A standardized genome architecture for bacterial synthetic biology (SEGA)

• Published in: Nature communications Vol. 12; no. 1; p. 5876
• Main Authors: Bayer, Carolyn N., Rennig, Maja, Ehrmann, Anja K., Nørholm, Morten H. H.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 07-10-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 13; 42; 42/44; 631/1647/1511; 631/61/185; 631/61/338/552; Bacteria; Bacteria - genetics; Biology; Chromosomes; Deoxyribonucleic acid; DNA; Engineering; Escherichia coli - genetics; Flow Cytometry - methods; Gene expression; Gene Expression Regulation, Bacterial; Genetic Engineering - methods; Genetic Vectors; Genome editing; Genome, Bacterial; Genomes; Humanities and Social Sciences; Inspection; Laboratory tests; multidisciplinary; Plasmids; Plates; Post-translation; Promoter Regions, Genetic; Reagents; Recombination, Genetic; Reference Standards; Science; Science (multidisciplinary); Screening; Standardization; Synthetic biology; Synthetic Biology - methods; Transcription; Translation
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-26155-5

Chromosomal recombinant gene expression offers a number of advantages over plasmid-based synthetic biology. However, the methods applied for bacterial genome engineering are still challenging and far from being standardized. Here, in an attempt to realize the simplest recombinant genome technology imaginable and facilitate the transition from recombinant plasmids to genomes, we create a simplistic methodology and a comprehensive strain collection called the Standardized Genome Architecture (SEGA). In its simplest form, SEGA enables genome engineering by combining only two reagents: a DNA fragment that can be ordered from a commercial vendor and a stock solution of bacterial cells followed by incubation on agar plates. Recombinant genomes are identified by visual inspection using green-white colony screening akin to classical blue-white screening for recombinant plasmids. The modular nature of SEGA allows precise multi-level control of transcriptional, translational, and post-translational regulation. The SEGA architecture simultaneously supports increased standardization of genetic designs and a broad application range by utilizing well-characterized parts optimized for robust performance in the context of the bacterial genome. Ultimately, its adaption and expansion by the scientific community should improve predictability and comparability of experimental outcomes across different laboratories.
Genome engineering is challenging compared to plasmid DNA manipulation. Here the authors create a simple methodology called SEGA that enables genome engineering by combining DNA and bacterial cells followed by identification of recombinant clones by a change in colour when grown on agar plates.