Genomes and Genes
Summary: Enzymes that catalyze the incorporation of deoxyribonucleotides into a chain of DNA. EC 2.7.7.-.
- Wong A, Draper B, Van Eenennaam A. FLPe functions in zebrafish embryos. Transgenic Res. 2011;20:409-15 pubmed publisher..Our results show that FLPe, which is derived from Saccharomyces cerevisiae, is an efficient recombinase in zebrafish maintained at 28.5°C. ..
- Kolb A. Genome engineering using site-specific recombinases. Cloning Stem Cells. 2002;4:65-80 pubmed..However, the vast repertoire of recombinases, which has recently become available as a result of large-scale sequencing projects, may provide a rich source for the development of novel strategies to precisely alter mammalian genomes. ..
- Voziyanov Y, Konieczka J, Stewart A, Jayaram M. Stepwise manipulation of DNA specificity in Flp recombinase: progressively adapting Flp to individual and combinatorial mutations in its target site. J Mol Biol. 2003;326:65-76 pubmed..Our results suggest that combined DNA shuffling and mutagenesis of libraries of Flp variants active on distinct mFRTs can yield variants that can recombine mFRTs containing combinations of the individual mutations. ..
- Merickel S, Johnson R. Topological analysis of Hin-catalysed DNA recombination in vivo and in vitro. Mol Microbiol. 2004;51:1143-54 pubmed..We also demonstrated that a single DNA exchange resulting in inversion in vitro is accompanied by a loss of four negative supercoils. ..
- Garcillán Barcia M, Jurado P, Gonzalez Perez B, Moncalian G, Fernandez L, de la Cruz F. Conjugative transfer can be inhibited by blocking relaxase activity within recipient cells with intrabodies. Mol Microbiol. 2007;63:404-16 pubmed..These findings demonstrate that the transferred relaxase plays an important role in the recipient cell and open a new approach to identify specific inhibitors of bacterial conjugation. ..
- Hekman K, Guja K, Larkin C, Schildbach J. An intrastrand three-DNA-base interaction is a key specificity determinant of F transfer initiation and of F TraI relaxase DNA recognition and cleavage. Nucleic Acids Res. 2008;36:4565-72 pubmed publisher..Oligonucleotide cleavage assay results suggest the essential function of the three-base interaction may be to position the scissile phosphate for cleavage, rather than to directly contribute to binding affinity. ..
- Patrick S, Parkhill J, McCoy L, Lennard N, Larkin M, Collins M, et al. Multiple inverted DNA repeats of Bacteroides fragilis that control polysaccharide antigenic variation are similar to the hin region inverted repeats of Salmonella typhimurium. Microbiology. 2003;149:915-24 pubmed..fragilis NCTC 9343, binds specifically to the invertible regions and the recombination sites have been designated as fragilis inversion cross-over (fix) sites. ..
- Gonzalez Perez B, Carballeira J, Moncalian G, de la Cruz F. Changing the recognition site of a conjugative relaxase by rational design. Biotechnol J. 2009;4:554-7 pubmed publisher..Using bacterial conjugation as an in vivo selection system, several TrwC variants were found that show changes in substrate specificity. These variants were also tested in a competitive assay to evaluate their conjugation efficiency. ..
- Vázquez Manrique R, Legg J, Olofsson B, Ly S, Baylis H. Improved gene targeting in C. elegans using counter-selection and Flp-mediated marker excision. Genomics. 2010;95:37-46 pubmed publisher..Using this strategy we have produced a knockout of the plc-4 gene, which encodes phospholipase C-delta in C. elegans, and demonstrated that conditional gene knockout is feasible in C. elegans. ..
- Boer R, Russi S, Guasch A, Lucas M, Blanco A, Perez Luque R, et al. Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site. J Mol Biol. 2006;358:857-69 pubmed
- Vetcher A, Lushnikov A, Navarra Madsen J, Scharein R, Lyubchenko Y, Darcy I, et al. DNA topology and geometry in Flp and Cre recombination. J Mol Biol. 2006;357:1089-104 pubmed..Only modest conformational changes within this structure are needed to form the symmetric, planar DNA junction, which may be characteristic of shorter-lived intermediates along the recombination pathway. ..
- Conway A, Chen Y, Rice P. Structural plasticity of the Flp-Holliday junction complex. J Mol Biol. 2003;326:425-34 pubmed..These results suggest a steric occlusion model for enforcement of half-of-the-sites activity. ..
- Rocco J, Churchward G. The integrase of the conjugative transposon Tn916 directs strand- and sequence-specific cleavage of the origin of conjugal transfer, oriT, by the endonuclease Orf20. J Bacteriol. 2006;188:2207-13 pubmed..Remarkably for a tyrosine recombinase, Tn916 Int acts as a specificity factor in the reaction, conferring both strand and sequence specificities on the endonucleolytic cleavage activity of Orf20. ..
- Rowland S, Boocock M, Stark W. Regulation of Sin recombinase by accessory proteins. Mol Microbiol. 2005;56:371-82 pubmed..We conclude that Sin bound at site II, and Hbsu, act together to control site I alignment and the topology of the synapse, and to stimulate strand exchange. ..
- Swalla B, Gumport R, Gardner J. Conservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain. Nucleic Acids Res. 2003;31:805-18 pubmed..In addition, the model predicts new residues that may participate in core-type DNA binding or dimerization, thereby providing hypotheses for future genetic and biochemical experiments. ..
- Kopke K, Hoff B, Kück U. Application of the Saccharomyces cerevisiae FLP/FRT recombination system in filamentous fungi for marker recycling and construction of knockout strains devoid of heterologous genes. Appl Environ Microbiol. 2010;76:4664-74 pubmed publisher..Here, we discuss the application of the optimized FLP/FRT recombination system as a molecular tool for the genetic manipulation of filamentous fungi. ..
- Akopian A, He J, Boocock M, Stark W. Chimeric recombinases with designed DNA sequence recognition. Proc Natl Acad Sci U S A. 2003;100:8688-91 pubmed..Our results demonstrate the functional autonomy of the resolvase catalytic domain and open the way to creating "custom-built" recombinases that act at chosen natural target sequences. ..
- Branda C, Dymecki S. Talking about a revolution: The impact of site-specific recombinases on genetic analyses in mice. Dev Cell. 2004;6:7-28 pubmed..By enabling high-fidelity DNA modifications to be induced in vitro or in vivo, these systems have incited a wave of new biology, advancing our understanding of gene function, genetic relationships, development, and disease. ..
- ElAntak L, Ansaldi M, Guerlesquin F, Mejean V, Morelli X. Structural and genetic analyses reveal a key role in prophage excision for the TorI response regulator inhibitor. J Biol Chem. 2005;280:36802-8 pubmed..Our findings suggest that TorI-related proteins identified in various pathogenic bacterial genomes define a new family of atypical excisionases. ..
- Xiong L, Chen X, Silver H, Ahmed N, Johnson E. Deficient SUMO attachment to Flp recombinase leads to homologous recombination-dependent hyperamplification of the yeast 2 microm circle plasmid. Mol Biol Cell. 2009;20:1241-51 pubmed publisher..This work also illustrates the importance of using cir(o) strains when studying mutants that affect the yeast SUMO pathway, to avoid confusing direct functions of the SUMO pathway with secondary effects of 2 microm amplification. ..
- Vanhooff V, Galloy C, Agaisse H, Lereclus D, Revet B, Hallet B. Self-control in DNA site-specific recombination mediated by the tyrosine recombinase TnpI. Mol Microbiol. 2006;60:617-29 pubmed..A model for the organization of TnpI/IRS recombination complex is presented. ..
- Burrus V, Waldor M. Control of SXT integration and excision. J Bacteriol. 2003;185:5045-54 pubmed..SXT excision and transfer from a donor containing pntB::SXT were reduced, suggesting that the SXT integration site may also influence the element's transmissibility. ..
- Gaj T, Mercer A, Gersbach C, Gordley R, Barbas C. Structure-guided reprogramming of serine recombinase DNA sequence specificity. Proc Natl Acad Sci U S A. 2011;108:498-503 pubmed publisher..These results demonstrate that unique resolvase and invertase derivatives can be developed to site-specifically modify the human genome in the context of zinc-finger recombinase fusion proteins. ..
- Du Q, Livshits A, Kwiatek A, Jayaram M, Vologodskii A. Protein-induced local DNA bends regulate global topology of recombination products. J Mol Biol. 2007;368:170-82 pubmed..Our findings have general implications in how small protein machines acting locally on large DNA molecules exploit statistical properties of their substrates to bring about directed global changes in topology. ..
- Luo K, Sun M, Deng W, Xu S. Excision of selectable marker gene from transgenic tobacco using the GM-gene-deletor system regulated by a heat-inducible promoter. Biotechnol Lett. 2008;30:1295-302 pubmed publisher..Our approach provides a reliable strategy for auto-excising a selectable marker gene from calli, shoots or other tissues of transgenic plants after transformation and producing marker-free transgenic plants. ..
- Schnütgen F, Stewart A, von Melchner H, Anastassiadis K. Engineering embryonic stem cells with recombinase systems. Methods Enzymol. 2006;420:100-36 pubmed..The upcoming ESC resource and the increasing sophistication of site-specific recombination technologies will greatly assist the functional annotation of the human genome and the animal modeling of human disease. ..
- Malchin N, Molotsky T, Borovok I, Voziyanov Y, Kotlyar A, Yagil E, et al. High efficiency of a sequential recombinase-mediated cassette exchange reaction in Escherichia coli. J Mol Microbiol Biotechnol. 2010;19:117-22 pubmed publisher..Atomic force microscopy images of Flp with its DNA substrates show that only 1 pair of recombination sites forms a synaptic complex with the recombinase. The results suggest that the RMCE reaction is sequential. ..
- Andreas S, Schwenk F, Küter Luks B, Faust N, Kühn R. Enhanced efficiency through nuclear localization signal fusion on phage PhiC31-integrase: activity comparison with Cre and FLPe recombinase in mammalian cells. Nucleic Acids Res. 2002;30:2299-306 pubmed
- Monzingo A, Ozburn A, Xia S, Meyer R, Robertus J. The structure of the minimal relaxase domain of MobA at 2.1 A resolution. J Mol Biol. 2007;366:165-78 pubmed..The model is consistent with observations of substrate base specificity, and provides a rationalization for elements of the likely enzyme mechanism. ..
- Hare P, Chua N. Excision of selectable marker genes from transgenic plants. Nat Biotechnol. 2002;20:575-80 pubmed..The implementation of these strategies in crops and their further improvement will help to expedite widespread public acceptance of agricultural biotechnology ..
- Guasch A, Lucas M, Moncalian G, Cabezas M, Perez Luque R, Gomis Ruth F, et al. Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Nat Struct Biol. 2003;10:1002-10 pubmed..Structural analysis combined with site-directed mutagenesis defines the architecture of the active site. ..
- Rowland S, Boocock M, Stark W. DNA bending in the Sin recombination synapse: functional replacement of HU by IHF. Mol Microbiol. 2006;59:1730-43 pubmed
- Lee L, Sadowski P. Strand selection by the tyrosine recombinases. Prog Nucleic Acid Res Mol Biol. 2005;80:1-42 pubmed
- Lujan S, Guogas L, Ragonese H, Matson S, Redinbo M. Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase. Proc Natl Acad Sci U S A. 2007;104:12282-7 pubmed..Thus, the inhibition of conjugative relaxases is a potentially novel antimicrobial approach, one that selectively targets bacteria capable of transferring antibiotic resistance and generating multidrug resistant strains. ..
- Cobellis G, Nicolaus G, Iovino M, Romito A, Marra E, Barbarisi M, et al. Tagging genes with cassette-exchange sites. Nucleic Acids Res. 2005;33:e44 pubmed..We believe that this system will facilitate in vivo studies of gene function and large-scale generation of mouse models of human diseases, caused by not only loss but also gain of function alleles. ..
- Takata Y, Kondo S, Goda N, Kanegae Y, Saito I. Comparison of efficiency between FLPe and Cre for recombinase-mediated cassette exchange in vitro and in adenovirus vector production. Genes Cells. 2011;16:765-77 pubmed publisher..Thus, although Cre is considered more active than, or similar to, FLPe, it may not be necessarily true for RMCE reaction. Possible reasons explaining these results are discussed. ..
- Ghosh K, Lau C, Guo F, Segall A, Van Duyne G. Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination. J Biol Chem. 2005;280:8290-9 pubmed..Peptide binding induces large conformational changes in the DNA strands of the HJ intermediate, which affect the active site geometries in the recombinase subunits. ..
- Dostál L, Schildbach J. Single-stranded DNA binding by F TraI relaxase and helicase domains is coordinately regulated. J Bacteriol. 2010;192:3620-8 pubmed publisher..These results suggest that the apparent negative cooperativity of binding to the two ssDNA binding sites of TraI serves a major regulatory function in F transfer. ..
- Venken K, Bellen H. Genome-wide manipulations of Drosophila melanogaster with transposons, Flp recombinase, and ?C31 integrase. Methods Mol Biol. 2012;859:203-28 pubmed publisher..This chapter focuses on genome-wide applications of transposons, Flp recombinase, and ?C31 integrase that greatly facilitate experimental manipulation of Drosophila. ..
- Yamamoto M, Shook N, Kanisicak O, Yamamoto S, Wosczyna M, Camp J, et al. A multifunctional reporter mouse line for Cre- and FLP-dependent lineage analysis. Genesis. 2009;47:107-14 pubmed publisher..Finally, by the simultaneous use of both Cre and FLP deleters, R26(NZG) allows lineage relationships to be interrogated with greater refinement than is possible with single recombinase reporter systems. ..
- Schucht R, Coroadinha A, Zanta Boussif M, Verhoeyen E, Carrondo M, Hauser H, et al. A new generation of retroviral producer cells: predictable and stable virus production by Flp-mediated site-specific integration of retroviral vectors. Mol Ther. 2006;14:285-92 pubmed..This method is compatible with other retroviral vectors, including self-inactivating vectors and marker-free vectors. Further, it provides a tool for evaluation of different retroviral vector designs. ..
- Djukanovic V, Lenderts B, Bidney D, Lyznik L. A Cre::FLP fusion protein recombines FRT or loxP sites in transgenic maize plants. Plant Biotechnol J. 2008;6:770-81 pubmed publisher..The crossing strategy proved to be suitable for the genetic engineering of maize using the FLP or Cre site-specific recombination system. ..
- Pinkney J, Zawadzki P, Mazuryk J, Arciszewska L, Sherratt D, Kapanidis A. Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence. Proc Natl Acad Sci U S A. 2012;109:20871-6 pubmed publisher..After recombination, the product synaptic complex was extremely stable and refractory to subsequent rounds of recombination. ..
- Anderson R, Voziyanova E, Voziyanov Y. Flp and Cre expressed from Flp-2A-Cre and Flp-IRES-Cre transcription units mediate the highest level of dual recombinase-mediated cassette exchange. Nucleic Acids Res. 2012;40:e62 pubmed publisher..The analysis shows that it is the relative Flp-to-Cre ratio that critically affects the efficiency of dual RMCE. Our results will be helpful for maximizing the efficiency of dual RMCE aimed to engineer and re-engineer genomes. ..
- Uemura M, Niwa Y, Kakazu N, Adachi N, Kinoshita K. Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors. PLoS ONE. 2010;5:e9846 pubmed publisher..g. embryonic stem cells). Experimental use of this system would open up new horizons in genome biology, including the establishment of cellular and animal models of diseases caused by translocations and copy-number variations. ..
- Sanders E, Johnson R. Stepwise dissection of the Hin-catalyzed recombination reaction from synapsis to resolution. J Mol Biol. 2004;340:753-66 pubmed..Subsequent steps of the reaction, including DNA exchange and ligation, are fast. Thus, post-synaptic step(s) required for DNA cleavage limit the overall rate of the recombination reaction. ..
- Hunter N, Awatramani R, Farley F, Dymecki S. Ligand-activated Flpe for temporally regulated gene modifications. Genesis. 2005;41:99-109 pubmed
- Rowland S, Stark W, Boocock M. Sin recombinase from Staphylococcus aureus: synaptic complex architecture and transposon targeting. Mol Microbiol. 2002;44:607-19 pubmed..Our model for the recombination synapse has at its core an assembly of four Sin dimers; Hbsu plays an architectural role that is taken by two resolvase dimers in models of the Tn3/gammadelta synapse. ..