301
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Thomason LC, Costantino N, Shaw DV, Court DL. Multicopy plasmid modification with phage lambda Red recombineering. Plasmid 2007; 58:148-58. [PMID: 17434584 PMCID: PMC2706537 DOI: 10.1016/j.plasmid.2007.03.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 02/28/2007] [Indexed: 12/01/2022]
Abstract
Recombineering, in vivo genetic engineering using the bacteriophage lambda Red generalized recombination system, was used to create various modifications of a multicopy plasmid derived from pBR322. All genetic modifications possible on the Escherichia coli chromosome and on bacterial artificial chromosomes (BACs) are also possible on multicopy plasmids and are obtained with similar frequencies to their chromosomal counterparts, including creation of point mutations (5-10% unselected frequency), deletions and substitutions. Parental and recombinant plasmids are nearly always present as a mixture following recombination, and circular multimeric plasmid molecules are often generated during the recombineering.
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Affiliation(s)
- Lynn C Thomason
- Gene Regulation and Chromosome Biology Laboratory, Building 539, Room 243, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
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302
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Chan W, Costantino N, Li R, Lee SC, Su Q, Melvin D, Court DL, Liu P. A recombineering based approach for high-throughput conditional knockout targeting vector construction. Nucleic Acids Res 2007; 35:e64. [PMID: 17426124 PMCID: PMC1885671 DOI: 10.1093/nar/gkm163] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Revised: 03/05/2007] [Accepted: 03/05/2007] [Indexed: 12/30/2022] Open
Abstract
Functional analysis of mammalian genes in vivo is primarily achieved through analysing knockout mice. Now that the sequencing of several mammalian genomes has been completed, understanding functions of all the genes represents the next major challenge in the post-genome era. Generation of knockout mutant mice has currently been achieved by many research groups but only by making individual knockouts, one by one. New technological advances and the refinements of existing technologies are critical for genome-wide targeted mutagenesis in the mouse. We describe here new recombineering reagents and protocols that enable recombineering to be carried out in a 96-well format. Consequently, we are able to construct 96 conditional knockout targeting vectors simultaneously. Our new recombineering system makes it a reality to generate large numbers of precisely engineered DNA constructs for functional genomics studies.
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Affiliation(s)
- Waiin Chan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Nina Costantino
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Ruixue Li
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Song Choon Lee
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Qin Su
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - David Melvin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Donald L. Court
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK and National Cancer Institute-Frederick, Frederick, MD 21702, USA
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303
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Bubunenko M, Baker T, Court DL. Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J Bacteriol 2007; 189:2844-53. [PMID: 17277072 PMCID: PMC1855809 DOI: 10.1128/jb.01713-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 01/18/2007] [Indexed: 11/20/2022] Open
Abstract
We describe here details of the method we used to identify and distinguish essential from nonessential genes on the bacterial Escherichia coli chromosome. Three key features characterize our method: high-efficiency recombination, precise replacement of just the open reading frame of a chromosomal gene, and the presence of naturally occurring duplications within the bacterial genome. We targeted genes encoding functions critical for processes of transcription and translation. Proteins from three complexes were evaluated to determine if they were essential to the cell by deleting their individual genes. The transcription elongation Nus proteins and termination factor Rho, which are involved in rRNA antitermination, the ribosomal proteins of the small 30S ribosome subunit, and minor ribosome-associated proteins were analyzed. It was concluded that four of the five bacterial transcription antitermination proteins are essential, while all four of the minor ribosome-associated proteins examined (RMF, SRA, YfiA, and YhbH), unlike most ribosomal proteins, are dispensable. Interestingly, although most 30S ribosomal proteins were essential, the knockouts of six ribosomal protein genes, rpsF (S6), rpsI (S9), rpsM (S13), rpsO (S15), rpsQ (S17), and rpsT (S20), were viable.
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Affiliation(s)
- Mikhail Bubunenko
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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304
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Weigele PR, Pope WH, Pedulla ML, Houtz JM, Smith AL, Conway JF, King J, Hatfull GF, Lawrence JG, Hendrix RW. Genomic and structural analysis of Syn9, a cyanophage infecting marineProchlorococcusandSynechococcus. Environ Microbiol 2007; 9:1675-95. [PMID: 17564603 DOI: 10.1111/j.1462-2920.2007.01285.x] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanobacteriophage Syn9 is a large, contractile-tailed bacteriophage infecting the widespread, numerically dominant marine cyanobacteria of the genera Prochlorococcus and Synechococcus. Its 177,300 bp genome sequence encodes 226 putative proteins and six tRNAs. Experimental and computational analyses identified genes likely involved in virion formation, nucleotide synthesis, and DNA replication and repair. Syn9 shows significant mosaicism when compared with related cyanophages S-PM2, P-SSM2 and P-SSM4, although shared genes show strong purifying selection and evidence for large population sizes relative to other phages. Related to coliphage T4 - which shares 19% of Syn9's genes - Syn9 shows evidence for different patterns of DNA replication and uses homologous proteins to assemble capsids with a different overall structure that shares topology with phage SPO1 and herpes virus. Noteworthy bacteria-related sequences in the Syn9 genome potentially encode subunits of the photosynthetic reaction centre, electron transport proteins, three pentose pathway enzymes and two tryptophan halogenases. These genes suggest that Syn9 is well adapted to the physiology of its photosynthetic hosts and may affect the evolution of these sequences within marine cyanobacteria.
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Affiliation(s)
- Peter R Weigele
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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305
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Phadtare S, Kazakov T, Bubunenko M, Court DL, Pestova T, Severinov K. Transcription antitermination by translation initiation factor IF1. J Bacteriol 2007; 189:4087-93. [PMID: 17384193 PMCID: PMC1913383 DOI: 10.1128/jb.00188-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial translation initiation factor IF1 is an S1 domain protein that belongs to the oligomer binding (OB) fold proteins. Cold shock domain (CSD)-containing proteins such as CspA (the major cold shock protein of Escherichia coli) and its homologues also belong to the OB fold protein family. The striking structural similarity between IF1 and CspA homologues suggests a functional overlap between these proteins. Certain members of the CspA family of cold shock proteins act as nucleic acid chaperones: they melt secondary structures in nucleic acids and act as transcription antiterminators. This activity may help the cell to acclimatize to low temperatures, since cold-induced stabilization of secondary structures in nascent RNA can impede transcription elongation. Here we show that the E. coli translation initiation factor, IF1, also has RNA chaperone activity and acts as a transcription antiterminator in vivo and in vitro. We further show that the RNA chaperone activity of IF1, although critical for transcription antitermination, is not essential for its role in supporting cell growth, which presumably functions in translation. The results thus indicate that IF1 may participate in transcription regulation and that cross talk and/or functional overlap may exist between the Csp family proteins, known to be involved in transcription regulation at cold shock, and S1 domain proteins, known to function in translation.
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Affiliation(s)
- Sangita Phadtare
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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306
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Korepanov AP, Gongadze GM, Garber MB, Court DL, Bubunenko MG. Importance of the 5 S rRNA-binding ribosomal proteins for cell viability and translation in Escherichia coli. J Mol Biol 2007; 366:1199-208. [PMID: 17198710 PMCID: PMC1939977 DOI: 10.1016/j.jmb.2006.11.097] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Revised: 11/15/2006] [Accepted: 11/21/2006] [Indexed: 10/23/2022]
Abstract
A specific complex of 5 S rRNA and several ribosomal proteins is an integral part of ribosomes in all living organisms. Here we studied the importance of Escherichia coli genes rplE, rplR and rplY, encoding 5 S rRNA-binding ribosomal proteins L5, L18 and L25, respectively, for cell growth, viability and translation. Using recombineering to create gene replacements in the E. coli chromosome, it was shown that rplE and rplR are essential for cell viability, whereas cells deleted for rplY are viable, but grow noticeably slower than the parental strain. The slow growth of these L25-defective cells can be stimulated by a plasmid expressing the rplY gene and also by a plasmid bearing the gene for homologous to L25 general stress protein CTC from Bacillus subtilis. The rplY mutant ribosomes are physically normal and contain all ribosomal proteins except L25. The ribosomes from L25-defective and parental cells translate in vitro at the same rate either poly(U) or natural mRNA. The difference observed was that the mutant ribosomes synthesized less natural polypeptide, compared to wild-type ribosomes both in vivo and in vitro. We speculate that the defect is at the ribosome recycling step.
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Affiliation(s)
- Alexey P. Korepanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
| | - George M. Gongadze
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
| | - Maria B. Garber
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russia
| | - Donald L. Court
- Gene Regulation and Chromosomal Biology Laboratory, National Cancer Institute at Frederick, Maryland 21702, USA
| | - Mikhail G. Bubunenko
- Gene Regulation and Chromosomal Biology Laboratory, National Cancer Institute at Frederick, Maryland 21702, USA
- Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
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307
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Semprini S, Troup T, Kotelevtseva N, King K, Davis J, Mullins L, Chapman K, Dunbar D, Mullins J. Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques. Nucleic Acids Res 2007; 35:1402-10. [PMID: 17284462 PMCID: PMC1865043 DOI: 10.1093/nar/gkl1108] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cre is widely used for DNA tailoring and, in combination with recombineering techniques, to modify BAC/PAC sequences for generating transgenic animals. However, mammalian genomes contain recombinase recognition sites (cryptic loxP sites) that can promote illegitimate DNA recombination and damage when cells express the Cre recombinase gene. We have created a new bioinformatic tool, FuzznucComparator, which searches for cryptic loxP sites and we have applied it to the analysis of the whole mouse genome. We found that cryptic loxP sites occur frequently and are homogeneously distributed in the genome. Given the mammalian nature of BAC/PAC genomic inserts, we hypothesised that the presence of cryptic loxP sites may affect the ability to grow and modify BAC and PAC clones in E. coli expressing Cre recombinase. We have observed a defect in bacterial growth when some BACs and PACs were transformed into EL350, a DH10B-derived bacterial strain that expresses Cre recombinase under the control of an arabinose-inducible promoter. In this study, we have demonstrated that Cre recombinase expression is leaky in un-induced EL350 cells and that some BAC/PAC sequences contain cryptic loxP sites, which are active and mediate the introduction of single-strand nicks in BAC/PAC genomic inserts.
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Affiliation(s)
- S. Semprini
- Molecular Physiology Group, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK, Current address: Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK, Endocrine Science Research Group, University of Manchester M13 9PT, UK and Endocrinology Unit, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK
| | - T.J. Troup
- Molecular Physiology Group, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK, Current address: Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK, Endocrine Science Research Group, University of Manchester M13 9PT, UK and Endocrinology Unit, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK
| | - N. Kotelevtseva
- Molecular Physiology Group, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK, Current address: Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK, Endocrine Science Research Group, University of Manchester M13 9PT, UK and Endocrinology Unit, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK
| | - K. King
- Molecular Physiology Group, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK, Current address: Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK, Endocrine Science Research Group, University of Manchester M13 9PT, UK and Endocrinology Unit, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK
| | - J.R.E. Davis
- Molecular Physiology Group, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK, Current address: Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK, Endocrine Science Research Group, University of Manchester M13 9PT, UK and Endocrinology Unit, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK
| | - L.J. Mullins
- Molecular Physiology Group, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK, Current address: Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK, Endocrine Science Research Group, University of Manchester M13 9PT, UK and Endocrinology Unit, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK
| | - K.E. Chapman
- Molecular Physiology Group, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK, Current address: Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK, Endocrine Science Research Group, University of Manchester M13 9PT, UK and Endocrinology Unit, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK
| | - D.R. Dunbar
- Molecular Physiology Group, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK, Current address: Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK, Endocrine Science Research Group, University of Manchester M13 9PT, UK and Endocrinology Unit, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK
| | - J.J. Mullins
- Molecular Physiology Group, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK, Current address: Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK, Endocrine Science Research Group, University of Manchester M13 9PT, UK and Endocrinology Unit, University of Edinburgh Medical School, Edinburgh EH16 4TJ, UK
- *To whom correspondence should be addressed. +44-131-242-6722+44-131-242-6782
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308
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309
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Sawitzke JA, Thomason LC, Costantino N, Bubunenko M, Datta S, Court DL. Recombineering: in vivo genetic engineering in E. coli, S. enterica, and beyond. Methods Enzymol 2007; 421:171-99. [PMID: 17352923 DOI: 10.1016/s0076-6879(06)21015-2] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
"Recombineering," in vivo genetic engineering with short DNA homologies, is changing how constructs are made. The methods are simple, precise, efficient, rapid, and inexpensive. Complicated genetic constructs that can be difficult or even impossible to make with in vitro genetic engineering can be created in days with recombineering. DNA molecules that are too large to manipulate with classical techniques are amenable to recombineering. This technology utilizes the phage lambda homologous recombination functions, proteins that can efficiently catalyze recombination between short homologies. Recombineering can be accomplished with linear PCR products or even single-stranded oligos. In this chapter we discuss methods of and ways to use recombineering.
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Affiliation(s)
- James A Sawitzke
- Molecular Control and Genetics, National Cancer Institute at Frederick, Frederick, MD, USA
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310
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Abstract
The piRNA class of small RNAs are distinct from other small RNAs by their approximately 26-31 nucleotide size, single-strandedness and strand-specificity as well as by the clustered arrangement of their origins. Here, we highlight how these features are reminiscent of the mechanisms of DNA replication, and then present three models suggesting that the origin of piRNAs may be mechanistically similar to key processes in DNA replication.
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Affiliation(s)
- Jack R Bateman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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311
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Abstract
The use of the recombination system from bacteriophage lambda, lambda-Red, allows for PCR-generated fragments to be targeted to specific chromosomal locations in sequenced genomes. A minimal region of homology of 30 to 50 bases flanking the fragment to be inserted is all that is required for targeted mutagenesis. Procedures for creating specific insertions, deletions, and site-directed changes are described.
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Affiliation(s)
- Joyce E Karlinsey
- Department of Microbiology, University of Washington, Seattle, WA, USA
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312
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van Kessel JC, Hatfull GF. Recombineering in Mycobacterium tuberculosis. Nat Methods 2006; 4:147-52. [PMID: 17179933 DOI: 10.1038/nmeth996] [Citation(s) in RCA: 407] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 11/09/2006] [Indexed: 01/26/2023]
Abstract
Genetic dissection of M. tuberculosis is complicated by its slow growth and its high rate of illegitimate recombination relative to homologous DNA exchange. We report here the development of a facile allelic exchange system by identification and expression of mycobacteriophage-encoded recombination proteins, adapting a strategy developed previously for recombineering in Escherichia coli. Identifiable recombination proteins are rare in mycobacteriophages, and only 1 of 30 genomically characterized mycobacteriophages (Che9c) encodes homologs of both RecE and RecT. Expression and biochemical characterization show that Che9c gp60 and gp61 encode exonuclease and DNA-binding activities, respectively, and expression of these proteins substantially elevates recombination facilitating allelic exchange in both M. smegmatis and M. tuberculosis. Mycobacterial recombineering thus provides a simple approach for the construction of gene replacement mutants in both slow- and fast-growing mycobacteria.
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Affiliation(s)
- Julia C van Kessel
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, 376 Crawford Hall, 4249 Fifth Ave., University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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313
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Nebert DW, Dalton TP. The role of cytochrome P450 enzymes in endogenous signalling pathways and environmental carcinogenesis. Nat Rev Cancer 2006; 6:947-60. [PMID: 17128211 DOI: 10.1038/nrc2015] [Citation(s) in RCA: 655] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Some cytochrome P450 (CYP) heme-thiolate enzymes participate in the detoxication and, paradoxically, the formation of reactive intermediates of thousands of chemicals that can damage DNA, as well as lipids and proteins. CYP expression can also affect the production of molecules derived from arachidonic acid, and alters various downstream signal-transduction pathways. Such changes can be precursors to malignancy. Recent studies in mice have changed our perceptions about the function of CYP1 enzymes. We suggest a two-tiered system to predict an overall inter-individual risk of tumorigenesis based on DNA variants in certain 'early defence' CYP genes, combined with polymorphisms in various downstream target genes.
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Affiliation(s)
- Daniel W Nebert
- Department of Environmental Health, and Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati, Ohio 45267-0056, USA.
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314
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Piuri M, Hatfull GF. A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells. Mol Microbiol 2006; 62:1569-85. [PMID: 17083467 PMCID: PMC1796659 DOI: 10.1111/j.1365-2958.2006.05473.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2006] [Indexed: 11/30/2022]
Abstract
The predominant morphotype of mycobacteriophage virions has a DNA-containing capsid attached to a long flexible non-contractile tail, features characteristic of the Siphoviridae. Within these phage genomes the tape measure protein (tmp) gene can be readily identified due to the well-established relationship between the length of the gene and the length of the phage tail--because these phages typically have long tails, the tmp gene is usually the largest gene in the genome. Many of these mycobacteriophage Tmp's contain small motifs with sequence similarity to host proteins. One of these motifs (motif 1) corresponds to the Rpf proteins that have lysozyme activity and function to stimulate growth of dormant bacteria, while the others (motifs 2 and 3) are related to proteins of unknown function, although some of the related proteins of the host are predicted to be involved in cell wall catabolism. We show here that motif 3-containing proteins have peptidoglycan-hydrolysing activity and that while this activity is not required for phage viability, it facilitates efficient infection and DNA injection into stationary phase cells. Tmp's of mycobacteriophages may thus have acquired these motifs in order to avoid a selective disadvantage that results from changes in peptidoglycan in non-growing cells.
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Affiliation(s)
- Mariana Piuri
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of PittsburghPittsburgh, PA 15260, USA
| | - Graham F Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of PittsburghPittsburgh, PA 15260, USA
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315
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Sarov M, Schneider S, Pozniakovski A, Roguev A, Ernst S, Zhang Y, Hyman AA, Stewart AF. A recombineering pipeline for functional genomics applied to Caenorhabditis elegans. Nat Methods 2006; 3:839-44. [PMID: 16990816 DOI: 10.1038/nmeth933] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Accepted: 08/07/2006] [Indexed: 12/28/2022]
Abstract
We present a new concept in DNA engineering based on a pipeline of serial recombineering steps in liquid culture. This approach is fast, straightforward and facilitates simultaneous processing of multiple samples in parallel. We validated the approach by generating green fluorescent protein (GFP)-tagged transgenes from Caenorhabditis briggsae genomic clones in a multistep pipeline that takes only 4 d. The transgenes were engineered with minimal disturbance to the natural genomic context so that the correct level and pattern of expression will be secured after transgenesis. An example transgene for the C. briggsae ortholog of lin-59 was used for ballistic transformation in Caenorhabditis elegans. We show that the cross-species transgene is correctly expressed and rescues RNA interference (RNAi)-mediated knockdown of the endogenous C. elegans gene. The strategy that we describe adapts the power of recombineering in Escherichia coli for fluent DNA engineering to a format that can be directly scaled up for genomic projects.
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Affiliation(s)
- Mihail Sarov
- Dresden University of Technology, BioInnovations Centre, Genomics Department, Tatzberg 47, 01307 Dresden, Germany
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316
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Huen MSY, Li XT, Lu LY, Watt RM, Liu DP, Huang JD. The involvement of replication in single stranded oligonucleotide-mediated gene repair. Nucleic Acids Res 2006; 34:6183-94. [PMID: 17088285 PMCID: PMC1693898 DOI: 10.1093/nar/gkl852] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Targeted gene repair mediated by single-stranded oligonucleotides (SSOs) has great potential for use in functional genomic studies and gene therapy. Genetic changes have been created using this approach in a number of prokaryotic and eukaryotic systems, including mouse embryonic stem cells. However, the underlying mechanisms remain to be fully established. In one of the current models, the ‘annealing-integration’ model, the SSO anneals to its target locus at the replication fork, serving as a primer for subsequent DNA synthesis mediated by the host replication machinery. Using a λ-Red recombination-based system in the bacterium Escherichia coli, we systematically examined several fundamental premises that form the mechanistic basis of this model. Our results provide direct evidence strongly suggesting that SSO-mediated gene repair is mechanistically linked to the process of DNA replication, and most likely involves a replication intermediate. These findings will help guide future experiments involving SSO-mediated gene repair in mammalian and prokaryotic cells, and suggest several mechanisms by which the efficiencies may be reliably and substantially increased.
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Affiliation(s)
- Michael S. Y. Huen
- Department of Biochemistry, The University of Hong Kong3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Xin-tian Li
- Department of Biochemistry, The University of Hong Kong3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC)Beijing 100005, P.R. China
| | - Lin-Yu Lu
- Department of Biochemistry, The University of Hong Kong3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Rory M. Watt
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong Pokfulam RoadHong Kong SAR, China
| | - De-Pei Liu
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC)Beijing 100005, P.R. China
| | - Jian-Dong Huang
- Department of Biochemistry, The University of Hong Kong3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- To whom correspondence should be addressed. Tel: +852 2819 2810; Fax: +852 2855 1254;
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317
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Ranallo RT, Barnoy S, Thakkar S, Urick T, Venkatesan MM. Developing liveShigellavaccines using λ Red recombineering. ACTA ACUST UNITED AC 2006; 47:462-9. [PMID: 16872384 DOI: 10.1111/j.1574-695x.2006.00118.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Live attenuated Shigella vaccines have shown promise in inducing protective immune responses in human clinical trials and as carriers of heterologous antigens from other mucosal pathogens. In the past, construction of Shigella vaccine strains relied on classical allelic exchange systems to genetically engineer the bacterial genome. These systems require extensive in vitro engineering of long homologous sequences to create recombinant replication-defective plasmids or phage. Alternatively, the lambda red recombination system from bacteriophage facilitates recombination with as little as 40 bp of homologous DNA. The process, referred to as recombineering, typically uses an inducible lambda red operon on a temperature-sensitive plasmid and optimal transformation conditions to integrate linear antibiotic resistance cassettes flanked by homologous sequences into a bacterial genome. Recent advances in recombineering have enabled modification of genomic DNA from bacterial pathogens including Salmonella, Yersinia, enteropathogenic Escherichia coli, or enterohemorrhagic E. coli and Shigella. These advances in recombineering have been used to systematically delete virulence-associated genes from Shigella, creating a number of isogenic strains from multiple Shigella serotypes. These strains have been characterized for attenuation using both in vivo and in vitro assays. Based on this data, prototypic Shigella vaccine strains containing multiple deletions in virulence-associated genes have been generated.
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Affiliation(s)
- Ryan T Ranallo
- Department of Enteric Infections, Division of Communicable Diseases and Immunology, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
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318
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Bubunenko M, Korepanov A, Court DL, Jagannathan I, Dickinson D, Chaudhuri BR, Garber MB, Culver GM. 30S ribosomal subunits can be assembled in vivo without primary binding ribosomal protein S15. RNA (NEW YORK, N.Y.) 2006; 12:1229-39. [PMID: 16682557 PMCID: PMC1484426 DOI: 10.1261/rna.2262106] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2005] [Accepted: 03/16/2006] [Indexed: 05/09/2023]
Abstract
Assembly of 30S ribosomal subunits from Escherichia coli has been dissected in detail using an in vitro system. Such studies have allowed characterization of the role for ribosomal protein S15 in the hierarchical assembly of 30S subunits; S15 is a primary binding protein that orchestrates the assembly of ribosomal proteins S6, S11, S18, and S21 with the central domain of 16S ribosomal RNA to form the platform of the 30S subunit. In vitro S15 is the sole primary binding protein in this cascade, performing a critical role during assembly of these four proteins. To investigate the role of S15 in vivo, the essential nature of rpsO, the gene encoding S15, was examined. Surprisingly, E. coli with an in-frame deletion of rpsO are viable, although at 37 degrees C this DeltarpsO strain has an exaggerated doubling time compared to its parental strain. In the absence of S15, the remaining four platform proteins are assembled into ribosomes in vivo, and the overall architecture of the 30S subunits formed in the DeltarpsO strain at 37 degrees C is not altered. Nonetheless, 30S subunits lacking S15 appear to be somewhat defective in subunit association in vivo and in vitro. In addition, this strain is cold sensitive, displaying a marked ribosome biogenesis defect at low temperature, suggesting that under nonideal conditions S15 is critical for assembly. The viability of this strain indicates that in vivo functional populations of 70S ribosomes must form in the absence of S15 and that 30S subunit assembly has a plasicity that has not previously been revealed or characterized.
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Affiliation(s)
- Mikhail Bubunenko
- Basic Research Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA
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319
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Bloor AE, Cranenburgh RM. An efficient method of selectable marker gene excision by Xer recombination for gene replacement in bacterial chromosomes. Appl Environ Microbiol 2006; 72:2520-5. [PMID: 16597952 PMCID: PMC1449051 DOI: 10.1128/aem.72.4.2520-2525.2006] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A simple, effective method of unlabeled, stable gene insertion into bacterial chromosomes has been developed. This utilizes an insertion cassette consisting of an antibiotic resistance gene flanked by dif sites and regions homologous to the chromosomal target locus. dif is the recognition sequence for the native Xer site-specific recombinases responsible for chromosome and plasmid dimer resolution: XerC/XerD in Escherichia coli and RipX/CodV in Bacillus subtilis. Following integration of the insertion cassette into the chromosomal target locus by homologous recombination, these recombinases act to resolve the two directly repeated dif sites to a single site, thus excising the antibiotic resistance gene. Previous approaches have required the inclusion of exogenous site-specific recombinases or transposases in trans; our strategy demonstrates that this is unnecessary, since an effective recombination system is already present in bacteria. The high recombination frequency makes the inclusion of a counter-selectable marker gene unnecessary.
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Affiliation(s)
- Alexandra E Bloor
- Cobra Biomanufacturing Plc, The Science Park, Keele, Staffordshire ST5 5SP, United Kingdom
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320
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Dolphin CT, Hope IA. Caenorhabditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones. Nucleic Acids Res 2006; 34:e72. [PMID: 16717278 PMCID: PMC1464416 DOI: 10.1093/nar/gkl352] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 03/06/2006] [Accepted: 04/19/2006] [Indexed: 11/13/2022] Open
Abstract
By determining spatial-temporal expression patterns, reporter constructs provide significant insights into gene function. Although additionally providing information on subcellular distribution, translational reporters, where the reporter is fused to the gene coding sequence, are used less frequently than simpler constructs containing only putative promoter sequences. Because these latter constructs may not contain all necessary regulatory elements, resulting expression patterns must be interpreted cautiously. To ensure inclusion of all such elements and provide details of subcellular localization, construction of translational reporters would, preferably, utilize genomic clones, containing the complete locus plus flanking regions and permit seamless insertion of the reporter anywhere within the gene. We have developed such a method based upon lambda Red-mediated recombineering coupled to a robust two-step counter-selection protocol. We have inserted either gfp or cfp precisely at the C-termini of three Caenorhabditis elegans target genes, each located within different fosmid clones, and examined previously with conventional reporter approaches. Resulting transgenic lines revealed reporter expression consistent with previously published data for the tagged genes and also provided additional information including subcellular distributions. This simple and straightforward method generates reporters highly likely to recapitulate endogenous gene expression and thus represents an important addition to the functional genomics toolbox.
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Affiliation(s)
- Colin T Dolphin
- Pharmaceutical Science Research Division, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
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321
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Datta S, Costantino N, Court DL. A set of recombineering plasmids for gram-negative bacteria. Gene 2006; 379:109-15. [PMID: 16750601 DOI: 10.1016/j.gene.2006.04.018] [Citation(s) in RCA: 367] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 04/21/2006] [Accepted: 04/22/2006] [Indexed: 11/23/2022]
Abstract
We have constructed a set of plasmids that can be used to express recombineering functions in some gram-negative bacteria, thereby facilitating in vivo genetic manipulations. These plasmids include an origin of replication and a segment of the bacteriophage lambda genome comprising the red genes (exo, bet and gam) under their native control. These constructs do not require the anti-termination event normally required for Red expression, making their application more likely in divergent species. Some of the plasmids have temperature-sensitive replicons to simplify curing. In creating these vectors we developed two useful recombineering applications. Any gene linked to a drug marker can be retrieved by gap-repair using only a plasmid origin and target homologies. A plasmid origin of replication can be changed to a different origin by targeted replacement, to potentially alter its copy number and host range. Both these techniques will prove useful for manipulation of plasmids in vivo. Most of the Red plasmid constructs catalyzed efficient recombination in E. coli with a low level of uninduced background recombination. These Red plasmids have been successfully tested in Salmonella, and we anticipate that that they will provide efficient recombination in other related gram-negative bacteria.
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Affiliation(s)
- Simanti Datta
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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322
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Penrod JT, Roth JR. Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica. J Bacteriol 2006; 188:2865-74. [PMID: 16585748 PMCID: PMC1447003 DOI: 10.1128/jb.188.8.2865-2874.2006] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonellae can use ethanolamine (EA) as a sole source of carbon and nitrogen. This ability is encoded by an operon (eut) containing 17 genes, only 6 of which are required under standard conditions (37 degrees C; pH 7.0). Five of the extra genes (eutM, -N, -L, -K, and -G) become necessary under conditions that favor loss of the volatile intermediate, acetaldehyde, which escapes as a gas during growth on EA and is lost at a higher rate from these mutants. The eutM, -N, -L, and -K genes encode homologues of shell proteins of the carboxysome, an organelle shown (in other organisms) to concentrate CO(2). We propose that carboxysome-like organelles help bacteria conserve certain volatile metabolites-CO(2) or acetaldehyde-perhaps by providing a low-pH compartment. The EutG enzyme converts acetaldehyde to ethanol, which may improve carbon retention by forming acetals; alternatively, EutG may recycle NADH within the carboxysome.
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Affiliation(s)
- Joseph T Penrod
- Microbiology Section, Division of Biological Sciences, University of California-Davis, Davis, CA, USA
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323
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Zhou Y, Shi T, Mozola MA, Olson ER, Henthorn K, Brown S, Gussin GN, Friedman DI. Evidence that the promoter can influence assembly of antitermination complexes at downstream RNA sites. J Bacteriol 2006; 188:2222-32. [PMID: 16513752 PMCID: PMC1428141 DOI: 10.1128/jb.188.6.2222-2232.2006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The N protein of phage lambda acts with Escherichia coli Nus proteins at RNA sites, NUT, to modify RNA polymerase (RNAP) to a form that overrides transcription terminators. These interactions have been thought to be the primary determinants of the effectiveness of N-mediated antitermination. We present evidence that the associated promoter, in this case the lambda early P(R) promoter, can influence N-mediated modification of RNAP even though modification occurs at a site (NUTR) located downstream of the intervening cro gene. As predicted by genetic analysis and confirmed by in vivo transcription studies, a combination of two mutations in P(R), at positions -14 and -45 (yielding P(R-GA)), reduces effectiveness of N modification, while an additional mutation at position -30 (yielding P(R-GCA)) suppresses this effect. In vivo, the level of P(R-GA)-directed transcription was twice as great as the wild-type level, while transcription directed by P(R-GCA) was the same as that directed by the wild-type promoter. However, the rate of open complex formation at P(R-GA) in vitro was roughly one-third the rate for wild-type P(R). We ascribe this apparent discrepancy to an effect of the mutations in P(R-GCA) on promoter clearance. Based on the in vivo experiments, one plausible explanation for our results is that increased transcription can lead to a failure to form active antitermination complexes with NUT RNA, which, in turn, causes failure to read through downstream termination sites. By blocking antitermination and thus expression of late functions, the effect of increased transcription through nut sites could be physiologically important in maintaining proper regulation of gene expression early in phage development.
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Affiliation(s)
- Ying Zhou
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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324
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Abstract
Experiments using phage lambda provided early insights into important molecular mechanisms, including genetic recombination and the control of gene expression. Before recombinant DNA technology, the use of lambda, most particularly lambda transducing phages, illustrated the importance of cloning bacterial genes, already providing some insight into how to use cloned genes to advantage. Subsequently, lambda made significant contributions to recombinant DNA technology, including the early generation of genomic and cDNA libraries. More recently, lambda genes associated with recombination have enabled techniques referred to as ‘recombineering’ to be developed. These techniques permit the refined manipulation, including mutation, of foreign genes in Escherichia coli and their subsequent return to the donor organism.
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325
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Burrus V, Marrero J, Waldor MK. The current ICE age: biology and evolution of SXT-related integrating conjugative elements. Plasmid 2006; 55:173-83. [PMID: 16530834 DOI: 10.1016/j.plasmid.2006.01.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Revised: 12/30/2005] [Accepted: 01/07/2006] [Indexed: 11/18/2022]
Abstract
SXT is an integrating conjugative element (ICE) that was initially isolated from a 1992 Vibrio cholerae O139 clinical isolate from India. This approximately 100-kb ICE encodes resistance to multiple antibiotics. SXT or closely related ICEs are now present in most clinical and some environmental V. cholerae isolates from Asia and Africa. SXT-related ICEs are not limited to V. cholerae. It is now clear that so-called IncJ elements such as R391 are closely related to SXT. More than 25 members of the SXT/R391 family of ICEs have now been identified in environmental and clinical isolates of diverse species of gamma-proteobacteria worldwide. In this review, we discuss the diversity, evolution and biology of this family of ICEs.
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Affiliation(s)
- Vincent Burrus
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, and Howard Hughes Medical Institute Boston, MA 02111, USA
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326
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Schwartz JA, Brittle EE, Reynolds AE, Enquist LW, Silverstein SJ. UL54-null pseudorabies virus is attenuated in mice but productively infects cells in culture. J Virol 2006; 80:769-84. [PMID: 16378979 PMCID: PMC1346835 DOI: 10.1128/jvi.80.2.769-784.2006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The pseudorabies virus (PRV) UL54 homologs are important multifunctional proteins with roles in shutoff of host protein synthesis, transactivation of virus and cellular genes, and regulation of splicing and translation. Here we describe the first genetic characterization of UL54. We constructed UL54 null mutations in a PRV bacterial artificial chromosome using sugar suicide and lambdaRed allele exchange systems. Surprisingly, UL54 is dispensable for growth in tissue culture but exhibits a small-plaque phenotype that can be complemented in trans by both the herpes simplex virus type 1 ICP27 and varicella-zoster virus open reading frame 4 proteins. Deletion of UL54 in the virus vJSdelta54 had no effect on the ability of the virus to shut off host cell protein synthesis but did affect virus gene expression. The glycoprotein gC accumulated to lower levels in cells infected with vJSdelta54 compared to those infected with wild-type virus, while gK levels were undetectable. Other late gene products, gB, gE, and Us9, accumulated to higher levels than those seen in cells infected with wild-type virus in a multiplicity-dependent manner. DNA replication is also reduced in cells infected with vJSdelta54. UL54 appears to regulate UL53 and UL52 at the transcriptional level as their respective RNAs are decreased in cells infected with vJSdelta54. Interestingly, vJSdelta54 is highly attenuated in a mouse model of PRV infection. Animals infected with vJSdelta54 survive twice as long as animals infected with wild-type virus, and this results in delayed accumulation of virus-specific antigens in skin, dorsal root ganglia, and spinal cord tissues.
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Affiliation(s)
- Jennifer A Schwartz
- Department of Microbiology, Columbia University, 701 W. 168th St., New York, NY 10032, USA
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327
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Savage PJ, Leong JM, Murphy KC. Rapid allelic exchange in enterohemorrhagic Escherichia coli (EHEC) and other E. coli using lambda red recombination. CURRENT PROTOCOLS IN MICROBIOLOGY 2006; Chapter 5:Unit5A.2. [PMID: 18770591 DOI: 10.1002/9780471729259.mc05a02s00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This unit describes an allelic exchange system for enterohemorrhagic E. coli (EHEC), and similar pathogenic species of bacteria. The phage lambda Red recombination system is expressed from a plasmid, inducing a hyper-recombinogenic state where electroporated PCR-generated substrates recombine with the bacterial chromosome at high efficiency. The technique can be used to substitute a drug marker for the gene of interest, or used to generate a clean in-frame deletion of the target gene. Single gene knockouts in EHEC, or deletions of whole pathogenicity islands, can be constructed. A procedure for the preparation of hyper-recombinogenic electrocompetent cells is also described. Besides E. coli K-12 and EHEC, this method has also been used for the construction of gene knockouts in enteropathogenic E. coli (EPEC), enteroaggregative E. coli, and uropathogenic E. coli, as well as Shigella flexneri and Salmonella enterica.
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Affiliation(s)
- Pamela J Savage
- University of Massachusetts MedicalSchool, Worcester, Massachusetts, USA
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328
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Maxwell KL, Reed P, Zhang RG, Beasley S, Walmsley AR, Curtis FA, Joachimiak A, Edwards AM, Sharples GJ. Functional similarities between phage lambda Orf and Escherichia coli RecFOR in initiation of genetic exchange. Proc Natl Acad Sci U S A 2005; 102:11260-5. [PMID: 16076958 PMCID: PMC1183564 DOI: 10.1073/pnas.0503399102] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Indexed: 11/18/2022] Open
Abstract
Genetic recombination in bacteriophage lambda relies on DNA end processing by Exo to expose 3'-tailed strands for annealing and exchange by beta protein. Phage lambda encodes an additional recombinase, Orf, which participates in the early stages of recombination by supplying a function equivalent to the Escherichia coli RecFOR complex. These host enzymes assist loading of the RecA strand exchange protein onto ssDNA coated with ssDNA-binding protein. In this study, we purified the Orf protein, analyzed its biochemical properties, and determined its crystal structure at 2.5 angstroms. The homodimeric Orf protein is arranged as a toroid with a shallow U-shaped cleft, lined with basic residues, running perpendicular to the central cavity. Orf binds DNA, favoring single-stranded over duplex and with no obvious preference for gapped, 3'-tailed, or 5'-tailed substrates. An interaction between Orf and ssDNA-binding protein was indicated by far Western analysis. The functional similarities between Orf and RecFOR are discussed in relation to the early steps of recombinational exchange and the interplay between phage and bacterial recombinases.
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Affiliation(s)
- Karen L Maxwell
- Centre for Infectious Diseases, Wolfson Research Institute, University of Durham, Queen's Campus, Stockton-on-Tees TS17 6BH, United Kingdom
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329
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Abstract
Gene fusion technology is a key tool in facilitating gene function studies. Hybrid molecules in which all the components are joined precisely, without the presence of intervening and unwanted extraneous sequences, enable accurate studies of molecules and the characterization of individual components. This article reviews situations in which seamlessly fused genes and proteins are required or desired and describes molecular approaches that are available for generating these hybrid molecules.
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Affiliation(s)
- Quinn Lu
- Gene Expression and Protein Biochemistry, Discovery Research, GlaxoSmithKline, Mail Code: UE0548, 709 Swedeland Road, King of Prussia, PA 19406, USA.
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330
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Parekh-Olmedo H, Ferrara L, Brachman E, Kmiec EB. Gene therapy progress and prospects: targeted gene repair. Gene Ther 2005; 12:639-46. [PMID: 15815682 DOI: 10.1038/sj.gt.3302511] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The capacity to correct a mutant gene within the context of the chromosome holds great promise as a therapy for inherited disorders but fulfilling this promise has proven to be challenging. However, steady progress is being made and the development of gene repair as a viable and robust approach is underway. Here, we present some of the recent advances that are helping to shape our thinking about the feasibility and the limitations of this technique. For the most part, these advances center on understanding the regulation of the reaction and validating its application in animal models.
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Affiliation(s)
- H Parekh-Olmedo
- Department of Biological Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
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331
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Wang PL, Lo BKC, Winter G. Generating molecular diversity by homologous recombination in Escherichia coli. Protein Eng Des Sel 2005; 18:397-404. [PMID: 15983006 DOI: 10.1093/protein/gzi042] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We explored the use of recE-mediated homologous recombination to generate molecular diversity in Escherichia coli. Two homologous genes were placed on different phagemid vectors each comprising multiple EcoRI restriction sites and overlapping N- and C-terminal portions of beta-lactamase. By co-infection of these phage into RecE+ EcoRI+ E.coli, we were able to introduce double-strand breaks into these vectors, allowing efficient homologous recombination (in up to 10% of bacteria) by the recE pathway and selection of the recombinants by resistance to ampicillin. Recombination gave single crossovers; these were more frequent near the EcoRI sites and the recombination frequency increased with the target length and degree of homology. The system was used to create a large combinatorial chicken antibody library (10(10)) for display on filamentous phage and to isolate several antibody fragments with binding affinities in the 10-100 nM range.
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Affiliation(s)
- Peter L Wang
- Centre for Protein Engineering, University of Cambridge, Hills Road, Cambridge CB2 2QH, UK.
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332
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Hayes S, Asai K, Chu AM, Hayes C. NinR- and red-mediated phage-prophage marker rescue recombination in Escherichia coli: recovery of a nonhomologous immlambda DNA segment by infecting lambdaimm434 phages. Genetics 2005; 170:1485-99. [PMID: 15956667 PMCID: PMC1449759 DOI: 10.1534/genetics.105.042341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We examined the requirement of lambda recombination functions for marker rescue of cryptic prophage genes within the Escherichia coli chromosome. We infected lysogenic host cells with lambdaimm434 phages and selected for recombinant immlambda phages that had exchanged the imm434 region of the infecting phage for the heterologous 2.6-kb immlambda region from the prophage. Phage-encoded activity, provided by either Red or NinR functions, was required for the substitution. Red(-) phages with DeltaNinR, internal NinR deletions of rap-ninH, or orf-ninC were 117-, 12-, and 5-fold reduced for immlambda rescue in a Rec(+) host, suggesting the participation of several NinR activities. RecA was essential for NinR-dependent immlambda rescue, but had slight influence on Red-dependent rescue. The host recombination activities RecBCD, RecJ, and RecQ participated in NinR-dependent recombination while they served to inhibit Red-mediated immlambda rescue. The opposite effects of several host functions toward NinR- and Red-dependent immlambda rescue explains why the independent pathways were not additive in a Rec(+) host and why the NinR-dependent pathway appeared dominant. We measured the influence of the host recombination functions and DnaB on the appearance of orilambda-dependent replication initiation and whether orilambda replication initiation was required for immlambda marker rescue.
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Affiliation(s)
- Sidney Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.
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333
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Adhya S, Black L, Friedman D, Hatfull G, Kreuzer K, Merril C, Oppenheim A, Rohwer F, Young R. 2004 ASM Conference on the New Phage Biology: the 'Phage Summit'. Mol Microbiol 2005; 55:1300-14. [PMID: 15720541 DOI: 10.1111/j.1365-2958.2005.04509.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In August, more than 350 conferees from 24 countries attended the ASM Conference on the New Phage Biology, in Key Biscayne, Florida. This meeting, also called the Phage Summit, was the first major international gathering in decades devoted exclusively to phage biology. What emerged from the 5 days of the Summit was a clear perspective on the explosive resurgence of interest in all aspects of bacteriophage biology. The classic phage systems like lambda and T4, reinvigorated by structural biology, bioinformatics and new molecular and cell biology tools, remain model systems of unequalled power and facility for studying fundamental biological issues. In addition, the New Phage Biology is also populated by basic and applied scientists focused on ecology, evolution, nanotechnology, bacterial pathogenesis and phage-based immunologics, therapeutics and diagnostics, resulting in a heightened interest in bacteriophages per se, rather than as a model system. Besides constituting another landmark in the long history of a field begun by d'Herelle and Twort during the early 20th century, the Summit provided a unique venue for establishment of new interactive networks for collaborative efforts between scientists of many different backgrounds, interests and expertise.
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Affiliation(s)
- Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, 37 Convent Dr., Rm 5138, Bethesda, MD 20892-4264, USA
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334
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MacAuley A, Ladiges WC. Approaches to determine clinical significance of genetic variants. Mutat Res 2005; 573:205-20. [PMID: 15829249 DOI: 10.1016/j.mrfmmm.2005.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Revised: 08/24/2004] [Indexed: 05/02/2023]
Abstract
The clinical significance of genetic variants (single nucleotide polymorphisms, SNPs) has implications for risk assessment and also for predicting the outcome of a disease process, especially in response to intervention. Approaches to determine the clinical significance of genetic polymorphisms are now beginning to be developed. The technology tools and procedures currently available have significant potential in identifying and validating polymorphisms associated with environmentally sensitive phenotypes. Numerous concepts can now provide the methodology to selectively identify SNPs with the potential for impacting gene function. These include computational algorithms, biochemical assays, yeast mutagenicity assays, and epidemiological studies, either as a stand-alone screen, or in various combinations depending on the gene of interest. Proof of principle will ultimately depend on large-scale epidemiological and clinical studies, but will require intensive resources. Therefore, the use of the mouse as a preclinical biological model is paramount in helping screen valid SNPs or combinations of SNPs for human studies. But more importantly, mouse modeling will help answer the question of what role gene variants play in sensitivity or resistance to a wide variety of environmental insults ranging from toxic chemicals and carcinogens to more mundane and routine exposure items, such as dietary factors, air quality, over the counter and prescription medications, and ultraviolet light. Our focus on SNPs that result in an amino acid change is a matter of expediency because these variants are more amenable to the prescreening approaches currently available that are expected to help identify SNPs that affect protein function. The mouse models generated to evaluate the environmental relevance of selected SNPs will be extremely valuable biological tools to validate gene variant and environment interaction in a variety of settings. Informative mouse models will also provide the basis of pursuing relevant SNPs in epidemiological and clinical investigations.
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Affiliation(s)
- Alasdair MacAuley
- Comparative Mouse Genomics Center, Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
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335
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Domi A, Moss B. Engineering of a vaccinia virus bacterial artificial chromosome in Escherichia coli by bacteriophage lambda-based recombination. Nat Methods 2005; 2:95-7. [PMID: 15782205 DOI: 10.1038/nmeth734] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 12/16/2004] [Indexed: 11/09/2022]
Abstract
The large capacity of vaccinia virus (VAC) for added DNA, cytoplasmic expression and broad host range make it a popular choice for gene delivery, despite the burdensome need for multiple plaque purifications to isolate recombinants. Here we describe how a bacterial artificial chromosome (BAC) containing the entire VAC genome can be engineered in Escherichia coli by homologous recombination using bacteriophage lambda-encoded enzymes. The engineered VAC genomes can then be used to produce clonally pure recombinant viruses in mammalian cells without the need for plaque purification.
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Affiliation(s)
- Arban Domi
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 4 Center Drive, Bethesda, Maryland 20892-0445, USA
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336
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Cukras AR, Green R. Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation. J Mol Biol 2005; 349:47-59. [PMID: 15876367 PMCID: PMC1687178 DOI: 10.1016/j.jmb.2005.03.075] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 03/25/2005] [Accepted: 03/25/2005] [Indexed: 11/20/2022]
Abstract
The ribosomal protein S13 is found in the head region of the small subunit, where it interacts with the central protuberance of the large ribosomal subunit and with the P site-bound tRNA through its extended C terminus. The bridging interactions between the large and small subunits are dynamic, and are thought to be critical in orchestrating the molecular motions of the translation cycle. S13 provides a direct link between the tRNA-binding site and the movements in the head of the small subunit seen during translocation, thereby providing a possible pathway of signal transduction. We have created and characterized an rpsM(S13)-deficient strain of Escherichia coli and have found significant defects in subunit association, initiation and translocation through in vitro assays of S13-deficient ribosomes. Targeted mutagenesis of specific bridge and tRNA contact elements in S13 provides evidence that these two interaction domains play critical roles in maintaining the fidelity of translation. This ribosomal protein thus appears to play a non-essential, yet important role by modulating subunit interactions in multiple steps of the translation cycle.
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337
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Wong QNY, Ng VCW, Lin MCM, Kung HF, Chan D, Huang JD. Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli. Nucleic Acids Res 2005; 33:e59. [PMID: 15800210 PMCID: PMC1072810 DOI: 10.1093/nar/gni059] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
λ-Red system-based recombinogenic engineering is a powerful new method to engineer DNA without the need for restriction enzymes or ligases. Here, we report the use of a single selectable marker to enhance the usefulness of this approach. The strategy is to utilize the thymidylate synthase A (thyA) gene, which encodes an enzyme involved in the synthesis of thymidine 5′-triphosphate, for both positive and negative selection. With this approach, we successfully created point mutations in plasmid and bacterial artificial chromosome (BAC) DNA containing the mouse Col10a1 gene. The results showed that the thyA selection system is highly efficient and accurate, giving an average of >90% selection efficiency. This selection system produces DNA that is free from permanent integration of unwanted sequences, thus allowing unlimited rounds of modifications if required.
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Affiliation(s)
- Queenie N. Y. Wong
- Institute of Molecular Biology, The University of Hong KongPokfulam, Hong Kong SAR, China
| | | | - Marie C. M. Lin
- Institute of Molecular Biology, The University of Hong KongPokfulam, Hong Kong SAR, China
| | - Hsiang-fu Kung
- Institute of Molecular Biology, The University of Hong KongPokfulam, Hong Kong SAR, China
| | - Danny Chan
- To whom correspondence should be addressed. Tel: +852 2819 9482; Fax: +852 2855 1254;
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338
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Svenningsen SL, Costantino N, Court DL, Adhya S. On the role of Cro in lambda prophage induction. Proc Natl Acad Sci U S A 2005; 102:4465-9. [PMID: 15728734 PMCID: PMC555511 DOI: 10.1073/pnas.0409839102] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lysogenic state of bacteriophage lambda is exceptionally stable yet the prophage is readily induced in response to DNA damage. This delicate epigenetic switch is believed to be regulated by two proteins; the lysogenic maintenance promoting protein CI and the early lytic protein Cro. First, we confirm, in the native configuration, the previous observation that the DNA loop mediated by oligomerization of CI bound to two distinct operator regions (O(L) and O(R)), increases repression of the early lytic promoters and is important for stable maintenance of lysogeny. Second, we show that the presence of the cro gene might be unimportant for the lysogenic to lytic switch during induction of the lambda prophage. We revisit the idea that Cro's primary role in induction is instead to mediate weak repression of the early lytic promoters.
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339
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Abstract
The popularity of Drosophila melanogaster as a model for understanding eukaryotic biology over the past 100 years has been accompanied by the development of numerous tools for manipulating the fruitfly genome. Here we review some recent technologies that will allow Drosophila melanogaster to be manipulated more easily than any other multicellular organism. These developments include the ability to create molecularly designed deletions, improved genetic mapping technologies, strategies for creating targeted mutations, new transgenic approaches and the means to clone and modify large fragments of DNA.
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Affiliation(s)
- Koen J T Venken
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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340
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Warming S, Costantino N, Court DL, Jenkins NA, Copeland NG. Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Res 2005; 33:e36. [PMID: 15731329 PMCID: PMC549575 DOI: 10.1093/nar/gni035] [Citation(s) in RCA: 968] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombineering allows DNA cloned in Escherichia coli to be modified via lambda (lambda) Red-mediated homologous recombination, obviating the need for restriction enzymes and DNA ligases to modify DNA. Here, we describe the construction of three new recombineering strains (SW102, SW105 and SW106) that allow bacterial artificial chromosomes (BACs) to be modified using galK positive/negative selection. This two-step selection procedure allows DNA to be modified without introducing an unwanted selectable marker at the modification site. All three strains contain an otherwise complete galactose operon, except for a precise deletion of the galK gene, and a defective temperature-sensitive lambda prophage that makes recombineering possible. SW105 and SW106 cells in addition carry l-arabinose-inducible Cre or Flp genes, respectively. The galK function can be selected both for and against. This feature greatly reduces the background seen in other negative-selection schemes, and galK selection is considerably more efficient than other related selection methods published. We also show how galK selection can be used to rapidly introduce point mutations, deletions and loxP sites into BAC DNA and thus facilitate functional studies of SNP and/or disease-causing point mutations, the identification of long-range regulatory elements and the construction of conditional targeting vectors.
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Affiliation(s)
| | - Nina Costantino
- Gene Regulation and Chromosome Biology Laboratory, National Cancer InstituteFrederick, MD 21702-1201, USA
| | - Donald L. Court
- Gene Regulation and Chromosome Biology Laboratory, National Cancer InstituteFrederick, MD 21702-1201, USA
| | | | - Neal G. Copeland
- To whom correspondence should be addressed at Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, West 7th Street at Fort Detrick, Bldg 539, PO Box B, Frederick, MD 21702-1201, USA. Tel: +1 301 846 1260; Fax: +1 301 846 6666;
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341
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Yosef I, Bloushtain N, Shapira M, Qimron U. Restoration of gene function by homologous recombination: from PCR to gene expression in one step. Appl Environ Microbiol 2005; 70:7156-60. [PMID: 15574912 PMCID: PMC535207 DOI: 10.1128/aem.70.12.7156-7160.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a simple method for single-step cloning of any PCR product into a plasmid. A novel selection principle has been applied, in which activation of a drug selection marker is achieved following homologous recombination. In this method a DNA fragment is amplified by PCR with standard oligonucleotides that contain flanking tails derived from the host plasmid and the complete lambdaPR or rrnA1 promoter regions. The resulting PCR product is then electroporated into an Escherichia coli strain harboring both the phage lambda Red functions and the host plasmid. Upon homologous recombination of the PCR fragment into the plasmid, expression of a drug selection marker is fully induced due to restoration of its truncated promoter, thus allowing appropriate selection. Recombinant plasmid vectors encoding beta-galactosidase and neomycin phosphotransferase were constructed by using this method in two well-known Red systems. This cloning strategy significantly reduces both the time and costs associated with cloning procedures.
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Affiliation(s)
- Ido Yosef
- Department of Microbiology and Immunology, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
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342
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Wu XS, Xin L, Yin WX, Shang XY, Lu L, Watt RM, Cheah KSE, Huang JD, Liu DP, Liang CC. Increased efficiency of oligonucleotide-mediated gene repair through slowing replication fork progression. Proc Natl Acad Sci U S A 2005; 102:2508-13. [PMID: 15695590 PMCID: PMC548982 DOI: 10.1073/pnas.0406991102] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Targeted gene modification mediated by single-stranded oligonucleotides (SSOs) holds great potential for widespread use in a number of biological and biomedical fields, including functional genomics and gene therapy. By using this approach, specific genetic changes have been created in a number of prokaryotic and eukaryotic systems. In mammalian cells, the precise mechanism of SSO-mediated chromosome alteration remains to be established, and there have been problems in obtaining reproducible targeting efficiencies. It has previously been suggested that the chromatin structure, which changes throughout the cell cycle, may be a key factor underlying these variations in efficiency. This hypothesis prompted us to systematically investigate SSO-mediated gene repair at various phases of the cell cycle in a mammalian cell line. We found that the efficiency of SSO-mediated gene repair was elevated by approximately 10-fold in thymidine-treated S-phase cells. The increase in repair frequency correlated positively with the duration of SSO/thymidine coincubation with host cells after transfection. We supply evidence suggesting that these increased repair frequencies arise from a thymidine-induced slowdown of replication fork progression. Our studies provide fresh insight into the mechanism of SSO-mediated gene repair in mammalian cells and demonstrate how its efficiency may be reliably and substantially increased.
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Affiliation(s)
- Xue-Song Wu
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, People's Republic of China
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343
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Volodin AA, Voloshin ON, Camerini-Otero RD. Homologous recombination and RecA protein: towards a new generation of tools for genome manipulations. Trends Biotechnol 2005; 23:97-102. [DOI: 10.1016/j.tibtech.2004.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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344
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Ferrara L, Parekh-Olmedo H, Kmiec EB. Enhanced oligonucleotide-directed gene targeting in mammalian cells following treatment with DNA damaging agents. Exp Cell Res 2004; 300:170-9. [PMID: 15383324 DOI: 10.1016/j.yexcr.2004.06.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2004] [Revised: 06/22/2004] [Indexed: 01/01/2023]
Abstract
Targeted gene repair, a form of oligonucleotide-directed mutagenesis, employs end-modified single-stranded DNA oligonucleotides to mediate single-base changes in chromosomal DNA. In this work, we use a specific 72-mer to direct the repair of a mutated eGFP gene stably integrated in the genome of DLD-1 cells. Corrected cells express eGFP that can be identified and quantitated by FACS. The repair of this mutant gene is dependent on the presence of a specifically designed oligonucleotide and the frequency with which the mutation is reversed is affected by the induction of DNA damage. We used hydroxyurea, VP16 (etoposide), and thymidine to modulate the rate of DNA replication through the stalling of the replication forks or the introduction of lesions. Addition of hydroxyurea or VP16 before the electroporation of the oligonucleotide, results in an accumulation of double-strand breaks (DSB) whose repair is facilitated by either nonhomologous end joining (NHEJ) or homologous recombination (HR). The addition of thymidine results in DNA damage within replication forks, damage that is repaired through the process of homologous recombination. Our data suggest that gene repair activity is elevated when DNA damage induces or activates the homologous recombination pathway.
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Affiliation(s)
- Luciana Ferrara
- Department of Biological Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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345
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Rybalchenko N, Golub EI, Bi B, Radding CM. Strand invasion promoted by recombination protein beta of coliphage lambda. Proc Natl Acad Sci U S A 2004; 101:17056-60. [PMID: 15574500 PMCID: PMC535401 DOI: 10.1073/pnas.0408046101] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Studies of phage lambda in vivo have indicated that its own recombination enzymes, beta protein and lambda exonuclease, are capable of catalyzing two dissimilar pathways of homologous recombination that are widely distributed in nature: single-strand annealing and strand invasion. The former is an enzymatic splicing of overlapping ends of broken homologous DNA molecules, whereas the latter is characterized by the formation of a three-stranded synaptic intermediate and subsequent strand exchange. Previous studies in vitro have shown that beta protein has annealing activity, and that lambda exonuclease, acting on branched substrates, can produce a perfect splice that requires only ligation for completion. The present study shows that beta protein can initiate strand invasion in vitro, as evidenced both by the formation of displacement loops (D-loops) in superhelical DNA and by strand exchange between colinear single-stranded and double-stranded molecules. Thus, beta protein can catalyze steps that are central to both strand annealing and strand invasion pathways of recombination. These observations add beta protein to a set of diverse proteins that appear to promote recognition of homology by a unitary mechanism governed by the intrinsic dynamic properties of base pairs in DNA.
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Affiliation(s)
- Nataliya Rybalchenko
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
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346
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Hope IA, Stevens J, Garner A, Hayes J, Cheo DL, Brasch MA, Vidal M. Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system. Genome Res 2004; 14:2070-5. [PMID: 15489328 PMCID: PMC528922 DOI: 10.1101/gr.2463804] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The understanding of gene function increasingly requires the characterization of DNA segments containing promoters and their associated regulatory sequences. We describe a novel approach for linking multiple DNA segments, here applied to the generation of promoter::reporter fusions. Promoters from Caenorhabditis elegans genes were cloned using the MultiSite Gateway cloning technology. The capacity for using this system for efficient construction of chimeric genes was explored by constructing promoter::reporter gene fusions with a gfp reporter. The promoters were found to provide appropriate expression of GFP upon introduction into C. elegans, demonstrating that the short Gateway recombination site between the promoter and the reporter did not interfere with transcription or translation. The recombinational cloning involved in the Gateway system, which permits the highly efficient and precise transfer of DNA segments between plasmid vectors, makes this technology ideal for genomics research programs.
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Affiliation(s)
- Ian A Hope
- School of Biology, University of Leeds, Leeds, LS2 9JT, UK.
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347
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Metzgar D, Bacher JM, Pezo V, Reader J, Döring V, Schimmel P, Marlière P, de Crécy-Lagard V. Acinetobacter sp. ADP1: an ideal model organism for genetic analysis and genome engineering. Nucleic Acids Res 2004; 32:5780-90. [PMID: 15514111 PMCID: PMC528786 DOI: 10.1093/nar/gkh881] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Revised: 08/30/2004] [Accepted: 09/21/2004] [Indexed: 11/15/2022] Open
Abstract
Acinetobacter sp. strain ADP1 is a naturally transformable gram-negative bacterium with simple culture requirements, a prototrophic metabolism and a compact genome of 3.7 Mb which has recently been sequenced. Wild-type ADP1 can be genetically manipulated by the direct addition of linear DNA constructs to log-phase cultures. This makes it an ideal organism for the automation of complex strain construction. Here, we demonstrate the flexibility and versatility of ADP1 as a genetic model through the construction of a broad variety of mutants. These include marked and unmarked insertions and deletions, complementary replacements, chromosomal expression tags and complex combinations thereof. In the process of these constructions, we demonstrate that ADP1 can effectively express a wide variety of foreign genes including antibiotic resistance cassettes, essential metabolic genes, negatively selectable catabolic genes and even intact operons from highly divergent bacteria. All of the described mutations were achieved by the same process of splicing PCR, direct transformation of growing cultures and plating on selective media. The simplicity of these tools make genetic analysis and engineering with Acinetobacter ADP1 accessible to laboratories with minimal microbial genetics expertise and very little equipment. They are also compatible with complete automation of genetic analysis and engineering protocols.
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Affiliation(s)
- David Metzgar
- The Scripps Research Institute, BCC-379, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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348
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Gust B, Chandra G, Jakimowicz D, Yuqing T, Bruton CJ, Chater KF. Lambda red-mediated genetic manipulation of antibiotic-producing Streptomyces. ADVANCES IN APPLIED MICROBIOLOGY 2004; 54:107-28. [PMID: 15251278 DOI: 10.1016/s0065-2164(04)54004-2] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Bertolt Gust
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, United Kingdom
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349
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Sparwasser T, Gong S, Li JYH, Eberl G. General method for the modification of different BAC types and the rapid generation of BAC transgenic mice. Genesis 2004; 38:39-50. [PMID: 14755803 DOI: 10.1002/gene.10249] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Most genome projects have relied on the sequencing of bacterial artificial chromosomes (BACs), which encompass 100-300 kb of genomic DNA. As a consequence, several thousand BAC clones are now mapped to the human and mouse genome. It is therefore possible to identify in silico a BAC clone that carries a particular gene and obtain it commercially. Given the large size of BACs, most if not all regulatory sequences of a gene are present and can be used to direct faithful and tissue-specific expression of heterologous genes in vitro in cell cultures and in vivo in BAC-transgenic mice. We describe here an optimized and comprehensive protocol to select, modify, and purify BACs in order to generate BAC-transgenic mice. Importantly, this protocol includes a method to generate, within 2 days, complex plasmid cassettes required to modify BACs, and to efficiently modify different types of BACs selected from the two major BAC libraries available. Altogether, using a combination of genomic database analysis, overlap PCR cloning, and BAC recombination in bacteria, our approach allows for the rapid and reliable generation of "pseudo knockin" mice. genesis 38:39-50, 2004.
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Affiliation(s)
- Tim Sparwasser
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
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350
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Campellone KG, Robbins D, Leong JM. EspFU Is a Translocated EHEC Effector that Interacts with Tir and N-WASP and Promotes Nck-Independent Actin Assembly. Dev Cell 2004; 7:217-28. [PMID: 15296718 DOI: 10.1016/j.devcel.2004.07.004] [Citation(s) in RCA: 263] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Revised: 05/28/2004] [Accepted: 05/28/2004] [Indexed: 02/08/2023]
Abstract
Several microbial pathogens including enteropathogenic E. coli (EPEC) exploit mammalian tyrosine-kinase signaling cascades to recruit Nck adaptor proteins and activate N-WASP-Arp2/3-mediated actin assembly. To promote localized actin "pedestal formation," EPEC translocates the bacterial effector protein Tir into the plasma membrane, where it is tyrosine-phosphorylated and binds Nck. Enterohemorrhagic E. coli (EHEC) also generates Tir-dependent pedestals, but in the absence of phosphotyrosines and Nck recruitment. To identify additional EHEC effectors that stimulate phosphotyrosine-independent actin assembly, we systematically generated EHEC mutants containing specific deletions in putative pathogenicity-islands. Among 0.33 Mb of deleted sequences, only one ORF was critical for pedestal formation. It lies within prophage-U, and encodes a protein similar to the known effector EspF. This proline-rich protein, EspFU, is the only EHEC effector of actin assembly absent from EPEC. Whereas EHEC Tir cannot efficiently recruit N-WASP or trigger actin polymerization, EspFU associates with Tir, binds N-WASP, and potently stimulates Nck-independent actin assembly.
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Affiliation(s)
- Kenneth G Campellone
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester 01655 USA
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