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Wacholder A, Parikh SB, Coelho NC, Acar O, Houghton C, Chou L, Carvunis AR. A vast evolutionarily transient translatome contributes to phenotype and fitness. Cell Syst 2023; 14:363-381.e8. [PMID: 37164009 PMCID: PMC10348077 DOI: 10.1016/j.cels.2023.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/30/2023] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Translation is the process by which ribosomes synthesize proteins. Ribosome profiling recently revealed that many short sequences previously thought to be noncoding are pervasively translated. To identify protein-coding genes in this noncanonical translatome, we combine an integrative framework for extremely sensitive ribosome profiling analysis, iRibo, with high-powered selection inferences tailored for short sequences. We construct a reference translatome for Saccharomyces cerevisiae comprising 5,400 canonical and almost 19,000 noncanonical translated elements. Only 14 noncanonical elements were evolving under detectable purifying selection. A representative subset of translated elements lacking signatures of selection demonstrated involvement in processes including DNA repair, stress response, and post-transcriptional regulation. Our results suggest that most translated elements are not conserved protein-coding genes and contribute to genotype-phenotype relationships through fast-evolving molecular mechanisms.
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Affiliation(s)
- Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Saurin Bipin Parikh
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Integrative Systems Biology Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Nelson Castilho Coelho
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Omer Acar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Joint CMU-Pitt PhD Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Carly Houghton
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Joint CMU-Pitt PhD Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Lin Chou
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Integrative Systems Biology Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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