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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 T. cruzi . Through tRNA sequencing and the integration of epigenomic and translatome data, we discovered that infective and noninfective forms of T. cruzi 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 T. cruzi .

This paper elucidates a close connection between two well-known facts that until now have seemed independent: (i) the quality control (“proofreading”) of the emerging amino acid sequence, occurring during the normal, elongation-factor-dependent ribosomal biosynthesis, which is performed by removing those Aa-tRNAs (aminoacyl tRNAs) whose anticodons are not complementary to the exhibited mRNA codons, and (ii) the in vitro discovered existence of the factor-free ribosomal synthesis of polypeptides. It is shown that a biological role of proofreading is played by a process that is exactly opposite to the step of factor-free binding of Aa-tRNA to the ribosome-exposed mRNA: a factor-free removal of that Aa-tRNA whose anticodon is not complementary to the ribosome-exhibited mRNA codon.