Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly

Published in Science in 2019, this paper developed a programmable method for splitting and rejoining bacterial chromosomes, enabling deliberate large-scale rearrangements and assembly of genomic DNA in E. coli.

Whole-genome engineering requires not just the ability to write new DNA sequences, but the ability to rearrange existing genomic architecture. Chromosomes are not simply linear strings of genes; their organisation affects replication, gene expression, and cell fitness. To build synthetic genomes with defined properties, researchers need tools that can restructure chromosomes at will: splitting a single chromosome into two, merging two chromosomes into one, or rearranging segments within a chromosome.

This paper provides those tools. The team demonstrated programmable chromosome fission (splitting one chromosome into two independent replicons) and chromosome fusion (merging two replicons into one), with precise control over where the breaks and joins occur. These operations work at scales of hundreds of kilobases, enabling rearrangements that would be difficult or unachievable with conventional recombination-based methods.

For Constructive Bio's genome engineering pipeline, chromosome-level tools are essential infrastructure. Building organisms like Syn61 and Syn57, where codons are removed and reassigned across the entire genome, requires the ability to manipulate genomic DNA at scales and configurations that go beyond simple gene insertion or deletion. Chromosome fission and fusion provide a layer of structural control that complements the sequence-level changes enabled by methods like continuous genome synthesis (CGS) and BAC stepwise insertion synthesis (BASIS).

This work broadens the design space for synthetic genomes by making chromosome architecture itself a programmable parameter, contributing to the toolkit that underpins Constructive Bio's ability to create and iterate on genome-recoded production strains.