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Payaslian F, Gradaschi V, Piuri M. Genetic manipulation of phages for therapy using BRED. Curr Opin Biotechnol 2020; 68:8-14. [PMID: 33039679 DOI: 10.1016/j.copbio.2020.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 02/08/2023]
Abstract
The alarming increase in antibiotic resistance has placed the focus on phages as an alternative antimicrobial therapy. Recently, the first patient treatment using engineered phages to combat a mycobacterial infection was successfully performed; genetic modifications were made using Bacteriophage Recombineering of Electroporated DNA (BRED). BRED is a simple technique that allows genetic manipulation of phages. The phage DNA and a recombination substrate, with short homology to the target, are co-electroporated into recombineering proficient bacteria promoting high levels of recombination. After electroporation, cells are recovered and plated in an infectious centre assay. Individual plaques are then screened by PCR to identify the mutant phage. The main characteristics of this technique, the advantages of engineered versus wild type phages for therapeutic purposes and the future perspective of BRED for doing such modifications, are reviewed here.
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Affiliation(s)
- Florencia Payaslian
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Victoria Gradaschi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
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52
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Fels U, Gevaert K, Van Damme P. Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics. Front Microbiol 2020; 11:548410. [PMID: 33013782 PMCID: PMC7516269 DOI: 10.3389/fmicb.2020.548410] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Serving a robust platform for reverse genetics enabling the in vivo study of gene functions primarily in enterobacteriaceae, recombineering -or recombination-mediated genetic engineering-represents a powerful and relative straightforward genetic engineering tool. Catalyzed by components of bacteriophage-encoded homologous recombination systems and only requiring short ∼40–50 base homologies, the targeted and precise introduction of modifications (e.g., deletions, knockouts, insertions and point mutations) into the chromosome and other episomal replicons is empowered. Furthermore, by its ability to make use of both double- and single-stranded linear DNA editing substrates (e.g., PCR products or oligonucleotides, respectively), lengthy subcloning of specific DNA sequences is circumvented. Further, the more recent implementation of CRISPR-associated endonucleases has allowed for more efficient screening of successful recombinants by the selective purging of non-edited cells, as well as the creation of markerless and scarless mutants. In this review we discuss various recombineering strategies to promote different types of gene modifications, how they are best applied, and their possible pitfalls.
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Affiliation(s)
- Ursula Fels
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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53
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Brewster JL, Tolun G. Half a century of bacteriophage lambda recombinase: In vitro studies of lambda exonuclease and Red-beta annealase. IUBMB Life 2020; 72:1622-1633. [PMID: 32621393 PMCID: PMC7496540 DOI: 10.1002/iub.2343] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/10/2020] [Accepted: 06/10/2020] [Indexed: 01/03/2023]
Abstract
DNA recombination, replication, and repair are intrinsically interconnected processes. From viruses to humans, they are ubiquitous and essential to all life on Earth. Single‐strand annealing homologous DNA recombination is a major mechanism for the repair of double‐stranded DNA breaks. An exonuclease and an annealase work in tandem, forming a complex known as a two‐component recombinase. Redβ annealase and λ‐exonuclease from phage lambda form the archetypal two‐component recombinase complex. In this short review article, we highlight some of the in vitro studies that have led to our current understanding of the lambda recombinase system. We synthesize insights from more than half a century of research, summarizing the state of our current understanding. From this foundation, we identify the gaps in our knowledge and cast an eye forward to consider what the next 50 years of research may uncover.
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Affiliation(s)
- Jodi L Brewster
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Keiraville, New South Wales, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Gökhan Tolun
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Keiraville, New South Wales, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
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54
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Bhat S, Bialy D, Sealy JE, Sadeyen JR, Chang P, Iqbal M. A ligation and restriction enzyme independent cloning technique: an alternative to conventional methods for cloning hard-to-clone gene segments in the influenza reverse genetics system. Virol J 2020; 17:82. [PMID: 32576218 PMCID: PMC7309217 DOI: 10.1186/s12985-020-01358-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reverse genetics is used in many laboratories around the world and enables the creation of tailor-made influenza viruses with a desired genotype or phenotype. However, the process is not flawless, and difficulties remain during cloning of influenza gene segments into reverse genetics vectors (pHW2000, pHH21, pCAGGS). Reverse genetics begins with making cDNA copies of influenza gene segments and cloning them into bi-directional (pHW2000) or uni-directional plasmids (pHH21, pCAGGS) followed by transfection of the recombinant plasmid(s) to HEK-293 T or any other suitable cells which are permissive to transfection. However, the presence of internal restriction sites in the gene segments of many field isolates of avian influenza viruses makes the cloning process difficult, if employing conventional methods. Further, the genetic instability of influenza gene-containing plasmids in bacteria (especially Polymerase Basic 2 and Polymerase Basic 1 genes; PB2 and PB1) also leads to erroneous incorporation of bacterial genomic sequences into the influenza gene of interest. METHODS Herein, we report an easy and efficient ligation and restriction enzyme independent (LREI) cloning method for cloning influenza gene segments into pHW2000 vector. The method involves amplification of megaprimers followed by PCR amplification of megaprimers using a bait plasmid, DpnI digestion and transformation. RESULTS Hard-to-clone genes: PB2 of A/chicken/Bangladesh/23527/2014 (H9N2) and PB1 of A/chicken/Bangladesh/23527/2014 (H9N2), A/chicken/Jiangxi/02.05YGYXG023-P/2015 (H5N6) and A/Chicken/Vietnam/H7F-14-BN4-315/2014 (H9N2) were cloned into pHW2000 using our LREI method and recombinant viruses were subsequently rescued. CONCLUSION The LREI cloning procedure represents an alternative strategy for cloning influenza gene segments which have internal restriction sites for the enzymes used in reverse genetics. Further, the problem of genetic instability in bacteria can be alleviated by growing recombinant bacterial cultures at a lower temperature. This technique can be applied to clone any influenza gene segment using universal primers, which would help in rapid generation of influenza viruses and facilitate influenza research and vaccine development.
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55
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Cianfanelli FR, Cunrath O, Bumann D. Efficient dual-negative selection for bacterial genome editing. BMC Microbiol 2020; 20:129. [PMID: 32448155 PMCID: PMC7245781 DOI: 10.1186/s12866-020-01819-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Gene editing is key for elucidating gene function. Traditional methods, such as consecutive single-crossovers, have been widely used to modify bacterial genomes. However, cumbersome cloning and limited efficiency of negative selection often make this method slower than other methods such as recombineering. Results Here, we established a time-effective variant of consecutive single-crossovers. This method exploits rapid plasmid construction using Gibson assembly, a convenient E. coli donor strain, and efficient dual-negative selection for improved suicide vector resolution. We used this method to generate in-frame deletions, insertions and point mutations in Salmonella enterica with limited hands-on time. Adapted versions enabled efficient gene editing also in Pseudomonas aeruginosa and multi-drug resistant (MDR) Escherichia coli clinical isolates. Conclusions Our method is time-effective and allows facile manipulation of multiple bacterial species including MDR clinical isolates. We anticipate that this method might be broadly applicable to additional bacterial species, including those for which recombineering has been difficult to implement.
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Affiliation(s)
| | - Olivier Cunrath
- Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | - Dirk Bumann
- Biozentrum, University of Basel, CH-4056, Basel, Switzerland.
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56
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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57
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Grigonyte AM, Harrison C, MacDonald PR, Montero-Blay A, Tridgett M, Duncan J, Sagona AP, Constantinidou C, Jaramillo A, Millard A. Comparison of CRISPR and Marker-Based Methods for the Engineering of Phage T7. Viruses 2020; 12:E193. [PMID: 32050613 PMCID: PMC7077284 DOI: 10.3390/v12020193] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 12/29/2022] Open
Abstract
With the recent rise in interest in using lytic bacteriophages as therapeutic agents, there is an urgent requirement to understand their fundamental biology to enable the engineering of their genomes. Current methods of phage engineering rely on homologous recombination, followed by a system of selection to identify recombinant phages. For bacteriophage T7, the host genes cmk or trxA have been used as a selection mechanism along with both type I and II CRISPR systems to select against wild-type phage and enrich for the desired mutant. Here, we systematically compare all three systems; we show that the use of marker-based selection is the most efficient method and we use this to generate multiple T7 tail fibre mutants. Furthermore, we found the type II CRISPR-Cas system is easier to use and generally more efficient than a type I system in the engineering of phage T7. These results provide a foundation for the future, more efficient engineering of bacteriophage T7.
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Affiliation(s)
- Aurelija M. Grigonyte
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (A.M.G.); (M.T.); (J.D.); (A.P.S.)
| | - Christian Harrison
- Department Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK;
| | - Paul R. MacDonald
- MOAC DTC, Senate House, University of Warwick, Coventry CV4 7AL, UK;
| | - Ariadna Montero-Blay
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain;
| | - Matthew Tridgett
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (A.M.G.); (M.T.); (J.D.); (A.P.S.)
| | - John Duncan
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (A.M.G.); (M.T.); (J.D.); (A.P.S.)
| | - Antonia P. Sagona
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (A.M.G.); (M.T.); (J.D.); (A.P.S.)
| | | | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (A.M.G.); (M.T.); (J.D.); (A.P.S.)
- Institute of Systems and Synthetic Biology (ISSB), CNRS, CEA, Université Paris-Saclay, 91025 Evry, France
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, 46980 Paterna, Spain
| | - Andrew Millard
- Department Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK;
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58
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Zheng K, Jiang FF, Su L, Wang X, Chen YX, Chen HC, Liu ZF. Highly Efficient Base Editing in Viral Genome Based on Bacterial Artificial Chromosome Using a Cas9-Cytidine Deaminase Fused Protein. Virol Sin 2019; 35:191-199. [PMID: 31792738 PMCID: PMC7198655 DOI: 10.1007/s12250-019-00175-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/09/2019] [Indexed: 02/04/2023] Open
Abstract
Viruses evolve rapidly and continuously threaten animal health and economy, posing a great demand for rapid and efficient genome editing technologies to study virulence mechanism and develop effective vaccine. We present a highly efficient viral genome manipulation method using CRISPR-guided cytidine deaminase. We cloned pseudorabies virus genome into bacterial artificial chromosome, and used CRISPR-guided cytidine deaminase to directly convert cytidine (C) to uridine (U) to induce premature stop mutagenesis in viral genes. The editing efficiencies were 100%. Comprehensive bioinformatic analysis revealed that a large number of editable sites exist in pseudorabies virus (PRV) genomes. Notably, in our study viral genome exists as a plasmid in E. coli, suggesting that this method is virus species-independent. This application of base-editing provided an alternative approach to generate mutant virus and might accelerate study on virulence and vaccine development.
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Affiliation(s)
- Ke Zheng
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Gene Editing Research Center, Hebei University of Science and Technology, Shijiazhuang, 050018, China
| | - Fang-Fang Jiang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Le Su
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu-Xin Chen
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huan-Chun Chen
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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Site-specific acylation of a bacterial virulence regulator attenuates infection. Nat Chem Biol 2019; 16:95-103. [PMID: 31740807 PMCID: PMC8439376 DOI: 10.1038/s41589-019-0392-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/23/2019] [Indexed: 12/27/2022]
Abstract
Microbiota generates millimolar concentrations of short-chain fatty acids (SCFAs) that can modulate host metabolism, immunity and susceptibility to infection. Butyrate in particular can function as a carbon source and anti-inflammatory metabolite, but the mechanism by which it inhibits pathogen virulence has been elusive. Using chemical proteomics, we discovered that several virulence factors encoded by Salmonella pathogenicity island-1 (SPI-1) are acylated by SCFAs. Notably, a transcriptional regulator of SPI-1, HilA, was acylated on several key lysine residues. Subsequent incorporation of stable butyryl-lysine analogs using CRISPR-Cas9 gene editing and unnatural amino acid mutagenesis revealed that site-specific modification of HilA impacts its genomic occupancy, expression of SPI-1 genes and attenuates Salmonella enterica serovar Typhimurium invasion of epithelial cells as well as dissemination in vivo. Moreover, a multiple-site HilA lysine-acylation mutant strain of S. Typhimurium was resistant to butyrate-mediated suppression in vivo. Our results suggest prominent microbiota-derived metabolites may directly acylate virulence factors to inhibit microbial pathogenesis in vivo.
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60
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Design of Experiments As a Tool for Optimization in Recombinant Protein Biotechnology: From Constructs to Crystals. Mol Biotechnol 2019; 61:873-891. [DOI: 10.1007/s12033-019-00218-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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61
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Fu L, Xie C, Jin Z, Tu Z, Han L, Jin M, Xiang Y, Zhang A. The prokaryotic Argonaute proteins enhance homology sequence-directed recombination in bacteria. Nucleic Acids Res 2019; 47:3568-3579. [PMID: 30698806 PMCID: PMC6468240 DOI: 10.1093/nar/gkz040] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 02/01/2023] Open
Abstract
Argonaute proteins are present and conserved in all domains of life. Recently characterized prokaryotic Argonaute proteins (pAgos) participates in host defense by DNA interference. Here, we report that the Natronobacterium gregoryi Argonaute (NgAgo) enhances gene insertions or deletions in Pasteurella multocida and Escherichia coli at efficiencies of 80–100%. Additionally, the effects are in a homologous arms-dependent but guide DNA- and potential enzyme activity-independent manner. Interestingly, such effects were also observed in other pAgos fragments including Thermus thermophilus Argonaute (TtAgo), Aquifex aeolicus Argonaute (AaAgo) and Pyrococcus furiosus Argonaute (PfAgo). The underlying mechanism of the NgAgo system is a positive selection process mainly through its PIWI-like domain interacting with recombinase A (recA) to enhance recA-mediated DNA strand exchange. Our study reveals a novel system for enhancing homologous sequence-guided gene editing in bacteria.
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Affiliation(s)
- Lei Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Caiyun Xie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zehua Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zizhuo Tu
- Shanghai East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China
| | - Li Han
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China.,Key Laboratory of Development of Veterinary Diagnostic Products (Ministry of Agriculture), International Research Center for Animal Disease (Ministry of Science and Technology), Wuhan, Hubei 430070, China
| | - Yaozu Xiang
- Shanghai East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China
| | - Anding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China.,Key Laboratory of Development of Veterinary Diagnostic Products (Ministry of Agriculture), International Research Center for Animal Disease (Ministry of Science and Technology), Wuhan, Hubei 430070, China
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62
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Wu T, Yang Y, Chen W, Wang J, Yang Z, Wang S, Xiao X, Li M, Zhao M. Noncanonical substrate preference of lambda exonuclease for 5'-nonphosphate-ended dsDNA and a mismatch-induced acceleration effect on the enzymatic reaction. Nucleic Acids Res 2019; 46:3119-3129. [PMID: 29490081 PMCID: PMC5888420 DOI: 10.1093/nar/gky154] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 02/19/2018] [Indexed: 01/01/2023] Open
Abstract
Lambda exonuclease (λ exo) plays an important role in the resection of DNA ends for DNA repair. Currently, it is also a widely used enzymatic tool in genetic engineering, DNA-binding protein mapping, nanopore sequencing and biosensing. Herein, we disclose two noncanonical properties of this enzyme and suggest a previously undescribed hydrophobic interaction model between λ exo and DNA substrates. We demonstrate that the length of the free portion of the substrate strand in the dsDNA plays an essential role in the initiation of digestion reactions by λ exo. A dsDNA with a 5' non-phosphorylated, two-nucleotide-protruding end can be digested by λ exo with very high efficiency. Moreover, we show that when a conjugated structure is covalently attached to an internal base of the dsDNA, the presence of a single mismatched base pair at the 5' side of the modified base may significantly accelerate the process of digestion by λ exo. A detailed comparison study revealed additional π-π stacking interactions between the attached label and the amino acid residues of the enzyme. These new findings not only broaden our knowledge of the enzyme but will also be very useful for research on DNA repair and in vitro processing of nucleic acids.
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Affiliation(s)
- Tongbo Wu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yufei Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing NMR Center, Peking University, Beijing 100871, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shenlin Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing NMR Center, Peking University, Beijing 100871, China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengyuan Li
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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63
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Egan M, Critelli B, Cleary SP, Marino M, Upreti C, Kalman D, Bhatt S. Transcriptional and posttranscriptional regulation of the locus of enterocyte effacement in Escherichia albertii. Microb Pathog 2019; 135:103643. [PMID: 31336143 DOI: 10.1016/j.micpath.2019.103643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 12/21/2022]
Abstract
The diarrheic bacterium Escherichia albertii is a recent addition to the attaching and effacing (A/E) morphotype of pathogens. A/E pathogens cause disease by tightly attaching to intestinal cells, destroying their actin-rich microvilli, and triggering re-localization and repolymerization of actin at the bacterial-host interface to form actin-filled membranous protrusions, termed A/E lesions, beneath the adherent bacterium. The locus of enterocyte effacement (LEE) is required for the biogenesis of these lesions. Whereas regulation of the LEE has been intensively investigated in EPEC and EHEC, it remains cryptic in E. albertii. In this study we characterized the very first transcriptional and posttranscriptional regulators of the LEE in this emerging pathogen. Our results suggest that Ler and GrlA globally activate transcription from the LEE, whereas GrlR negatively regulates the LEE. Additionally, we demonstrate that the RNA chaperone Hfq posttranscriptionally represses the LEE by specifically targeting the 5' UTR of grlR. In summary, our findings provide the very first glimpse of the regulatory landscape of the LEE in E. albertii - a bacterium that has been implicated in multiple diarrheal outbreaks worldwide.
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Affiliation(s)
- Marisa Egan
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, 19131, PA, USA; Department of Microbiology, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA
| | - Brian Critelli
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, 19131, PA, USA
| | - Sean P Cleary
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, 19131, PA, USA
| | - Mary Marino
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, 19131, PA, USA
| | - Chirag Upreti
- Department of Neuroscience, New York State Psychiatric Institute, Columbia University Medical Center, New York, 10032, USA
| | - Daniel Kalman
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, 30341, GA, USA
| | - Shantanu Bhatt
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, 19131, PA, USA.
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64
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Bressan RB, Pollard SM. Genome Editing in Human Neural Stem and Progenitor Cells. Results Probl Cell Differ 2019; 66:163-182. [PMID: 30209659 DOI: 10.1007/978-3-319-93485-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Experimental tools for precise manipulation of mammalian genomes enable reverse genetic approaches to explore biology and disease. Powerful genome editing technologies built upon designer nucleases, such as CRISPR/Cas9, have recently emerged. Parallel progress has been made in methodologies for the expansion and differentiation of human pluripotent and tissue stem cells. Together these innovations provide a remarkable new toolbox for human cellular genetics and are opening up vast opportunities for discoveries and applications across the breadth of life sciences research. In this chapter, we review the emergence of genome editing technologies and how these are being deployed in studies of human neurobiology, neurological disease, and neuro-oncology. We focus our discussion on CRISPR/Cas9 and its application in studies of human neural stem and progenitor cells.
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Affiliation(s)
- Raul Bardini Bressan
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, UK.
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65
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Buckley KM, Dong P, Cameron RA, Rast JP. Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms. Brief Funct Genomics 2019; 17:362-371. [PMID: 29045542 DOI: 10.1093/bfgp/elx031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome sequences contain all the necessary information-both coding and regulatory sequences-to construct an organism. The developmental process translates this genomic information into a three-dimensional form. One interpretation of this translation process can be described using gene regulatory network (GRN) models, which are maps of interactions among regulatory gene products in time and space. As high throughput investigations reveal increasing complexity within these GRNs, it becomes apparent that efficient methods are required to test the necessity and sufficiency of regulatory interactions. One of the most complete GRNs for early development has been described in the purple sea urchin, Strongylocentrotus purpuratus. This work has been facilitated by two resources: a well-annotated genome sequence and transgenes generated in bacterial artificial chromosome (BAC) constructs. BAC libraries played a central role in assembling the S. purpuratus genome sequence and continue to serve as platforms for generating reporter constructs for use in expression and regulatory analyses. Optically transparent echinoderm larvae are highly amenable to transgenic approaches and are therefore particularly well suited for experiments that rely on BAC-based reporter transgenes. Here, we discuss the experimental utility of BAC constructs in the context of understanding developmental processes in echinoderm embryos and larvae.
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Affiliation(s)
- Katherine M Buckley
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Ping Dong
- California Institute of Technology, California, USA
| | - R Andrew Cameron
- Beckman Institute Center for Computational Regulatory Genomics, California Institute for Technology, California, USA
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66
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Barriers to genome editing with CRISPR in bacteria. J Ind Microbiol Biotechnol 2019; 46:1327-1341. [PMID: 31165970 DOI: 10.1007/s10295-019-02195-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
Abstract
Genome editing is essential for probing genotype-phenotype relationships and for enhancing chemical production and phenotypic robustness in industrial bacteria. Currently, the most popular tools for genome editing couple recombineering with DNA cleavage by the CRISPR nuclease Cas9 from Streptococcus pyogenes. Although successful in some model strains, CRISPR-based genome editing has been slow to extend to the multitude of industrially relevant bacteria. In this review, we analyze existing barriers to implementing CRISPR-based editing across diverse bacterial species. We first compare the efficacy of current CRISPR-based editing strategies. Next, we discuss alternatives when the S. pyogenes Cas9 does not yield colonies. Finally, we describe different ways bacteria can evade editing and how elucidating these failure modes can improve CRISPR-based genome editing across strains. Together, this review highlights existing obstacles to CRISPR-based editing in bacteria and offers guidelines to help achieve and enhance editing in a wider range of bacterial species, including non-model strains.
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67
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Li L, Liu X, Wei K, Lu Y, Jiang W. Synthetic biology approaches for chromosomal integration of genes and pathways in industrial microbial systems. Biotechnol Adv 2019; 37:730-745. [PMID: 30951810 DOI: 10.1016/j.biotechadv.2019.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
Industrial biotechnology is reliant on native pathway engineering or foreign pathway introduction for efficient biosynthesis of target products. Chromosomal integration, with intrinsic genetic stability, is an indispensable step for reliable expression of homologous or heterologous genes and pathways in large-scale and long-term fermentation. With advances in synthetic biology and CRISPR-based genome editing approaches, a wide variety of novel enabling technologies have been developed for single-step, markerless, multi-locus genomic integration of large biochemical pathways, which significantly facilitate microbial overproduction of chemicals, pharmaceuticals and other value-added biomolecules. Notably, the newly discovered homology-mediated end joining strategy could be widely applicable for high-efficiency genomic integration in a number of homologous recombination-deficient microbes. In this review, we explore the fundamental principles and characteristics of genomic integration, and highlight the development and applications of targeted integration approaches in the three representative industrial microbial systems, including Escherichia coli, actinomycetes and yeasts.
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Affiliation(s)
- Lei Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaocao Liu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Keke Wei
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 200232, China.
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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68
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Buckley KM, Ettensohn CA. Techniques for analyzing gene expression using BAC-based reporter constructs. Methods Cell Biol 2019; 151:197-218. [PMID: 30948008 PMCID: PMC7215881 DOI: 10.1016/bs.mcb.2019.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To characterize the complex regulatory control of gene expression using fluorescent protein reporters, it is often necessary to analyze large genomic regions. Bacteria artificial chromosome (BAC) vectors, which are able to support DNA fragments of up to 300kb, provide stable platforms for experimental manipulation. Using phage-based systems of homologous recombination, BACs can be efficiently engineered for a variety of aims. These include expressing fluorescent proteins to delineate gene expression boundaries using high-resolution, in vivo microscopy, tracing cell lineages using stable fluorescent proteins, perturbing endogenous protein function by expressing dominant negative forms, interfering with development by mis-expressing transcription factors, and identifying regulatory regions through deletion analysis. Here, we present a series of protocols for identifying BAC clones that contain genes of interest, modifying BACs for use as reporter constructs, and preparing BAC DNA for microinjection into fertilized eggs. Although the protocols here are tailored for use in echinoderm embryonic and larval stages, these methods are easily adaptable for use in other transgenic systems. As fluorescent protein technology continues to expand, so do the potential applications for recombinant BACs.
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Affiliation(s)
- Katherine M Buckley
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
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69
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Chen W, Li Y, Wu G, Zhao L, Lu L, Wang P, Zhou J, Cao C, Li S. Simple and efficient genome recombineering using kil counter-selection in Escherichia coli. J Biotechnol 2019; 294:58-66. [PMID: 30768999 DOI: 10.1016/j.jbiotec.2019.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 01/04/2019] [Accepted: 01/19/2019] [Indexed: 01/01/2023]
Abstract
Seamless modification of the Escherichia coli genome using positive selection / negative selection is widely used in metabolic engineering and functional genome analysis. Some excellent negative selection systems have been reported, of which tetA-sacB and inducible toxins system are prominent. To expand the existing negative selection toolkit, we constructed a new negative selection marker system based on kil gene of lambda prophage. The selection stringency of kil was measured and compared with the most widely used counter-selection gene, sacB, at the lacI, ack, and dbpa loci using different E. coli strains. At all these loci of tested strains, the selection stringency of kil significantly exceeds that of sacB by 2- to 28-fold. When dsDNA fragments were employed for recombination, the efficiency for isolating the correct recombinant of kil was significantly higher than that of sacB. This new negative selection system does not require special media or extended incubation time. However, our system cannot be used in host strains containing temperature-sensitive kil gene. A Red system providing plasmid without kil gene is recommended for use together with our system. Our counter-selection system is expected to be an addition to the engineering arsenal of E. coli.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China; Beijing Institute of Biotechnology, Beijing 100850, China
| | - Yujuan Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Guangjin Wu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Lingfeng Zhao
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Li Lu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Peng Wang
- Beijing Institute of Biotechnology, Beijing 100850, China
| | - Jianguang Zhou
- Beijing Institute of Biotechnology, Beijing 100850, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, Beijing 100850, China.
| | - Shanhu Li
- Beijing Institute of Biotechnology, Beijing 100850, China.
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70
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Abstract
Bacterial Artificial Chromosome (BAC) libraries are a valuable research resource. Any one of the clones in these libraries can carry hundreds of thousands of base pairs of genetic information. Often the entire coding sequence and significant upstream and downstream regions, including regulatory elements, can be found in a single BAC clone. BACs can be put to many uses, such as to study the function of human genes in knockout mice, to drive reporter gene expression in transgenic animals, and for gene discovery. In order to use BACs for experimental purposes it is often desirable to genetically modify them by introducing reporter elements or heterologous cDNA sequences. It is not feasible to use conventional DNA cloning approaches to modify BACs due to their size and complexity, thus a specialized field "recombineering" has developed to modify BAC clones through the use of homologous recombination in bacteria with short homology regions. Genetically engineered BACs can then be used in cell culture, mouse, or rat models to study cancer, neurology, and genetics.
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71
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Marinelli LJ, Piuri M, Hatfull GF. Genetic Manipulation of Lytic Bacteriophages with BRED: Bacteriophage Recombineering of Electroporated DNA. Methods Mol Biol 2019; 1898:69-80. [PMID: 30570724 DOI: 10.1007/978-1-4939-8940-9_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We describe a recombineering-based method for the genetic manipulation of lytically replicating bacteriophages, focusing on mycobacteriophages. The approach utilizes recombineering-proficient strains of Mycobacterium smegmatis and employs a cotransformation strategy with purified phage genomic DNA and a mutagenic substrate, which selects for only those cells that are competent to take up DNA. The cotransformation method, combined with the high rates of recombination obtained in M. smegmatis recombineering strains, allows for the efficient and rapid generation of bacteriophage mutants.
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Affiliation(s)
- Laura J Marinelli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
- Laboratorio "Bacteriófagos y Aplicaciones Biotecnológicas", Departamento de Química Biológica, FCEyN, UBA, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires, Argentina
| | - Graham F Hatfull
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA, USA
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72
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Herpes simplex virus 1 ICP8 mutant lacking annealing activity is deficient for viral DNA replication. Proc Natl Acad Sci U S A 2018; 116:1033-1042. [PMID: 30598436 DOI: 10.1073/pnas.1817642116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most DNA viruses that use recombination-dependent mechanisms to replicate their DNA encode a single-strand annealing protein (SSAP). The herpes simplex virus (HSV) single-strand DNA binding protein (SSB), ICP8, is the central player in all stages of DNA replication. ICP8 is a classical replicative SSB and interacts physically and/or functionally with the other viral replication proteins. Additionally, ICP8 can promote efficient annealing of complementary ssDNA and is thus considered to be a member of the SSAP family. The role of annealing during HSV infection has been difficult to assess in part, because it has not been possible to distinguish between the role of ICP8 as an SSAP from its role as a replicative SSB during viral replication. In this paper, we have characterized an ICP8 mutant, Q706A/F707A (QF), that lacks annealing activity but retains many other functions characteristic of replicative SSBs. Like WT ICP8, the QF mutant protein forms filaments in vitro, binds ssDNA cooperatively, and stimulates the activities of other replication proteins including the viral polymerase, helicase-primase complex, and the origin binding protein. Interestingly, the QF mutant does not complement an ICP8-null virus for viral growth, replication compartment formation, or DNA replication. Thus, we have been able to separate the activities of ICP8 as a replicative SSB from its annealing activity. Taken together, our data indicate that the annealing activity of ICP8 is essential for viral DNA replication in the context of infection and support the notion that HSV-1 uses recombination-dependent mechanisms during DNA replication.
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73
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Li L, Wei K, Liu X, Wu Y, Zheng G, Chen S, Jiang W, Lu Y. aMSGE: advanced multiplex site-specific genome engineering with orthogonal modular recombinases in actinomycetes. Metab Eng 2018; 52:153-167. [PMID: 30529239 DOI: 10.1016/j.ymben.2018.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 11/18/2022]
Abstract
Chromosomal integration of genes and pathways is of particular importance for large-scale and long-term fermentation in industrial biotechnology. However, stable, multi-copy integration of long DNA segments (e.g., large gene clusters) remains challenging. Here, we describe a plug-and-play toolkit that allows for high-efficiency, single-step, multi-locus integration of natural product (NP) biosynthetic gene clusters (BGCs) in actinomycetes, based on the innovative concept of "multiple integrases-multiple attB sites". This toolkit consists of 27 synthetic modular plasmids, which contain single- or multi-integration modules (from two to four) derived from five orthogonal site-specific recombination (SSR) systems. The multi-integration modules can be readily ligated into plasmids containing large BGCs by Gibson assembly, which can be simultaneously inserted into multiple native attB sites in a single step. We demonstrated the applicability of this toolkit by performing stabilized amplification of acetyl-CoA carboxylase genes to facilitate actinorhodin biosynthesis in Streptomyces coelicolor. Furthermore, using this toolkit, we achieved a 185.6% increase in 5-oxomilbemycin titers (from 2.23 to 6.37 g/L) in Streptomyces hygroscopicus via the multi-locus integration of the entire 5-oxomilbemycin BGC (72 kb) (up to four copies). Compared with previously reported methods, the advanced multiplex site-specific genome engineering (aMSGE) method does not require the introduction of any modifications into host genomes before the amplification of target genes or BGCs, which will drastically simplify and accelerate efforts to improve NP production. Considering that SSR systems are widely distributed in a variety of industrial microbes, this novel technique also promises to be a valuable tool for the enhanced biosynthesis of other high-value bioproducts.
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Affiliation(s)
- Lei Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Keke Wei
- School of Pharmacy, Fudan University, Shanghai 201203, China; Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Xiaocao Liu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science, Henan University, Kaifeng 475004, China
| | - Yuanjie Wu
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Guosong Zheng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shaoxin Chen
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Jiangsu National Synergetic Innovation Center for Advanced Materials, SICAM, Nanjing 210009, China.
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai 200232, China.
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74
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Snoeck N, De Mol ML, Van Herpe D, Goormans A, Maryns I, Coussement P, Peters G, Beauprez J, De Maeseneire SL, Soetaert W. Serine integrase recombinational engineering (SIRE): A versatile toolbox for genome editing. Biotechnol Bioeng 2018; 116:364-374. [PMID: 30345503 DOI: 10.1002/bit.26854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/24/2018] [Accepted: 10/18/2018] [Indexed: 12/20/2022]
Abstract
Chromosomal integration of biosynthetic pathways for the biotechnological production of high-value chemicals is a necessity to develop industrial strains with a high long-term stability and a low production variability. However, the introduction of multiple transcription units into the microbial genome remains a difficult task. Despite recent advances, current methodologies are either laborious or efficiencies highly fluctuate depending on the length and the type of the construct. Here we present serine integrase recombinational engineering (SIRE), a novel methodology which combines the ease of recombinase-mediated cassette exchange (RMCE) with the selectivity of orthogonal att sites of the PhiC31 integrase. As a proof of concept, this toolbox is developed for Escherichia coli. Using SIRE we were able to introduce a 10.3 kb biosynthetic gene cluster on different locations throughout the genome with an efficiency of 100% for the integrating step and without the need for selection markers on the knock-in cassette. Next to integrating large fragments, the option for multitargeting, for deleting operons, as well as for performing in vivo assemblies further expand and proof the versatility of the SIRE toolbox for E. coli. Finally, the serine integrase PhiC31 was also applied in the yeast Saccharomyces cerevisiae as a marker recovery tool, indicating the potential and portability of this toolbox.
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Affiliation(s)
- Nico Snoeck
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Maarten L De Mol
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Dries Van Herpe
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anke Goormans
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Isabelle Maryns
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | | | | | - Sofie L De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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75
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Naorem SS, Han J, Zhang SY, Zhang J, Graham LB, Song A, Smith CV, Rashid F, Guo H. Efficient transposon mutagenesis mediated by an IPTG-controlled conditional suicide plasmid. BMC Microbiol 2018; 18:158. [PMID: 30355324 PMCID: PMC6201506 DOI: 10.1186/s12866-018-1319-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/16/2018] [Indexed: 11/17/2022] Open
Abstract
Background Transposon mutagenesis is highly valuable for bacterial genetic and genomic studies. The transposons are usually delivered into host cells through conjugation or electroporation of a suicide plasmid. However, many bacterial species cannot be efficiently conjugated or transformed for transposon saturation mutagenesis. For this reason, temperature-sensitive (ts) plasmids have also been developed for transposon mutagenesis, but prolonged incubation at high temperatures to induce ts plasmid loss can be harmful to the hosts and lead to enrichment of mutants with adaptive genetic changes. In addition, the ts phenotype of a plasmid is often strain- or species-specific, as it may become non-ts or suicidal in different bacterial species. Results We have engineered several conditional suicide plasmids that have a broad host range and whose loss is IPTG-controlled. One construct, which has the highest stability in the absence of IPTG induction, was then used as a curable vector to deliver hyperactive miniTn5 transposons for insertional mutagenesis. Our analyses show that these new tools can be used for efficient and regulatable transposon mutagenesis in Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. In P. aeruginosa PAO1, we have used this method to generate a Tn5 insertion library with an estimated diversity of ~ 108, which is ~ 2 logs larger than the best transposon insertional library of PAO1 and related Pseudomonas strains previously reported. Conclusion We have developed a number of IPTG-controlled conditional suicide plasmids. By exploiting one of them for transposon delivery, a highly efficient and broadly useful mutagenesis system has been developed. As the assay condition is mild, we believe that our methodology will have broad applications in microbiology research. Electronic supplementary material The online version of this article (10.1186/s12866-018-1319-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santa S Naorem
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Jin Han
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Stephanie Y Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Junyi Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Lindsey B Graham
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Angelou Song
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Cameron V Smith
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Fariha Rashid
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Huatao Guo
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA.
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76
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Zhu Z, Ji X, Wu Z, Zhang J, Du G. Improved acid-stress tolerance of Lactococcus lactis NZ9000 and Escherichia coli BL21 by overexpression of the anti-acid component recT. J Ind Microbiol Biotechnol 2018; 45:1091-1101. [PMID: 30232653 DOI: 10.1007/s10295-018-2075-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/22/2018] [Indexed: 12/01/2022]
Abstract
Acid accumulation caused by carbon metabolism severely affects the fermentation performance of microbial cells. Here, different sources of the recT gene involved in homologous recombination were functionally overexpressed in Lactococcus lactis NZ9000 and Escherichia coli BL21, and their acid-stress tolerances were investigated. Our results showed that L. lactis NZ9000 (ERecT and LRecT) strains showed 1.4- and 10.4-fold higher survival rates against lactic acid (pH 4.0), respectively, and that E. coli BL21 (ERecT) showed 16.7- and 9.4-fold higher survival rates than the control strain against lactic acid (pH 3.8) for 40 and 60 min, respectively. Additionally, we found that recT overexpression in L. lactis NZ9000 improved their growth under acid-stress conditions, as well as increased salt- and ethanol-stress tolerance and intracellular ATP concentrations in L. lactis NZ9000. These findings demonstrated the efficacy of recT overexpression for enhancing acid-stress tolerance and provided a promising strategy for insertion of anti-acid components in different hosts.
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Affiliation(s)
- Zhengming Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Xiaomei Ji
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Zhimeng Wu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Guocheng Du
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
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77
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Single-Homology-Arm Linear DNA Recombination by the Nonhomologous End Joining Pathway as a Novel and Simple Gene Inactivation Method: a Proof-of-Concept Study in Dietzia sp. Strain DQ12-45-1b. Appl Environ Microbiol 2018; 84:AEM.00795-18. [PMID: 30030230 DOI: 10.1128/aem.00795-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/04/2018] [Indexed: 02/06/2023] Open
Abstract
Nonhomologous end joining (NHEJ) is critical for genome stability because of its roles in double-strand break repair. Ku and ligase D (LigD) are the crucial proteins in this process, and strains expressing Ku and LigD can cyclize linear DNA in vivo Here, we established a proof-of-concept single-homology-arm linear DNA recombination for gene inactivation or genome editing by which cyclization of linear DNA in vivo by NHEJ could be used to generate nonreplicable circular DNA and could allow allelic exchanges between the circular DNA and the chromosome. We achieved this approach in Dietzia sp. strain DQ12-45-1b, which expresses Ku and LigD homologs and presents NHEJ activity. By transforming the strain with a linear DNA single homolog to the sequence in the chromosome, we mutated the genome. This method did not require the screening of suitable plasmids and was easy and time-effective. Bioinformatic analysis showed that more than 20% of prokaryotic organisms contain Ku and LigD, suggesting the wide distribution of NHEJ activities. Moreover, an Escherichia coli strain also showed NHEJ activity when the Ku and LigD of Dietzia sp. DQ12-45-1b were introduced and expressed in it. Therefore, this method may be a widely applicable genome editing tool for diverse prokaryotic organisms, especially for nonmodel microorganisms.IMPORTANCE Many nonmodel Gram-positive bacteria lack efficient genetic manipulation systems, but they express genes encoding Ku and LigD. The NHEJ pathway in Dietzia sp. DQ12-45-1b was evaluated and was used to successfully knock out 11 genes in the genome. Since bioinformatic studies revealed that the putative genes encoding Ku and LigD ubiquitously exist in phylogenetically diverse bacteria and archaea, the single-homology-arm linear DNA recombination by the NHEJ pathway could be a potentially applicable genetic manipulation method for diverse nonmodel prokaryotic organisms.
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Ou B, Garcia C, Wang Y, Zhang W, Zhu G. Techniques for chromosomal integration and expression optimization in Escherichia coli. Biotechnol Bioeng 2018; 115:2467-2478. [PMID: 29981268 DOI: 10.1002/bit.26790] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/30/2018] [Accepted: 07/04/2018] [Indexed: 12/31/2022]
Abstract
Due to the inherent expression stability and low metabolic burden to the host cell, the expression of heterologous proteins in the bacterial chromosome in a precise and efficient manner is highly desirable for metabolic engineering and live bacterial applications. However, obtaining suitable chromosome expression levels is particularly challenging. In this minireview, we briefly present the technologies available for the integration of heterologous genes into Escherichia coli chromosomes and strategies to optimize the expression levels of heterologous proteins.
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Affiliation(s)
- Bingming Ou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China.,Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Carolina Garcia
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Weiping Zhang
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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79
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Rao P, Rozgaja TA, Alqahtani A, Grimwade JE, Leonard AC. Low Affinity DnaA-ATP Recognition Sites in E. coli oriC Make Non-equivalent and Growth Rate-Dependent Contributions to the Regulated Timing of Chromosome Replication. Front Microbiol 2018; 9:1673. [PMID: 30093890 PMCID: PMC6070618 DOI: 10.3389/fmicb.2018.01673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/04/2018] [Indexed: 11/13/2022] Open
Abstract
Although the mechanisms that precisely time initiation of chromosome replication in bacteria remain unclear, most clock models are based on accumulation of the active initiator protein, DnaA-ATP. During each cell division cycle, sufficient DnaA-ATP must become available to interact with a distinct set of low affinity recognition sites in the unique chromosomal replication origin, oriC, and assemble the pre-replicative complex (orisome) that unwinds origin DNA and helps load the replicative helicase. The low affinity oriC-DnaA-ATP interactions are required for the orisome's mechanical functions, and may also play a role in timing of new rounds of DNA synthesis. To further examine this possibility, we constructed chromosomal oriCs with equal preference for DnaA-ADP or DnaA-ATP at one or more low affinity recognition sites, thereby lowering the DnaA-ATP requirement for orisome assembly, and measured the effect of the mutations on cell cycle timing of DNA synthesis. Under slow growth conditions, mutation of any one of the six low affinity DnaA-ATP sites in chromosomal oriC resulted in initiation earlier in the cell cycle, but the shift was not equivalent for every recognition site. Mutation of τ2 caused a greater change in initiation age, suggesting its occupation by DnaA-ATP is a temporal bottleneck during orisome assembly. In contrast, during rapid growth, all origins with a single mutated site displayed wild-type initiation timing. Based on these observations, we propose that E. coli uses two different, DnaA-ATP-dependent initiation timing mechanisms; a slow growth timer that is directly coupled to individual site occupation, and a fast growth timer comprising DnaA-ATP and additional factors that regulate DnaA access to oriC. Analysis of origins with paired mutated sites suggests that Fis is an important component of the fast growth timing mechanism.
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Affiliation(s)
- Prassanna Rao
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | | | - Abdulaziz Alqahtani
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Julia E Grimwade
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Alan C Leonard
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, United States
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80
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Mancini G, Horvath TL. Viral Vectors for Studying Brain Mechanisms that Control Energy Homeostasis. Cell Metab 2018; 27:1168-1175. [PMID: 29874565 DOI: 10.1016/j.cmet.2018.05.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 03/18/2018] [Accepted: 05/16/2018] [Indexed: 12/26/2022]
Abstract
Viral vectors have been shown to be potent and versatile tools for genome editing. In the present Minireview, we focus on lentiviruses and adeno-associated viruses as vectors and their use in the study of the hypothalamic circuits involved in the regulation of energy homeostasis.
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Affiliation(s)
- Giacomo Mancini
- Program in Integrative Cell Signalling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Tamas L Horvath
- Program in Integrative Cell Signalling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Anatomy and Histology, University of Veterinary Medicine, Budapest 1078, Hungary.
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81
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Zheng K, Wang Y, Li N, Jiang FF, Wu CX, Liu F, Chen HC, Liu ZF. Highly efficient base editing in bacteria using a Cas9-cytidine deaminase fusion. Commun Biol 2018; 1:32. [PMID: 30271918 PMCID: PMC6123677 DOI: 10.1038/s42003-018-0035-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/21/2018] [Indexed: 12/02/2022] Open
Abstract
The ability to precisely edit individual bases of bacterial genomes would accelerate the investigation of the function of genes. Here we utilized a nickase Cas9-cytidine deaminase fusion protein to direct the conversion of cytosine to thymine within prokaryotic cells, resulting in high mutagenesis frequencies in Escherichia coli and Brucella melitensis. Our study suggests that CRISPR/Cas9-guided base-editing is a viable alternative approach to generate mutant bacterial strains. Ke Zheng and colleagues repurposed a nickase Cas9-cytidine deaminase fusion protein to effectively direct the conversion of cytosine to thymine on bacterial genome. This study suggests that CRISPR/Cas9-guided base-editing can be used to generate viable mutant bacterial strains.
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Affiliation(s)
- Ke Zheng
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yang Wang
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Na Li
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang-Fang Jiang
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang-Xian Wu
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Liu
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huan-Chun Chen
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology and Key laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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82
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Hijacking CRISPR-Cas for high-throughput bacterial metabolic engineering: advances and prospects. Curr Opin Biotechnol 2018; 50:146-157. [DOI: 10.1016/j.copbio.2018.01.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 12/18/2022]
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83
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Gorshkova NV, Lobanova JS, Tokmakova IL, Smirnov SV, Akhverdyan VZ, Krylov AA, Mashko SV. Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome. Appl Microbiol Biotechnol 2018; 102:2867-2884. [PMID: 29392386 PMCID: PMC5847225 DOI: 10.1007/s00253-018-8767-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 02/05/2023]
Abstract
A dual-component Mu-transposition system was modified for the integration/amplification of genes in Corynebacterium. The system consists of two types of plasmids: (i) a non-replicative integrative plasmid that contains the transposing mini-Mu(LR) unit bracketed by the L/R Mu ends or the mini-Mu(LER) unit, which additionally contains the enhancer element, E, and (ii) an integration helper plasmid that expresses the transposition factor genes for MuA and MuB. Efficient transposition in the C. glutamicum chromosome (≈ 2 × 10−4 per cell) occurred mainly through the replicative pathway via cointegrate formation followed by possible resolution. Optimizing the E location in the mini-Mu unit significantly increased the efficiency of Mu-driven intramolecular transposition–amplification in C. glutamicum as well as in gram-negative bacteria. The new C. glutamicum genome modification strategy that was developed allows the consequent independent integration/amplification/fixation of target genes at high copy numbers. After integration/amplification of the first mini-Mu(LER) unit in the C. glutamicum chromosome, the E-element, which is bracketed by lox-like sites, is excised by Cre-mediated fashion, thereby fixing the truncated mini-Mu(LR) unit in its position for the subsequent integration/amplification of new mini-Mu(LER) units. This strategy was demonstrated using the genes for the citrine and green fluorescent proteins, yECitrine and yEGFP, respectively.
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Affiliation(s)
- Natalya V Gorshkova
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Juliya S Lobanova
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Irina L Tokmakova
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Sergey V Smirnov
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Valerii Z Akhverdyan
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Alexander A Krylov
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Sergey V Mashko
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545.
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84
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Selection-Enhanced Mutagenesis of lac Genes Is Due to Their Coamplification with dinB Encoding an Error-Prone DNA Polymerase. Genetics 2018; 208:1009-1021. [PMID: 29301907 DOI: 10.1534/genetics.117.300409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022] Open
Abstract
To test whether growth limitation induces mutations, Cairns and Foster constructed an Escherichia coli strain whose mutant lac allele provides 1-2% of normal ability to use lactose. This strain cannot grow on lactose, but produces ∼50 Lac+ revertant colonies per 108 plated cells over 5 days. About 80% of revertants carry a stable lac+ mutation made by the error-prone DinB polymerase, which may be induced during growth limitation; 10% of Lac+ revertants are stable but form without DinB; and the remaining 10% grow by amplifying their mutant lac allele and are unstably Lac+ Induced DinB mutagenesis has been explained in two ways: (1) upregulation of dinB expression in nongrowing cells ("stress-induced mutagenesis") or (2) selected local overreplication of the lac and dinB+ genes on lactose medium (selected amplification) in cells that are not dividing. Transcription of dinB is necessary but not sufficient for mutagenesis. Evidence is presented that DinB enhances reversion only when encoded somewhere on the F'lac plasmid that carries the mutant lac gene. A new model will propose that rare preexisting cells (1 in a 1000) have ∼10 copies of the F'lac plasmid, providing them with enough energy to divide, mate, and overreplicate their F'lac plasmid under selective conditions. In these clones, repeated replication of F'lac in nondividing cells directs opportunities for lac reversion and increases the copy number of the dinB+ gene. Amplification of dinB+ increases the error rate of replication and increases the number of lac+ revertants. Thus, reversion is enhanced in nondividing cells not by stress-induced mutagenesis, but by selected coamplification of the dinB and lac genes, both of which happen to lie on the F'lac plasmid.
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85
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Gamboa-Melendez H, Larroude M, Park YK, Trebul P, Nicaud JM, Ledesma-Amaro R. Synthetic Biology to Improve the Production of Lipases and Esterases (Review). Methods Mol Biol 2018; 1835:229-242. [PMID: 30109656 DOI: 10.1007/978-1-4939-8672-9_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic biology is an emergent field of research whose aim is to make biology an engineering discipline, thus permitting to design, control, and standardize biological processes. Synthetic biology is therefore expected to boost the development of biotechnological processes such as protein production and enzyme engineering, which can be significantly relevant for lipases and esterases.
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Affiliation(s)
- Heber Gamboa-Melendez
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Macarena Larroude
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Young Kyoung Park
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Pauline Trebul
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Sythetic Biology, Imperial College London, London, UK.
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86
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Novel Metabolic Pathway for N-Methylpyrrolidone Degradation in Alicycliphilus sp. Strain BQ1. Appl Environ Microbiol 2017; 84:AEM.02136-17. [PMID: 29030443 DOI: 10.1128/aem.02136-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022] Open
Abstract
The molecular mechanisms underlying the biodegradation of N-methylpyrrolidone (NMP), a widely used industrial solvent that produces skin irritation in humans and is teratogenic in rats, are unknown. Alicycliphilus sp. strain BQ1 degrades NMP. By studying a transposon-tagged mutant unable to degrade NMP, we identified a six-gene cluster (nmpABCDEF) that is transcribed as a polycistronic mRNA and encodes enzymes involved in NMP biodegradation. nmpA and the transposon-affected gene nmpB encode an N-methylhydantoin amidohydrolase that transforms NMP to γ-N-methylaminobutyric acid; this is metabolized by an amino acid oxidase (NMPC), either by demethylation to produce γ-aminobutyric acid (GABA) or by deamination to produce succinate semialdehyde (SSA). If GABA is produced, the activity of a GABA aminotransferase (GABA-AT), not encoded in the nmp gene cluster, is needed to generate SSA. SSA is transformed by a succinate semialdehyde dehydrogenase (SSDH) (NMPF) to succinate, which enters the Krebs cycle. The abilities to consume NMP and to utilize it for growth were complemented in the transposon-tagged mutant by use of the nmpABCD genes. Similarly, Escherichia coli MG1655, which has two SSDHs but is unable to grow in NMP, acquired these abilities after functional complementation with these genes. In wild-type (wt) BQ1 cells growing in NMP, GABA was not detected, but SSA was present at double the amount found in cells growing in Luria-Bertani medium (LB), suggesting that GABA is not an intermediate in this pathway. Moreover, E. coli GABA-AT deletion mutants complemented with nmpABCD genes retained the ability to grow in NMP, supporting the possibility that γ-N-methylaminobutyric acid is deaminated to SSA instead of being demethylated to GABA.IMPORTANCEN-Methylpyrrolidone is a cyclic amide reported to be biodegradable. However, the metabolic pathway and enzymatic activities for degrading NMP are unknown. By developing molecular biology techniques for Alicycliphilus sp. strain BQ1, an environmental bacterium able to grow in NMP, we identified a six-gene cluster encoding enzymatic activities involved in NMP degradation. These findings set the basis for the study of new enzymatic activities and for the development of biotechnological processes with potential applications in bioremediation.
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87
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Yurieva O, Nikiforov V, Nikiforov V, O'Donnell M, Mustaev A. Insights into RNA polymerase catalysis and adaptive evolution gained from mutational analysis of a locus conferring rifampicin resistance. Nucleic Acids Res 2017; 45:11327-11340. [PMID: 29036608 PMCID: PMC5737076 DOI: 10.1093/nar/gkx813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/06/2017] [Indexed: 01/25/2023] Open
Abstract
S531 of Escherichia coli RNA polymerase (RNAP) β subunit is a part of RNA binding domain in transcription complex. While highly conserved, S531 is not involved in interactions within the transcription complex as suggested by X-ray analysis. To understand the basis for S531 conservation we performed systematic mutagenesis of this residue. We find that the most of the mutations significantly decreased initiation-to-elongation transition by RNAP. Surprisingly, some changes enhanced the production of full-size transcripts by suppressing abortive loss of short RNAs. S531-R increased transcript retention by establishing a salt bridge with RNA, thereby explaining the R substitution at the equivalent position in extremophilic organisms, in which short RNAs retention is likely to be an issue. Generally, the substitutions had the same effect on bacterial doubling time when measured at 20°. Raising growth temperature to 37° ablated the positive influence of some mutations on the growth rate in contrast to their in vitro action, reflecting secondary effects of cellular environment on transcription and complex involvement of 531 locus in the cell biology. The properties of generated RNAP variants revealed an RNA/protein interaction network that is crucial for transcription, thereby explaining the details of initiation-to-elongation transition on atomic level.
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Affiliation(s)
- Olga Yurieva
- Laboratory of DNA Replication, The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065 USA
| | - Vadim Nikiforov
- Laboratory of DNA Replication, The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065 USA
| | - Vadim Nikiforov
- Public Health Research Institute, Newark, NJ 07103, USA.,Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA.,Institute of molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Michael O'Donnell
- Laboratory of DNA Replication, The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065 USA
| | - Arkady Mustaev
- Public Health Research Institute, Newark, NJ 07103, USA.,Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
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88
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An enhanced vector-free allele exchange (VFAE) mutagenesis protocol for genome editing in a wide range of bacterial species. AMB Express 2017. [PMID: 28629206 PMCID: PMC5474227 DOI: 10.1186/s13568-017-0425-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Vector-free allele exchange (VFAE) is a newly developed protocol for genome editing in Pseudomonas species. Although several parameters have been determined to optimize the procedures for obtaining a stable and high-frequency mutation, numerous false-positive clones still appear on the plate, which increases the difficulty of finding the desired mutants. It has also not been established whether this protocol can be used for genome editing in other bacterial species. In the current study, the protocol was modified to dramatically decrease the occurrence of false-positive colonies using Pseudomonas stutzeri A1501 as a model strain. This improvement was reached by increasing the occurrence of circular-DNA cassettes of the correct size. Furthermore, the enhanced protocol was used to construct mutants in both the gram-negative Escherichia coli BL21 and gram-positive Bacillus subtilis 168 strains. The protocol works well in both strains, yielding ideal results with a low percentage of false-positive colonies. In summary, the enhanced VFAE mutagenesis protocol is a potential tool for use in bacterial genome editing.
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89
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Abstract
ABSTRACT
The
Lactobacillus
genus is a diverse group of microorganisms, many of which are of industrial and medical relevance. Several
Lactobacillus
species have been used as probiotics, organisms that when present in sufficient quantities confer a health benefit to the host. A significant limitation to the mechanistic understanding of how these microbes provide health benefits to their hosts and how they can be used as therapeutic delivery systems has been the lack of genetic strategies to efficiently manipulate their genomes. This article will review the development and employment of traditional genetic tools in lactobacilli and highlight the latest methodologies that are allowing for precision genome engineering of these probiotic organisms. The application of these tools will be key in providing mechanistic insights into probiotics as well as maximizing the value of lactobacilli as either a traditional probiotic or as a platform for the delivery of therapeutic proteins. Finally, we will discuss concepts that we consider relevant for the delivery of engineered therapeutics to the human gut.
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90
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Abstract
Homologous recombination methods enable modifications to be made to the bacterial chromosome. Commonly, the λ phage RED proteins are employed as a site-specific recombinase system, to facilitate recombination of linear DNA fragments with targeted regions of the chromosome. Here we describe methods for the efficient delivery of linear DNA segments containing homology to the chromosome into the cell as substrates for the λRED proteins. Combined with antibiotic selection and counterselection, we demonstrate that using this method facilitates accurate, rapid editing of the chromosome.
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91
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Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas12a (Cpf1) has emerged as an effective genome editing tool in many organisms. Here, we developed and optimized a CRISPR-Cas12a-assisted recombineering system to facilitate genetic manipulation in bacteria. Using this system, point mutations, deletions, insertions, and gene replacements can be easily generated on the chromosome or native plasmids in Escherichia coli, Yersinia pestis, and Mycobacterium smegmatis Because CRISPR-Cas12a-assisted recombineering does not require introduction of an antibiotic resistance gene into the chromosome to select for recombinants, it is an efficient approach for generating markerless and scarless mutations in bacteria.IMPORTANCE The CRISPR-Cas9 system has been widely used to facilitate genome editing in many bacteria. CRISPR-Cas12a (Cpf1), a new type of CRISPR-Cas system, allows efficient genome editing in bacteria when combined with recombineering. Cas12a and Cas9 recognize different target sites, which allows for more precise selection of the cleavage target and introduction of the desired mutation. In addition, CRISPR-Cas12a-assisted recombineering can be used for genetic manipulation of plasmids and plasmid curing. Finally, Cas12a-assisted recombineering in the generation of point mutations, deletions, insertions, and replacements in bacteria has been systematically analyzed. Taken together, our findings will guide efficient Cas12a-mediated genome editing in bacteria.
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92
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Zerbini F, Zanella I, Fraccascia D, König E, Irene C, Frattini LF, Tomasi M, Fantappiè L, Ganfini L, Caproni E, Parri M, Grandi A, Grandi G. Large scale validation of an efficient CRISPR/Cas-based multi gene editing protocol in Escherichia coli. Microb Cell Fact 2017; 16:68. [PMID: 28438207 PMCID: PMC5404680 DOI: 10.1186/s12934-017-0681-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The exploitation of the CRISPR/Cas9 machinery coupled to lambda (λ) recombinase-mediated homologous recombination (recombineering) is becoming the method of choice for genome editing in E. coli. First proposed by Jiang and co-workers, the strategy has been subsequently fine-tuned by several authors who demonstrated, by using few selected loci, that the efficiency of mutagenesis (number of mutant colonies over total number of colonies analyzed) can be extremely high (up to 100%). However, from published data it is difficult to appreciate the robustness of the technology, defined as the number of successfully mutated loci over the total number of targeted loci. This information is particularly relevant in high-throughput genome editing, where repetition of experiments to rescue missing mutants would be impractical. This work describes a "brute force" validation activity, which culminated in the definition of a robust, simple and rapid protocol for single or multiple gene deletions. RESULTS We first set up our own version of the CRISPR/Cas9 protocol and then we evaluated the mutagenesis efficiency by changing different parameters including sequence of guide RNAs, length and concentration of donor DNAs, and use of single stranded and double stranded donor DNAs. We then validated the optimized conditions targeting 78 "dispensable" genes. This work led to the definition of a protocol, featuring the use of double stranded synthetic donor DNAs, which guarantees mutagenesis efficiencies consistently higher than 10% and a robustness of 100%. The procedure can be applied also for simultaneous gene deletions. CONCLUSIONS This work defines for the first time the robustness of a CRISPR/Cas9-based protocol based on a large sample size. Since the technical solutions here proposed can be applied to other similar procedures, the data could be of general interest for the scientific community working on bacterial genome editing and, in particular, for those involved in synthetic biology projects requiring high throughput procedures.
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Affiliation(s)
- Francesca Zerbini
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Ilaria Zanella
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Davide Fraccascia
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Enrico König
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Carmela Irene
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Luca F. Frattini
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Michele Tomasi
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Laura Fantappiè
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Luisa Ganfini
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Elena Caproni
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
| | - Matteo Parri
- Toscana Life Sciences Scientific Park, Via Fiorentina, 1, 53100 Siena, Italy
| | - Alberto Grandi
- Toscana Life Sciences Scientific Park, Via Fiorentina, 1, 53100 Siena, Italy
| | - Guido Grandi
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Povo, 38123 Trento, Italy
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93
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Tso D, Peebles CL, Maurer JB, Duda RL, Hendrix RW. On the catalytic mechanism of bacteriophage HK97 capsid crosslinking. Virology 2017; 506:84-91. [PMID: 28359902 DOI: 10.1016/j.virol.2017.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 10/19/2022]
Abstract
During maturation of the phage HK97 capsid, each of the 415 capsid subunits forms covalent bonds to neighboring subunits, stabilizing the capsid. Crosslinking is catalyzed not by a separate enzyme but by subunits of the assembled capsid in response to conformational rearrangements during maturation. This report investigates the catalytic mechanism. Earlier work established that the crosslinks are isopeptide (amide) bonds between side chains of a lysine on one subunit and an asparagine on another subunit, aided by a catalytic glutamate on a third subunit. The mature capsid structure suggests that the reaction may be facilitated by the arrival of a valine with the lysine to complete a hydrophobic pocket surrounding the glutamate, lysine and asparagine. We show that this valine has an essential role for efficient crosslinking, and that any of six other amino acids can successfully substitute for valine. Evidently none of the remaining 13 amino acids will work.
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Affiliation(s)
- DanJu Tso
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Craig L Peebles
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Joshua B Maurer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robert L Duda
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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94
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A Cre Transcription Fidelity Reporter Identifies GreA as a Major RNA Proofreading Factor in Escherichia coli. Genetics 2017; 206:179-187. [PMID: 28341651 PMCID: PMC5419468 DOI: 10.1534/genetics.116.198960] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/04/2017] [Indexed: 12/21/2022] Open
Abstract
We made a coupled genetic reporter that detects rare transcription misincorporation errors to measure RNA polymerase transcription fidelity in Escherichia coli. Using this reporter, we demonstrated in vivo that the transcript cleavage factor GreA, but not GreB, is essential for proofreading of a transcription error where a riboA has been misincorporated instead of a riboG. A greA mutant strain had more than a 100-fold increase in transcription errors relative to wild-type or a greB mutant. However, overexpression of GreB in ΔgreA cells reduced the misincorporation errors to wild-type levels, demonstrating that GreB at high concentration could substitute for GreA in RNA proofreading activity in vivo.
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95
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Wilkinson M, Troman LA, Wan Nur Ismah WAK, Chaban Y, Avison MB, Dillingham MS, Wigley DB. Structural basis for the inhibition of RecBCD by Gam and its synergistic antibacterial effect with quinolones. eLife 2016; 5:e22963. [PMID: 28009252 PMCID: PMC5218532 DOI: 10.7554/elife.22963] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 12/22/2016] [Indexed: 12/11/2022] Open
Abstract
Our previous paper (Wilkinson et al, 2016) used high-resolution cryo-electron microscopy to solve the structure of the Escherichia coli RecBCD complex, which acts in both the repair of double-stranded DNA breaks and the degradation of bacteriophage DNA. To counteract the latter activity, bacteriophage λ encodes a small protein inhibitor called Gam that binds to RecBCD and inactivates the complex. Here, we show that Gam inhibits RecBCD by competing at the DNA-binding site. The interaction surface is extensive and involves molecular mimicry of the DNA substrate. We also show that expression of Gam in E. coli or Klebsiella pneumoniae increases sensitivity to fluoroquinolones; antibacterials that kill cells by inhibiting topoisomerases and inducing double-stranded DNA breaks. Furthermore, fluoroquinolone-resistance in K. pneumoniae clinical isolates is reversed by expression of Gam. Together, our data explain the synthetic lethality observed between topoisomerase-induced DNA breaks and the RecBCD gene products, suggesting a new co-antibacterial strategy.
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Affiliation(s)
- Martin Wilkinson
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Luca A Troman
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Wan AK Wan Nur Ismah
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Yuriy Chaban
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Mark S Dillingham
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Dale B Wigley
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
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96
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Bhatt S, Egan M, Ramirez J, Xander C, Jenkins V, Muche S, El-Fenej J, Palmer J, Mason E, Storm E, Buerkert T. Hfq and three Hfq-dependent small regulatory RNAs-MgrR, RyhB and McaS-coregulate the locus of enterocyte effacement in enteropathogenic Escherichia coli. Pathog Dis 2016; 75:ftw113. [PMID: 27956465 DOI: 10.1093/femspd/ftw113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/28/2016] [Accepted: 12/10/2016] [Indexed: 11/15/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a significant cause of infantile diarrhea and death in developing countries. The pathogenicity island locus of enterocyte effacement (LEE) is essential for EPEC to cause diarrhea. Besides EPEC, the LEE is also present in other gastrointestinal pathogens, most notably enterohemorrhagic E. coli (EHEC). Whereas transcriptional control of the LEE has been meticulously examined, posttranscriptional regulation, including the role of Hfq-dependent small RNAs, remains undercharacterized. However, the past few years have witnessed a surge in the identification of riboregulators of the LEE in EHEC. Contrastingly, the posttranscriptional regulatory landscape of EPEC remains cryptic. Here we demonstrate that the RNA-chaperone Hfq represses the LEE of EPEC by targeting the 5' untranslated leader region of grlR in the grlRA mRNA. Three conserved small regulatory RNAs (sRNAs)-MgrR, RyhB and McaS-are involved in the Hfq-dependent regulation of grlRA MgrR and RyhB exert their effects by directly base-pairing to the 5' region of grlR Whereas MgrR selectively represses grlR but activates grlA, RyhB represses gene expression from the entire grlRA transcript. Meanwhile, McaS appears to target the grlRA mRNA indirectly. Thus, our results provide the first definitive evidence that implicates multiple sRNAs in regulating the LEE and the resulting virulence of EPEC.
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Affiliation(s)
- Shantanu Bhatt
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Marisa Egan
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Jasmine Ramirez
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Christian Xander
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Valerie Jenkins
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Sarah Muche
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Jihad El-Fenej
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Jamie Palmer
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Elisabeth Mason
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Elizabeth Storm
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
| | - Thomas Buerkert
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Science Center, Philadelphia, PA 19131, USA
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97
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Zhao D, Yuan S, Xiong B, Sun H, Ye L, Li J, Zhang X, Bi C. Development of a fast and easy method for Escherichia coli genome editing with CRISPR/Cas9. Microb Cell Fact 2016; 15:205. [PMID: 27908280 PMCID: PMC5134288 DOI: 10.1186/s12934-016-0605-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 11/25/2016] [Indexed: 11/24/2022] Open
Abstract
Background Microbial genome editing is a powerful tool to modify chromosome in way of deletion, insertion or replacement, which is one of the most important techniques in metabolic engineering research. The emergence of CRISPR/Cas9 technique inspires various genomic editing methods. Results In this research, the goal of development of a fast and easy method for Escherichia coli genome editing with high efficiency is pursued. For this purpose, we designed modular plasmid assembly strategy, compared effects of different length of homologous arms for recombination, and tested different sets of recombinases. The final technique we developed only requires one plasmid construction and one transformation of practice to edit a genomic locus with 3 days and minimal lab work. In addition, the single temperature sensitive plasmid is easy to eliminate for another round of editing. Especially, process of the modularized editing plasmid construction only takes 4 h. Conclusion In this study, we developed a fast and easy genome editing procedure based on CRISPR/Cas9 system that only required the work of one plasmid construction and one transformation, which allowed modification of a chromosome locus within 3 days and could be performed continuously for multiple loci. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0605-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Shenli Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Bin Xiong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Hongnian Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Lijun Ye
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Jing Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
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98
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Arias-Cartin R, Ceccaldi P, Schoepp-Cothenet B, Frick K, Blanc JM, Guigliarelli B, Walburger A, Grimaldi S, Friedrich T, Receveur-Brechot V, Magalon A. Redox cofactors insertion in prokaryotic molybdoenzymes occurs via a conserved folding mechanism. Sci Rep 2016; 6:37743. [PMID: 27886223 PMCID: PMC5123574 DOI: 10.1038/srep37743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/01/2016] [Indexed: 01/28/2023] Open
Abstract
A major gap of knowledge in metalloproteins is the identity of the prefolded state of the protein before cofactor insertion. This holds for molybdoenzymes serving multiple purposes for life, especially in energy harvesting. This large group of prokaryotic enzymes allows for coordination of molybdenum or tungsten cofactors (Mo/W-bisPGD) and Fe/S clusters. Here we report the structural data on a cofactor-less enzyme, the nitrate reductase respiratory complex and characterize the conformational changes accompanying Mo/W-bisPGD and Fe/S cofactors insertion. Identified conformational changes are shown to be essential for recognition of the dedicated chaperone involved in cofactors insertion. A solvent-exposed salt bridge is shown to play a key role in enzyme folding after cofactors insertion. Furthermore, this salt bridge is shown to be strictly conserved within this prokaryotic molybdoenzyme family as deduced from a phylogenetic analysis issued from 3D structure-guided multiple sequence alignment. A biochemical analysis with a distantly-related member of the family, respiratory complex I, confirmed the critical importance of the salt bridge for folding. Overall, our results point to a conserved cofactors insertion mechanism within the Mo/W-bisPGD family.
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Affiliation(s)
| | - Pierre Ceccaldi
- Aix-Marseille Univ, CNRS, IMM, LCB UMR7283, Marseille, France.,Aix-Marseille Univ, CNRS, IMM, BIP UMR7281, Marseille, France
| | | | - Klaudia Frick
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
| | | | | | - Anne Walburger
- Aix-Marseille Univ, CNRS, IMM, LCB UMR7283, Marseille, France
| | | | | | | | - Axel Magalon
- Aix-Marseille Univ, CNRS, IMM, LCB UMR7283, Marseille, France
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99
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Bott M, Eggeling L. Novel Technologies for Optimal Strain Breeding. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:227-254. [PMID: 27872965 DOI: 10.1007/10_2016_33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The implementation of a knowledge-based bioeconomy requires the rapid development of highly efficient microbial production strains that are able to convert renewable carbon sources to value-added products, such as bulk and fine chemicals, pharmaceuticals, or proteins at industrial scale. Starting from classical strain breeding by random mutagenesis and screening in the 1950s via rational design by metabolic engineering initiated in the 1970s, a range of powerful new technologies have been developed in the past two decades that can revolutionize future strain engineering. In particular, next-generation sequencing technologies combined with new methods of genome engineering and high-throughput screening based on genetically encoded biosensors have allowed for new concepts. In this chapter, selected new technologies relevant for breeding microbial production strains with a special emphasis on amino acid producers will be summarized.
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Affiliation(s)
- Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany.
| | - Lothar Eggeling
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany
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100
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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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