Synthetic genome engineering gets infectious

Abstract

Since the start of this century, a handful of research groups have pursued the synthesis and large-scale engineering of genomes. Work on synthetic genomes has seen the field scale-up from the full synthesis of the small poliovirus genome (2002) (1), to a complete working synthetic bacterial genome (2010) (2), and more recently to the construction and validation of multiple rewritten eukaryote chromosomes for the model organism Saccharomyces cerevisiae (2014, 2017) (3⇓⇓⇓⇓–8). The costs and time-scales for assembling entire bacterial genomes and eukaryotic chromosomes mean that synthetic genome engineering is not yet a routine approach to manipulating cells for research or biotechnology. However, by stepping down a scale from bacteria to viruses, opportunities quickly arise, even for those viruses with comparatively large genomes, like the double-stranded DNA herpes simplex virus (HSV) type 1 genome, over 150 kb in length. In PNAS, Oldfield et al. (9) engineer the HSV KOS strain genome, leveraging synthetic genomic cloning approaches to rapidly construct HSV variants with combinatorial mutations for functional evaluation. Large-scale genomic engineering has been achieved by a handful of groups taking different approaches, but broadly the strategies employed fall into two categories: multiplexed editing and hierarchical assembly. For editing, new technologies, such as multiplex automated genome engineering-based targeted mutation (10) and the new genome editing tools of CRISPR-Cas9 allow existing genomes to be extensively modified toward a target sequence over several generations within their host cells (11). This can be an efficient approach if the cell grows fast and is easy to manipulate with molecular biology methods. For the alternative hierarchical assembly strategy, a designed or modified target genome sequence is instead put together gradually from smaller subgenomic fragments that are linked together by various DNA assembly methods. Depending on the size of the genome or chromosome … [↵][1]1To whom correspondence should be addressed. Email: t.ellis{at}imperial.ac.uk. [1]: #xref-corresp-1-1