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Abstract
The technology of recombineering, in vivo genetic engineering, was initially developed in Escherichia coli and uses bacteriophage-encoded homologous recombination proteins to efficiently recombine DNA at short homologies (35 to 50 nt). Because the technology is homology driven, genomic DNA can be modified precisely and independently of restriction site location. Recombineering uses linear DNA substrates that are introduced into the cell by electroporation; these can be PCR products, synthetic double-strand DNA (dsDNA), or single-strand DNA (ssDNA). Here we describe the applications, challenges, and factors affecting ssDNA and dsDNA recombineering in a variety of non-model bacteria, both Gram-negative and -positive, and recent breakthroughs in the field. We list different microbes in which the widely used phage λ Red and Rac RecET recombination systems have been used for in vivo genetic engineering. New homologous ssDNA and dsDNA recombineering systems isolated from non-model bacteria are also described. The Basic Protocol outlines a method for ssDNA recombineering in the non-model species of Shewanella. The Alternate Protocol describes the use of CRISPR/Cas as a counter-selection system in conjunction with recombineering to enhance recovery of recombinants. We provide additional background information, pertinent considerations for experimental design, and parameters critical for success. The design of ssDNA oligonucleotides (oligos) and various internet-based tools for oligo selection from genome sequences are also described, as is the use of oligo-mediated recombination. This simple form of genome editing uses only ssDNA oligo(s) and does not require an exogenous recombination system. The information presented here should help researchers identify a recombineering system suitable for their microbe(s) of interest. If no system has been characterized for a specific microbe, researchers can find guidance in developing a recombineering system from scratch. We provide a flowchart of decision-making paths for strategically applying annealase-dependent or oligo-mediated recombination in non-model and undomesticated bacteria. © 2022 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol: ssDNA recombineering in Shewanella species Alternate Protocol: ssDNA recombineering coupled to CRISPR/Cas9 in Shewanella species.
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Affiliation(s)
- Anna Corts
- Cultivarium, 490 Arsenal Way, Ste 110, Watertown, Massachusetts 02472
| | - Lynn C. Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Nina Costantino
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Donald L. Court
- Emeritus, Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
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Bird LJ, Kundu BB, Tschirhart T, Corts AD, Su L, Gralnick JA, Ajo-Franklin CM, Glaven SM. Engineering Wired Life: Synthetic Biology for Electroactive Bacteria. ACS Synth Biol 2021; 10:2808-2823. [PMID: 34637280 DOI: 10.1021/acssynbio.1c00335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.
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Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Biki B. Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Tanya Tschirhart
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Anna D. Corts
- Joyn Bio, Boston, Massachusetts 02210, United States
| | - Lin Su
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210018, People’s Republic of China
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | | | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
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Thomason LC, Costantino N, Court DL. Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli. mBio 2016; 7:e01443-16. [PMID: 27624131 PMCID: PMC5021808 DOI: 10.1128/mbio.01443-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/16/2016] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Recombineering, in vivo genetic engineering with bacteriophage homologous recombination systems, is a powerful technique for making genetic modifications in bacteria. Two systems widely used in Escherichia coli are the Red system from phage λ and RecET from the defective Rac prophage. We investigated the in vivo dependence of recombineering on DNA replication of the recombining substrate using plasmid targets. For λ Red recombination, when DNA replication of a circular target plasmid is prevented, recombination with single-stranded DNA oligonucleotides is greatly reduced compared to that under replicating conditions. For RecET recombination, when DNA replication of the targeted plasmid is prevented, the recombination frequency is also reduced, to a level identical to that seen for the Red system in the absence of replication. The very low level of oligonucleotide recombination observed in the absence of any phage recombination functions is the same in the presence or absence of DNA replication. In contrast, both the Red and RecET systems recombine a nonreplicating linear dimer plasmid with high efficiency to yield a circular monomer. Therefore, the DNA replication requirement is substrate dependent. Our data are consistent with recombination by both the Red and RecET systems occurring predominately by single-strand annealing rather than by strand invasion. IMPORTANCE Bacteriophage homologous recombination systems are widely used for in vivo genetic engineering in bacteria. Single- or double-stranded linear DNA substrates containing short flanking homologies to chromosome targets are used to generate precise and accurate genetic modifications when introduced into bacteria expressing phage recombinases. Understanding the molecular mechanism of these recombination systems will facilitate improvements in the technology. Here, two phage-specific systems are shown to require exposure of complementary single-strand homologous targets for efficient recombination; these single-strand regions may be created during DNA replication or by single-strand exonuclease digestion of linear duplex DNA. Previously, in vitro studies reported that these recombinases promote the single-strand annealing of two complementary DNAs and also strand invasion of a single DNA strand into duplex DNA to create a three-stranded region. Here, in vivo experiments show that recombinase-mediated annealing of complementary single-stranded DNA is the predominant recombination pathway in E. coli.
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Affiliation(s)
- Lynn C Thomason
- Basic Science Program, GRCBL-Molecular Control and Genetics Section, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland, USA
| | - Nina Costantino
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland, USA
| | - Donald L Court
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland, USA
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Krylov AA, Kolontaevsky EE, Mashko SV. Oligonucleotide recombination in corynebacteria without the expression of exogenous recombinases. J Microbiol Methods 2014; 105:109-15. [PMID: 25087479 DOI: 10.1016/j.mimet.2014.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 11/24/2022]
Abstract
Brevibacterium lactofermentum and Corynebacterium glutamicum are important biotechnology species of the genus Corynebacterium. The single-strand DNA annealing protein (SSAP)-independent oligonucleotide-mediated recombination procedure was successfully applied to the commonly used wild-type strains B. lactofermentum AJ1511 and C. glutamicum ATCC13032. When the rpsL gene was used as a target, the optimized protocol yielded up to (1.4±0.3)×10(3) and (6.7±1.3)×10(3) streptomycin-resistant colonies per 10(8) viable cells for the corresponding strains. We tested the influence of several parameters that are known to enhance the efficiency of oligonucleotide-mediated recombination in other bacterial species. Among them, increasing the concentration of oligonucleotides and targeting the lagging strand of the chromosome have proven to have positive effects on both of the tested species. No difference in the efficiency of recombination was observed between the oligonucleotides phosphorothiorated at the 5' ends and the unmodified oligonucleotides or between the oligonucleotides with four mutated nucleotides and those with one mutated nucleotide. The described approach demonstrates that during the adaptation of the recombineering technique, testing SSAP-independent oligonucleotide-mediated recombination could be a good starting point. Such testing could decrease the probability of an incorrect interpretation of the effect of exogenous protein factors (such as SSAP and/or corresponding exonucleases) due to non-optimal experimental conditions. In addition, SSAP-independent recombination itself could be useful in combination with suitable selection/enrichment methods.
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Affiliation(s)
- Alexander A Krylov
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd 1, Moscow 117545, Russia.
| | - Egor E Kolontaevsky
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd 1, Moscow 117545, Russia
| | - Sergey V Mashko
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd 1, Moscow 117545, Russia
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Ryu YS, Biswas RK, Shin K, Parisutham V, Kim SM, Lee SK. A simple and effective method for construction of Escherichia coli strains proficient for genome engineering. PLoS One 2014; 9:e94266. [PMID: 24747264 PMCID: PMC3991648 DOI: 10.1371/journal.pone.0094266] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/13/2014] [Indexed: 11/25/2022] Open
Abstract
Multiplex genome engineering is a standalone recombineering tool for large-scale programming and accelerated evolution of cells. However, this advanced genome engineering technique has been limited to use in selected bacterial strains. We developed a simple and effective strain-independent method for effective genome engineering in Escherichia coli. The method involves introducing a suicide plasmid carrying the λ Red recombination system into the mutS gene. The suicide plasmid can be excised from the chromosome via selection in the absence of antibiotics, thus allowing transient inactivation of the mismatch repair system during genome engineering. In addition, we developed another suicide plasmid that enables integration of large DNA fragments into the lacZ genomic locus. These features enable this system to be applied in the exploitation of the benefits of genome engineering in synthetic biology, as well as the metabolic engineering of different strains of E. coli.
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Affiliation(s)
- Young Shin Ryu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Rajesh Kumar Biswas
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Kwangsu Shin
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Vinuselvi Parisutham
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- * E-mail:
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Abstract
Recombineering refers to a strategy for engineering DNA sequences using a specialized mode of homologous recombination. This technology can be used for rapidly constructing precise changes in bacterial genome sequences in vivo. Oligonucleotide recombination is one type of recombineering that uses ssDNA oligonucleotides to direct chromosomal mutations. Oligo recombination occurs without addition of any exogenous functions, making this approach potentially useful in many different bacteria. Here we describe the basic technique for constructing a site-specific genomic mutation in Pseudomonas syringae.
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Affiliation(s)
- Bryan M Swingle
- United States Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA.
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Van Pijkeren JP, Neoh KM, Sirias D, Findley AS, Britton RA. Exploring optimization parameters to increase ssDNA recombineering in Lactococcus lactis and Lactobacillus reuteri. Bioengineered 2012; 3:209-17. [PMID: 22750793 PMCID: PMC3476877 DOI: 10.4161/bioe.21049] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Single-stranded DNA (ssDNA) recombineering is a technology which is used to make subtle changes in the chromosome of several bacterial genera. Cells which express a single-stranded DNA binding protein (RecT or Bet) are transformed with an oligonucleotide which is incorporated via an annealing and replication-dependent mechanism. By in silico analysis we identified ssDNA binding protein homologs in the genus Lactobacillus and Lactococcus lactis. To assess whether we could further improve the recombineering efficiency in Lactobacillus reuteri ATCC PTA 6475 we expressed several RecT homologs in this strain. RecT derived from Enterococcus faecalis CRMEN 19 yielded comparable efficiencies compared with a native RecT protein, but none of the other proteins further increased the recombineering efficiency. We successfully improved recombineering efficiency 10-fold in L. lactis by increasing oligonucleotide concentration combined with the use of oligonucleotides containing phosphorothioate-linkages (PTOs). Surprisingly, neither increased oligonucleotide concentration nor PTO linkages enhanced recombineering in L. reuteri 6475. To emphasize the utility of this technology in improving probiotic features we modified six bases in a transcriptional regulatory element region of the pdu-operon of L. reuteri 6475, yielding a 3-fold increase in the production of the antimicrobial compound reuterin. Directed genetic modification of lactic acid bacteria through ssDNA recombineering will simplify strain improvement in a way that, when mutating a single base, is genetically indistinguishable from strains obtained through directed evolution.
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Affiliation(s)
- Jan-Peter Van Pijkeren
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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Bryan A, Swanson MS. Oligonucleotides stimulate genomic alterations of Legionella pneumophila. Mol Microbiol 2011; 80:231-47. [PMID: 21306445 DOI: 10.1111/j.1365-2958.2011.07573.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Genetic variation generates diversity in all kingdoms of life. The corresponding mechanisms can also be harnessed for laboratory studies of fundamental cellular processes. Here we report that oligonucleotides (oligos) generate mutations on the Legionella pneumophila chromosome by a mechanism that requires homologous DNA, but not RecA, RadA or any known phage recombinase. Instead we propose that DNA replication contributes, as oligo-induced mutagenesis required ≥ 21 nucleotides of homology, was strand-dependent, and was most efficient in exponential phase. Mutagenesis did not require canonical 5' phosphate or 3' hydroxyl groups, but the primosomal protein PriA and DNA Pol I contributed. After electroporation, oligos stimulated excision of 2.1 kb of chromosomal DNA or insertion of 18 bp, and non-homologous flanking sequences were also processed. We exploited this endogenous activity to generate chromosomal deletions and to insert an epitope into a chromosomal coding sequence. Compared with Escherichia coli, L. pneumophila encodes fewer canonical single-stranded exonucleases, and the frequency of mutagenesis increased substantially when either its RecJ and ExoVII nucleases were inactivated or the oligos modified by nuclease-resistant bases. In addition to genetic engineering, oligo-induced mutagenesis may have evolutionary implications as a mechanism to incorporate divergent DNA sequences with only short regions of homology.
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Affiliation(s)
- Andrew Bryan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109-5620, USA
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