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

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

Biomedical Engineering

Research output: Contribution to journal › Article › peer-review

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 language	English (US)
Pages (from-to)	5237-5253.e22
Journal	Cell
Volume	186
Issue number	24
DOIs	https://doi.org/10.1016/j.cell.2023.10.015
State	Published - Nov 22 2023

Keywords

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

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.1016/j.cell.2023.10.015

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Schindler, D., Walker, R. S. K., Jiang, S., Brooks, A. N., Wang, Y., Müller, C. A., Cockram, C., Luo, Y., García, A., Schraivogel, D., Mozziconacci, J., Pena, N., Assari, M., Sánchez Olmos, M. D. C., Zhao, Y., Ballerini, A., Blount, B. A., Cai, J., Ogunlana, L., ... 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

Schindler, D, Walker, RSK, Jiang, S, Brooks, AN, Wang, Y, Müller, CA, Cockram, C, Luo, Y, García, A, Schraivogel, D, Mozziconacci, J, Pena, N, Assari, M, Sánchez Olmos, MDC, Zhao, Y, Ballerini, A, Blount, BA, Cai, J, Ogunlana, L, Liu, W, Jönsson, K, Abramczyk, D, Garcia-Ruiz, E, Turowski, TW, Swidah, R, Ellis, T, Pan, T, Antequera, F, Shen, Y, Nieduszynski, CA, Koszul, R, Dai, J, Steinmetz, LM, Boeke, JD & Cai, Y 2023, 'Design, construction, and functional characterization of a tRNA neochromosome in yeast', Cell, vol. 186, no. 24, pp. 5237-5253.e22. https://doi.org/10.1016/j.cell.2023.10.015

@article{673aa72f909940bab3e5740a67c5849c,

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

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",

author = "Daniel Schindler and Walker, {Roy S.K.} and Shuangying Jiang and Brooks, {Aaron N.} and Yun Wang and M{\"u}ller, {Carolin A.} and Charlotte Cockram and Yisha Luo and Alicia Garc{\'i}a and Daniel Schraivogel and Julien Mozziconacci and Noah Pena and Mahdi Assari and {S{\'a}nchez Olmos}, {Mar{\'i}a del Carmen} and Yu Zhao and Alba Ballerini and Blount, {Benjamin A.} and Jitong Cai and Lois Ogunlana and Wei Liu and Katarina J{\"o}nsson and Dariusz Abramczyk and Eva Garcia-Ruiz and Turowski, {Tomasz W.} and Reem Swidah and Tom Ellis and Tao Pan and Francisco Antequera and Yue Shen and Nieduszynski, {Conrad A.} and Romain Koszul and Junbiao Dai and Steinmetz, {Lars M.} and Boeke, {Jef D.} and Yizhi Cai",

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year = "2023",

month = nov,

day = "22",

doi = "10.1016/j.cell.2023.10.015",

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T1 - Design, construction, and functional characterization of a tRNA neochromosome in yeast

AU - Schindler, Daniel

AU - Walker, Roy S.K.

AU - Jiang, Shuangying

AU - Brooks, Aaron N.

AU - Wang, Yun

AU - Müller, Carolin A.

AU - Cockram, Charlotte

AU - Luo, Yisha

AU - García, Alicia

AU - Schraivogel, Daniel

AU - Mozziconacci, Julien

AU - Pena, Noah

AU - Assari, Mahdi

AU - Sánchez Olmos, María del Carmen

AU - Zhao, Yu

AU - Ballerini, Alba

AU - Blount, Benjamin A.

AU - Cai, Jitong

AU - Ogunlana, Lois

AU - Liu, Wei

AU - Jönsson, Katarina

AU - Abramczyk, Dariusz

AU - Garcia-Ruiz, Eva

AU - Turowski, Tomasz W.

AU - Swidah, Reem

AU - Ellis, Tom

AU - Pan, Tao

AU - Antequera, Francisco

AU - Shen, Yue

AU - Nieduszynski, Conrad A.

AU - Koszul, Romain

AU - Dai, Junbiao

AU - Steinmetz, Lars M.

AU - Boeke, Jef D.

AU - Cai, Yizhi

PY - 2023/11/22

Y1 - 2023/11/22

N2 - 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.

AB - 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.

KW - Sc2.0

KW - Yeast 2.0

KW - cellular burden

KW - genome reorganization

KW - neochromosome

KW - ploidy changes

KW - rational chromosome design

KW - synthetic biology

KW - synthetic genomics

KW - tRNA

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U2 - 10.1016/j.cell.2023.10.015

DO - 10.1016/j.cell.2023.10.015

M3 - Article

C2 - 37944512

AN - SCOPUS:85175614875

SN - 0092-8674

VL - 186

SP - 5237-5253.e22

JO - Cell

JF - Cell

IS - 24

ER -

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

Abstract

Keywords

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