CRISPR SWAPnDROP -- A multifunctional system for genome editing and large-scale interspecies gene transfer

TL;DR

CRISPR SWAPnDROP is a versatile genome editing system enabling large-scale DNA transfer and modifications across bacterial species, demonstrated in E. coli and Vibrio natriegens, with high efficiency and broad application scope.

Contribution

It introduces a modular, multifunctional platform for large-scale in-vivo DNA transfer and genome editing across species, expanding capabilities beyond existing technologies.

Findings

Transferred 151kb chromosomal DNA between bacteria.

Enabled V. natriegens to metabolize lactose and galactose.

Achieved up to 92% editing efficiency with multi-color co-selection.

Abstract

The need for diverse chromosomal modifications in biotechnology, synthetic biology and basic research requires the development of new technologies. With CRISPR SWAPnDROP, we extend the limits of genome editing to large-scale in-vivo DNA transfer between bacterial species. Its modular platform approach facilitates species specific adaptation to confer genome editing in various species. In this study, we show the implementation of the CRISPR SWAPnDROP concept for the model organism Escherichia coli and the currently fastest growing and biotechnologically relevant organism Vibrio natriegens. We demonstrate the excision, transfer and integration of 151kb chromosomal DNA between E. coli strains and from E. coli to V. natriegens without size-limiting intermediate DNA extraction. With the transfer of the E. coli MG1655 wild type lac operon, we establish a functional lactose and galactose degradation pathway in V. natriegens to extend its biotechnological spectrum. We also transfer the E. coli DH5alpha lac operon and make V. natriegens capable of alpha-complementation - a step towards an ultra-fast cloning strain. Furthermore, CRISPR SWAPnDROP is designed to be the swiss army knife of genome engineering. Its spectrum of application comprises scarless, marker-free, iterative and parallel insertions and deletions, genome rearrangements, as well as gene transfer between strains and across species. The modular character facilitates DNA library applications and the recycling of standardized parts. Its novel multi-color scarless co-selection system significantly improves editing efficiency to 92% for single edits and 83% for quadruple edits and provides visual quality controls throughout the assembly and editing process.