4.3  Synthetic yeast neochromosomes
Neochromosomes represent a new concept of designer biological structure that exists both in abstraction, and in addition, to their natural chromosomal complement. In contrast to existing synthetic chromosomes of the Yeast 2.0 project, neochromosomes are generally not based on any natural template and, as such, in silico bio-design approaches play a central role due to their de novo nature. Furthermore, in contrast to classical synthetic biology approaches that view DNA as a ‘code’ to be written, these bio-design efforts extent to treating neochromosomes as a physical entity and therefore require approaches more closely resembling structural engineering performed at the molecular scale. The point-like nature of S. cerevisiaecentromeres and the great power of homologous recombination also render yeast the perfect host. Notable recent advances have demonstrated their application in the systematic refactoring of genetic components (Postma et al., 2021) , the introduction of novel characteristics (Kutyna et al., 2022) and can be used to construct human biosynthetic pathways (Agmon et al., 2020).
Neochromosomes present novel opportunities and advantages to rapidly scale DNA synthesis. In their circular form, these entities can be readily extracted and chemically transformed into a new host chassis at will (Noskov et al., 2011), facilitating the direct transfer of large amounts of genetic information between host biological systems. Subsequently, these chromosomal circles can be converted into functional linear chromosomes by introducing synthetic telomere seed sequences using the telomerator system (Mitchell and Boeke, 2014).
The radical re-engineering approaches of the Sc2.0 consortium have enabled the removal and relocation of all 275 tRNA genes onto a dedicated ‘tRNA neochromosome’ (Schindler and Walker et al., 2022). This project has led to unique insights into tRNA, cell and chromosomal biology that would not have been possible through ‘traditional’ approaches. Following synthetic chromosome consolidation into one host cell, it’s anticipated that the tRNA neochromosome will provide new insights into host-cell tRNA supply and demand through an orthogonal SCRaMbLE system based on the Dre-rox recombination. Thus, the tRNA neochromosome will provide novel insights into cell stress and industrial biotechnology and improve our understanding of minimal genome dynamics once the two SCRaMbLE systems are activated.