101
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Matsubara K, Malay AD, Curtis FA, Sharples GJ, Heddle JG. Structural and functional characterization of the Redβ recombinase from bacteriophage λ. PLoS One 2013; 8:e78869. [PMID: 24244379 PMCID: PMC3823998 DOI: 10.1371/journal.pone.0078869] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/23/2013] [Indexed: 11/18/2022] Open
Abstract
The Red system of bacteriophage λ is responsible for the genetic rearrangements that contribute to its rapid evolution and has been successfully harnessed as a research tool for genome manipulation. The key recombination component is Redβ, a ring-shaped protein that facilitates annealing of complementary DNA strands. Redβ shares functional similarities with the human Rad52 single-stranded DNA (ssDNA) annealing protein although their evolutionary relatedness is not well established. Alignment of Rad52 and Redβ sequences shows an overall low level of homology, with 15% identity in the N-terminal core domains as well as important similarities with the Rad52 homolog Sak from phage ul36. Key conserved residues were chosen for mutagenesis and their impact on oligomer formation, ssDNA binding and annealing was probed. Two conserved regions were identified as sites important for binding ssDNA; a surface basic cluster and an intersubunit hydrophobic patch, consistent with findings for Rad52. Surprisingly, mutation of Redβ residues in the basic cluster that in Rad52 are involved in ssDNA binding disrupted both oligomer formation and ssDNA binding. Mutations in the equivalent of the intersubunit hydrophobic patch in Rad52 did not affect Redβ oligomerization but did impair DNA binding and annealing. We also identified a single amino acid substitution which had little effect on oligomerization and DNA binding but which inhibited DNA annealing, indicating that these two functions of Redβ can be separated. Taken together, the results provide fresh insights into the structural basis for Redβ function and the important role of quaternary structure.
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Affiliation(s)
| | - Ali D. Malay
- Heddle Initiative Research Unit, RIKEN, Wako, Saitama, Japan
| | - Fiona A. Curtis
- School of Biological and Biomedical Sciences, Department of Chemistry, Durham University, Durham, United Kingdom
| | - Gary J. Sharples
- School of Biological and Biomedical Sciences, Department of Chemistry, Durham University, Durham, United Kingdom
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102
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Li XT, Thomason LC, Sawitzke JA, Costantino N, Court DL. Positive and negative selection using the tetA-sacB cassette: recombineering and P1 transduction in Escherichia coli. Nucleic Acids Res 2013; 41:e204. [PMID: 24203710 PMCID: PMC3905872 DOI: 10.1093/nar/gkt1075] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The two-step process of selection and counter-selection is a standard way to enable genetic modification and engineering of bacterial genomes using homologous recombination methods. The tetA and sacB genes are contained in a DNA cassette and confer a novel dual counter-selection system. Expression of tetA confers bacterial resistance to tetracycline (TcR) and also causes sensitivity to the lipophillic chelator fusaric acid; sacB causes sensitivity to sucrose. These two genes are introduced as a joint DNA cassette into Escherichia coli by selection for TcR. A medium containing both fusaric acid and sucrose has been developed, in which, coexpression of tetA-sacB is orders of magnitude more sensitive as a counter-selection agent than either gene alone. In conjunction with the homologous recombination methods of recombineering and P1 transduction, this powerful system has been used to select changes in the bacterial genome that cannot be directly detected by other counter-selection systems.
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Affiliation(s)
- Xin-Tian Li
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA and Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA
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103
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Poteete AR. Involvement of Escherichia coli DNA Replication Proteins in Phage Lambda Red-Mediated Homologous Recombination. PLoS One 2013; 8:e67440. [PMID: 23840702 PMCID: PMC3686724 DOI: 10.1371/journal.pone.0067440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/20/2013] [Indexed: 11/19/2022] Open
Abstract
The Red recombination system of bacteriophage lambda is widely used for genetic engineering because of its ability to promote recombination between bacterial chromosomes or plasmids and linear DNA species introduced by electroporation. The process is known to be intimately tied to replication, but the cellular functions which participate with Red in this process are largely unknown. Here two such functions are identified: the GrpE-DnaK-DnaJ chaperone system, and DNA polymerase I. Mutations in either function are found to decrease the efficiency of Red recombination. grpE and dnaJ mutations which greatly decrease Red recombination with electroporated DNA species have only small effects on Red-mediated transduction. This recombination event specificity suggests that the involvement of GrpE-DnaJ-DnaK is not simply an effect on Red structure or stability.
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Affiliation(s)
- Anthony R. Poteete
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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104
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Li XT, Thomason LC, Sawitzke JA, Costantino N, Court DL. Bacterial DNA polymerases participate in oligonucleotide recombination. Mol Microbiol 2013; 88:906-20. [PMID: 23634873 PMCID: PMC7523544 DOI: 10.1111/mmi.12231] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2013] [Indexed: 02/01/2023]
Abstract
Synthetic single-strand oligonucleotides (oligos) with homology to genomic DNA have proved to be highly effective for constructing designed mutations in targeted genomes, a process referred to as recombineering. The cellular functions important for this type of homologous recombination have yet to be determined. Towards this end, we have identified Escherichia coli functions that process the recombining oligo and affect bacteriophage λ Red-mediated oligo recombination. To determine the nature of oligo processing during recombination, each oligo contained multiple nucleotide changes: a single base change allowing recombinant selection, and silent changes serving as genetic markers to determine the extent of oligo processing during the recombination. Such oligos were often not incorporated into the host chromosome intact; many were partially degraded in the process of recombination. The position and number of these silent nucleotide changes within the oligo strongly affect both oligo processing and recombination frequency. Exonucleases, especially those associated with DNA Polymerases I and III, affect inheritance of the silent nucleotide changes in the oligos. We demonstrate for the first time that the major DNA polymerases (Pol I and Pol III) and DNA ligase are directly involved with oligo recombination.
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Affiliation(s)
- Xin-tian Li
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lynn C. Thomason
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Basic Science Program, SAIC-Frederick, Inc., Frederick, MD 21702, USA
| | - James A. Sawitzke
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nina Costantino
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Donald L. Court
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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105
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Binder S, Siedler S, Marienhagen J, Bott M, Eggeling L. Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation. Nucleic Acids Res 2013; 41:6360-9. [PMID: 23630315 PMCID: PMC3695502 DOI: 10.1093/nar/gkt312] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recombineering in bacteria is a powerful technique for genome reconstruction, but until now, it was not generally applicable for development of small-molecule producers because of the inconspicuous phenotype of most compounds of biotechnological relevance. Here, we establish recombineering for Corynebacterium glutamicum using RecT of prophage Rac and combine this with our recently developed nanosensor technology, which enables the detection and isolation of productive mutants at the single-cell level via fluorescence-activated cell sorting (FACS). We call this new technology RecFACS, which we use for genomic site-directed saturation mutagenesis without relying on pre-constructed libraries to directly isolate L-lysine-producing cells. A mixture of 19 different oligonucleotides was used targeting codon 81 in murE of the wild-type, at a locus where one single mutation is known to cause L-lysine production. Using RecFACS, productive mutants were screened and isolated. Sequencing revealed 12 different amino acid exchanges in the targeted murE codon, which caused different L-lysine production titers. Apart from introducing a rapid genome construction technology for C. glutamicum, the present work demonstrates that RecFACS is suitable to simply create producers as well as genetic diversity in one single step, thus establishing a new general concept in synthetic biology.
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Affiliation(s)
- Stephan Binder
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
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106
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Ross W, Vrentas CE, Sanchez-Vazquez P, Gaal T, Gourse RL. The magic spot: a ppGpp binding site on E. coli RNA polymerase responsible for regulation of transcription initiation. Mol Cell 2013; 50:420-9. [PMID: 23623682 DOI: 10.1016/j.molcel.2013.03.021] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 02/17/2013] [Accepted: 03/19/2013] [Indexed: 10/26/2022]
Abstract
The global regulatory nucleotide ppGpp ("magic spot") regulates transcription from a large subset of Escherichia coli promoters, illustrating how small molecules can control gene expression promoter-specifically by interacting with RNA polymerase (RNAP) without binding to DNA. However, ppGpp's target site on RNAP, and therefore its mechanism of action, has remained unclear. We report here a binding site for ppGpp on E. coli RNAP, identified by crosslinking, protease mapping, and analysis of mutant RNAPs that fail to respond to ppGpp. A strain with a mutant ppGpp binding site displays properties characteristic of cells defective for ppGpp synthesis. The binding site is at an interface of two RNAP subunits, ω and β', and its position suggests an allosteric mechanism of action involving restriction of motion between two mobile RNAP modules. Identification of the binding site allows prediction of bacterial species in which ppGpp exerts its effects by targeting RNAP.
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Affiliation(s)
- Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
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107
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Jeong J, Cho N, Jung D, Bang D. Genome-scale genetic engineering in Escherichia coli. Biotechnol Adv 2013; 31:804-10. [PMID: 23624241 DOI: 10.1016/j.biotechadv.2013.04.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 04/13/2013] [Accepted: 04/15/2013] [Indexed: 12/23/2022]
Abstract
Genome engineering has been developed to create useful strains for biological studies and industrial uses. However, a continuous challenge remained in the field: technical limitations in high-throughput screening and precise manipulation of strains. Today, technical improvements have made genome engineering more rapid and efficient. This review introduces recent advances in genome engineering technologies applied to Escherichia coli as well as multiplex automated genome engineering (MAGE), a recent technique proposed as a powerful toolkit due to its straightforward process, rapid experimental procedures, and highly efficient properties.
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Affiliation(s)
- Jaehwan Jeong
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
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108
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Tyler JS, Beeri K, Reynolds JL, Alteri CJ, Skinner KG, Friedman JH, Eaton KA, Friedman DI. Prophage induction is enhanced and required for renal disease and lethality in an EHEC mouse model. PLoS Pathog 2013; 9:e1003236. [PMID: 23555250 PMCID: PMC3610611 DOI: 10.1371/journal.ppat.1003236] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 01/22/2013] [Indexed: 11/23/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC), particularly serotype O157:H7, causes hemorrhagic colitis, hemolytic uremic syndrome, and even death. In vitro studies showed that Shiga toxin 2 (Stx2), the primary virulence factor expressed by EDL933 (an O157:H7 strain), is encoded by the 933W prophage. And the bacterial subpopulation in which the 933W prophage is induced is the producer of Stx2. Using the germ-free mouse, we show the essential role 933W induction plays in the virulence of EDL933 infection. An EDL933 derivative with a single mutation in its 933W prophage, resulting specifically in that phage being uninducible, colonizes the intestines, but fails to cause any of the pathological changes seen with the parent strain. Hence, induction of the 933W prophage is the primary event leading to disease from EDL933 infection. We constructed a derivative of EDL933, SIVET, with a biosensor that specifically measures induction of the 933W prophage. Using this biosensor to measure 933W induction in germ-free mice, we found an increase three logs greater than was expected from in vitro results. Since the induced population produces and releases Stx2, this result indicates that an activity in the intestine increases Stx2 production.
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Affiliation(s)
- Jessica S. Tyler
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Karen Beeri
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jared L. Reynolds
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christopher J. Alteri
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Katherine G. Skinner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jonathan H. Friedman
- Department of Mathwork, Mathworks, Natick, Massachusetts, United States of America
| | - Kathryn A. Eaton
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David I. Friedman
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
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109
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Boyle NR, Reynolds TS, Evans R, Lynch M, Gill RT. Recombineering to homogeneity: extension of multiplex recombineering to large-scale genome editing. Biotechnol J 2013; 8:515-22. [PMID: 23436787 DOI: 10.1002/biot.201200237] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/17/2012] [Accepted: 01/22/2013] [Indexed: 11/08/2022]
Abstract
Recombineering has been an essential tool for genetic engineering in microbes for many years and has enabled faster, more efficient engineering than previous techniques. There have been numerous studies that focus on improving recombineering efficiency, which can be divided into three main areas: (i) optimizing the oligo used for recombineering to enhance replication fork annealing and limit proofreading; (ii) mechanisms to modify the replisome itself, enabling an increased rate of annealing; and (iii) multiplexing recombineering targets and automation. These efforts have increased the efficiency of recombineering several hundred-fold. One area that has received far less attention is the problem of multiple chromosomes, which effectively decrease efficiency on a chromosomal basis, resulting in more sectored colonies, which require longer outgrowth to obtain clonal populations. Herein, we describe the problem of multiple chromosomes, discuss calculations predicting how many generations are needed to obtain a pure colony, and how changes in experimental procedure or genetic background can minimize the effect of multiple chromosomes.
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Affiliation(s)
- Nanette R Boyle
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
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110
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Cenens W, Mebrhatu MT, Makumi A, Ceyssens PJ, Lavigne R, Van Houdt R, Taddei F, Aertsen A. Expression of a novel P22 ORFan gene reveals the phage carrier state in Salmonella typhimurium. PLoS Genet 2013; 9:e1003269. [PMID: 23483857 PMCID: PMC3573128 DOI: 10.1371/journal.pgen.1003269] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 12/08/2012] [Indexed: 01/13/2023] Open
Abstract
We discovered a novel interaction between phage P22 and its host Salmonella Typhimurium LT2 that is characterized by a phage mediated and targeted derepression of the host dgo operon. Upon further investigation, this interaction was found to be instigated by an ORFan gene (designated pid for phage P22 encoded instigator of dgo expression) located on a previously unannotated moron locus in the late region of the P22 genome, and encoding an 86 amino acid protein of 9.3 kDa. Surprisingly, the Pid/dgo interaction was not observed during strict lytic or lysogenic proliferation of P22, and expression of pid was instead found to arise in cells that upon infection stably maintained an unintegrated phage chromosome that segregated asymmetrically upon subsequent cell divisions. Interestingly, among the emerging siblings, the feature of pid expression remained tightly linked to the cell inheriting this phage carrier state and became quenched in the other. As such, this study is the first to reveal molecular and genetic markers authenticating pseudolysogenic development, thereby exposing a novel mechanism, timing, and populational distribution in the realm of phage-host interactions.
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Affiliation(s)
- William Cenens
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mehari T. Mebrhatu
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Angella Makumi
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rob Van Houdt
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | | | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
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111
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Zhou YN, Lubkowska L, Hui M, Court C, Chen S, Court DL, Strathern J, Jin DJ, Kashlev M. Isolation and characterization of RNA polymerase rpoB mutations that alter transcription slippage during elongation in Escherichia coli. J Biol Chem 2013; 288:2700-10. [PMID: 23223236 PMCID: PMC3554936 DOI: 10.1074/jbc.m112.429464] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Indexed: 01/05/2023] Open
Abstract
Transcription fidelity is critical for maintaining the accurate flow of genetic information. The study of transcription fidelity has been limited because the intrinsic error rate of transcription is obscured by the higher error rate of translation, making identification of phenotypes associated with transcription infidelity challenging. Slippage of elongating RNA polymerase (RNAP) on homopolymeric A/T tracts in DNA represents a special type of transcription error leading to disruption of open reading frames in Escherichia coli mRNA. However, the regions in RNAP involved in elongation slippage and its molecular mechanism are unknown. We constructed an A/T tract that is out of frame relative to a downstream lacZ gene on the chromosome to examine transcriptional slippage during elongation. Further, we developed a genetic system that enabled us for the first time to isolate and characterize E. coli RNAP mutants with altered transcriptional slippage in vivo. We identified several amino acid residues in the β subunit of RNAP that affect slippage in vivo and in vitro. Interestingly, these highly clustered residues are located near the RNA strand of the RNA-DNA hybrid in the elongation complex. Our E. coli study complements an accompanying study of slippage by yeast RNAP II and provides the basis for future studies on the mechanism of transcription fidelity.
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Affiliation(s)
- Yan Ning Zhou
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Lucyna Lubkowska
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Monica Hui
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Carolyn Court
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Shuo Chen
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Donald L. Court
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Jeffrey Strathern
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Ding Jun Jin
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Mikhail Kashlev
- From the Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
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112
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Abstract
Recombineering refers to a strategy for engineering DNA sequences using a specialized mode of homologous recombination. This technology can be used for rapidly constructing precise changes in bacterial genome sequences in vivo. Oligonucleotide recombination is one type of recombineering that uses ssDNA oligonucleotides to direct chromosomal mutations. Oligo recombination occurs without addition of any exogenous functions, making this approach potentially useful in many different bacteria. Here we describe the basic technique for constructing a site-specific genomic mutation in Pseudomonas syringae.
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Affiliation(s)
- Bryan M Swingle
- United States Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA.
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113
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Mansell TJ, Warner JR, Gill RT. Trackable multiplex recombineering for gene-trait mapping in E. coli. Methods Mol Biol 2013; 985:223-246. [PMID: 23417807 DOI: 10.1007/978-1-62703-299-5_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent advances in homologous recombination in Escherichia coli have enabled improved genome engineering by multiplex recombineering. In this chapter, we present trackable multiplex recombineering (TRMR), a method for gene-trait mapping which creates simulated knockdown and overexpression mutants for virtually all genes in the E. coli genome. The method combines oligonucleotide synthesis with multiplex recombineering to create two libraries comprising of over 8,000 E. coli strains in total that can be selected for traits of interest via high-throughput screening or selection. DNA barcodes included in the recombineering cassette allow for rapid characterization of a naïve or selected population via DNA microarray analysis. Important considerations for oligonucleotide design, DNA library construction, recombineering, strain characterization, and selection are discussed.
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Affiliation(s)
- Thomas J Mansell
- Department of Chemical and Biological Engineering, Engineering Center, University of Colorado Boulder, Boulder, CO, USA
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114
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Substrate and target sequence length influence RecTE(Psy) recombineering efficiency in Pseudomonas syringae. PLoS One 2012; 7:e50617. [PMID: 23226333 PMCID: PMC3511549 DOI: 10.1371/journal.pone.0050617] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/23/2012] [Indexed: 01/25/2023] Open
Abstract
We are developing a new recombineering system to assist experimental manipulation of the Pseudomonas syringae genome. P. syringae is a globally dispersed plant pathogen and an important model species used to study the molecular biology of bacteria-plant interactions. We previously identified orthologs of the lambda Red bet/exo and Rac recET genes in P. syringae and confirmed that they function in recombineering using ssDNA and dsDNA substrates. Here we investigate the properties of dsDNA substrates more closely to determine how they influence recombineering efficiency. We find that the length of flanking homologies and length of the sequences being inserted or deleted have a large effect on RecTEPsy mediated recombination efficiency. These results provide information about the design elements that should be considered when using recombineering.
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115
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Abstract
The homologous recombination systems of linear double-stranded (ds)DNA bacteriophages are required for the generation of genetic diversity, the repair of dsDNA breaks, and the formation of concatemeric chromosomes, the immediate precursor to packaging. These systems have been studied for decades as a means to understand the basic principles of homologous recombination. From the beginning, it was recognized that these recombinases are linked intimately to the mechanisms of phage DNA replication. In the last decade, however, investigators have exploited these recombination systems as tools for genetic engineering of bacterial chromosomes, bacterial artificial chromosomes, and plasmids. This recombinational engineering technology has been termed "recombineering" and offers a new paradigm for the genetic manipulation of bacterial chromosomes, which is far more efficient than the classical use of nonreplicating integration vectors for gene replacement. The phage λ Red recombination system, in particular, has been used to construct gene replacements, deletions, insertions, inversions, duplications, and single base pair changes in the Escherichia coli chromosome. This chapter discusses the components of the recombination systems of λ, rac prophage, and phage P22 and properties of single-stranded DNA annealing proteins from these and other phage that have been instrumental for the development of this technology. The types of genetic manipulations that can be made are described, along with proposed mechanisms for both double-stranded DNA- and oligonucleotide-mediated recombineering events. Finally, the impact of this technology to such diverse fields as bacterial pathogenesis, metabolic engineering, and mouse genomics is discussed.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
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116
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Boyle NR, Gill RT. Tools for genome-wide strain design and construction. Curr Opin Biotechnol 2012; 23:666-71. [DOI: 10.1016/j.copbio.2012.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 01/21/2012] [Accepted: 01/23/2012] [Indexed: 11/25/2022]
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117
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Mosberg JA, Gregg CJ, Lajoie MJ, Wang HH, Church GM. Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases. PLoS One 2012; 7:e44638. [PMID: 22957093 PMCID: PMC3434165 DOI: 10.1371/journal.pone.0044638] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/06/2012] [Indexed: 11/19/2022] Open
Abstract
Lambda Red recombineering is a powerful technique for making targeted genetic changes in bacteria. However, many applications are limited by the frequency of recombination. Previous studies have suggested that endogenous nucleases may hinder recombination by degrading the exogenous DNA used for recombineering. In this work, we identify ExoVII as a nuclease which degrades the ends of single-stranded DNA (ssDNA) oligonucleotides and double-stranded DNA (dsDNA) cassettes. Removing this nuclease improves both recombination frequency and the inheritance of mutations at the 3′ ends of ssDNA and dsDNA. Extending this approach, we show that removing a set of five exonucleases (RecJ, ExoI, ExoVII, ExoX, and Lambda Exo) substantially improves the performance of co-selection multiplex automatable genome engineering (CoS-MAGE). In a given round of CoS-MAGE with ten ssDNA oligonucleotides, the five nuclease knockout strain has on average 46% more alleles converted per clone, 200% more clones with five or more allele conversions, and 35% fewer clones without any allele conversions. Finally, we use these nuclease knockout strains to investigate and clarify the effects of oligonucleotide phosphorothioation on recombination frequency. The results described in this work provide further mechanistic insight into recombineering, and substantially improve recombineering performance.
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Affiliation(s)
- Joshua A. Mosberg
- Program in Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Christopher J. Gregg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marc J. Lajoie
- Program in Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Harris H. Wang
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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118
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Lima BP, Thanh Huyen TT, Bäsell K, Becher D, Antelmann H, Wolfe AJ. Inhibition of acetyl phosphate-dependent transcription by an acetylatable lysine on RNA polymerase. J Biol Chem 2012; 287:32147-60. [PMID: 22829598 DOI: 10.1074/jbc.m112.365502] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ability of bacteria to adapt to environmental changes has allowed these organisms to thrive in all parts of the globe. By monitoring their extracellular and intracellular environments, bacteria assure their most appropriate response for each environment. Post-translational modification of proteins is one mechanism by which cells respond to their changing environments. Here, we report that two post-translational modifications regulate transcription of the extracytoplasmic stress-responsive promoter cpxP: (i) acetyl phosphate-dependent phosphorylation of the response regulator CpxR and (ii) acetyl coenzyme A-dependent acetylation of the α subunit of RNA polymerase. Together, these two post-translational modifications fine-tune cpxP transcription in response to changes in the intracellular environment.
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Affiliation(s)
- Bruno P Lima
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois 60153, USA
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119
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Van Pijkeren JP, Neoh KM, Sirias D, Findley AS, Britton RA. Exploring optimization parameters to increase ssDNA recombineering in Lactococcus lactis and Lactobacillus reuteri. Bioengineered 2012; 3:209-17. [PMID: 22750793 PMCID: PMC3476877 DOI: 10.4161/bioe.21049] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Single-stranded DNA (ssDNA) recombineering is a technology which is used to make subtle changes in the chromosome of several bacterial genera. Cells which express a single-stranded DNA binding protein (RecT or Bet) are transformed with an oligonucleotide which is incorporated via an annealing and replication-dependent mechanism. By in silico analysis we identified ssDNA binding protein homologs in the genus Lactobacillus and Lactococcus lactis. To assess whether we could further improve the recombineering efficiency in Lactobacillus reuteri ATCC PTA 6475 we expressed several RecT homologs in this strain. RecT derived from Enterococcus faecalis CRMEN 19 yielded comparable efficiencies compared with a native RecT protein, but none of the other proteins further increased the recombineering efficiency. We successfully improved recombineering efficiency 10-fold in L. lactis by increasing oligonucleotide concentration combined with the use of oligonucleotides containing phosphorothioate-linkages (PTOs). Surprisingly, neither increased oligonucleotide concentration nor PTO linkages enhanced recombineering in L. reuteri 6475. To emphasize the utility of this technology in improving probiotic features we modified six bases in a transcriptional regulatory element region of the pdu-operon of L. reuteri 6475, yielding a 3-fold increase in the production of the antimicrobial compound reuterin. Directed genetic modification of lactic acid bacteria through ssDNA recombineering will simplify strain improvement in a way that, when mutating a single base, is genetically indistinguishable from strains obtained through directed evolution.
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Affiliation(s)
- Jan-Peter Van Pijkeren
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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120
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In the fast lane: Large-scale bacterial genome engineering. J Biotechnol 2012; 160:72-9. [DOI: 10.1016/j.jbiotec.2012.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/16/2012] [Accepted: 02/21/2012] [Indexed: 11/15/2022]
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121
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Strategy for directing combinatorial genome engineering in Escherichia coli. Proc Natl Acad Sci U S A 2012; 109:10540-5. [PMID: 22689973 DOI: 10.1073/pnas.1206299109] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe a directed genome-engineering approach that combines genome-wide methods for mapping genes to traits [Warner JR, Reeder PJ, Karimpour-Fard A, Woodruff LBA, Gill RT (2010) Nat Biotechnol 28:856-862] with strategies for rapidly creating combinatorial ribosomal binding site (RBS) mutation libraries containing billions of targeted modifications [Wang HH, et al. (2009) Nature 460:894-898]. This approach should prove broadly applicable to various efforts focused on improving production of fuels, chemicals, and pharmaceuticals, among other products. We used barcoded promoter mutation libraries to map the effect of increased or decreased expression of nearly every gene in Escherichia coli onto growth in several model environments (cellulosic hydrolysate, low pH, and high acetate). Based on these data, we created and evaluated RBS mutant libraries (containing greater than 100,000,000 targeted mutations), targeting the genes identified to most affect growth. On laboratory timescales, we successfully identified a broad range of mutations (>25 growth-enhancing mutations confirmed), which improved growth rate 10-200% for several different conditions. Although successful, our efforts to identify superior combinations of growth-enhancing genes emphasized the importance of epistatic interactions among the targeted genes (synergistic, antagonistic) for taking full advantage of this approach to directed genome engineering.
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122
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Valledor M, Hu Q, Schiller P, Myers RS. Fluorescent protein engineering by in vivo site-directed mutagenesis. IUBMB Life 2012; 64:684-9. [PMID: 22639380 DOI: 10.1002/iub.1041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 03/30/2012] [Indexed: 02/03/2023]
Abstract
In vivo site-directed mutagenesis by single-stranded deoxyribonucleic acid recombineering is a facile method to change the color of fluorescent proteins (FPs) without cloning. Two different starting alleles of GFP were targeted for mutagenesis: gfpmut3* residing in the Escherichia coli genome and egfp carried by a bacterial/mammalian dual expression lentiviral plasmid vector. Fluorescent protein spectra were shifted by subtle modification of the chromophore region and residues interacting with the chromophore of the FP. Eight different FPs (Violeta, Azure, Aqua, Mar, Celeste, Amarillo, Mostaza, and Bronze) were isolated and shown to be useful in multicolor imaging and flow cytometry of bacteria and transgenic human stem cells. To make in vivo site-directed mutagenesis more efficient, the recombineering method was optimized using the fluorescence change as a sensitive quantitative assay for recombination. A set of rules to simplify mutant isolation by recombineering is provided.
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Affiliation(s)
- Melvys Valledor
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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123
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Carr PA, Wang HH, Sterling B, Isaacs FJ, Lajoie MJ, Xu G, Church GM, Jacobson JM. Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Res 2012; 40:e132. [PMID: 22638574 PMCID: PMC3458525 DOI: 10.1093/nar/gks455] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Genome-scale engineering of living organisms requires precise and economical methods to efficiently modify many loci within chromosomes. One such example is the directed integration of chemically synthesized single-stranded deoxyribonucleic acid (oligonucleotides) into the chromosome of Escherichia coli during replication. Herein, we present a general co-selection strategy in multiplex genome engineering that yields highly modified cells. We demonstrate that disparate sites throughout the genome can be easily modified simultaneously by leveraging selectable markers within 500 kb of the target sites. We apply this technique to the modification of 80 sites in the E. coli genome.
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Affiliation(s)
- Peter A Carr
- The Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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124
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Abstract
The ability to efficiently generate targeted point mutations in the chromosome without the need for antibiotics, or other means of selection, is a powerful strategy for genome engineering. Although oligonucleotide-mediated recombineering (ssDNA recombineering) has been utilized in Escherichia coli for over a decade, the successful adaptation of ssDNA recombineering to Gram-positive bacteria has not been reported. Here we describe the development and application of ssDNA recombineering in lactic acid bacteria. Mutations were incorporated in the chromosome of Lactobacillus reuteri and Lactococcus lactis without selection at frequencies ranging between 0.4% and 19%. Whole genome sequence analysis showed that ssDNA recombineering is specific and not hypermutagenic. To highlight the utility of ssDNA recombineering we reduced the intrinsic vancomymycin resistance of L. reuteri >100-fold. By creating a single amino acid change in the d-Ala-d-Ala ligase enzyme we reduced the minimum inhibitory concentration for vancomycin from >256 to 1.5 µg/ml, well below the clinically relevant minimum inhibitory concentration. Recombineering thus allows high efficiency mutagenesis in lactobacilli and lactococci, and may be used to further enhance beneficial properties and safety of strains used in medicine and industry. We expect that this work will serve as a blueprint for the adaptation of ssDNA recombineering to other Gram-positive bacteria.
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Affiliation(s)
- Jan-Peter van Pijkeren
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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125
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Synthetic biology: new strategies for directing design. Metab Eng 2011; 14:205-11. [PMID: 22227399 DOI: 10.1016/j.ymben.2011.12.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 10/25/2011] [Accepted: 12/18/2011] [Indexed: 11/22/2022]
Abstract
The advancement of synthetic biology is thanks, in large part, to continuing improvements in DNA synthesis. The expansion of synthetic biology into the realm of metabolic engineering has shifted the focus from simply making novel synthetic biological parts to answering the question of how we employ these biological parts to construct genomes that ultimately give rise to useful phenotypes. Much like protein engineering, the answer to this will be arrived at following the combination of rational design and evolutionary approaches. This review will highlight some of the new DNA synthesis-enabled search methods and discuss the application of such methods to the creation of synthetic gene networks and genomes.
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126
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Abstract
The increasing interest in genetic manipulation of bacterial host metabolic pathways for protein or small molecule production has led to a need to add new genes to a chromosome quickly and easily without leaving behind a selectable marker. The present report describes a vector and four-day procedure that enable site-specific chromosomal insertion of cloned genes in a context insulated from external transcription, usable once in a construction series. The use of rhamnose-inducible transcription from rhaBp allows regulation of the inserted genes independently of the commonly used IPTG and arabinose strategies. Using lacZ as a reporter, we first show that expression from the rhamnose promoter is tightly regulatable, exhibiting very low leakage of background expression compared with background, and moderate rhamnose-induced expression compared with IPTG-induced expression from lacp. Second, the expression of a DNA methyltransferase was used to show that rhamnose regulation yielded on-off expression of this enzyme, such that a resident high-copy plasmid was either fully sensitive or fully resistant to isoschizomer restriction enzyme cleavage. In both cases, growth medium manipulation allows intermediate levels of expression. The vehicle can also be adapted as an ORF-cloning vector.
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Affiliation(s)
- Marion H Sibley
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
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127
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Cai Y, Boeke JD. Genome remodeling. Nat Biotechnol 2011; 29:807-8. [DOI: 10.1038/nbt.1964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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128
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Engineering genomes in multiplex. Curr Opin Biotechnol 2011; 22:576-83. [DOI: 10.1016/j.copbio.2011.04.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 03/25/2011] [Accepted: 04/20/2011] [Indexed: 12/31/2022]
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129
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Wang HH, Xu G, Vonner AJ, Church G. Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion. Nucleic Acids Res 2011; 39:7336-47. [PMID: 21609953 PMCID: PMC3167615 DOI: 10.1093/nar/gkr183] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome engineering using single-stranded oligonucleotides is an efficient method for generating small chromosomal and episomal modifications in a variety of host organisms. The efficiency of this allelic replacement strategy is highly dependent on avoidance of the endogenous mismatch repair (MMR) machinery. However, global MMR inactivation generally results in significant accumulation of undesired background mutations. Here, we present a novel strategy using oligos containing chemically modified bases (2′-Fluoro-Uridine, 5-Methyl-deoxyCytidine, 2,6-Diaminopurine or Iso-deoxyGuanosine) in place of the standard T, C, A or G to avoid mismatch detection and repair, which we tested in Escherichia coli. This strategy increases transient allelic-replacement efficiencies by up to 20-fold, while maintaining a 100-fold lower background mutation level. We further show that the mismatched bases between the full length oligo and the chromosome are often not incorporated at the target site, probably due to nuclease activity at the 5′ and 3′ termini of the oligo. These results further elucidate the mechanism of oligo-mediated allelic replacement (OMAR) and enable improved methodologies for efficient, large-scale engineering of genomes.
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Affiliation(s)
- Harris H Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
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