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Genome shuffling leads to rapid phenotypic improvement in bacteria


For millennia, selective breeding, on the basis of biparental mating, has led to the successful improvement of plants and animals to meet societal needs1. At a molecular level, DNA shuffling mimics, yet accelerates, evolutionary processes, and allows the breeding and improvement of individual genes and subgenomic DNA fragments. We describe here whole-genome shuffling; a process that combines the advantage of multi-parental crossing allowed by DNA shuffling with the recombination of entire genomes normally associated with conventional breeding. We show that recursive genomic recombination within a population of bacteria can efficiently generate combinatorial libraries of new strains. When applied to a population of phenotypically selected bacteria, many of these new strains show marked improvements in the selected phenotype. We demonstrate the use of this approach through the rapid improvement of tylosin production from Streptomyces fradiae. This approach has the potential to facilitate cell and metabolic engineering and provide a non-recombinant alternative to the rapid production of improved organisms.

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Figure 1: Asexual versus sexual evolution.
Figure 2: Genome shuffling versus classical strain improvement.


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The authors would like to thank D. Hopwood for the S. coelicolor strains, E. Lilly for S. fradiae SF1 and SF21, R. Baltz, E. Cundliffe, G. Huisman, V. Gavrilovic, R. Patnaik, M. Lassner, T. Cox and S. Louie for technical discussion and assistance, and the National Institute of Standards and Technology Advanced Technology Program for financial assistance.

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Correspondence to Stephen B. del Cardayré.

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Zhang, YX., Perry, K., Vinci, V. et al. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415, 644–646 (2002).

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