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.