The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation

• Published in: Genome Biology Vol. 25; no. 1; pp. 268 - 25
• Main Authors: Papadopoulos, Chris, Arbes, Hugo, Cornu, David, Chevrollier, Nicolas, Blanchet, Sandra, Roginski, Paul, Rabier, Camille, Atia, Safiya, Lespinet, Olivier, Namy, Olivier, Lopes, Anne
• Format: Journal Article
• Language: English
• Published: England BioMed Central 14-10-2024; BMC
• Subjects: Biochemistry, Molecular Biology; De novo coding products; Genome evolution; Genomics; Life Sciences; Microbiology and Parasitology; Mycology; Non-canonical translation signals; Noncoding genome; Open Reading Frames; Pervasive translation; Protein Biosynthesis; Ribosome Profiling; Ribosomes - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Non-canonical translation signals; Genome evolution; De novo coding products; Noncoding genome; Pervasive translation; Noncanonical translation signals
• ISSN: 1474-760X; 1465-6906; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-024-03403-7

Pervasive translation is a widespread phenomenon that plays a critical role in the emergence of novel microproteins, but the diversity of translation patterns contributing to their generation remains unclear. Based on 54 ribosome profiling (Ribo-Seq) datasets, we investigated the yeast Ribo-Seq landscape using a representation framework that allows the comprehensive inventory and classification of the entire diversity of Ribo-Seq signals, including non-canonical ones.
We show that if coding regions occupy specific areas of the Ribo-Seq landscape, noncoding regions encompass a wide diversity of Ribo-Seq signals and, conversely, populate the entire landscape. Our results show that pervasive translation can, nevertheless, be associated with high specificity, with 1055 noncoding ORFs exhibiting canonical Ribo-Seq signals. Using mass spectrometry under standard conditions or proteasome inhibition with an in-house analysis protocol, we report 239 microproteins originating from noncoding ORFs that display canonical but also non-canonical Ribo-Seq signals. Each condition yields dozens of additional microprotein candidates with comparable translation properties, suggesting a larger population of volatile microproteins that are challenging to detect. Our findings suggest that non-canonical translation signals may harbor valuable information and underscore the significance of considering them in proteogenomic studies. Finally, we show that the translation outcome of a noncoding ORF is primarily determined by the initiating codon and the codon distribution in its two alternative frames, rather than features indicative of functionality.
Our results enable us to propose a topology of a species' Ribo-Seq landscape, opening the way to comparative analyses of this translation landscape under different conditions.