Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast

Schindler, D.; Walker, R. S. K.; Jiang, S.; Brooks, A. N.; Wang, Y.; Mueller, C. A.; Cockram, C.; Luo, Y.; Garcia, A.; Schraivogel, D.; Mozziconacci, J.; Blount, B. A.; Cai, J.; Ogunlana, L.; Liu, W.; Joensson, K.; Abramczyk, D.; Garcia-Ruiz, E.; Turowski, T. W.; Swidah, R.; Ellis, T.; Antequera, F.; Shen, Y.; Nieduszynski, C. A.; Koszul, R.; Dai, J.; Steinmetz, L. M.; Boeke, J. D.; Cai, Y.

doi:10.1101/2022.10.03.510608

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bioRxiv · 10.1101/2022.10.03.510608

Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast

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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 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. HighlightsO_LIDe novo design, construction and functional characterization of a neochromosome containing all 275 nuclear tRNA genes of Saccharomyces cerevisiae. C_LIO_LIIncreasing 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. C_LIO_LIThe 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. C_LIO_LIComprehensive 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. C_LI

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Schindler, D., Walker, R. S. K., Jiang, S., Brooks, A. N., Wang, Y., Mueller, C. A., Cockram, C., Luo, Y., Garcia, A., Schraivogel, D., Mozziconacci, J., Blount, B. A., Cai, J., Ogunlana, L., Liu, W., Joensson, K., Abramczyk, D., Garcia-Ruiz, E., Turowski, T. W., Swidah, R., Ellis, T., Antequera, F., Shen, Y., Nieduszynski, C. A., Koszul, R., Dai, J., Steinmetz, L. M., Boeke, J. D., Cai, Y.. 2022-10-03. Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast. https://doi.org/10.1101/2022.10.03.510608

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