New Technique Helps Solve a Long-Standing Obstacle for Microbial Genetic Engineering

SEER, a new method to rapidly search for proteins involved in rearranging DNA molecules, increases genome-editing efficiency.

The Science

Using genetic engineering, scientists can alter genes and transfer them from one organism to another. To do this, genetic engineers use proteins that can move fragments of DNA between organisms. Once scientists find a gene that carries out a desired function, for example, in a wild microbe, they can take the DNA fragment that contains that gene or synthesize a copy and insert it into the genome of an industrially useful organism. Scientists can then modify the gene however they want. This process, called DNA recombination, refers to the natural or artificial way that DNA moves and changes. Now scientists have developed a fast method to find new proteins involved in DNA recombination that can improve the efficiency of genetic engineering.

The Impact

For decades, scientists have used a tool called recombination-mediated genetic engineering, or recombineering. This technique works well in Escherichia coli, a type of bacteria often used in laboratory experiments. However, it does not work well for a long list of microbes that are used in industry. A new technique called Serial Enrichment for Efficient Recombineering (SEER) should help. SEER allows biologists to apply recombineering to many different species of bacteria and will help speed up the engineering of microbes for biotechnology applications.


Recombineering  allows scientists to introduce genetic material from different species into bacterial genomes, as well as to make edits to existing DNA, conferring new functions to edited bacteria. For example, scientists can add genetic material for the synthesis of biofuels or other valuable compounds. Although they are useful and flexible, these recombineering approaches do not work well in other microbial species, including many industrially relevant microorganisms. To solve this problem, scientists have now developed the high-throughput SEER screening method. SEER allows researchers to identify new single-stranded DNA-annealing proteins (SSAPs) that promote efficient recombineering. SSAPs are often found in phages, which are viruses that infect bacteria. Using SEER, the investigators rapidly tested more than 200 SSAPs and found two promising recombineering proteins that greatly improve gene-editing efficiency in diverse bacterial species, including E. coli, Pseudomonas aeruginosa (a human pathogen), and Citrobacter freundii (an industrially relevant bacterium). SEER will facilitate the discovery of many recombineering proteins in new and different bacteria that will expand their use to other industrial microbes. Using these new proteins in combination with multiplex recombineering technologies, such as multiplex automated genome engineering (MAGE), will enable scientists to simultaneously edit multiple genes, for applications such as whole metabolic pathway optimization, in important bacterial species in a single experiment.

Principal Investigator

Timothy Wannier
Harvard Medical School
[email protected]

Co-Principal Investigator

George M. Church
Harvard Medical School
[email protected]

Related Links

BER Program Manager

Pablo Rabinowicz

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Funding for this research was provided by the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy Office of Science. Funding for individual researchers was provided by the European Research Council, the Lendület (Momentum) Program of the Hungarian Academy of Sciences, a Ph.D. fellowship from the Boehringer Ingelheim Fonds, a European Molecular Biology Organization (EMBO) Long-Term Fellowship, the Szeged Scientists Academy under the sponsorship of the Hungarian Ministry of Human Capacities, the New National Excellence Program of the Hungarian Ministry of Human Capacities, and the New National Excellence Program of the Hungarian Ministry for Innovation and Technology.


Wannier, T. M., A. Nyerges, H. M. Kuchwara, M. Czikkely, D. Balogh, G. T. Filsinger, N. C. Borders, C. J. Gregg, M. J. Lajoie, X. Rios, C. Pál and G. M. Church. 2020. “Improved Bacterial Recombineering by Parallelized Protein Discovery,Proceedings of the National Academy of Sciences USA 117(24), 13689–98. DOI:10.1073/pnas.2001588117.