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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)
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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.

Original languageEnglish
Pages (from-to)5237-5253.e22
Number of pages39
JournalCell
Volume186
Issue number24
Early online date8 Nov 2023
DOIs
Publication statusPublished - 22 Nov 2023

Bibliographical note

Copyright the Author(s) 2023. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

  • cellular burden
  • genome reorganization
  • neochromosome
  • ploidy changes
  • rational chromosome design
  • Sc2.0
  • synthetic biology
  • synthetic genomics
  • tRNA
  • Yeast 2.0

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  • COESB: ARC Centre of Excellence in Synthetic Biology

    Paulsen, I., Filipovska, A., Parker, R., Nielsen, L. K., Neilan, B. A., Alexandrov, K., Jackson , C., Wodak, J., Rackham, O., Marcellin, E., Gillings, M., Rogers, W., Lee, L., Packer, N., O'Hara, I. M., Speight, R., Vickers, C. E., Beliaev, A., Scott, C., Lacey, J., Mankad, A., Calvert, J., Thomas, G., Rodriguez-Concepcion, M., Fleishman, S., Koepke, M., Ball, M., Turner, N. J., Borneman, A. R., Holowko, M., Goold, H., Ellis, T., Mitchell, L. A. & Dai, J.

    9/11/208/11/27

    Project: Research

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