Design, construction, and functional characterization of a tRNA neochromosome in yeast

Schindler, Daniel; Walker, Roy S.K.; Jiang, Shuangying; Brooks, Aaron N.; Wang, Yun; Müller, Carolin A.; Cockram, Charlotte; Luo, Yisha; García, Alicia; Schraivogel, Daniel; Mozziconacci, Julien; Pena, Noah; Assari, Mahdi; Sánchez Olmos, María del Carmen; Zhao, Yu; Ballerini, Alba; Blount, Benjamin A.; Cai, Jitong; Ogunlana, Lois; Liu, Wei; Jönsson, Katarina; Abramczyk, Dariusz; Garcia-Ruiz, Eva; Turowski, Tomasz W.; Swidah, Reem; Ellis, Tom; Pan, Tao; Antequera, Francisco; Shen, Yue; Nieduszynski, Conrad A.; Koszul, Romain; Dai, Junbiao; Steinmetz, Lars M.; Boeke, Jef D.; Cai, Yizhi

Abstract

Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190-kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enables an orthogonal tRNA SCRaMbLE system. Following construction in yeast, we obtained evidence of a potent selective force, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH, and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs.

Citation

Schindler, D., Walker, R. S., Jiang, S., Brooks, A. N., Wang, Y., Müller, C. A., …Cai, Y. (2023). Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell, 186(24), 5237-5253.e22. https://doi.org/10.1016/j.cell.2023.10.015

• Journal Article Type: Article
• Acceptance Date: Oct 12, 2023
• Online Publication Date: Nov 8, 2023
• Publication Date: Nov 22, 2023
• Deposit Date: Nov 10, 2023
• Publicly Available Date: Nov 10, 2023
• Journal: Cell
• Print ISSN: 0092-8674
• Electronic ISSN: 1097-4172
• Publisher: Cell Press
• Peer Reviewed: Peer Reviewed
• Volume: 186
• Issue: 24
• Pages: 5237-5253.e22
• DOI: https://doi.org/10.1016/j.cell.2023.10.015
• Keywords: Ssynthetic biology; synthetic genomics; tRNA; neochromosome; Sc2.0; Yeast 2.0; cellular burden; rational chromosome design; genome reorganization; ploidy changes
• Public URL: https://nottingham-repository.worktribe.com/output/27086102
• Publisher URL: https://www.cell.com/cell/fulltext/S0092-8674(23)01130-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867423011303%3Fshowall%3Dtrue
• Additional Information: This article is maintained by: Elsevier; Article Title: Design, construction, and functional characterization of a tRNA neochromosome in yeast; Journal Title: Cell; CrossRef DOI link to publisher maintained version: https://doi.org/10.1016/j.cell.2023.10.015; Content Type: article; Copyright: © 2023 The Author(s). Published by Elsevier Inc.