A new toolbox allows engineering genomes without CRISPR

Leuven/Ghent, ​ 08 Febuary 2024 – Belgian researchers from VIB-KU Leuven Center for Microbiology and VIB-UGent Center for Plant Systems Biology have developed a new toolbox of 16 different short DNA sequences that allow triggering controlled and specific recombination events in any genome. This new patented toolbox, complementing – and for certain applications surpassing – CRISPR, is now available for researchers and industry in the field of genome engineering. The results are reported today in two concurrent papers in the prestigious journal Nature Communications.

Site-specific recombinases enable efficient cutting and pasting of DNA at specific locations in the genome, where each recombinase recognizes one precise DNA sequence. Due to their sequence-specificity, CRISPR systems have overshadowed site-specific recombinases in the past decade as a genome engineering tool. CRISPR systems caused a revolution in the field because they can very easily be targeted to different genomic loci. However, because site-specific recombinases operate differently, they circumvent some of the major issues of CRISPR, including the toxicity of DNA double strand breaks causing undesired point mutations and structural variation, the low editing efficiencies faced in many non-conventional organisms and non-dividing cells and the difficulty to insert large DNA fragments. Moreover, the very complex patenting of CRISPR makes its use in research and industry often difficult and expensive.

The research groups of VIB-KU Leuven Center for Microbiology and their colleagues at VIB-UGent Center for Plant Systems Biology have now addressed the shortcomings of earlier site-specific recombination as a means for genomic engineering. The team has expanded the toolbox that uses a viral recombinase (Cre) so that it can now specifically recognize, cut, and paste multiple DNA sites. The team has identified a set of 16 sites that efficiently recombine with the same site, but not with any other site of this set, and this for different organisms.

Due to these orthogonal recombination systems, we can avoid the unpredictable way in which multiple recombination sites in a genome interact with each other. This opens routes for many research projects to install many small or large genomic edits simultaneously or to repeatedly recycle markers during genome engineering efforts. - Professor Kevin Verstrepen, Director of VIB-KU Leuven Center for Microbiology

Applications for research and industry

Charlotte Cautereels, PhD student at the lab of Kevin Verstrepen, established the new toolbox in yeast and tested these in bacterial cells, and collaborated with the VIB-UGent PSB center to also demonstrate its efficiency in plant cells. In her latest publication, she demonstrates how it can be used to optimize the expression of metabolic pathway genes and production titers of industrially relevant molecules. A single round of shuffling dedicated gene regulators with the new recombination sites already doubled the production titers.

We were able to corroborate that modifying expression through our recombination-based setup allows for a rapid and efficient gene expression optimization in heterologous biosynthetic pathways. Not only does this new toolbox offer possibilities to improve microbial cell factories, it also validates our toolbox for scientists and industry working in the field of genome engineering. - Charlotte Cautereels


Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast - https://doi.org/10.1038/s41467-024-44997-7

Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts - https://doi.org/10.1038/s41467-024-44996-8

Joran Lauwers

Joran Lauwers

Science & Business Communications Expert, VIB

Steve Bers

Steve Bers

Science Communications Expert, VIB

About the VIB-KU Leuven Center for Microbiology

The big impact of bacteria on our health, the use of yeasts to enhance the production of chocolate, beer or bioethanol, yeast as a model system for studying human disease ... these are just a few of the research areas for the scientists at the VIB-KU Leuven Center for Microbiology. Their research also has important implications in various fields of application.

About VIB

VIB’s core mission is to generate disruptive insights in the molecular underpinning of life and to translate these actively into impactful innovations for patients and society. VIB is an independent research institute where some 1,800 top scientists from Belgium and abroad conduct pioneering basic research. As such, they are pushing the boundaries of what we know about molecular mechanisms and how they rule living organisms such as human beings, animals, plants, and microorganisms. Based on a close partnership with five Flemish universities – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel, and Hasselt University – and supported by a solid funding program, VIB unites the expertise of all its collaborators and research groups in a single institute. VIB’s technology transfer activities translate research results into concrete benefits for society such as new diagnostics and therapies and agricultural innovations. These applications are often developed by young start-ups from VIB or through collaborations with other companies. This also leads to additional employment and bridges the gap between scientific research and entrepreneurship. VIB also engages actively in the public debate on biotechnology by developing and disseminating a wide range of science-based information. 

More info can be found on www.vib.be.


About VIB

VIB is an independent research institute that translates insights in biology into impactful innovations for society. Collaborating with the five Flemish universities, it conducts research in plant biology, cancer, neuroscience, microbiology, inflammatory diseases, artificial intelligence and more. VIB connects science with entrepreneurship and stimulates the growth of the Flemish biotech ecosystem. The institute contributes to solutions for societal challenges such as new methods for diagnostics and treatments, as well as innovations for agriculture. 

Learn more at www.vib.be.