4.2 Synthetic minimal genomes
Synthetic genome minimalization
efforts seek to overcome the limitations of genetic redundancy inherent
to several billion years of natural evolution. This includes uncovering
the minimal number of genes required for cell viability. Notable past
efforts include the construction of the bacterium, Mycoplasma
mycoides, which unexpectedly revealed many genes with unknown function
that were essential for life (Hutchison et al., 2016). By reducing
complexity and improving engineerability through the removal of
unnecessary genetic elements, a streamlined minimalised genome will
enable opportunities in both basic and applied research, with the latter
enabling the creation of novel platform chassis of use in industrial
biotechnology. Such advantages include an increased predictability in
rational design, freeing-up unnecessary genetic components for increased
biosynthetic capacity, improved genome stability through the removal of
repetitive genetic elements and generating fundamental insights into
genome function for future genome synthesis (Xu et al., 2023).
Additional research value can be derived through the implementation of
biosecurity layers built into organism design. By removing all genetic
material that does not support the laboratory- or bioreactor-based
growth of the organism, the fitness of the organism in natural and wild
environments is notably reduced (Torres et al., 2016). This
significantly lowers the risk of unintentional releases of engineered
organisms into the wild, an important trait for all industrial organisms
to have when the world is on the cusp of rolling out next-generation
fermentation infrastructure across regional areas that are proximate to
feedstocks, but also proximate to natural and agricultural environments.
Combined with research into other biosecurity techniques, such as kill
switches (Moe-Behrens et al., 2013), this provides the researcher with a
toolkit of biosecurity methodologies for layering over any given
biological design.
Both ‘top-down’ and ‘bottom-up’ represent the fundamental two approaches
to minimal genome design. ‘Top-down’ refers to the reduction of existing
gene content, and ‘bottom-up’ describes the application of whole genome
synthesis and design through de novo DNA synthesis. Notably,
these two approaches can be combined into one chassis, with the Yeast
2.0 project minimalizing existing genome content by removing
transposable elements and implementing one of the more important method
discoveries to arise out of the Yeast 2.0 project, the SCRaMbLE
technique (Shen et al., 2016, 2019; Wu et al., 2018). SCRaMbLE can
generate significant diversity in minimal genome structure, order, and
content, or even alter the composition of essential gene variance within
those designs (Xu et al., 2023). This is due to genomic deletion being
the most commonly occurring SCRaMbLE-related event, leading to a
near-infinite number of variable minimal genomes. However, a key
challenge in this area is ensuring cell viability after deployment of
SCRaMbLE, with a significant proportion of the cells dying following
induction. This is an area of active research and the overall promise of
standardising a minimal genome chassis for industrial biodesign will
both complement in silico design through improved understanding
of minimal content while ensuring biosecurity features are engineered in
from the start.