Integrating tRNA gene epigenomics and expression with codon usage unravels an intricate connection with translatome dynamics in <i>Trypanosoma cruzi</i>

Trypanosomatids primarily regulate protein expression at the posttranscriptional level, with codon bias playing a crucial role in controlling protein production across all life forms. This study investigated how codon usage, tRNA abundance, and codon pairing modes influence protein production in <i>T. cruzi</i>. Through tRNA sequencing and the integration of epigenomic and translatome data, we discovered that infective and noninfective forms of <i>T. cruzi</i> exhibit similar codon usage and tRNA pool preferences, despite having different proteomes. We developed pipelines applicable to any organism to measure codon adaptation to tRNA pools and pairing modes. Our analysis revealed that highly expressed genes are better aligned with more abundant tRNAs and favor Watson-Crick or inosine pairing. These findings suggest an additional layer of gene regulation based on tRNA availability and pairing modes, which impacts protein expression in the different life forms of <i>T. cruzi</i>.