51
|
Sharma A, Raman V, Lee J, Forbes NS. Mucus blocks probiotics but increases penetration of motile pathogens and induces TNF-α and IL-8 secretion. Biotechnol Bioeng 2020; 117:2540-2555. [PMID: 32396232 PMCID: PMC7806204 DOI: 10.1002/bit.27383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 12/29/2022]
Abstract
The mucosal barrier in combination with innate immune system are the first line of defense against luminal bacteria at the intestinal mucosa. Dysfunction of the mucus layer and bacterial infiltration are linked to tissue inflammation and disease. To study host-bacterial interactions at the mucosal interface, we created an experimental model that contains luminal space, a mucus layer, an epithelial layer, and suspended immune cells. Reconstituted porcine small intestinal mucus formed an 880 ± 230 µm thick gel layer and had a porous structure. In the presence of mucus, sevenfold less probiotic and nonmotile VSL#3 bacteria transmigrated across the epithelial barrier compared to no mucus. The higher bacterial transmigration caused immune cell differentiation and increased the concentration of interleukin-8 (IL-8) and tumor necrosis factor-alpha (TNF-α; p < .01). Surprisingly, the mucus layer increased transmigration of pathogenic Salmonella and increased secretion of TNF-α and IL-8 (p < .05). Nonmotile, flagella knockout Salmonella had lower transmigration and caused lower IL-8 and TNF-α secretion (p < .05). These results demonstrate that motility enables pathogenic bacteria to cross the mucus and epithelial layers, which could lead to infection. Using an in vitro coculture platform to understand the interactions of bacteria with the intestinal mucosa has the potential to improve the treatment of intestinal diseases.
Collapse
Affiliation(s)
- Abhinav Sharma
- Department of Chemical Engineering, University of Massachusetts, Amherst
| | - Vishnu Raman
- Department of Chemical Engineering, University of Massachusetts, Amherst
| | - Jungwoo Lee
- Department of Chemical Engineering, University of Massachusetts, Amherst
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst
- Institute for Applied Life Sciences, University of Massachusetts, Amherst
| | - Neil S. Forbes
- Department of Chemical Engineering, University of Massachusetts, Amherst
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst
- Institute for Applied Life Sciences, University of Massachusetts, Amherst
| |
Collapse
|
52
|
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.
Collapse
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
| |
Collapse
|
53
|
Wannier TM, Nyerges A, Kuchwara HM, Czikkely M, Balogh D, Filsinger GT, Borders NC, Gregg CJ, Lajoie MJ, Rios X, Pál C, Church GM. Improved bacterial recombineering by parallelized protein discovery. Proc Natl Acad Sci U S A 2020; 117:13689-13698. [PMID: 32467157 PMCID: PMC7306799 DOI: 10.1073/pnas.2001588117] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Exploiting bacteriophage-derived homologous recombination processes has enabled precise, multiplex editing of microbial genomes and the construction of billions of customized genetic variants in a single day. The techniques that enable this, multiplex automated genome engineering (MAGE) and directed evolution with random genomic mutations (DIvERGE), are however, currently limited to a handful of microorganisms for which single-stranded DNA-annealing proteins (SSAPs) that promote efficient recombineering have been identified. Thus, to enable genome-scale engineering in new hosts, efficient SSAPs must first be found. Here we introduce a high-throughput method for SSAP discovery that we call "serial enrichment for efficient recombineering" (SEER). By performing SEER in Escherichia coli to screen hundreds of putative SSAPs, we identify highly active variants PapRecT and CspRecT. CspRecT increases the efficiency of single-locus editing to as high as 50% and improves multiplex editing by 5- to 10-fold in E. coli, while PapRecT enables efficient recombineering in Pseudomonas aeruginosa, a concerning human pathogen. CspRecT and PapRecT are also active in other, clinically and biotechnologically relevant enterobacteria. We envision that the deployment of SEER in new species will pave the way toward pooled interrogation of genotype-to-phenotype relationships in previously intractable bacteria.
Collapse
Affiliation(s)
| | - Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged HU-6726, Hungary
| | | | - Márton Czikkely
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged HU-6726, Hungary
| | - Dávid Balogh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged HU-6726, Hungary
| | | | | | | | - Marc J Lajoie
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Xavier Rios
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged HU-6726, Hungary
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
| |
Collapse
|
54
|
Bashir A, Tian T, Yu X, Meng C, Ali M, Li L. Pyoverdine-Mediated Killing of Caenorhabditis elegans by Pseudomonas syringae MB03 and the Role of Iron in Its Pathogenicity. Int J Mol Sci 2020; 21:ijms21062198. [PMID: 32235814 PMCID: PMC7139650 DOI: 10.3390/ijms21062198] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/28/2022] Open
Abstract
The pathogenicity of the common phytopathogenic bacterium Pseudomonas syringae toward Caenorhabditis elegans has been recently demonstrated. However, the major virulence factors involved in this interaction remain unknown. In this study, we investigated the nematocidal activity of P. syringae against C. elegans under iron-sufficient/limited conditions, primarily focusing on the role of the ferric chelator pyoverdine in a P. syringae–C. elegans liquid-based pathogenicity model. Prediction-based analysis of pyoverdine-encoding genes in the genome of the wild-type P. syringae strain MB03 revealed that the genes are located in one large cluster. Two non-ribosomal peptide synthetase genes (pvdD and pvdJ) were disrupted via a Rec/TE recombination system, resulting in mutant strains with abrogated pyoverdine production and attenuated virulence against C. elegans. When used alone, pure pyoverdine also showed nematocidal activity. The role of iron used alone or with pyoverdine was further investigated in mutant and MB03-based bioassays. The results indicated that pyoverdine in P. syringae MB03 is a robust virulence factor that promotes the killing of C. elegans. We speculate that pyoverdine functions as a virulence determinant by capturing environmentally available iron for host bacterial cells, by limiting its availability for C. elegans worms, and by regulating and/or activating other intracellular virulence factors that ultimately kills C. elegans worms.
Collapse
Affiliation(s)
- Anum Bashir
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.B.); (T.T.); (X.Y.); (M.A.)
| | - Tian Tian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.B.); (T.T.); (X.Y.); (M.A.)
| | - Xun Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.B.); (T.T.); (X.Y.); (M.A.)
| | - Cui Meng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.B.); (T.T.); (X.Y.); (M.A.)
| | - Muhammad Ali
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.B.); (T.T.); (X.Y.); (M.A.)
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.B.); (T.T.); (X.Y.); (M.A.)
- Correspondence: ; Tel.: +86-27-8728-6952
| |
Collapse
|
55
|
Homing endonuclease I-SceI-mediated Corynebacterium glutamicum ATCC 13032 genome engineering. Appl Microbiol Biotechnol 2020; 104:3597-3609. [PMID: 32146493 DOI: 10.1007/s00253-020-10517-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/11/2020] [Accepted: 03/01/2020] [Indexed: 10/24/2022]
Abstract
Corynebacterium glutamicum is widely used to produce amino acids and is a chassis for the production of value-added compounds. Effective genome engineering methods are crucial to metabolic engineering and synthetic biology studies of C. glutamicum. Herein, a homing endonuclease I-SceI-mediated genome engineering strategy was established for the model strain C. glutamicum ATCC 13032. A vegetative R6K replicon-based, suicide plasmid was employed. The plasmid, pLS3661, contains both tightly regulated, IPTG (isopropyl-β-D-1-thiogalactopyranoside)-inducible I-SceI expression elements and two I-SceI recognition sites. Following cloning of the homologous arms into pLS3661 and transfer the recombinant vector into C. glutamicum ATCC 13032, through the homologous recombination between the cloned fragment and its chromosomal allele, a merodiploid was selected under kanamycin selection. Subsequently, a merodiploid was resolved by double-stranded break repair stimulated by IPTG-stimulated I-SceI expression, generating desired mutants. The protocol obviates a pre-generated strain, transfer of a second I-SceI expression plasmid, and there is not any strain, medium, and temperature restrictions. We validated the approach via deletions of five genes (up to ~ 13.0 kb) and knock-in of one DNA fragment. Furthermore, through kanamycin resistance repair, the ssDNA recombineering parameters were optimized. We hope the highly efficient method will be helpful for the studies of C. glutamicum, and potentially, to other bacteria. KEY POINTS: • Counterselection marker I-SceI-mediated C. glutamicum genome engineering • A suicide vector contains I-SceI expression elements and its recognition sites • Gene deletions and knock-in were conducted; efficiency was as high as 90% • Through antibiotic resistance repair, ssDNA recombineering parameters were optimized.
Collapse
|
56
|
Choudhury A, Fenster JA, Fankhauser RG, Kaar JL, Tenaillon O, Gill RT. CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli. Mol Syst Biol 2020; 16:e9265. [PMID: 32175691 PMCID: PMC7073797 DOI: 10.15252/msb.20199265] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/14/2023] Open
Abstract
Deep mutational scanning can provide significant insights into the function of essential genes in bacteria. Here, we developed a high-throughput method for mutating essential genes of Escherichia coli in their native genetic context. We used Cas9-mediated recombineering to introduce a library of mutations, created by error-prone PCR, within a gene fragment on the genome using a single gRNA pre-validated for high efficiency. Tracking mutation frequency through deep sequencing revealed biases in the position and the number of the introduced mutations. We overcame these biases by increasing the homology arm length and blocking mismatch repair to achieve a mutation efficiency of 85% for non-essential genes and 55% for essential genes. These experiments also improved our understanding of poorly characterized recombineering process using dsDNA donors with single nucleotide changes. Finally, we applied our technology to target rpoB, the beta subunit of RNA polymerase, to study resistance against rifampicin. In a single experiment, we validate multiple biochemical and clinical observations made in the previous decades and provide insights into resistance compensation with the study of double mutants.
Collapse
Affiliation(s)
- Alaksh Choudhury
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- IAMEINSERMUniversité de ParisParisFrance
| | - Jacob A Fenster
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Joel L Kaar
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Ryan T Gill
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- Renewable & Sustainable Energy InstituteUniversity of ColoradoBoulderCOUSA
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityCopenhagenDenmark
| |
Collapse
|
57
|
Des Soye BJ, Gerbasi VR, Thomas PM, Kelleher NL, Jewett MC. A Highly Productive, One-Pot Cell-Free Protein Synthesis Platform Based on Genomically Recoded Escherichia coli. Cell Chem Biol 2019; 26:1743-1754.e9. [PMID: 31706984 DOI: 10.1016/j.chembiol.2019.10.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 06/05/2019] [Accepted: 10/18/2019] [Indexed: 12/26/2022]
Abstract
The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins via amber suppression provides access to novel protein properties, structures, and functions. Historically, poor protein expression yields resulting from release factor 1 (RF1) competition has limited this technology. To address this limitation, we develop a high-yield, one-pot cell-free platform for synthesizing proteins bearing ncAAs based on genomically recoded Escherichia coli lacking RF1. A key feature of this platform is the independence on the addition of purified T7 DNA-directed RNA polymerase (T7RNAP) to catalyze transcription. Extracts derived from our final strain demonstrate high productivity, synthesizing 2.67 ± 0.06 g/L superfolder GFP in batch mode without supplementation of purified T7RNAP. Using an optimized one-pot platform, we demonstrate multi-site incorporation of the ncAA p-acetyl-L-phenylalanine into an elastin-like polypeptide with high accuracy of incorporation and yield. Our work has implications for chemical and synthetic biology.
Collapse
Affiliation(s)
- Benjamin J Des Soye
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Vincent R Gerbasi
- Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
| | - Paul M Thomas
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|
58
|
Abstract
Recombineering inserts PCR products into DNA using homologous recombination. A pair of short homology arms (50 base pairs) on the ends of a PCR cassette target the cassette to its intended location. These homology arms can be easily introduced as 5' primer overhangs during the PCR reaction. The flexibility to choose almost any pair of homology arms enables the precise modification of virtually any DNA for purposes of sequence deletion, replacement, insertion, or point mutation. Recombineering often offers significant advantages relative to previous homologous recombination methods that require the construction of cassettes with large homology arms, and relative to traditional cloning methods that become intractable for large plasmids or DNA sequences. However, the tremendous number of variables, options, and pitfalls that can be encountered when designing and performing a recombineering protocol for the first time introduce barriers that can make recombineering a challenging technique for new users to adopt. This article focuses on three recombineering protocols we have found to be particularly robust, providing a detailed guide for choosing the simplest recombineering method for a given application and for performing and troubleshooting experiments. © 2019 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Louis J Papa
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts
| | - Matthew D Shoulders
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts
| |
Collapse
|
59
|
Xia Y, Li K, Li J, Wang T, Gu L, Xun L. T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis. Nucleic Acids Res 2019; 47:e15. [PMID: 30462336 PMCID: PMC6379645 DOI: 10.1093/nar/gky1169] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/31/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
The assembly of DNA fragments with homologous arms is becoming popular in routine cloning. For an in vitro assembly reaction, a DNA polymerase is often used either alone for its 3'-5' exonuclease activity or together with a 5'-3' exonuclease for its DNA polymerase activity. Here, we present a 'T5 exonuclease DNA assembly' (TEDA) method that only uses a 5'-3' exonuclease. DNA fragments with short homologous ends were treated by T5 exonuclease and then transformed into Escherichia coli to produce clone colonies. The cloning efficiency was similar to that of the commercial In-Fusion method employing a proprietary DNA polymerase, but higher than that of the Gibson method utilizing T5 exonuclease, Phusion DNA polymerase, and DNA ligase. It also assembled multiple DNA fragments and did simultaneous site-directed mutagenesis at multiple sites. The reaction mixture was simple, and each reaction used 0.04 U of T5 exonuclease that cost 0.25 US cents. The simplicity, cost effectiveness, and cloning efficiency should promote its routine use, especially for labs with a budget constraint. TEDA may trigger further development of DNA assembly methods that employ single exonucleases.
Collapse
Affiliation(s)
- Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Kai Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Jingjing Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China.,School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| |
Collapse
|
60
|
Caldwell BJ, Bell CE. Structure and mechanism of the Red recombination system of bacteriophage λ. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:33-46. [PMID: 30904699 DOI: 10.1016/j.pbiomolbio.2019.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/05/2019] [Accepted: 03/15/2019] [Indexed: 01/27/2023]
Abstract
While much of this volume focuses on mammalian DNA repair systems that are directly involved in genome stability and cancer, it is important to still be mindful of model systems from prokaryotes. Herein we review the Red recombination system of bacteriophage λ, which consists of an exonuclease for resecting dsDNA ends, and a single-strand annealing protein (SSAP) for binding the resulting 3'-overhang and annealing it to a complementary strand. The genetics and biochemistry of Red have been studied for over 50 years, in work that has laid much of the foundation for understanding DNA recombination in higher eukaryotes. In fact, the Red exonuclease (λ exo) is homologous to Dna2, a nuclease involved in DNA end-resection in eukaryotes, and the Red annealing protein (Redβ) is homologous to Rad52, the primary SSAP in eukaryotes. While eukaryotic recombination involves an elaborate network of proteins that is still being unraveled, the phage systems are comparatively simple and streamlined, yet still encompass the fundamental features of recombination, namely DNA end-resection, homologous pairing (annealing), and a coupling between them. Moreover, the Red system has been exploited in powerful methods for bacterial genome engineering that are important for functional genomics and systems biology. However, several mechanistic aspects of Red, particularly the action of the annealing protein, remain poorly understood. This review will focus on the proteins of the Red recombination system, with particular attention to structural and mechanistic aspects, and how the lessons learned can be applied to eukaryotic systems.
Collapse
Affiliation(s)
- Brian J Caldwell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA; Department of Chemistry and Biochemistry, 484 West 12th Avenue, 1060 Carmack Road, Columbus, OH, 43210, USA.
| |
Collapse
|
61
|
Coupling ssDNA recombineering with CRISPR-Cas9 for Escherichia coli DnaG mutations. Appl Microbiol Biotechnol 2019; 103:3559-3570. [DOI: 10.1007/s00253-019-09744-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/18/2019] [Accepted: 03/06/2019] [Indexed: 10/27/2022]
|
62
|
Combination of ssDNA recombineering and CRISPR-Cas9 for Pseudomonas putida KT2440 genome editing. Appl Microbiol Biotechnol 2019; 103:2783-2795. [DOI: 10.1007/s00253-019-09654-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 12/17/2022]
|
63
|
Guo T, Xin Y, Zhang Y, Gu X, Kong J. A rapid and versatile tool for genomic engineering in Lactococcus lactis. Microb Cell Fact 2019; 18:22. [PMID: 30704485 PMCID: PMC6357491 DOI: 10.1186/s12934-019-1075-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/24/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lactococcus lactis is one of the most extensively characterized lactic acid bacteria, from physiological traits to industrial exploitation. Since last decade, L. lactis has been developed into cell factories for the production of bioactive compounds such as enzymes, vaccine antigens and natural products. However, its precise and efficient genome editing tools is still required to make L. lactis more suitable candidate for engineered functionality. RESULTS A high active recombinase, RecT of Enterococcus faecalis ATCC14506, was selected from six candidates and mediated homologous recombination between single-stranded DNA (ssDNA) and the L. lactis chromosomal rpoB locus with an efficiency of 100% after rifampin selection. To screen mutants without an externally selectable phenotype, the CRISPR/Cas9 system was used for counterselection, yielding an upp mutant with an efficiency of 46%. By optimization of the copy number of plasmid carrying the CRISPR/Cas9 system and the length of spacer sequence, the off-target efficiency of the recA, galK, hemN and noxD genes were eliminated. The ability of this optimized tool to perform sequential point mutation was demonstrated using the upp and galK gene loci as targets with improved efficiencies > 75%. Moreover, seamless genomic DNA deletions (50/100 bp) or insertion (a loxP site, 34 bp) was efficiently accomplished within 72 h. CONCLUSIONS The work provided a rapid, versatile and precise tool for L. lactis genomic engineering by combination of ssDNA recombineering with improved CRISPR/Cas9 counterselection. This tool will simplify the production of isogenic strains for assessment of gene function or construction of biosynthetic host.
Collapse
Affiliation(s)
- Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Yongping Xin
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Yi Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Xinyi Gu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China.
| |
Collapse
|
64
|
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.
Collapse
|
65
|
Liu J, Mu X, Wang X, Huan H, Gao Q, Chen J, Qiao P, Jiang L, Gao S, Liu X. Unexpected transcriptome pompT' contributes to the increased pathogenicity of a pompT mutant of avian pathogenic Escherichia coli. Vet Microbiol 2018; 228:61-68. [PMID: 30593381 DOI: 10.1016/j.vetmic.2018.11.011] [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] [Received: 06/29/2018] [Revised: 11/10/2018] [Accepted: 11/15/2018] [Indexed: 11/17/2022]
Abstract
The lambda red recombination system makes it suitable for screening virulence gene utility in avian pathogenic Escherichia coli (APEC) on account of its wide applicability, simplicity and high efficiency. In APEC E058 (O2 serogroup), there are two copies of the outer membrane protease (ompT) gene, compT encoding cOmpT that is located on the chromosome and pompT encoding pOmpT that is located on a ColV plasmid. However, the relationship between pathogenesis and pompT expression in APEC E058 has yet to be elucidated. Here, we successfully constructed two pompT gene mutants: E058ΔpompT containing a chloramphenicol (cat) resistance gene and E058ΔpompT' without the cat gene. By RT-PCR and sequencing analysis, an unexpected transcriptome pompT' was detected in mutant strain E058ΔpompT' after deletion of the cat gene induced by the lambda red recombination system. Surprisingly, the pathogenicity of mutant E058ΔpompT was significantly attenuated compared to its parental strain in the chicken infection model and HD11 cell model then the pompT gene was knocked out, while the pathogenicity of the other mutant strain E058ΔpompT' had no difference. Furthermore, the presence of unexpected transcriptome pompT' influenced the bactericidal activity of SPF chicken serum and decreased the transcription level of TLR2 in the heart tissue of chickens. Our study identifies the pompT gene plays an important role in the virulence of APEC E058, and the unexpected transcriptome pompT' contributes to the increased pathogenicity of APEC E058 mutants following deletion of the cat gene induced by the lambda red recombination system, which suggests that this system still has some limitations for construction of mutant strains particularly where these are used in development of live vaccine.
Collapse
Affiliation(s)
- Juanhua Liu
- Key Laboratory for Avian Bioproducts Development, Animal Infectious Disease Laboratory, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, China; The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory for Zoonosis, Jiangsu Key Laboratory of Preventive Veterinary Medicine, Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xiaohui Mu
- Key Laboratory for Avian Bioproducts Development, Animal Infectious Disease Laboratory, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, China; The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory for Zoonosis, Jiangsu Key Laboratory of Preventive Veterinary Medicine, Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xiaobo Wang
- Key Laboratory for Avian Bioproducts Development, Animal Infectious Disease Laboratory, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, China; The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory for Zoonosis, Jiangsu Key Laboratory of Preventive Veterinary Medicine, Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Haixia Huan
- College of Life Science, Huaiyin Normal University, Huaian, China
| | - Qingqing Gao
- Key Laboratory for Avian Bioproducts Development, Animal Infectious Disease Laboratory, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, China; The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory for Zoonosis, Jiangsu Key Laboratory of Preventive Veterinary Medicine, Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Juan Chen
- Key Laboratory for Avian Bioproducts Development, Animal Infectious Disease Laboratory, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, China; The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory for Zoonosis, Jiangsu Key Laboratory of Preventive Veterinary Medicine, Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Peizhuang Qiao
- Key Laboratory for Avian Bioproducts Development, Animal Infectious Disease Laboratory, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, China; The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory for Zoonosis, Jiangsu Key Laboratory of Preventive Veterinary Medicine, Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Luyao Jiang
- Key Laboratory for Avian Bioproducts Development, Animal Infectious Disease Laboratory, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, China; The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory for Zoonosis, Jiangsu Key Laboratory of Preventive Veterinary Medicine, Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Song Gao
- Key Laboratory for Avian Bioproducts Development, Animal Infectious Disease Laboratory, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, China; The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory for Zoonosis, Jiangsu Key Laboratory of Preventive Veterinary Medicine, Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.
| | - Xiufan Liu
- Key Laboratory for Avian Bioproducts Development, Animal Infectious Disease Laboratory, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, China; The International Joint Laboratory for Cooperation in Agriculture and Agricultural Product Safety, Ministry of Education, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory for Zoonosis, Jiangsu Key Laboratory of Preventive Veterinary Medicine, Jiangsu Research Centre of Engineering and Technology for Prevention and Control of Poultry Disease, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| |
Collapse
|
66
|
CRISPR-Cas9 and CRISPR-Assisted Cytidine Deaminase Enable Precise and Efficient Genome Editing in Klebsiella pneumoniae. Appl Environ Microbiol 2018; 84:AEM.01834-18. [PMID: 30217854 DOI: 10.1128/aem.01834-18] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/10/2018] [Indexed: 12/21/2022] Open
Abstract
Klebsiella pneumoniae is a promising industrial microorganism as well as a major human pathogen. The recent emergence of carbapenem-resistant K. pneumoniae has posed a serious threat to public health worldwide, emphasizing a dire need for novel therapeutic means against drug-resistant K. pneumoniae Despite the critical importance of genetics in bioengineering, physiology studies, and therapeutic-means development, genome editing, in particular, the highly desirable scarless genetic manipulation in K. pneumoniae, is often time-consuming and laborious. Here, we report a two-plasmid system, pCasKP-pSGKP, used for precise and iterative genome editing in K. pneumoniae By harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome cleavage system and the lambda Red recombination system, pCasKP-pSGKP enabled highly efficient genome editing in K. pneumoniae using a short repair template. Moreover, we developed a cytidine base-editing system, pBECKP, for precise C→T conversion in both the chromosomal and plasmid-borne genes by engineering the fusion of the cytidine deaminase APOBEC1 and a Cas9 nickase. By using both the pCasKP-pSGKP and the pBECKP tools, the bla KPC-2 gene was confirmed to be the major factor that contributed to the carbapenem resistance of a hypermucoviscous carbapenem-resistant K. pneumoniae strain. The development of the two editing tools will significantly facilitate the genetic engineering of K. pneumoniae IMPORTANCE Genetics is a key means to study bacterial physiology. However, the highly desirable scarless genetic manipulation is often time-consuming and laborious for the major human pathogen K. pneumoniae We developed a CRISPR-Cas9-mediated genome-editing method and a cytidine base-editing system, enabling rapid, highly efficient, and iterative genome editing in both industrial and clinically isolated K. pneumoniae strains. We applied both tools in dissecting the drug resistance mechanism of a hypermucoviscous carbapenem-resistant K. pneumoniae strain, elucidating that the bla KPC-2 gene was the major factor that contributed to the carbapenem resistance of the hypermucoviscous carbapenem-resistant K. pneumoniae strain. Utilization of the two tools will dramatically accelerate a wide variety of investigations in diverse K. pneumoniae strains and relevant Enterobacteriaceae species, such as gene characterization, drug discovery, and metabolic engineering.
Collapse
|
67
|
Kang SY, Heo KT, Hong YS. Optimization of Artificial Curcumin Biosynthesis in E. coli by Randomized 5'-UTR Sequences To Control the Multienzyme Pathway. ACS Synth Biol 2018; 7:2054-2062. [PMID: 30160937 DOI: 10.1021/acssynbio.8b00198] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the optimization strategies of an artificial biosynthetic metabolic flux with a multienzyme pathway is when the enzyme concentrations are present at the appropriate ratios rather than at their maximum expression. Thus, many recent research efforts have focused on the development of tools that fine-tune the enzyme expression, and these research efforts have facilitated the search for the optimum balance between pathway expression and cell viability. However, the rational approach has some limitations in finding the most optimized expression ratio in in vivo systems. In our study, we focused on fine-tuning the expression level of a six-enzyme reaction for the artificial biosynthesis of curcumin by screening a library of 5'-untranslational region (UTR) sequence mutants made by a multiplex automatic genome engineering (MAGE) tool. From the screening results, a variant (6M08rv) showed about a 38.2-fold improvement in the production of curcumin compared to the parent strain, in which the calculated expression levels of 4-coumarate:CoA ligase (4CL) and phenyldiketide-CoA synthase (DCS), two of the six enzymes, were much lower than those of the parent strain.
Collapse
Affiliation(s)
- Sun-Young Kang
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungbuk 28116, Korea
| | - Kyung Taek Heo
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungbuk 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Young-Soo Hong
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungbuk 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34141, Korea
| |
Collapse
|
68
|
Application of chromosomal gene insertion into Escherichia coli for expression of recombinant proteins. J Biosci Bioeng 2018; 126:266-272. [DOI: 10.1016/j.jbiosc.2018.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/13/2018] [Accepted: 02/19/2018] [Indexed: 11/20/2022]
|
69
|
Zebec Z, Scrutton NS. Genome Editing for the Production of Natural Products inEscherichia coli. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Ziga Zebec
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; Manchester M1 7DN UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; Manchester M1 7DN UK
| |
Collapse
|
70
|
Mehrer CR, Incha MR, Politz MC, Pfleger BF. Anaerobic production of medium-chain fatty alcohols via a β-reduction pathway. Metab Eng 2018; 48:63-71. [PMID: 29807110 DOI: 10.1016/j.ymben.2018.05.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/11/2018] [Accepted: 05/23/2018] [Indexed: 11/17/2022]
Abstract
In this report, we identify the relevant factors to increase production of medium chain n-alcohols through an expanded view of the reverse β-oxidation pathway. We began by creating a base strain capable of producing medium chain n-alcohols from glucose using a redox-balanced and growth-coupled metabolic engineering strategy. By dividing the heterologous enzymes in the pathway into different modules, we were able to identify and evaluate homologs of each enzyme within the pathway and identify several capable of enhancing medium chain alcohol titers and/or selectivity. In general, the identity of the trans-2-enoyl-CoA reductase (TER) and the direct overexpression of the thiolase (FadA) and β-hydroxy-acyl-CoA reductase (FadB) improved alcohol titer and the identity of the FadBA complex influenced the dominant chain length. Next, we linked the anaerobically induced VHb promoter from Vitreoscilla hemoglobin to each gene to remove the need for chemical inducers and ensure robust expression. The highest performing strain with the autoinduced reverse β-oxidation pathway produced n-alcohols at titers of 1.8 g/L with an apparent molar yield of 0.2 on glucose consumed in rich medium (52% of theoretical yield).
Collapse
Affiliation(s)
- Christopher R Mehrer
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, United States
| | - Matthew R Incha
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, United States
| | - Mark C Politz
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, United States
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, United States.
| |
Collapse
|
71
|
Freed EF, Pines G, Eckert CA, Gill RT. Trackable Multiplex Recombineering (TRMR) and Next-Generation Genome Design Technologies: Modifying Gene Expression inE. coliby Inserting Synthetic DNA Cassettes and Molecular Barcodes. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Affiliation(s)
- Emily F. Freed
- Biosciences Center, National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401 USA
| | - Gur Pines
- University of Colorado; Chemical and Biological Engineering; 3415 Colorado Ave Boulder CO 80303 USA
- University of Colorado; Renewable and Sustainable Energy Institute; 4001 Discovery Dr Boulder CO 80303 USA
| | - Carrie A. Eckert
- Biosciences Center, National Renewable Energy Laboratory; 15013 Denver West Parkway Golden CO 80401 USA
- University of Colorado; Renewable and Sustainable Energy Institute; 4001 Discovery Dr Boulder CO 80303 USA
| | - Ryan T. Gill
- University of Colorado; Chemical and Biological Engineering; 3415 Colorado Ave Boulder CO 80303 USA
- University of Colorado; Renewable and Sustainable Energy Institute; 4001 Discovery Dr Boulder CO 80303 USA
| |
Collapse
|
72
|
Translocation through the Conjugative Type IV Secretion System Requires Unfolding of Its Protein Substrate. J Bacteriol 2018; 200:JB.00615-17. [PMID: 29311273 PMCID: PMC5826034 DOI: 10.1128/jb.00615-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
Bacterial conjugation, a mechanism of horizontal gene transfer, is the major means by which antibiotic resistance spreads among bacteria (1, 2). Conjugative plasmids are transferred from one bacterium to another through a type IV secretion system (T4SS) in the form of single-stranded DNA covalently attached to a protein called relaxase. The relaxase is fully functional both in a donor cell (prior to conjugation) and recipient cell (after conjugation). Here, we demonstrate that the protein substrate has to unfold for efficient translocation through the conjugative T4SS. Furthermore, we present various relaxase modifications that preserve the function of the relaxase but block substrate translocation. This study brings us a step closer to deciphering the complete mechanism of T4SS substrate translocation, which is vital for the development of new therapies against multidrug-resistant pathogenic bacteria. IMPORTANCE Conjugation is the principal means by which antibiotic resistance genes spread from one bacterium to another (1, 2). During conjugation, a covalent complex of single-stranded DNA and a protein termed relaxase is transported by a type IV secretion system. To date, it is not known whether the relaxase requires unfolding prior to transport. In this report, we use functional assays to monitor the transport of wild-type relaxase and variants containing unfolding-resistant domains and show that these domains reduce conjugation and protein transport dramatically. Mutations that lower the free energy of unfolding in these domains do not block translocation and can even promote it. We thus conclude that the unfolding of the protein substrate is required during transport.
Collapse
|
73
|
Reisch CR, Prather KL. Scarless Cas9 Assisted Recombineering (no‐SCAR) in
Escherichia coli
, an Easy‐to‐Use System for Genome Editing. ACTA ACUST UNITED AC 2018; 117:31.8.1-31.8.20. [DOI: 10.1002/cpmb.29] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Christopher R. Reisch
- Department of Chemical Engineering, Massachusetts Institute of Technology Cambridge Massachusetts
- Department of Microbiology and Cell Science, University of Florida Gainesville Florida
| | - Kristala L.J. Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology Cambridge Massachusetts
| |
Collapse
|
74
|
Alonso‐Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS. Toward industrial production of isoprenoids in
Escherichia coli
: Lessons learned from CRISPR‐Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnol Bioeng 2018; 115:1000-1013. [DOI: 10.1002/bit.26530] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/18/2017] [Accepted: 12/22/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Jorge Alonso‐Gutierrez
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Daisuke Koma
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- Osaka Municipal Technical Research InstituteOsakaJapan
| | - Qijun Hu
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Yuchen Yang
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Leanne J. G. Chan
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Christopher J. Petzold
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Paul D. Adams
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Jay D. Keasling
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkHorsholmDenmark
- Department of Chemical and Biomolecular EngineeringUniversity of CaliforniaBerkeleyCalifornia
- Department of BioengineeringUniversity of CaliforniaBerkeleyCalifornia
| | - Taek S. Lee
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| |
Collapse
|
75
|
Abstract
Lambda Red recombineering is an easy and efficient method for generating genetic modifications in Escherichia coli. For gene deletions, lambda Red recombineering is combined with the use of selectable markers, which are removed through the action of, e.g., flippase (Flp) recombinase. This PCR-based engineering method has also been applied to a number of other bacteria. In this chapter, we describe a recently developed one plasmid-based method as well as the use of a strain with genomically integrated recombineering genes, which significantly speeds up the engineering of strains with multiple genomic alterations.
Collapse
Affiliation(s)
- Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| |
Collapse
|
76
|
Moreb EA, Hoover B, Yaseen A, Valyasevi N, Roecker Z, Menacho-Melgar R, Lynch MD. Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity. ACS Synth Biol 2017; 6:2209-2218. [PMID: 28915012 DOI: 10.1021/acssynbio.7b00174] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes, and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well as mutation rates through induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants. We report an approach to inhibiting the SOS response and RecA activity through the expression of a mutant dominant negative form of RecA, which incorporates into wild type RecA filaments and inhibits activity. Using a plasmid-based system in which Cas9 and recA mutants are coexpressed, we can achieve increased efficiency and consistency of CRISPR-Cas9-mediated selection and recombineering in E. coli, while reducing the induction of the SOS response. To date, this approach has been shown to be independent of recA genotype and host strain lineage. Using this system, we demonstrate increased CRISPR-Cas selection efficacy with over 10 000 guides covering the E. coli chromosome. The use of dominant negative RecA or homologues may be of broad use in bacterial CRISPR-Cas-based genome editing where the SOS pathways are present.
Collapse
Affiliation(s)
- Eirik Adim Moreb
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Benjamin Hoover
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Adam Yaseen
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Nisakorn Valyasevi
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Zoe Roecker
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Romel Menacho-Melgar
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Michael D. Lynch
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
77
|
Lin D, Izadpanah R, Braun SE, Alt E. A novel model to characterize structure and function of BRCA1. Cell Biol Int 2017; 42:34-44. [PMID: 28833843 DOI: 10.1002/cbin.10846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 08/14/2017] [Indexed: 01/19/2023]
Abstract
BRCA1 plays a central role in DNA repair. Although N-terminal RING and C-terminal BRCT domains are studied well, the functions of the central region of BRCA1 are poorly characterized. Here, we report a structural and functional analysis of BRCA1 alleles and functional human BRCA1 in chicken B-lymphocyte cell line DT40. The combination of "homologous recombineering" and "RT-cassette" enables modifications of chicken BRCA1 gene in Escherichia coli. Mutant BRCA1 knock-in DT40 cell lines were generated using BRCA1 mutation constructs by homologous recombination with a targeting efficiency of up to 100%. Our study demonstrated that deletion of motifs 2-9 BRCA1Δ/Δ181-1415 (Caenorhabditis elegans BRCA1 mimic) or deletion of motif 1 BRCA1Δ/Δ126-136 decreased cell viability following cisplatin treatment. Furthermore, deletion of motifs 5 and 6 BRCA1Δ/Δ525-881 within DNA-binding region, even the conserved 7-amino acid deletion BRCA1Δ/Δ872-878 within motif 6, caused a decreased cell viability upon cisplatin treatment. Surprisingly, human BRCA1 is functional in DT40 cells as indicated by DNA damage-induced Rad 51 foci formation in human BRCA1 knock-in DT40 cells. These results demonstrate that those conserved motifs within the central region are essential for DNA repair functions of BRCA1. These findings provide a valuable tool for the development of new therapeutic modalities of breast cancer linked to BRCA1.
Collapse
Affiliation(s)
- Dong Lin
- Department of Radiation Oncology, The University of Chicago, 5801 South Ellis Avenue, Chicago, IL, 60637, USA
| | - Reza Izadpanah
- Department of Medicine, Tulane University, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Stephen E Braun
- Division of Regenerative Medicine, Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA, 70433, USA
| | - Eckhard Alt
- Isar Klinikum, Sonnenstr 24-26, Munich, 80331, Germany
| |
Collapse
|
78
|
Higgins SA, Ouonkap SVY, Savage DF. Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering. ACS Synth Biol 2017; 6:1825-1833. [PMID: 28707884 DOI: 10.1021/acssynbio.7b00112] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Comprehensive and programmable protein mutagenesis is critical for understanding structure-function relationships and improving protein function. There is thus a need for robust and unbiased molecular biological approaches for the construction of the requisite comprehensive protein libraries. Here we demonstrate that plasmid recombineering is a simple and robust in vivo method for the generation of protein mutants for both comprehensive library generation as well as programmable targeting of sequence space. Using the fluorescent protein iLOV as a model target, we build a complete mutagenesis library and find it to be specific and comprehensive, detecting 99.8% of our intended mutations. We then develop a thermostability screen and utilize our comprehensive mutation data to rapidly construct a targeted and multiplexed library that identifies significantly improved variants, thus demonstrating rapid protein engineering in a simple protocol.
Collapse
Affiliation(s)
- Sean A. Higgins
- Department
of Molecular and Cell Biology, and ‡Department of Chemistry, UC Berkeley, Berkeley, California 94720, United States
| | - Sorel V. Y. Ouonkap
- Department
of Molecular and Cell Biology, and ‡Department of Chemistry, UC Berkeley, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, and ‡Department of Chemistry, UC Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
79
|
Chien T, Doshi A, Danino T. Advances in bacterial cancer therapies using synthetic biology. CURRENT OPINION IN SYSTEMS BIOLOGY 2017; 5:1-8. [PMID: 29881788 PMCID: PMC5986102 DOI: 10.1016/j.coisb.2017.05.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Synthetic biology aims to apply engineering principles to biology by modulating the behavior of living organisms. An emerging application of this field is the engineering of bacteria as a cancer therapy by the programming of therapeutic, safety, and specificity features through genetic modification. Here, we review progress in this engineering including the targeting of bacteria to tumors, specific sensing and response to tumor microenvironments, remote induction methods, and controllable release of therapeutics. We discuss the most prominent bacteria strains used and their specific properties and the types of therapeutics tested thus far. Finally, we note current challenges, such as genetic stability, that researchers must address for successful clinical implementation of this novel therapy in humans.
Collapse
Affiliation(s)
- Tiffany Chien
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Anjali Doshi
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
- Data Science Institute, Columbia University, New York, NY 10027, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA
| |
Collapse
|
80
|
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.
Collapse
|
81
|
Valero-Rello A, López-Sanz M, Quevedo-Olmos A, Sorokin A, Ayora S. Molecular Mechanisms That Contribute to Horizontal Transfer of Plasmids by the Bacteriophage SPP1. Front Microbiol 2017; 8:1816. [PMID: 29018417 PMCID: PMC5615212 DOI: 10.3389/fmicb.2017.01816] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/06/2017] [Indexed: 01/02/2023] Open
Abstract
Natural transformation and viral-mediated transduction are the main avenues of horizontal gene transfer in Firmicutes. Bacillus subtilis SPP1 is a generalized transducing bacteriophage. Using this lytic phage as a model, we have analyzed how viral replication and recombination systems contribute to the transfer of plasmid-borne antibiotic resistances. Phage SPP1 DNA replication relies on essential phage-encoded replisome organizer (G38P), helicase loader (G39P), hexameric replicative helicase (G40P), recombinase (G35P) and in less extent on the partially dispensable 5′→3′ exonuclease (G34.1P), the single-stranded DNA binding protein (G36P) and the Holliday junction resolvase (G44P). Correspondingly, the accumulation of linear concatemeric plasmid DNA, and the formation of transducing particles were blocked in the absence of G35P, G38P, G39P, and G40P, greatly reduced in the G34.1P, G36P mutants, and slightly reduced in G44P mutants. In contrast, establishment of injected linear plasmid DNA in the recipient host was independent of viral-encoded functions. DNA homology between SPP1 and the plasmid, rather than a viral packaging signal, enhanced the accumulation of packagable plasmid DNA. The transfer efficiency was also dependent on plasmid copy number, and rolling-circle plasmids were encapsidated at higher frequencies than theta-type replicating plasmids.
Collapse
Affiliation(s)
- Ana Valero-Rello
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain.,Micalis Institute, INRA, AgroParisTech, Universite Paris-SaclayJouy-en-Josas, France
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Alvaro Quevedo-Olmos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Alexei Sorokin
- Micalis Institute, INRA, AgroParisTech, Universite Paris-SaclayJouy-en-Josas, France
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| |
Collapse
|
82
|
Näsvall J. Direct and Inverted Repeat stimulated excision (DIRex): Simple, single-step, and scar-free mutagenesis of bacterial genes. PLoS One 2017; 12:e0184126. [PMID: 28854250 PMCID: PMC5576700 DOI: 10.1371/journal.pone.0184126] [Citation(s) in RCA: 13] [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: 06/14/2017] [Accepted: 08/18/2017] [Indexed: 11/29/2022] Open
Abstract
The need for generating precisely designed mutations is common in genetics, biochemistry, and molecular biology. Here, I describe a new λ Red recombineering method (Direct and Inverted Repeat stimulated excision; DIRex) for fast and easy generation of single point mutations, small insertions or replacements as well as deletions of any size, in bacterial genes. The method does not leave any resistance marker or scar sequence and requires only one transformation to generate a semi-stable intermediate insertion mutant. Spontaneous excision of the intermediate efficiently and accurately generates the final mutant. In addition, the intermediate is transferable between strains by generalized transductions, enabling transfer of the mutation into multiple strains without repeating the recombineering step. Existing methods that can be used to accomplish similar results are either (i) more complicated to design, (ii) more limited in what mutation types can be made, or (iii) require expression of extrinsic factors in addition to λ Red. I demonstrate the utility of the method by generating several deletions, small insertions/replacements, and single nucleotide exchanges in Escherichia coli and Salmonella enterica. Furthermore, the design parameters that influence the excision frequency and the success rate of generating desired point mutations have been examined to determine design guidelines for optimal efficiency.
Collapse
Affiliation(s)
- Joakim Näsvall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail:
| |
Collapse
|
83
|
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.
Collapse
|
84
|
Näsvall J, Knöppel A, Andersson DI. Duplication-Insertion Recombineering: a fast and scar-free method for efficient transfer of multiple mutations in bacteria. Nucleic Acids Res 2017; 45:e33. [PMID: 27899661 PMCID: PMC5389514 DOI: 10.1093/nar/gkw1078] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/25/2016] [Indexed: 11/18/2022] Open
Abstract
We have developed a new λ Red recombineering methodology for generating transient selection markers that can be used to transfer mutations between bacterial strains of both Escherichia coli and Salmonella enterica. The method is fast, simple and allows for the construction of strains with several mutations without any unwanted sequence changes (scar-free). The method uses λ Red recombineering to generate a marker-held tandem duplication, termed Duplication-Insertion (Dup-In). The Dup-Ins can easily be transferred between strains by generalized transduction and are subsequently rapidly lost by homologous recombination between the two copies of the duplicated sequence, leaving no scar sequence or antibiotic resistance cassette behind. We demonstrate the utility of the method by generating several Dup-Ins in E. coli and S. enterica to transfer genetically linked mutations in both essential and non-essential genes. We have successfully used this methodology to re-construct mutants found after various types of selections, and to introduce foreign genes into the two species. Furthermore, recombineering with two overlapping fragments was as efficient as recombineering with the corresponding single large fragment, allowing more complicated constructions without the need for overlap extension PCR.
Collapse
Affiliation(s)
- Joakim Näsvall
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Anna Knöppel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
85
|
Abstract
Genome integration is a powerful tool in both basic and applied biological research. However, traditional genome integration, which is typically mediated by homologous recombination, has been constrained by low efficiencies and limited host range. In recent years, the emergence of homing endonucleases and programmable nucleases has greatly enhanced integration efficiencies and allowed alternative integration mechanisms such as nonhomologous end joining and microhomology-mediated end joining, enabling integration in hosts deficient in homologous recombination. In this review, we will highlight recent advances and breakthroughs in genome integration methods made possible by programmable nucleases, and their new applications in synthetic biology and metabolic engineering.
Collapse
Affiliation(s)
- Zihe Liu
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | - Youyun Liang
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | - Ee Lui Ang
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
| | - Huimin Zhao
- Metabolic
Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
86
|
Genome reprogramming for synthetic biology. Front Chem Sci Eng 2017. [DOI: 10.1007/s11705-017-1618-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
87
|
Oesterle S, Wuethrich I, Panke S. Toward Genome-Based Metabolic Engineering in Bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2017; 101:49-82. [PMID: 29050667 DOI: 10.1016/bs.aambs.2017.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Prokaryotes modified stably on the genome are of great importance for production of fine and commodity chemicals. Traditional methods for genome engineering have long suffered from imprecision and low efficiencies, making construction of suitable high-producer strains laborious. Here, we review the recent advances in discovery and refinement of molecular precision engineering tools for genome-based metabolic engineering in bacteria for chemical production, with focus on the λ-Red recombineering and the clustered regularly interspaced short palindromic repeats/Cas9 nuclease systems. In conjunction, they enable the integration of in vitro-synthesized DNA segments into specified locations on the chromosome and allow for enrichment of rare mutants by elimination of unmodified wild-type cells. Combination with concurrently developing improvements in important accessory technologies such as DNA synthesis, high-throughput screening methods, regulatory element design, and metabolic pathway optimization tools has resulted in novel efficient microbial producer strains and given access to new metabolic products. These new tools have made and will likely continue to make a big impact on the bioengineering strategies that transform the chemical industry.
Collapse
|
88
|
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.
Collapse
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
| |
Collapse
|
89
|
Ng IS, Hung YH, Kao PH, Zhou Y, Zhang X. CRISPR/Cas9 nuclease cleavage enables marker-free genome editing in Escherichia coli : A sequential study. J Taiwan Inst Chem Eng 2016. [DOI: 10.1016/j.jtice.2016.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
90
|
Subramaniam S, Erler A, Fu J, Kranz A, Tang J, Gopalswamy M, Ramakrishnan S, Keller A, Grundmeier G, Müller D, Sattler M, Stewart AF. DNA annealing by Redβ is insufficient for homologous recombination and the additional requirements involve intra- and inter-molecular interactions. Sci Rep 2016; 6:34525. [PMID: 27708411 PMCID: PMC5052646 DOI: 10.1038/srep34525] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/15/2016] [Indexed: 01/09/2023] Open
Abstract
Single strand annealing proteins (SSAPs) like Redβ initiate homologous recombination by annealing complementary DNA strands. We show that C-terminally truncated Redβ, whilst still able to promote annealing and nucleoprotein filament formation, is unable to mediate homologous recombination. Mutations of the C-terminal domain were evaluated using both single- and double stranded (ss and ds) substrates in recombination assays. Mutations of critical amino acids affected either dsDNA recombination or both ssDNA and dsDNA recombination indicating two separable functions, one of which is critical for dsDNA recombination and the second for recombination per se. As evaluated by co-immunoprecipitation experiments, the dsDNA recombination function relates to the Redα-Redβ protein-protein interaction, which requires not only contacts in the C-terminal domain but also a region near the N-terminus. Because the nucleoprotein filament formed with C-terminally truncated Redβ has altered properties, the second C-terminal function could be due to an interaction required for functional filaments. Alternatively the second C-terminal function could indicate a requirement for a Redβ-host factor interaction. These data further advance the model for Red recombination and the proposition that Redβ and RAD52 SSAPs share ancestral and mechanistic roots.
Collapse
Affiliation(s)
| | - Axel Erler
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Andrea Kranz
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Jing Tang
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Mohanraj Gopalswamy
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstr.4, 85747 Garching, Germany
| | - Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Daniel Müller
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstraße 26, 4058 Basel, Switzerland
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstr.4, 85747 Garching, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| |
Collapse
|
91
|
Csörgő B, Nyerges Á, Pósfai G, Fehér T. System-level genome editing in microbes. Curr Opin Microbiol 2016; 33:113-122. [PMID: 27472027 DOI: 10.1016/j.mib.2016.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/09/2016] [Accepted: 07/06/2016] [Indexed: 11/16/2022]
Abstract
The release of the first complete microbial genome sequences at the end of the past century opened the way for functional genomics and systems-biology to uncover the genetic basis of various phenotypes. The surge of available sequence data facilitated the development of novel genome editing techniques for system-level analytical studies. Recombineering allowed unprecedented throughput and efficiency in microbial genome editing and the recent discovery and widespread use of RNA-guided endonucleases offered several further perspectives: (i) previously recalcitrant species became editable, (ii) the efficiency of recombineering could be elevated, and as a result (iii) diverse genomic libraries could be generated more effectively. Supporting recombineering by RNA-guided endonucleases has led to success stories in metabolic engineering, but their use for system-level analysis is mostly unexplored. For the full exploitation of opportunities that are offered by the genome editing proficiency, future development of large scale analytical procedures is also vitally needed.
Collapse
Affiliation(s)
- Bálint Csörgő
- Systems and Synthetic Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ákos Nyerges
- Systems and Synthetic Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - György Pósfai
- Systems and Synthetic Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
| | - Tamás Fehér
- Systems and Synthetic Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| |
Collapse
|
92
|
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.
Collapse
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
| |
Collapse
|
93
|
Abstract
The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics.
Collapse
Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
| |
Collapse
|
94
|
Egan M, Ramirez J, Xander C, Upreti C, Bhatt S. Lambda Red-mediated Recombineering in the Attaching and Effacing Pathogen Escherichia albertii. Biol Proced Online 2016; 18:3. [PMID: 26843851 PMCID: PMC4739404 DOI: 10.1186/s12575-015-0032-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/29/2015] [Indexed: 02/06/2023] Open
Abstract
Background The ability to introduce site-specific mutations in bacterial pathogens is essential towards understanding their molecular mechanisms of pathogenicity. This has been greatly facilitated by the genetic engineering technique of recombineering. In recombineering, linear double- or single-stranded DNA molecules with two terminal homology arms are electroporated into hyperrecombinogenic bacteria that express a phage-encoded recombinase. The recombinase catalyzes the replacement of the endogenous allele with the exogenous allele to generate selectable or screenable recombinants. In particular, lambda red recombinase has been instrumental in engineering mutations to characterize the virulence arsenal of the attaching and effacing (A/E) pathogens enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC), and Citrobacter rodentium. Escherichia albertii is another member of this taxon; however, the virulence of E. albertii remains cryptic despite accumulating evidence that E. albertii is an emerging pathogen. Multiple retrospective studies have reported that a substantial number of EPEC and EHEC isolates (~15 %) that were previously incriminated in human outbreaks actually belong to the E. albertii lineage. Thus, there is increased urgency to reliably identify and rapidly engineer mutations in E. albertii to systematically characterize its virulence determinants. To the best of our knowledge not a single chromosomal gene has been altered by targeted mutagenesis in E. albertii since it was first isolated almost 25 years ago. This is disconcerting because an E. albertii outbreak could cause significant morbidity and mortality owing to our inadequate understanding of its virulence program. Results In this report we describe a modified lambda red recombineering protocol to mutagenize E. albertii. As proof of principle, we successfully deleted three distinct virulence-associated genetic loci – ler, grlRA, and hfq – and replaced each wild type allele by a mutant allele with an encodable drug resistance cassette bracketed by FRT sites. Subsequently, the FRT-site flanked drug resistance marker was evicted by FLP-dependent site-specific recombination to generate excisants containing a solitary FRT site. Conclusions Our protocol will enable researchers to construct marked and unmarked genome-wide mutations in E. albertii, which, in turn, will illuminate its molecular mechanisms of pathogenicity and aid in developing appropriate preventative and therapeutic approaches to combat E. albertii outbreaks.
Collapse
Affiliation(s)
- Marisa Egan
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA ; Department of Mathematics, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA
| | - Jasmine Ramirez
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA ; Present address: Microbiology Department, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, 221 Johnson Pavilion, Philadelphia, PA 19104 USA
| | - Christian Xander
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA ; Present address: Bluemle Life Sciences Building, Thomas Jefferson University, 233 South Tenth Street, Philadelphia, PA 19107 USA
| | - Chirag Upreti
- Howard Hughes Medical Institute, Columbia University Medical Center, Columbia, USA ; Columbia University Medical Center, 1051 Riverside Drive, New York, NY 10032 USA
| | - Shantanu Bhatt
- Department of Biology, Saint Joseph's University, 5600 City Avenue, Philadelphia, PA 19131 USA
| |
Collapse
|
95
|
Ronda C, Pedersen LE, Sommer MOA, Nielsen AT. CRMAGE: CRISPR Optimized MAGE Recombineering. Sci Rep 2016; 6:19452. [PMID: 26797514 PMCID: PMC4726160 DOI: 10.1038/srep19452] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/14/2015] [Indexed: 12/23/2022] Open
Abstract
A bottleneck in metabolic engineering and systems biology approaches is the lack of efficient genome engineering technologies. Here, we combine CRISPR/Cas9 and λ Red recombineering based MAGE technology (CRMAGE) to create a highly efficient and fast method for genome engineering of Escherichia coli. Using CRMAGE, the recombineering efficiency was between 96.5% and 99.7% for gene recoding of three genomic targets, compared to between 0.68% and 5.4% using traditional recombineering. For modulation of protein synthesis (small insertion/RBS substitution) the efficiency was increased from 6% to 70%. CRMAGE can be multiplexed and enables introduction of at least two mutations in a single round of recombineering with similar efficiencies. PAM-independent loci were targeted using degenerate codons, thereby making it possible to modify any site in the genome. CRMAGE is based on two plasmids that are assembled by a USER-cloning approach enabling quick and cost efficient gRNA replacement. CRMAGE furthermore utilizes CRISPR/Cas9 for efficient plasmid curing, thereby enabling multiple engineering rounds per day. To facilitate the design process, a web-based tool was developed to predict both the λ Red oligos and the gRNAs. The CRMAGE platform enables highly efficient and fast genome editing and may open up promising prospective for automation of genome-scale engineering.
Collapse
Affiliation(s)
- Carlotta Ronda
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970 Hørsholm, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970 Hørsholm, Denmark
| | - Morten O. A. Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970 Hørsholm, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970 Hørsholm, Denmark
| |
Collapse
|
96
|
Weninger A, Killinger M, Vogl T. Key Methods for Synthetic Biology: Genome Engineering and DNA Assembly. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
|
97
|
Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress. Sci Rep 2015; 5:17874. [PMID: 26643270 PMCID: PMC4672327 DOI: 10.1038/srep17874] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/06/2015] [Indexed: 11/08/2022] Open
Abstract
Generation of multiple genomic alterations is currently a time consuming process. Here, a method was established that enables highly efficient and simultaneous deletion of multiple genes in Escherichia coli. A temperature sensitive plasmid containing arabinose inducible lambda Red recombineering genes and a rhamnose inducible flippase recombinase was constructed to facilitate fast marker-free deletions. To further speed up the procedure, we integrated the arabinose inducible lambda Red recombineering genes and the rhamnose inducible FLP into the genome of E. coli K-12 MG1655. This system enables growth at 37 °C, thereby facilitating removal of integrated antibiotic cassettes and deletion of additional genes in the same day. Phosphorothioated primers were demonstrated to enable simultaneous deletions during one round of electroporation. Utilizing these methods, we constructed strains in which four to seven genes were deleted in E. coli W and E. coli K-12. The growth rate of an E. coli K-12 quintuple deletion strain was significantly improved in the presence of high concentrations of acetate and NaCl. In conclusion, we have generated a method that enables efficient and simultaneous deletion of multiple genes in several E. coli variants. The method enables deletion of up to seven genes in as little as seven days.
Collapse
|
98
|
Pines G, Freed EF, Winkler JD, Gill RT. Bacterial Recombineering: Genome Engineering via Phage-Based Homologous Recombination. ACS Synth Biol 2015; 4:1176-85. [PMID: 25856528 DOI: 10.1021/acssynbio.5b00009] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ability to specifically modify bacterial genomes in a precise and efficient manner is highly desired in various fields, ranging from molecular genetics to metabolic engineering and synthetic biology. Much has changed from the initial realization that phage-derived genes may be employed for such tasks to today, where recombineering enables complex genetic edits within a genome or a population. Here, we review the major developments leading to recombineering becoming the method of choice for in situ bacterial genome editing while highlighting the various applications of recombineering in pushing the boundaries of synthetic biology. We also present the current understanding of the mechanism of recombineering. Finally, we discuss in detail issues surrounding recombineering efficiency and future directions for recombineering-based genome editing.
Collapse
Affiliation(s)
- Gur Pines
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Emily F. Freed
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - James D. Winkler
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Ryan T. Gill
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| |
Collapse
|
99
|
The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli. Sci Rep 2015; 5:15096. [PMID: 26463009 PMCID: PMC4604488 DOI: 10.1038/srep15096] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/15/2015] [Indexed: 02/02/2023] Open
Abstract
Genome engineering methods in E. coli allow for easy to perform manipulations of the chromosome in vivo with the assistance of the λ-Red recombinase system. These methods generally rely on the insertion of an antibiotic resistance cassette followed by removal of the same cassette, resulting in a two-step procedure for genomic manipulations. Here we describe a method and plasmid system that can edit the genome of E. coli without chromosomal markers. This system, known as Scarless Cas9 Assisted Recombineering (no-SCAR), uses λ-Red to facilitate genomic integration of donor DNA and double stranded DNA cleavage by Cas9 to counterselect against wild-type cells. We show that point mutations, gene deletions, and short sequence insertions were efficiently performed in several genomic loci in a single-step with regards to the chromosome and did not leave behind scar sites. The single-guide RNA encoding plasmid can be easily cured due to its temperature sensitive origin of replication, allowing for iterative chromosomal manipulations of the same strain, as is often required in metabolic engineering. In addition, we demonstrate the ability to efficiently cure the second plasmid in the system by targeting with Cas9, leaving the cells plasmid-free.
Collapse
|
100
|
Liu R, Bassalo MC, Zeitoun RI, Gill RT. Genome scale engineering techniques for metabolic engineering. Metab Eng 2015; 32:143-154. [PMID: 26453944 DOI: 10.1016/j.ymben.2015.09.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/15/2015] [Accepted: 09/02/2015] [Indexed: 12/18/2022]
Abstract
Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in genome-scale engineering technologies. Metabolic engineering has been generally defined by the use of iterative cycles of rational genome modifications, strain analysis and characterization, and a synthesis step that fuels additional hypothesis generation. This cycle mirrors the Design-Build-Test-Learn cycle followed throughout various engineering fields that has recently become a defining aspect of synthetic biology. This review will attempt to summarize recent genome-scale design, build, test, and learn technologies and relate their use to a range of metabolic engineering applications.
Collapse
Affiliation(s)
- Rongming Liu
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States.
| | - Marcelo C Bassalo
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, United States.
| | - Ramsey I Zeitoun
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States.
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States.
| |
Collapse
|