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 Liu; Katarina 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

doi:10.1016/j.cell.2023.10.015

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

Cell. 2023 Nov 22;186(24):5237-5253.e22. doi: 10.1016/j.cell.2023.10.015. Epub 2023 Nov 8.

Authors

Daniel Schindler¹, Roy S K Walker², Shuangying Jiang³, Aaron N Brooks⁴, Yun Wang⁵, Carolin A Müller⁶, Charlotte Cockram⁷, Yisha Luo⁸, Alicia García⁹, Daniel Schraivogel⁴, Julien Mozziconacci⁷, Noah Pena¹⁰, Mahdi Assari¹¹, María Del Carmen Sánchez Olmos¹², Yu Zhao¹³, Alba Ballerini⁸, Benjamin A Blount¹⁴, Jitong Cai¹⁵, Lois Ogunlana¹⁶, Wei Liu¹⁶, Katarina Jönsson¹⁶, Dariusz Abramczyk¹⁶, Eva Garcia-Ruiz⁸, Tomasz W Turowski¹⁷, Reem Swidah⁸, Tom Ellis¹⁴, Tao Pan¹⁸, Francisco Antequera⁹, Yue Shen¹⁹, Conrad A Nieduszynski⁶, Romain Koszul⁷, Junbiao Dai³, Lars M Steinmetz²⁰, Jef D Boeke²¹, Yizhi Cai²²

Affiliations

¹ Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, 35032 Marburg, Germany.
² School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3BF, Scotland; School of Natural Sciences and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia.
³ CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
⁴ European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany.
⁵ BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China.
⁶ Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK.
⁷ Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France.
⁸ Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
⁹ Instituto de Biología Funcional y Genómica (IBFG), CSIC, Universidad de Salamanca, Salamanca, Spain.
¹⁰ Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA.
¹¹ Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.
¹² Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
¹³ Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
¹⁴ Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK.
¹⁵ Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.
¹⁶ School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland.
¹⁷ Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland.
¹⁸ Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
¹⁹ Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China.
²⁰ European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics and Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.
²¹ Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA.
²² Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK. Electronic address: yizhi.cai@manchester.ac.uk.

PMID: 37944512
DOI: 10.1016/j.cell.2023.10.015

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.

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

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosomes, Artificial, Yeast* / genetics
Gene Expression Profiling
Genome, Fungal*
Proteomics
RNA, Transfer / genetics
Saccharomyces cerevisiae* / genetics
Synthetic Biology

Substances

RNA, Transfer

Abstract

Publication types

MeSH terms

Substances

Grants and funding