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.