1
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Rodgers KK. Riches in RAGs: Revealing the V(D)J Recombinase through High-Resolution Structures. Trends Biochem Sci 2016; 42:72-84. [PMID: 27825771 DOI: 10.1016/j.tibs.2016.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/04/2016] [Accepted: 10/17/2016] [Indexed: 12/15/2022]
Abstract
Development of the adaptive immune system is dependent on V(D)J recombination, which forms functional antigen receptor genes through rearrangement of component gene segments. The V(D)J recombinase, comprising recombination-activating proteins RAG1 and RAG2, guides the initial DNA cleavage events to the recombination signal sequence (RSS), which flanks each gene segment. Although the enzymatic steps for RAG-mediated endonucleolytic activity were established over two decades ago, only recently have high-resolution structural studies of the catalytically active core regions of the RAG proteins shed light on conformational requirements for the reaction. While outstanding questions remain, we have a clearer picture of how RAG proteins function in generating the diverse repertoires of antigen receptors, the underlying foundation of the adaptive immune system.
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Affiliation(s)
- Karla K Rodgers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA.
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2
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Morris ER, Grey H, McKenzie G, Jones AC, Richardson JM. A bend, flip and trap mechanism for transposon integration. eLife 2016; 5. [PMID: 27223327 PMCID: PMC5481204 DOI: 10.7554/elife.15537] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022] Open
Abstract
Cut-and-paste DNA transposons of the mariner/Tc1 family are useful tools for genome engineering and are inserted specifically at TA target sites. A crystal structure of the mariner transposase Mos1 (derived from Drosophila mauritiana), in complex with transposon ends covalently joined to target DNA, portrays the transposition machinery after DNA integration. It reveals severe distortion of target DNA and flipping of the target adenines into extra-helical positions. Fluorescence experiments confirm dynamic base flipping in solution. Transposase residues W159, R186, F187 and K190 stabilise the target DNA distortions and are required for efficient transposon integration and transposition in vitro. Transposase recognises the flipped target adenines via base-specific interactions with backbone atoms, offering a molecular basis for TA target sequence selection. Our results will provide a template for re-designing mariner/Tc1 transposases with modified target specificities. DOI:http://dx.doi.org/10.7554/eLife.15537.001 The complete set of DNA in a cell is referred to as its genome. Most genomes contain short fragments of DNA called transposons that can jump from one place to another. Transposons carry sections of DNA with them when they move, which creates diversity and can influence the evolution of a species. Transposons are also being exploited to develop tools for biotechnology and medical applications. One family of transposons – the Mariner/Tc1 family – has proved particularly useful in these endeavours because it is widespread in nature and can jump around the genomes of a broad range of species, including mammals. DNA transposons are cut out of their position and then pasted at a new site by an enzyme called transposase, which is encoded by some of the DNA within the transposon. DNA is made up of strings of molecules called bases and Mariner/Tc1-family transposons can only insert into a new position in the genome at sites that have a specific sequence of two bases. However, it was not known how this target sequence is chosen and how the transposon inserts into it. Morris et al. have now used a technique called X-ray crystallography to build a three-dimensional model of a Mariner/Tc1-family transposon as it inserts into a new position. The model shows that, as the transposon is pasted into its new site, the surrounding DNA bends. This causes two DNA bases in the surrounding DNA to flip out from their normal position in the DNA molecule, which enables them to be recognised by the transposase. Further experiments showed that this base-flipping is dynamic, that is, the two bases continuously flip in and out of position. Furthermore, Morris et al. identified which parts of the transposase enzyme are required for the transposon to be efficiently pasted into the genome. Together these findings may help researchers to alter the transposase so that it can insert the transposon into different locations in a genome. This will hopefully lead to new tools for biotechnology and medical applications. DOI:http://dx.doi.org/10.7554/eLife.15537.002
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Affiliation(s)
- Elizabeth R Morris
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Heather Grey
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Anita C Jones
- EaStCHEM School of Chemistry, Edinburgh, United Kingdom
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
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3
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Abstract
The IS630-Tc1-mariner (ITm) family of transposons is one of the most widespread in nature. The phylogenetic distribution of its members shows that they do not persist for long in a given lineage, but rely on frequent horizontal transfer to new hosts. Although they are primarily selfish genomic-parasites, ITm transposons contribute to the evolution of their hosts because they generate variation and contribute protein domains and regulatory regions. Here we review the molecular mechanism of ITm transposition and its regulation. We focus mostly on the mariner elements, which are understood in the greatest detail owing to in vitro reconstitution and structural analysis. Nevertheless, the most important characteristics are probably shared across the grouping. Members of the ITm family are mobilized by a cut-and-paste mechanism and integrate at 5'-TA dinucleotide target sites. The elements encode a single transposase protein with an N-terminal DNA-binding domain and a C-terminal catalytic domain. The phosphoryl-transferase reactions during the DNA-strand breaking and joining reactions are performed by the two metal-ion mechanism. The metal ions are coordinated by three or four acidic amino acid residues located within an RNase H-like structural fold. Although all of the strand breaking and joining events at a given transposon end are performed by a single molecule of transposase, the reaction is coordinated by close communication between transpososome components. During transpososome assembly, transposase dimers compete for free transposon ends. This helps to protect the host by dampening an otherwise exponential increase in the rate of transposition as the copy number increases.
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4
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Biochemical Characterization of Kat1: a Domesticated hAT-Transposase that Induces DNA Hairpin Formation and MAT-Switching. Sci Rep 2016; 6:21671. [PMID: 26902909 PMCID: PMC4763223 DOI: 10.1038/srep21671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 01/28/2016] [Indexed: 11/08/2022] Open
Abstract
Kluyveromyces lactis hAT-transposase 1 (Kat1) generates hairpin-capped DNA double strand breaks leading to MAT-switching (MATa to MATα). Using purified Kat1, we demonstrate the importance of terminal inverted repeats and subterminal repeats for its endonuclease activity. Kat1 promoted joining of the transposon end into a target DNA molecule in vitro, a biochemical feature that ties Kat1 to transposases. Gas-phase Electrophoretic Mobility Macromolecule analysis revealed that Kat1 can form hexamers when complexed with DNA. Kat1 point mutants were generated in conserved positions to explore structure-function relationships. Mutants of predicted catalytic residues abolished both DNA cleavage and strand-transfer. Interestingly, W576A predicted to be impaired for hairpin formation, was active for DNA cleavage and supported wild type levels of mating-type switching. In contrast, the conserved CXXH motif was critical for hairpin formation because Kat1 C402A/H405A completely blocked hairpinning and switching, but still generated nicks in the DNA. Mutations in the BED zinc-finger domain (C130A/C133A) resulted in an unspecific nuclease activity, presumably due to nonspecific DNA interaction. Kat1 mutants that were defective for cleavage in vitro were also defective for mating-type switching. Collectively, this study reveals Kat1 sharing extensive biochemical similarities with cut and paste transposons despite being domesticated and evolutionary diverged from active transposons.
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5
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Crystal structure of the V(D)J recombinase RAG1-RAG2. Nature 2015; 518:507-11. [PMID: 25707801 DOI: 10.1038/nature14174] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/22/2014] [Indexed: 01/30/2023]
Abstract
V(D)J recombination in the vertebrate immune system generates a highly diverse population of immunoglobulins and T-cell receptors by combinatorial joining of segments of coding DNA. The RAG1-RAG2 protein complex initiates this site-specific recombination by cutting DNA at specific sites flanking the coding segments. Here we report the crystal structure of the mouse RAG1-RAG2 complex at 3.2 Å resolution. The 230-kilodalton RAG1-RAG2 heterotetramer is 'Y-shaped', with the amino-terminal domains of the two RAG1 chains forming an intertwined stalk. Each RAG1-RAG2 heterodimer composes one arm of the 'Y', with the active site in the middle and RAG2 at its tip. The RAG1-RAG2 structure rationalizes more than 60 mutations identified in immunodeficient patients, as well as a large body of genetic and biochemical data. The architectural similarity between RAG1 and the hairpin-forming transposases Hermes and Tn5 suggests the evolutionary conservation of these DNA rearrangements.
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6
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Hickman AB, Ewis HE, Li X, Knapp JA, Laver T, Doss AL, Tolun G, Steven AC, Grishaev A, Bax A, Atkinson PW, Craig NL, Dyda F. Structural basis of hAT transposon end recognition by Hermes, an octameric DNA transposase from Musca domestica. Cell 2014; 158:353-367. [PMID: 25036632 DOI: 10.1016/j.cell.2014.05.037] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/10/2014] [Accepted: 05/12/2014] [Indexed: 11/25/2022]
Abstract
Hermes is a member of the hAT transposon superfamily that has active representatives, including McClintock's archetypal Ac mobile genetic element, in many eukaryotic species. The crystal structure of the Hermes transposase-DNA complex reveals that Hermes forms an octameric ring organized as a tetramer of dimers. Although isolated dimers are active in vitro for all the chemical steps of transposition, only octamers are active in vivo. The octamer can provide not only multiple specific DNA-binding domains to recognize repeated subterminal sequences within the transposon ends, which are important for activity, but also multiple nonspecific DNA binding surfaces for target capture. The unusual assembly explains the basis of bipartite DNA recognition at hAT transposon ends, provides a rationale for transposon end asymmetry, and suggests how the avidity provided by multiple sites of interaction could allow a transposase to locate its transposon ends amidst a sea of chromosomal DNA.
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Affiliation(s)
- Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hosam E Ewis
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xianghong Li
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joshua A Knapp
- Graduate Program in Biochemistry and Molecular Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Thomas Laver
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California Riverside, Riverside, CA 92521, USA
| | - Anna-Louise Doss
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Gökhan Tolun
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander Grishaev
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter W Atkinson
- Graduate Program in Biochemistry and Molecular Biology, University of California Riverside, Riverside, CA 92521, USA; Graduate Program in Genetics, Genomics, and Bioinformatics, University of California Riverside, Riverside, CA 92521, USA; Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside, Riverside, CA 92521, USA; Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Nancy L Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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7
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Simon Davis DA, Parish CR. Heparan sulfate: a ubiquitous glycosaminoglycan with multiple roles in immunity. Front Immunol 2013; 4:470. [PMID: 24391644 PMCID: PMC3866581 DOI: 10.3389/fimmu.2013.00470] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/05/2013] [Indexed: 12/20/2022] Open
Abstract
Heparan sulfate (HS) is a highly acidic linear polysaccharide with a very variable structure. It is ubiquitously expressed on cell surfaces and in the extracellular matrix and basement membrane of mammalian tissues. Synthesized attached to various core proteins to form HS-proteoglycans, HS is capable of interacting with various polypeptides and exerting diverse functions. In fact, a bioinformatics analysis of mammalian proteins that express a heparin/HS-binding motif and are associated with the immune system identified 235 candidate proteins, the majority having an intracellular location. This simple analysis suggests that HS may, in fact, interact with many more components of the immune system than previously realized. Numerous studies have also directly demonstrated that HS plays multiple prominent functional roles in the immune system that are briefly reviewed in this article. In particular, the molecule has been shown to regulate leukocyte development, leukocyte migration, immune activation, and inflammatory processes.
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Affiliation(s)
- David Anak Simon Davis
- Cancer and Vascular Biology Group, Department of Immunology, The John Curtin School of Medical Research, Australian National University , Canberra, ACT , Australia
| | - Christopher R Parish
- Cancer and Vascular Biology Group, Department of Immunology, The John Curtin School of Medical Research, Australian National University , Canberra, ACT , Australia
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8
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Shi K, Huang WM, Aihara H. An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation. PLoS Biol 2013; 11:e1001472. [PMID: 23382649 PMCID: PMC3558466 DOI: 10.1371/journal.pbio.1001472] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 12/12/2012] [Indexed: 12/19/2022] Open
Abstract
Crystal structures reveal catalysis of DNA refolding in the molecular mechanism underlying generation of bacterial hairpin telomeres. Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting–rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions. Linear chromosomes capped by hairpin telomeres are widespread in prokaryotes and are found in important bacterial pathogens. However, three-dimensional structure of the hairpin telomere, as well as the molecular mechanisms underlying its generation, has remained poorly understood. In this work, we investigated how the enzyme responsible for generating the bacterial hairpin telomeres (protelomerase, also known as telomere resolvase) transforms a linear double-stranded DNA molecule into sharp hairpin turns. Our X-ray crystallographic and biochemical data collectively suggest that protelomerase employs a multistep DNA strand-refolding mechanism as described below. Protelomerase first cleaves both strands of a double-helical DNA substrate and reshapes the DNA strands into a transition state conformation (refolding intermediate) stabilized by specific protein–DNA and DNA–DNA interactions including noncanonical (non-Watson–Crick) base-pairs. The DNA strands are then refolded into extremely compact hairpin products, stabilized by a set of interactions distinct from those stabilizing the refolding intermediate. We believe that an enzyme “catalyzing” not only the chemical reactions of DNA strand cutting/rejoining but also the ordered transition between different DNA conformations to guide refolding of the DNA strand is a novel concept, and we suspect that similar mechanisms may be employed by other enzymes involved in conformational changes/refolding of biological macromolecules.
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Affiliation(s)
- Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Wai Mun Huang
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah, United States of America
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
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9
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Abstract
Maize Activator (Ac) is one of the prototype transposable elements of the hAT transposon superfamily, members of which were identified in plants, fungi, and animals. The autonomous Ac and nonautonomous Dissociation (Ds) elements are mobilized by the single transposase protein encoded by Ac. To date Ac/Ds transposons were shown to be functional in approximately 20 plant species and have become the most widely used transposable elements for gene tagging and functional genomics approaches in plants. In this chapter we review the biology, regulation, and transposition mechanism of Ac/Ds elements in maize and heterologous plants. We discuss the parameters that are known to influence the functionality and transposition efficiency of Ac/Ds transposons and need to be considered when designing Ac transposase expression constructs and Ds elements for application in heterologous plant species.
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Affiliation(s)
- Katina Lazarow
- Leibniz-Institute for Molecular Pharmacology (FMP), Berlin, Germany
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10
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Abstract
V(D)J recombination assembles immunoglobulin and T cell receptor genes during lymphocyte development through a series of carefully orchestrated DNA breakage and rejoining events. DNA cleavage requires a series of protein-DNA complexes containing the RAG1 and RAG2 proteins and recombination signals that flank the recombining gene segments. In this review, we discuss recent advances in our understanding of the function and domain organization of the RAG proteins, the composition and structure of RAG-DNA complexes, and the pathways that lead to the formation of these complexes. We also consider the functional significance of RAG-mediated histone recognition and ubiquitin ligase activities, and the role played by RAG in ensuring proper repair of DNA breaks made during V(D)J recombination. Finally, we propose a model for the formation of RAG-DNA complexes that involves anchoring of RAG1 at the recombination signal nonamer and RAG2-dependent surveillance of adjoining DNA for suitable spacer and heptamer sequences.
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Affiliation(s)
- David G Schatz
- Department of Immunobiology and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06520-8011, USA.
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11
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Desiderio S. Temporal and spatial regulatory functions of the V(D)J recombinase. Semin Immunol 2010; 22:362-9. [PMID: 21036059 DOI: 10.1016/j.smim.2010.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 12/20/2022]
Abstract
In developing lymphocytes, V(D)J recombination is subject to tight spatial and temporal regulation. An emerging body of evidence indicates that some of these constraints, particularly with respect to locus specificity and cell cycle phase, are enforced by regulatory cues that converge directly on the RAG proteins themselves. Active chromatin is bound by RAG-2 through a specific histone modification that may serve the recombinase as an allosteric activator as well as a docking site. RAG-1 possesses intrinsic histone ubiquitin ligase activity, suggesting that the recombinase not only responds to chromatin modification but is itself able to modify chromatin. The cyclin A/Cdk2 component of the cell cycle clock triggers periodic destruction of RAG-2, thereby restricting V(D)J recombination to the G0/G1 cell cycle phases. These examples illustrate that the RAG proteins, in addition to their direct actions on DNA, are able to detect and respond to intracellular signals, thereby coordinating recombinase activity with intracellular processes such as cell division and transcription.
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Affiliation(s)
- Stephen Desiderio
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21210, United States
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12
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Hickman AB, Chandler M, Dyda F. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 2010; 45:50-69. [PMID: 20067338 DOI: 10.3109/10409230903505596] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA rearrangements are important in genome function and evolution. Genetic material can be rearranged inadvertently during processes such as DNA repair, or can be moved in a controlled manner by enzymes specifically dedicated to the task. DNA transposases comprise one class of such enzymes. These move DNA segments known as transposons to new locations, without the need for sequence homology between transposon and target site. Several biochemically distinct pathways have evolved for DNA transposition, and genetic and biochemical studies have provided valuable insights into many of these. However, structural information on transposases - particularly with DNA substrates - has proven elusive in most cases. On the other hand, large-scale genome sequencing projects have led to an explosion in the number of annotated prokaryotic and eukaryotic mobile elements. Here, we briefly review biochemical and mechanistic aspects of DNA transposition, and propose that integrating sequence information with structural information using bioinformatics tools such as secondary structure prediction and protein threading can lead not only to an additional level of understanding but possibly also to testable hypotheses regarding transposition mechanisms. Detailed understanding of transposition pathways is a prerequisite for the long-term goal of exploiting DNA transposons as genetic tools and as a basis for genetic medical applications.
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Affiliation(s)
- Alison Burgess Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.
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13
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Arnal SM, Holub AJ, Salus SS, Roth DB. Non-consensus heptamer sequences destabilize the RAG post-cleavage complex, making ends available to alternative DNA repair pathways. Nucleic Acids Res 2010; 38:2944-54. [PMID: 20139091 PMCID: PMC2875030 DOI: 10.1093/nar/gkp1252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
V(D)J recombination entails double-stranded DNA cleavage at the antigen receptor loci by the RAG1/2 proteins, which recognize conserved recombination signal sequences (RSSs) adjoining variable (V), diversity (D) and joining (J) gene segments. After cleavage, RAG1/2 remain associated with the coding and signal ends (SE) in a post-cleavage complex (PCC), which is critical for their proper joining by classical non-homologous end joining (NHEJ). Certain mutations in RAG1/2 destabilize the PCC, allowing DNA ends to access inappropriate repair pathways such as alternative NHEJ, an error-prone pathway implicated in chromosomal translocations. The PCC is thus thought to discourage aberrant rearrangements by controlling repair pathway choice. Since interactions between RAG1/2 and the RSS heptamer element are especially important in forming the RAG-SE complex, we hypothesized that non-consensus heptamer sequences might affect PCC stability. We find that certain non-consensus heptamers, including a cryptic heptamer implicated in oncogenic chromosomal rearrangements, destabilize the PCC, allowing coding and SEs to be repaired by non-standard pathways, including alternative NHEJ. These data suggest that some non-consensus RSS, frequently present at chromosomal translocations in lymphoid neoplasms, may promote genomic instability by a novel mechanism, disabling the PCC’s ability to restrict repair pathway choice.
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Affiliation(s)
- Suzzette M Arnal
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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14
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Base flipping in V(D)J recombination: insights into the mechanism of hairpin formation, the 12/23 rule, and the coordination of double-strand breaks. Mol Cell Biol 2009; 29:5889-99. [PMID: 19720743 DOI: 10.1128/mcb.00187-09] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tn5 transposase cleaves the transposon end using a hairpin intermediate on the transposon end. This involves a flipped base that is stacked against a tryptophan residue in the protein. However, many other members of the cut-and-paste transposase family, including the RAG1 protein, produce a hairpin on the flanking DNA. We have investigated the reversed polarity of the reaction for RAG recombination. Although the RAG proteins appear to employ a base-flipping mechanism using aromatic residues, the putatively flipped base is not at the expected location and does not appear to stack against any of the said aromatic residues. We propose an alternative model in which a flipped base is accommodated in a nonspecific pocket or cleft within the recombinase. This is consistent with the location of the flipped base at position -1 in the coding flank, which can be occupied by purine or pyrimidine bases that would be difficult to stabilize using a single, highly specific, interaction. Finally, during this work we noticed that the putative base-flipping events on either side of the 12/23 recombination signal sequence paired complex are coupled to the nicking steps and serve to coordinate the double-strand breaks on either side of the complex.
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15
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Grundy GJ, Ramón-Maiques S, Dimitriadis EK, Kotova S, Biertümpfel C, Heymann JB, Steven AC, Gellert M, Yang W. Initial stages of V(D)J recombination: the organization of RAG1/2 and RSS DNA in the postcleavage complex. Mol Cell 2009; 35:217-27. [PMID: 19647518 DOI: 10.1016/j.molcel.2009.06.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 05/27/2009] [Accepted: 06/25/2009] [Indexed: 11/30/2022]
Abstract
To obtain structural information on the early stages of V(D)J recombination, we isolated a complex of the core RAG1 and RAG2 proteins with DNA containing a pair of cleaved recombination signal sequences (RSS). Stoichiometric and molecular mass analysis established that this signal-end complex (SEC) contains two protomers each of RAG1 and RAG2. Visualization of the SEC by negative-staining electron microscopy revealed an anchor-shaped particle with approximate two-fold symmetry. Consistent with a parallel arrangement of DNA and protein subunits, the N termini of RAG1 and RAG2 are positioned at opposing ends of the complex, and the DNA chains beyond the RSS nonamer emerge from the same face of the complex, near the RAG1 N termini. These first images of the V(D)J recombinase in its postcleavage state provide a framework for modeling RAG domains and their interactions with DNA.
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Affiliation(s)
- Gabrielle J Grundy
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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16
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Gwyn LM, Peak MM, De P, Rahman NS, Rodgers KK. A zinc site in the C-terminal domain of RAG1 is essential for DNA cleavage activity. J Mol Biol 2009; 390:863-78. [PMID: 19500590 PMCID: PMC2782368 DOI: 10.1016/j.jmb.2009.05.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 05/28/2009] [Indexed: 11/24/2022]
Abstract
The recombination-activating protein, RAG1, a key component of the V(D)J recombinase, binds multiple Zn(2+) ions in its catalytically required core region. However, the role of zinc in the DNA cleavage activity of RAG1 is not well resolved. To address this issue, we determined the stoichiometry of Zn(2+) ions bound to the catalytically active core region of RAG1 under various conditions. Using metal quantitation methods, we determined that core RAG1 can bind up to four Zn(2+) ions. Stripping the full complement of bound Zn(2+) ions to produce apoprotein abrogated DNA cleavage activity. Moreover, even partial removal of zinc-binding equivalents resulted in a significant diminishment of DNA cleavage activity, as compared to holo-Zn(2+) core RAG1. Mutants of the intact core RAG1 and the isolated core RAG1 domains were studied to identify the location of zinc-binding sites. Significantly, the C-terminal domain in core RAG1 binds at least two Zn(2+) ions, with one zinc-binding site containing C902 and C907 as ligands (termed the CC zinc site) and H937 and H942 coordinating a Zn(2+) ion in a separate site (HH zinc site). The latter zinc-binding site is essential for DNA cleavage activity, given that the H937A and H942A mutants were defective in both in vitro DNA cleavage assays and cellular recombination assays. Furthermore, as mutation of the active-site residue E962 reduces Zn(2+) coordination, we propose that the HH zinc site is located in close proximity to the DDE active site. Overall, these results demonstrate that Zn(2+) serves an important auxiliary role for RAG1 DNA cleavage activity. Furthermore, we propose that one of the zinc-binding sites is linked to the active site of core RAG1 directly or indirectly by E962.
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Affiliation(s)
| | | | - Pallabi De
- Department of Biochemistry and Molecular Biology The University of Oklahoma Health Sciences Center Oklahoma City, Oklahoma 73190
| | - Negar S. Rahman
- Department of Biochemistry and Molecular Biology The University of Oklahoma Health Sciences Center Oklahoma City, Oklahoma 73190
| | - Karla K. Rodgers
- Department of Biochemistry and Molecular Biology The University of Oklahoma Health Sciences Center Oklahoma City, Oklahoma 73190
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17
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Bischerour J, Chalmers R. Base flipping in tn10 transposition: an active flip and capture mechanism. PLoS One 2009; 4:e6201. [PMID: 19593448 PMCID: PMC2705183 DOI: 10.1371/journal.pone.0006201] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 05/25/2009] [Indexed: 11/19/2022] Open
Abstract
The bacterial Tn5 and Tn10 transposases have a single active site that cuts both strands of DNA at their respective transposon ends. This is achieved using a hairpin intermediate that requires the DNA to change conformation during the reaction. In Tn5 these changes are controlled in part by a flipped nucleoside that is stacked on a tryptophan residue in a hydrophobic pocket of the transposase. Here we have investigated the base flipping mechanism in Tn10 transposition. As in Tn5 transposition, we find that base flipping takes place after the first nick and is required for efficient hairpin formation and resolution. Experiments with an abasic substrate show that the role of base flipping in hairpin formation is to remove the base from the DNA helix. Specific interactions between the flipped base and the stacking tryptophan residue are required for hairpin resolution later in the reaction. We show that base flipping in Tn10 transposition is not a passive reaction in which a spontaneously flipped base is captured and retained by the protein. Rather, it is driven in part by a methionine probe residue that helps to force the flipped base from the base stack. Overall, it appears that base flipping in Tn10 transposition is similar to that in Tn5 transposition.
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Affiliation(s)
- Julien Bischerour
- University of Nottingham, School of Biomedical Sciences, The Medical School, Queens Medical Centre (QMC), Nottingham, United Kingdom
| | - Ronald Chalmers
- University of Nottingham, School of Biomedical Sciences, The Medical School, Queens Medical Centre (QMC), Nottingham, United Kingdom
- * E-mail:
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18
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Paleo-immunology: evidence consistent with insertion of a primordial herpes virus-like element in the origins of acquired immunity. PLoS One 2009; 4:e5778. [PMID: 19492059 PMCID: PMC2686171 DOI: 10.1371/journal.pone.0005778] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 04/22/2009] [Indexed: 11/29/2022] Open
Abstract
Background The RAG encoded proteins, RAG-1 and RAG-2 regulate site-specific recombination events in somatic immune B- and T-lymphocytes to generate the acquired immune repertoire. Catalytic activities of the RAG proteins are related to the recombinase functions of a pre-existing mobile DNA element in the DDE recombinase/RNAse H family, sometimes termed the “RAG transposon”. Methodology/Principal Findings Novel to this work is the suggestion that the DDE recombinase responsible for the origins of acquired immunity was encoded by a primordial herpes virus, rather than a “RAG transposon.” A subsequent “arms race” between immunity to herpes infection and the immune system obscured primary amino acid similarities between herpes and immune system proteins but preserved regulatory, structural and functional similarities between the respective recombinase proteins. In support of this hypothesis, evidence is reviewed from previous published data that a modern herpes virus protein family with properties of a viral recombinase is co-regulated with both RAG-1 and RAG-2 by closely linked cis-acting co-regulatory sequences. Structural and functional similarity is also reviewed between the putative herpes recombinase and both DDE site of the RAG-1 protein and another DDE/RNAse H family nuclease, the Argonaute protein component of RISC (RNA induced silencing complex). Conclusions/Significance A “co-regulatory” model of the origins of V(D)J recombination and the acquired immune system can account for the observed linked genomic structure of RAG-1 and RAG-2 in non-vertebrate organisms such as the sea urchin that lack an acquired immune system and V(D)J recombination. Initially the regulated expression of a viral recombinase in immune cells may have been positively selected by its ability to stimulate innate immunity to herpes virus infection rather than V(D)J recombination Unlike the “RAG-transposon” hypothesis, the proposed model can be readily tested by comparative functional analysis of herpes virus replication and V(D)J recombination.
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19
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Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG. Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Nat Struct Mol Biol 2009; 16:499-508. [PMID: 19396172 PMCID: PMC2715281 DOI: 10.1038/nsmb.1593] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 03/20/2009] [Indexed: 12/23/2022]
Abstract
The products of recombination-activating genes RAG1 and RAG2 mediate the assembly of antigen receptor genes during lymphocyte development in a process known as V(D)J recombination. Lack of structural information for the RAG proteins has hindered mechanistic studies of this reaction. We report here the crystal structure of an essential DNA binding domain of the RAG1 catalytic core bound to its nonamer DNA recognition motif. The RAG1 nonamer binding domain (NBD) forms a tightly interwoven dimer that binds and synapses two nonamer elements, with each NBD making contact with both DNA molecules. Biochemical and biophysical experiments confirm that the two nonamers are in close proximity in the RAG1/2-DNA synaptic complex and demonstrate the functional importance of the protein-DNA contacts revealed in the structure. These findings reveal a previously unsuspected function for the NBD in DNA synapsis and have implications for the regulation of DNA binding and cleavage by RAG1 and RAG2.
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Affiliation(s)
- Fang Fang Yin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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20
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Zhao S, Gwyn LM, De P, Rodgers KK. A non-sequence-specific DNA binding mode of RAG1 is inhibited by RAG2. J Mol Biol 2009; 387:744-58. [PMID: 19232525 DOI: 10.1016/j.jmb.2009.02.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 02/03/2009] [Accepted: 02/06/2009] [Indexed: 11/29/2022]
Abstract
RAG1 and RAG2 proteins catalyze site-specific DNA cleavage reactions in V(D)J recombination, a process that assembles antigen receptor genes from component gene segments during lymphocyte development. The first step towards the DNA cleavage reaction is the sequence-specific association of the RAG proteins with the conserved recombination signal sequence (RSS), which flanks each gene segment in the antigen receptor loci. Questions remain as to the contribution of each RAG protein to recognition of the RSS. For example, while RAG1 alone is capable of recognizing the conserved elements of the RSS, it is not clear if or how RAG2 may enhance sequence-specific associations with the RSS. To shed light on this issue, we examined the association of RAG1, with and without RAG2, with consensus RSS versus non-RSS substrates using fluorescence anisotropy and gel mobility shift assays. The results indicate that while RAG1 can recognize the RSS, the sequence-specific interaction under physiological conditions is masked by a high-affinity non-sequence-specific DNA binding mode. Significantly, addition of RAG2 effectively suppressed the association of RAG1 with non-sequence-specific DNA, resulting in a large differential in binding affinity for the RSS versus the non-RSS sites. We conclude that this represents a major means by which RAG2 contributes to the initial recognition of the RSS and that, therefore, association of RAG1 with RAG2 is required for effective interactions with the RSS in developing lymphocytes.
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Affiliation(s)
- Shuying Zhao
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA
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21
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Swanson PC, Kumar S, Raval P. Early steps of V(D)J rearrangement: insights from biochemical studies of RAG-RSS complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 650:1-15. [PMID: 19731797 DOI: 10.1007/978-1-4419-0296-2_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
V(D)J recombination is initiated by the synapsis and cleavage of a complementary (12/23) pair of recombination signal sequences (RSSs) by the RAG1 and RAG2 proteins. Our understanding of these processes has been greatly aided by the development of in vitro biochemical assays of RAG binding and cleavage activity. Accumulating evidence suggests that synaptic complex assembly occurs in a step-wise manner and that the RAG proteins catalyze RSS cleavage by mechanisms similar to those used by bacterial transposases. In this chapter we will review the molecular mechanisms of RAG synaptic complex assembly and 12/23-regulated RSS cleavage, focusing on recent advances that shed new light on these processes.
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Affiliation(s)
- Patrick C Swanson
- Department of Medical Microbiology and Immunology, Creighton University Medical Center, Omaha, Nebraska 68178, USA.
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22
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Wong SY, Lu CP, Roth DB. A RAG1 mutation found in Omenn syndrome causes coding flank hypersensitivity: a novel mechanism for antigen receptor repertoire restriction. THE JOURNAL OF IMMUNOLOGY 2008; 181:4124-30. [PMID: 18768869 DOI: 10.4049/jimmunol.181.6.4124] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Hypomorphic RAG mutants with severely reduced V(D)J recombination activity cause Omenn Syndrome (OS), an immunodeficiency with features of immune dysregulation and a restricted TCR repertoire. Precisely how RAG mutants produce autoimmune and allergic symptoms has been unclear. Current models posit that the severe recombination defect restricts the number of lymphocyte clones, a few of which are selected upon Ag exposure. We show that murine RAG1 R972Q, corresponding to an OS mutation, renders the recombinase hypersensitive to selected coding sequences at the hairpin formation step. Other RAG1 OS mutants tested do not manifest this sequence sensitivity. These new data support a novel mechanism for OS: by selectively impairing recombination at certain coding flanks, a RAG mutant can cause primary repertoire restriction, as opposed to a more random, limited repertoire that develops secondary to severely diminished recombination activity.
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Affiliation(s)
- Serre-Yu Wong
- Program in Molecular Pathogenesis, Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute for Biomolecular Medicine, and Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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23
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Pavlicek JW, Lyubchenko YL, Chang Y. Quantitative analyses of RAG-RSS interactions and conformations revealed by atomic force microscopy. Biochemistry 2008; 47:11204-11. [PMID: 18831563 PMCID: PMC2648828 DOI: 10.1021/bi801426x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During V(D)J recombination, site specific DNA excision is dictated by the binding of RAG1/2 proteins to the conserved recombination signal sequence (RSS) within the genome. The interaction between RAG1/2 and RSS is thought to involve a large DNA distortion that is permissive for DNA cleavage. In this study, using atomic force microscopy imaging (AFM), we analyzed individual RAG-RSS complexes, in which the bending angle of RAG-associated RSS substrates could be visualized and quantified. We provided the quantitative measurement on the conformations of specific RAG-12RSS complexes. Previous data indicating the necessity of RAG2 for recombination implies a structural role in the RAG-RSS complex. Surprisingly, however, no significant difference was observed in conformational bending with AFM between RAG1-12RSS and RAG1/2-12RSS. RAG1 was found sufficient to induce DNA bending, and the addition of RAG2 did not change the bending profile. In addition, a prenicked 12RSS bound by RAG1/2 proteins displayed a conformation similar to the one observed with the intact 12RSS, implying that no greater DNA bending occurs after the nicking step in the signal complex. Taken together, the quantitative AFM results on the components of the recombinase emphasize a tightly held complex with a bend angle value near 60 degrees , which may be a prerequisite step for the site-specific nicking by the V(D)J recombinase.
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Affiliation(s)
- Jeffrey W. Pavlicek
- School of Life Sciences, Center for Infectious Disease and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5501 USA
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center. Omaha, NE 68198-6025, USA
| | - Yung Chang
- School of Life Sciences, Center for Infectious Disease and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5501 USA
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24
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Klenchin VA, Czyz A, Goryshin IY, Gradman R, Lovell S, Rayment I, Reznikoff WS. Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif. Nucleic Acids Res 2008; 36:5855-62. [PMID: 18790806 PMCID: PMC2566895 DOI: 10.1093/nar/gkn577] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bacterial DNA transposition is an important model system for studying DNA recombination events such as HIV-1 DNA integration and RAG-1-mediated V(D)J recombination. This communication focuses on the role of protein-phosphate contacts in manipulating DNA structure as a requirement for transposition catalysis. In particular, the participation of the nontransferred strand (NTS) 5' phosphate in Tn5 transposition strand transfer is analyzed. The 5' phosphate plays no direct catalytic role, nonetheless its presence stimulates strand transfer approximately 30-fold. X-ray crystallography indicates that transposase-DNA complexes formed with NTS 5' phosphorylated DNA have two properties that contrast with structures formed with complexes lacking the 5' phosphate or complexes generated from in-crystal hairpin cleavage. Transposase residues R210, Y319 and R322 of the (R)YREK motif coordinate the 5' phosphate rather than the subterminal NTS phosphate, and the 5' NTS end is moved away from the 3' transferred strand end. Mutation R210A impairs the 5' phosphate stimulation. It is posited that DNA phosphate coordination by R210, Y319 and R322 results in movement of the 5' NTS DNA away from the 3'-end thus allowing efficient target DNA binding. It is likely that this role for the newly identified RYR triad is utilized by other transposase-related proteins.
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Affiliation(s)
- Vadim A Klenchin
- Department of Biochemistry, University of Wisconsin at Madison, 433 Babcock Drive, Madison, WI 53706, USA
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25
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Mitra R, Fain-Thornton J, Craig NL. piggyBac can bypass DNA synthesis during cut and paste transposition. EMBO J 2008; 27:1097-109. [PMID: 18354502 PMCID: PMC2323262 DOI: 10.1038/emboj.2008.41] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 02/07/2008] [Indexed: 12/20/2022] Open
Abstract
DNA synthesis is considered a defining feature in the movement of transposable elements. In determining the mechanism of piggyBac transposition, an insect transposon that is being increasingly used for genome manipulation in a variety of systems including mammalian cells, we have found that DNA synthesis can be avoided during piggyBac transposition, both at the donor site following transposon excision and at the insertion site following transposon integration. We demonstrate that piggyBac transposon excision occurs through the formation of transient hairpins on the transposon ends and that piggyBac target joining occurs by the direct attack of the 3'OH transposon ends on to the target DNA. This is the same strategy for target joining used by the members of DDE superfamily of transposases and retroviral integrases. Analysis of mutant piggyBac transposases in vitro and in vivo using a piggyBac transposition system we have established in Saccharomyces cerevisiae suggests that piggyBac transposase is a member of the DDE superfamily of recombinases, an unanticipated result because of the lack of sequence similarity between piggyBac and DDE family of recombinases.
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Affiliation(s)
- Rupak Mitra
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer Fain-Thornton
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nancy L Craig
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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26
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Lu CP, Posey JE, Roth DB. Understanding how the V(D)J recombinase catalyzes transesterification: distinctions between DNA cleavage and transposition. Nucleic Acids Res 2008; 36:2864-73. [PMID: 18375979 PMCID: PMC2396405 DOI: 10.1093/nar/gkn128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Rag1 and Rag2 proteins initiate V(D)J recombination by introducing site-specific DNA double-strand breaks. Cleavage occurs by nicking one DNA strand, followed by a one-step transesterification reaction that forms a DNA hairpin structure. A similar reaction allows Rag transposition, in which the 3'-OH groups produced by Rag cleavage are joined to target DNA. The Rag1 active site DDE triad clearly plays a catalytic role in both cleavage and transposition, but no other residues in Rag1 responsible for transesterification have been identified. Furthermore, although Rag2 is essential for both cleavage and transposition, the nature of its involvement is unknown. Here, we identify basic amino acids in the catalytic core of Rag1 specifically important for transesterification. We also show that some Rag1 mutants with severe defects in hairpin formation nonetheless catalyze substantial levels of transposition. Lastly, we show that a catalytically defective Rag2 mutant is impaired in target capture and displays a novel form of coding flank sensitivity. These findings provide the first identification of components of Rag1 that are specifically required for transesterification and suggest an unexpected role for Rag2 in DNA cleavage and transposition.
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Affiliation(s)
- Catherine P Lu
- Program in Molecular Pathogenesis, Department of Pathology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
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27
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Chen S, Li X. Molecular characterization of the first intact Transib transposon from Helicoverpa zea. Gene 2008; 408:51-63. [DOI: 10.1016/j.gene.2007.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/06/2007] [Accepted: 10/12/2007] [Indexed: 01/10/2023]
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28
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Nishihara T, Nagawa F, Imai T, Sakano H. RAG-heptamer interaction in the synaptic complex is a crucial biochemical checkpoint for the 12/23 recombination rule. J Biol Chem 2007; 283:4877-85. [PMID: 18089566 DOI: 10.1074/jbc.m709890200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In V(D)J recombination, the RAG1 and RAG2 protein complex cleaves the recombination signal sequences (RSSs), generating a hairpin structure at the coding end. The cleavage occurs only between two RSSs with different spacer lengths of 12 and 23 bp. Here we report that in the synaptic complex, recombination-activating gene (RAG) proteins interact with the 7-mer and unstack the adjacent base in the coding region. We generated a RAG1 mutant that exhibits reduced RAG-7-mer interaction, unstacking of the coding base, and hairpin formation. Mutation of the 23-RSS at the first position of the 7-mer, which has been reported to impair the cleavage of the partner 12-RSS, demonstrated phenotypes similar to those of the RAG1 mutant; the RAG interaction and base unstacking in the partner 12-RSS are reduced. We propose that the RAG-7-mer interaction is a critical step for coding DNA distortion and hairpin formation in the context of the 12/23 rule.
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Affiliation(s)
- Tadashi Nishihara
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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29
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Khiong K, Murakami M, Kitabayashi C, Ueda N, Sawa SI, Sakamoto A, Kotzin BL, Rozzo SJ, Ishihara K, Verella-Garcia M, Kappler J, Marrack P, Hirano T. Homeostatically proliferating CD4 T cells are involved in the pathogenesis of an Omenn syndrome murine model. J Clin Invest 2007; 117:1270-81. [PMID: 17476359 PMCID: PMC1857265 DOI: 10.1172/jci30513] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 02/20/2007] [Indexed: 11/17/2022] Open
Abstract
Patients with Omenn syndrome (OS) have hypomorphic RAG mutations and develop varying manifestations of severe combined immunodeficiency. It is not known which symptoms are caused directly by the RAG mutations and which depend on other polymorphic genes. Our current understanding of OS is limited by the lack of an animal model. In the present study, we identified a C57BL/10 mouse with a spontaneous mutation in, and reduced activity of, RAG1. Mice bred from this animal contained high numbers of memory-phenotype T cells and experienced hepatosplenomegaly and eosinophilia, had oligoclonal T cells, and demonstrated elevated levels of IgE, major symptoms of OS. Depletion of CD4+ T cells in the mice caused a reduction in their IgE levels. Hence these "memory mutant" mice are a model for human OS; many symptoms of their disease were direct results of the Rag hypomorphism and some were caused by malfunctions of their CD4+ T cells.
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Affiliation(s)
- Khie Khiong
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Masaaki Murakami
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Chika Kitabayashi
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Naoko Ueda
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Shin-ichiro Sawa
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Akemi Sakamoto
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Brian L. Kotzin
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Stephen J. Rozzo
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Katsuhiko Ishihara
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Marileila Verella-Garcia
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - John Kappler
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Philippa Marrack
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Toshio Hirano
- Department of Developmental Immunology, Graduate School of Medicine and Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
Integrated Department of Immunology, University of Colorado Health Sciences Center, Howard Hughes Medical Institute, and National Jewish Medical and Research Center, Denver, Colorado, USA.
Division of Clinical Immunology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
Lung Cancer Program, Department of Medicine, University of Colorado Cancer Center, Denver, Colorado, USA.
Laboratory of Cytokine Signaling, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
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30
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Abstract
In the 40 years since Harvard medical student Gilbert Omenn first described a rare, inherited disorder producing a paradoxical combination of immunodeficiency and immune dysregulation, the pathogenesis of Omenn syndrome (OS) has remained mysterious. In separate studies reported in this issue of the JCI, two mouse models bearing mutations in the V(D)J recombinase analogous to those causing human OS have been shown to recapitulate the disease and provide insight into the genesis of immunodeficiency combined with autoimmunity and atopy in OS and other disease settings (see the related articles beginning on pages 1260 and 1270).
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Affiliation(s)
- Serre-Yu Wong
- Program in Molecular Pathogenesis, Skirball Institute of Biomolecular Medicine, and Department of Pathology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
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31
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Abstract
The rearrangement of antigen receptor genes is initiated by double-strand breaks catalyzed by the RAG1/2 complex at the junctions of recombination signal sequences and coding segments. As with some "cut-and-paste" transposases, such as Tn5 and Hermes, a DNA hairpin is formed at one end of the break via a nicked intermediate. By using abasic DNA substrates, we show that different base positions are important for the two steps of cleavage. Removal of one base in the coding flank enhances hairpin formation, bypassing a requirement for a paired complex of two signal sequences. Rescue by abasic substrates is consistent with a base-flip mechanism seen in the crystal structure of the Tn5 postcleavage complex and may mimic the DNA changes on paired complex formation. We have searched for a tryptophan residue in RAG1 that would be the functional equivalent of W298 in Tn5, which stabilizes the DNA interaction by stacking the flipped base on the indole ring. A W956A mutation in RAG1 had an inhibitory effect on both nicking and hairpin stages that could be rescued by abasic substrates. W956 is therefore a likely candidate for interacting with this base during hairpin formation.
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Affiliation(s)
- Gabrielle J. Grundy
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 241, Bethesda, MD 20892
| | - Joanne E. Hesse
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 241, Bethesda, MD 20892
| | - Martin Gellert
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 241, Bethesda, MD 20892
- *To whom correspondence may be addressed. E-mail:
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