Emergent Properties of Reduced-Genome Escherichia coli

Abstract

With the use of synthetic biology, we reduced the Escherichia coli K-12 genome by making planned, precise deletions. The multiple-deletion series (MDS) strains, with genome reductions up to 15%, were designed by identifying nonessential genes and sequences for elimination, including recombinogenic or mobile DNA and cryptic virulence genes, while preserving good growth profiles and protein production. Genome reduction also led to unanticipated beneficial properties: high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains. Eradication of stress-induced transposition evidently stabilized the MDS genomes and provided some of the new properties.

Biofuel alternatives to ethanol: pumping the microbial well

“…For success in the production of alternative biofuels, similar metabolic engineering strategies will be necessary; for example, the development of targeted and efficient transport systems, the improvement of the resistance of biofuels producers to the toxic effects of accumulating biomolecules, the optimization of carbon flux to the desired products, and the construction of strains that are robust under industrial process conditions [14,[72][73][74]. Some advances that might have enormous potential in the field of microbial biofuel production include the engineer-ing of a reduced-genome E. coli strain that can be used for the systematic design of desired phenotypes [75], and the inter-microbial genome transplantation demonstrated in Mycoplasma caprilocum [76]. These examples represent the first steps towards engineering an entire biological system from the ground up.…”

Building the blueprint of life

“…Efforts are under way in many labs throughout the world to produce a living strain with a minimal genome [1,7,8,14,[49][50][51]. These efforts are applying various approaches, depending on the organisms being used as a starting point and the specific scientific or industrial objectives motivating the effort.All the approaches can be classified as either top down or bottom up [4].…”

“…These efforts are applying various approaches, depending on the organisms being used as a starting point and the specific scientific or industrial objectives motivating the effort.All the approaches can be classified as either top down or bottom up [4]. Top-down approaches involve starting with the genome of an existing (often far from minimal) organism and combining deletions to produce progressively smaller genomes [7,8,14,[49][50][51]. Bottom-up approaches involve starting with a very small genome and engineering a reduced version of the entire genome for implantation and viability testing [1].…”

“…These efforts are already helping to improve genome annotations [5,6,11], correct models ( [12,13] and Tanaka et al, unpublished results), and gain insights into global cell regulation [8,14].…”

“…A minimal organism will lack mobile DNA elements (e.g., insertion elements, transposases, phages, integrases, and site-specific recombinases) that plague efforts to control strains used in the industrial setting over the long term [14]. A minimal organism will also lack competing metabolic pathways that drive raw materials away from desired end products and toward useless or even toxic byproducts [2].…”