University of Massachusetts Medical School Faculty Publications
UMMS Affiliation
Department of Microbiology and Physiological Systems
Publication Date
2018-01-16
Document Type
Article Preprint
Disciplines
Bacterial Infections and Mycoses | Computational Biology | Genetic Phenomena | Genetics | Genomics | Microbiology | Molecular, Cellular, and Tissue Engineering | Molecular Genetics
Abstract
Current methods for genome engineering in mycobacteria rely on relatively inefficient recombination systems that require the laborious construction of a long double-stranded DNA substrate for each desired modification. We combined two efficient recombination systems to produce a versatile method for high-throughput chromosomal engineering that obviates the need for the preparation of double-stranded DNA recombination substrates. A synthetic targeting oligonucleotide is incorporated into the chromosome via homologous recombination mediated by the phage Che9c RecT annelase. This oligo contains a site-specific recombination site for the directional Bxb1 integrase (Int), which allows the simultaneous integration of a payload plasmid that contains a cognate recombination site and selectable marker. The targeting oligo and payload plasmid are co-transformed into a RecT- and Int- expressing strain, and drug-resistant homologous recombinants are selected in a single step. A library of reusable target-independent payload plasmids is available to generate knockouts and promoter replacements, or to fuse the C-terminal-encoding regions of target genes with tags of various functionalities. This new system is called ORBIT (Oligo-mediated Recombineering followed by Bxb1 Integrase Targeting) and is ideally suited for the creation of libraries consisting of large numbers of deletions, insertions or fusions in a target bacterium. We demonstrate the utility of ORBIT by the construction of insertions or deletions in over 100 genes in M. tuberculosis and M. smegmatis. The report describes the first genetic engineering technique for making selectable chromosomal fusions and deletions that does not require the construction of target- or modification-specific double-stranded DNA recombination substrates.
Keywords
genetics, Oligo-mediated Recombineering followed by Bxb1 Integrase Targeting, ORBIT, genetic engineering, mycobacterial chromosomes, oligonucleotides, bacteria
Rights and Permissions
The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
DOI of Published Version
10.1101/249292
Source
bioRxiv 249292; doi: https://doi.org/10.1101/249292. Link to preprint on bioRxiv service.
Journal/Book/Conference Title
bioRxiv
Repository Citation
Murphy, Kenan C.; Nelson, Samantha J.; Nambi, Subhalaxmi; Papavinasasundaram, Kadamba; Baer, Christina E.; and Sassetti, Christopher M., "ORBIT: a new paradigm for genetic engineering of mycobacterial chromosomes" (2018). University of Massachusetts Medical School Faculty Publications. 1526.
https://escholarship.umassmed.edu/faculty_pubs/1526
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
Included in
Bacterial Infections and Mycoses Commons, Computational Biology Commons, Genetic Phenomena Commons, Genetics Commons, Genomics Commons, Microbiology Commons, Molecular, Cellular, and Tissue Engineering Commons, Molecular Genetics Commons