TY - UNPB
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 - 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 - 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 - 2022/10/3
Y1 - 2022/10/3
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 incorporated orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enable an orthogonal SCRaMbLE system capable of adjusting tRNA abundance. Following construction, we obtained evidence of a potent selective force once the neochromosome was introduced into yeast cells, 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 new opportunities to directly test hypotheses surrounding these essential non-coding RNAs. HighlightsDe novo design, construction and functional characterization of a neochromosome containing all 275 nuclear tRNA genes of Saccharomyces cerevisiae.Increasing the copy number of the 275 highly expressed tRNA genes causes cellular burden, which the host cell likely buffers either by selecting for partial tRNA neochromosome deletions or by increasing its ploidy.The tRNA neochromosome can be chemically extracted and transformed into new strain backgrounds, enabling its transplantation into multi-synthetic chromosome strains to finalize the Sc2.0 strain.Comprehensive functional characterization does not pinpoint a singular cause for the cellular burden caused by the tRNA neochromosome, but does reveal novel insights into its tRNA and structural chromosome biology.
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 incorporated orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enable an orthogonal SCRaMbLE system capable of adjusting tRNA abundance. Following construction, we obtained evidence of a potent selective force once the neochromosome was introduced into yeast cells, 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 new opportunities to directly test hypotheses surrounding these essential non-coding RNAs. HighlightsDe novo design, construction and functional characterization of a neochromosome containing all 275 nuclear tRNA genes of Saccharomyces cerevisiae.Increasing the copy number of the 275 highly expressed tRNA genes causes cellular burden, which the host cell likely buffers either by selecting for partial tRNA neochromosome deletions or by increasing its ploidy.The tRNA neochromosome can be chemically extracted and transformed into new strain backgrounds, enabling its transplantation into multi-synthetic chromosome strains to finalize the Sc2.0 strain.Comprehensive functional characterization does not pinpoint a singular cause for the cellular burden caused by the tRNA neochromosome, but does reveal novel insights into its tRNA and structural chromosome biology.
U2 - 10.1101/2022.10.03.510608
DO - 10.1101/2022.10.03.510608
M3 - Preprint
BT - Design, construction, and functional characterization of a tRNA neochromosome in yeast
PB - bioRxiv
ER -