Although Escherichia coli has been a popular tool
for plasmid construction, this bacterium was believed to be “unsuitable”
for constructing a large plasmid whose size exceeds 500 kilobases.
We assumed that traditional plasmid vectors may lack some regulatory
DNA elements required for the stable replication and segregation of
such a large plasmid. In addition, the use of a few site-specific
recombination systems may facilitate cloning of large DNA segments.
Here we show two strategies for constructing 1-megabase (1-Mb) secondary
chromosomes by using new bacterial artificial chromosome (BAC) vectors.
First, the 3-Mb genome of a genome-reduced E. coli strain was split into two chromosomes (2-Mb and 1-Mb), of which
the smaller one has the origin of replication and the partitioning
locus of the Vibrio tubiashii secondary chromosome.
This chromosome fission method (Flp-POP cloning) works via flippase-mediated excision, which coincides with the reassembly
of a split chloramphenicol resistance gene, allowing chloramphenicol
selection. Next, we developed a new cloning method (oriT-POP cloning) and a fully equipped BAC vector (pMegaBAC1H) for developing
a 1-Mb plasmid. Two 0.5-Mb genomic regions were sequentially transferred
from two donor strains to a recipient strain via conjugation
and captured by pMegaBAC1H in the recipient strain to produce a 1-Mb
plasmid. This 1-Mb plasmid was transmissible to another E. coli strain via conjugation. Furthermore, these 1-Mb
secondary chromosomes were amplifiable in vitro by
using the reconstituted E. coli chromosome replication
cycle reaction (RCR). These strategies and technologies would make
popular E. coli cells a productive factory for
designer chromosome engineering.