The Synthetic Yeast Genome Project – Sc2.0 is a state-of-the-art initiative in which scientists from all around the world are collaborating to synthesize an entire eukaryotic genome, specifically that of Saccharomyces cerevisiae. This endeavor aims to empower researchers to understand and overcome obstacles in genome improvement, fostering the creation of more robust organisms for key purposes such as developing new medicines or biofuels.
As part of this project, a collaborative effort was recently published in Cell, presenting an entire neochromosome containing the tRNAs for S. cerevisiae. Fascinating, isn’t it?
tRNA genes are highly conserved across life forms as they are vital for protein synthesis. In S. cerevisiae, there are 275 nuclear tRNA genes. But why synthesize an entire tRNA neochromosome? tRNA genes acts as DNA damage hotspots since they are highly transcribed by RNA polymerase III, and collisions between the transcription elements and the replication fork occur frequently, leading to DNA breakage. Highly repetitive sequences, retrotransposons, and long terminal repeats (LTRs) can also act as hotspots for chromosomal recombination.
To build this neochromosome tRNA genes are organized in arrays placed in tandem, and the neochromosome is synthesized circular, then linearized. To avoid homology with S. cerevisiae sequences, the flanking sequences of the genes are from non-S. cerevisiae yeast species. The chromosome was designed to maintain the tRNA copy number and codon specificity of all wild-type tRNA genes of S. cerevisiae. To address the repetitive sequences problem, researchers used the flanking sequences of another yeast species, A. gossypii, which lacks retrotransposons and LTRs. The tRNA genes on the neochromosome successfully compensated for the loss of function of their wild-type counterparts. The DNA damage caused by collisions between transcription machinery and the replication fork was resolved by directing the arrays of tRNAs so that the direction of transcription and the replication fork were in agreement. Another scientific significance of this neochromosome is that it serves as a chassis for studying tRNA genetics and chromosomal biology.
Without delving too deeply into technicalities, the neochromosome was efficiently integrated into the S. cerevisiae genome, as confirmed by transcriptomic and proteomic analyses. The chromosome affected the overall growth of the cell, as a whole new set of tRNAs now has to be transcribed. However, the downregulation of RNA polymerases I and III can compensate to recover the growth phenotype.
Another aspect to consider is the ethical one. This successful synthesis and integration of a neochromosome into the genome of S. cerevisiae is one example of how far science has progressed and how close we are to creating and designing new organisms. This point raises numerous ethical concerns about how far we can go and how this may affect the ecosystem and life on Earth if things were to go out of control. Other concerns may be ideological and religious.
In conclusion, this fascinating work opens new doors in RNA biology to study various families of RNAs and their functions, as well as the quite interesting and central idea of synthesizing the entire genome of the yeast S. cerevisiae. The ability to manipulate life, as we have known for thousands of years, is very intriguing and enjoyable.
References:
Schindler, D. et al. Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell (2023)
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