of translation, and (ii) differential protein degradation, supported by proteomics following proteasome inhibition with lactacystin. Lactacystin impaired amastigote-to-promastigote differentiation, highlighting the importance of proteasomal activity. Overall, our analysis links Leishmania development to coordinated post-transcriptional regulatory networks. Our findings provide a powerful new resource for research programs that aim to dissect the emergent properties of regulatory networks and feedback loops underlying Leishmania stage differentiation, serving as a blueprint for other vector-borne pathogens that rely on disease-associated developmental transitions.