1
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Van Duyne GD, Landy A. Bacteriophage lambda site-specific recombination. Mol Microbiol 2024; 121:895-911. [PMID: 38372210 PMCID: PMC11096046 DOI: 10.1111/mmi.15241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
The site-specific recombination pathway of bacteriophage λ encompasses isoenergetic but highly directional and tightly regulated integrative and excisive reactions that integrate and excise the vial chromosome into and out of the bacterial chromosome. The reactions require 240 bp of phage DNA and 21 bp of bacterial DNA comprising 16 protein binding sites that are differentially used in each pathway by the phage-encoded Int and Xis proteins and the host-encoded integration host factor and factor for inversion stimulation proteins. Structures of higher-order protein-DNA complexes of the four-way Holliday junction recombination intermediates provided clarifying insights into the mechanisms, directionality, and regulation of these two pathways, which are tightly linked to the physiology of the bacterial host cell. Here we review our current understanding of the mechanisms responsible for regulating and executing λ site-specific recombination, with an emphasis on key studies completed over the last decade.
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Affiliation(s)
- Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arthur Landy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
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2
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Williams JD, Voziyanova E, Voziyanov Y. The bacteriophage lambda integrase catalytic domain can be modified to act with the regulatory domain as a recombination-competent binary recombinase. J Biol Chem 2022; 299:102721. [PMID: 36410432 PMCID: PMC9791396 DOI: 10.1016/j.jbc.2022.102721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
Site-specific recombinase Int mediates integration of the bacteriophage λ genome into the Escherichia coli chromosome. Integration occurs once the Int tetramer, assisted by the integration host factor IHF, forms the intasome, a higher order structure, within which Int, a heterobivalent protein, interacts with two nonhomologous DNA sequences: the core recombination sites and the accessory arm sites. The binding to these sites is mediated by the catalytic C-terminal domain (CTD) and the regulatory N-terminal domain (NTD) of Int, respectively. Within Int, the NTD can activate or inhibit the recombination activity of the CTD depending on whether the NTD is bound to the arm sites. The CTD alone cannot mediate recombination, and even when the NTD and the CTD are mixed together as individual polypeptides, the NTD cannot trigger recombination in the CTD. In this work, we set to determine what modifications can unlock the recombination activity in the CTD alone and how the CTD can be modified to respond to recombination-triggering signals from the NTD. For this, we performed a series of genetic analyses, which showed that a single mutation that stabilizes the CTD on DNA, E174K, allows the CTD to recombine the core DNA sequences. When the NTD is paired with the CTD (E174K) that also bears a short polypeptide from the C terminus of the NTD, the resulting binary Int can recombine arm-bearing substrates. Our results provide insights into the molecular basis of the regulation of the Int activity and suggest how binary recombinases of the integrase type can be engineered.
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Affiliation(s)
- Joe D Williams
- School of Biosciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Eugenia Voziyanova
- School of Biosciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Yuri Voziyanov
- School of Biosciences, Louisiana Tech University, Ruston, Louisiana, USA.
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3
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Hancock SP, Cascio D, Johnson RC. Cooperative DNA binding by proteins through DNA shape complementarity. Nucleic Acids Res 2019; 47:8874-8887. [PMID: 31616952 PMCID: PMC7145599 DOI: 10.1093/nar/gkz642] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 01/13/2023] Open
Abstract
Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein-protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage λ from the chromosome, the bacterial DNA architectural protein Fis recruits multiple λ-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis β-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.
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MESH Headings
- Allosteric Site
- Bacteriophage lambda/genetics
- Bacteriophage lambda/metabolism
- Base Sequence
- Binding Sites
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/metabolism
- Cloning, Molecular
- Crystallography, X-Ray
- DNA Nucleotidyltransferases/chemistry
- DNA Nucleotidyltransferases/genetics
- DNA Nucleotidyltransferases/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Factor For Inversion Stimulation Protein/chemistry
- Factor For Inversion Stimulation Protein/genetics
- Factor For Inversion Stimulation Protein/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Kinetics
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Recombinational DNA Repair
- Sequence Alignment
- Thermodynamics
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
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Affiliation(s)
- Stephen P Hancock
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
- Department of Chemistry, Towson University, 8000 York Rd., Towson, MD 21252, USA
| | - Duilio Cascio
- University of California at Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095-1570, USA
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095-1737, USA
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
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4
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Resolution of Mismatched Overlap Holliday Junction Intermediates by the Tyrosine Recombinase IntDOT. J Bacteriol 2017; 199:JB.00873-16. [DOI: 10.1128/jb.00873-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 02/19/2017] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
CTnDOT is an integrated conjugative element found in
Bacteroides
species. CTnDOT contains and transfers antibiotic resistance genes. The element integrates into and excises from the host chromosome via a Holliday junction (HJ) intermediate as part of a site-specific recombination mechanism. The CTnDOT integrase, IntDOT, is a tyrosine recombinase with core-binding, catalytic, and amino-terminal (N) domains. Unlike well-studied tyrosine recombinases, such as lambda integrase (Int), IntDOT is able to resolve Holliday junctions containing heterology (mismatched bases) between the sites of strand exchange. All known natural isolates of CTnDOT contain mismatches in the overlap region between the sites of strand exchange. Previous work showed that IntDOT was unable to resolve synthetic Holliday junctions containing mismatched bases to products in the absence of the arm-type sites and a DNA-bending protein. We constructed synthetic HJs with the arm-type sites and tested them with the
Bacteroides
host factor (BHFa). We found that the addition of BHFa stimulated resolution of HJ intermediates with mismatched overlap regions to products. In addition, the L1 site is required for directionality of the reaction, particularly when the HJ contains mismatches. BHFa is required for product formation when the overlap region contains mismatches, and it stimulates resolution to products when the overlap region is identical. Without this DNA bending, the N domain of IntDOT is likely unable to bind the L1 arm-type site. These findings suggest that BHFa bends DNA into the necessary conformation for the higher-order complexes, including the L1 site, that are required for product formation.
IMPORTANCE
CTnDOT is a mobile element that carries antibiotic resistance genes and moves by site-selective recombination and subsequent conjugation. The recombination reaction is catalyzed by an integrase IntDOT that is a member of the tyrosine recombinase family. The reaction proceeds through ordered strand exchanges that generate a Holliday junction (HJ) intermediate. Unlike other tyrosine recombinases, IntDOT can resolve HJs containing mismatched bases in the overlap region
in vivo
, as is the case under natural conditions. However, HJ intermediates including only IntDOT core-type sites cannot be resolved to products if the HJ intermediate contains mismatched bases. We added arm-type sites in
cis
and in
trans
to the HJ intermediates and the protein BHFa to study the requirements for higher-order nucleoprotein complexes.
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5
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Laxmikanthan G, Xu C, Brilot AF, Warren D, Steele L, Seah N, Tong W, Grigorieff N, Landy A, Van Duyne GD. Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction. eLife 2016; 5. [PMID: 27223329 PMCID: PMC4880445 DOI: 10.7554/elife.14313] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/07/2016] [Indexed: 11/13/2022] Open
Abstract
The molecular machinery responsible for DNA expression, recombination, and compaction has been difficult to visualize as functionally complete entities due to their combinatorial and structural complexity. We report here the structure of the intact functional assembly responsible for regulating and executing a site-specific DNA recombination reaction. The assembly is a 240-bp Holliday junction (HJ) bound specifically by 11 protein subunits. This higher-order complex is a key intermediate in the tightly regulated pathway for the excision of bacteriophage λ viral DNA out of the E. coli host chromosome, an extensively studied paradigmatic model system for the regulated rearrangement of DNA. Our results provide a structural basis for pre-existing data describing the excisive and integrative recombination pathways, and they help explain their regulation. DOI:http://dx.doi.org/10.7554/eLife.14313.001 Some viruses can remain dormant inside an infected cell and only become active when conditions are right to multiply and infect other cells. Bacteriophage λ is a much-studied model virus that adopts this lifecycle by inserting its genetic information into the chromosome of a bacterium called Escherichia coli. Certain signals can later trigger the viral DNA to be removed from the bacterial chromosome, often after many generations, so that it can replicate and make new copies of the virus. Specific sites on the viral and bacterial DNA earmark where the virus’s genetic information will insert and how it will be removed. Remarkably, each of these two site-specific reactions (i.e. insertion and removal) cannot be reversed once started, and their onset is precisely controlled. These reactions involve a molecular machine or complex that consists of four enzymes that cut and reconnect the DNA strands and seven DNA-bending proteins that bring distant sites closer together. Despite decades of work by many laboratories, no one had provided a three-dimensional image of this complete molecular machine together with the DNA it acts upon. Now, Laxmikanthan et al. reveal a three-dimensional structure of this machine with all its components by trapping and purifying the complex at the halfway point in the removal process, when the DNA forms a structure known as a “Holliday junction”. The structure was obtained using electron microscopy of complexes frozen in ice. The structure answers many of the long-standing questions about the removal and insertion reactions. For example, it shows how the DNA-bending proteins and enzymes assemble into a large complex to carry out the removal reaction, which is different from the complex that carries out the insertion reaction. It also shows that the removal and insertion reactions are each prevented from acting in the opposite direction because the two complexes have different requirements. These new findings improve our understanding of how the insertion and removal reactions are precisely regulated. Laxmikanthan et al.’s results also serve as examples for thinking about the complicated regulatory machines that are widespread in biology. DOI:http://dx.doi.org/10.7554/eLife.14313.002
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Affiliation(s)
- Gurunathan Laxmikanthan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, United States.,Division of Biology and Medicine, Brown University, Providence, United States
| | - Chen Xu
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
| | - Axel F Brilot
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
| | - David Warren
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, United States.,Division of Biology and Medicine, Brown University, Providence, United States
| | - Lindsay Steele
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, United States.,Division of Biology and Medicine, Brown University, Providence, United States
| | - Nicole Seah
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, United States.,Division of Biology and Medicine, Brown University, Providence, United States
| | - Wenjun Tong
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, United States.,Division of Biology and Medicine, Brown University, Providence, United States
| | - Nikolaus Grigorieff
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Arthur Landy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, United States.,Division of Biology and Medicine, Brown University, Providence, United States
| | - Gregory D Van Duyne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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6
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Abstract
The site-specific recombinase encoded by bacteriophage λ (Int) is responsible for integrating and excising the viral chromosome into and out of the chromosome of its Escherichia coli host. Int carries out a reaction that is highly directional, tightly regulated, and depends upon an ensemble of accessory DNA bending proteins acting on 240 bp of DNA encoding 16 protein binding sites. This additional complexity enables two pathways, integrative and excisive recombination, whose opposite, and effectively irreversible, directions are dictated by different physiological and environmental signals. Int recombinase is a heterobivalent DNA binding protein and each of the four Int protomers, within a multiprotein 400 kDa recombinogenic complex, is thought to bind and, with the aid of DNA bending proteins, bridge one arm- and one core-type DNA site. In the 12 years since the publication of the last review focused solely on the λ site-specific recombination pathway in Mobile DNA II, there has been a great deal of progress in elucidating the molecular details of this pathway. The most dramatic advances in our understanding of the reaction have been in the area of X-ray crystallography where protein-DNA structures have now been determined for of all of the DNA-protein interfaces driving the Int pathway. Building on this foundation of structures, it has been possible to derive models for the assembly of components that determine the regulatory apparatus in the P-arm, and for the overall architectures that define excisive and integrative recombinogenic complexes. The most fundamental additional mechanistic insights derive from the application of hexapeptide inhibitors and single molecule kinetics.
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7
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Identification and characterization of episomal forms of integrative genomic islands in the genus Francisella. Int J Med Microbiol 2015; 305:874-80. [PMID: 26358917 DOI: 10.1016/j.ijmm.2015.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 08/05/2015] [Accepted: 08/27/2015] [Indexed: 02/07/2023] Open
Abstract
Recently, we identified a putative prophage on a genomic island (GI) within the genome sequence of Francisella hispaniensis isolate AS0-814 (Francisella tularensis subsp. novicida-like 3523) by the analysis of the CRISPR-Cas systems of Francisella. Various spacer DNAs within the CRISPR region of different F. tularensis subsp. novicida strains were found to be homologous to the putative prophage (Schunder et al., 2013, Int. J. Med. Microbiol. 303:51-60). Now we identified the GI (FhaGI-1) as a mobile element which is able to form a circular episomal structure. The circular episomal form of FhaGI-1 is generated by F. hispaniensis, and the excision of the island is an integrase-dependent and site-specific process. Furthermore, we could demonstrate that the excision of the island is also possible in other bacterial species (Escherichia coli). In addition, we could show that a genetically generated small variant of the island is also functional and, after its electroporation into strain F. tularensis subsp. holarctica LVS, the GI was stable and site-specifically integrated into the genome of the transformants. The integrase is sufficient for the integration and excision of the small variant into and from the DNA backbone, respectively. Thus, the element may be suitable to be used as a genetic tool in F. tularensis research. Furthermore, we identified the tRNA(Val) gene of Francisella as an integration site for GIs. Genomic island FphGI-1 was identified in Francisella philomiragia ATCC 25016. We were not able to detect the episomal form of this GI, probably due to a mutated attR site. However, we could demonstrate that integrative GIs are present in Francisella and that they may allow horizontal gene transfer between different Francisella species.
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8
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Nucleoprotein architectures regulating the directionality of viral integration and excision. Proc Natl Acad Sci U S A 2014; 111:12372-7. [PMID: 25114241 DOI: 10.1073/pnas.1413019111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The virally encoded site-specific recombinase Int collaborates with its accessory DNA bending proteins IHF, Xis, and Fis to assemble two distinct, very large, nucleoprotein complexes that carry out either integrative or excisive recombination along regulated and essentially unidirectional pathways. The core of each complex consists of a tetramer of Integrase protein (Int), which is a heterobivalent DNA binding protein that binds and bridges a core-type DNA site (where strand cleavage and ligation are executed), and a distal arm-type site, that is brought within range by one or more DNA bending proteins. The recent determination of the patterns of these Int bridges has made it possible to think realistically about the global architecture of the recombinogenic complexes. Here, we combined the previously determined Int bridging patterns with in-gel FRET experiments and in silico modeling to characterize and differentiate the two 400-kDa multiprotein Holiday junction recombination intermediates formed during λ integration and excision. The results lead to architectural models that explain how integration and excision are regulated in λ site-specific recombination. Our confidence in the basic features of these architectures is based on the redundancy and self-consistency of the underlying data from two very different experimental approaches to establish bridging interactions, a set of strategic intracomplex distances from FRET experiments, and the model's ability to explain key aspects of the integrative and excisive recombination pathways, such as topological changes, the mechanism of capturing attB, and the features of asymmetry and flexibility within the complexes.
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9
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Lee SY. Structural and functional views of salt-bridge interactions of λ integrase in the higher order recombinogenic complexes visualized by genetic method. Biochem Biophys Res Commun 2010; 400:1-6. [PMID: 20708599 DOI: 10.1016/j.bbrc.2010.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 08/07/2010] [Indexed: 05/29/2023]
Abstract
The integrase protein encoded by bacteriophage λ (Int) catalyzes site a specific DNA recombination by which the viral chromosome is inserted into and excised out of the host genome through the formation of higher order recombinogenic nucleoprotein complexes. Genetic and biochemical studies on the Int carried out by isolating "multimer-specific" mutants had revealed informative functional characteristics of specific electrostatic interactions occurring among the functional domains of Int. The λ Int recombination system shows the usefulness of structural and functional investigation of multimeric protein complexes through genetic studies on the electrostatic interactions of proteins comprising multimeric complexes. This approach is especially powerful when combined with NMR and X-ray crystallography results providing biological evidences of specific molecular interactions among proteins.
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Affiliation(s)
- Sang Yeol Lee
- Department of Life Science, Kyungwon University, San 65, Bokjeong-Dong, Sujeong-Gu, Seongnam-Si, Kyeonggi-Do 461-701, Republic of Korea.
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10
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Matovina M, Seah N, Hamilton T, Warren D, Landy A. Stoichiometric incorporation of base substitutions at specific sites in supercoiled DNA and supercoiled recombination intermediates. Nucleic Acids Res 2010; 38:e175. [PMID: 20693535 PMCID: PMC2952878 DOI: 10.1093/nar/gkq674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Supercoiled DNA is the relevant substrate for a large number of DNA transactions and has additionally been found to be a favorable form for delivering DNA and protein-DNA complexes to cells. We report here a facile method for stoichiometrically incorporating several different modifications at multiple, specific, and widely spaced sites in supercoiled DNA. The method is based upon generating an appropriately gapped circular DNA, starting from single-strand circular DNA from two phagemids with oppositely oriented origins of replication. The gapped circular DNA is annealed with labeled and unlabeled synthetic oligonucleotides to make a multiply nicked circle, which is covalently sealed and supercoiled. The method is efficient, robust and can be readily scaled up to produce large quantities of labeled supercoiled DNA for biochemical and structural studies. We have applied this method to generate dye-labeled supercoiled DNA with heteroduplex bubbles for a Förster resonance energy transfer (FRET) analysis of supercoiled Holliday junction intermediates in the λ integrative recombination reaction. We found that a higher-order structure revealed by FRET in the supercoiled Holliday junction intermediate is preserved in the linear recombination product. We suggest that in addition to studies on recombination complexes, these methods will be generally useful in other reactions and systems involving supercoiled DNA.
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Affiliation(s)
- Mihaela Matovina
- Division of Molecular Medicine, Laboratory of Molecular Virology and Bacteriology, Rudjer Boskovic Institute, Zagreb, Croatia
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11
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Fadeev EA, Sam MD, Clubb RT. NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove. J Mol Biol 2009; 388:682-90. [PMID: 19324050 DOI: 10.1016/j.jmb.2009.03.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 03/12/2009] [Accepted: 03/13/2009] [Indexed: 10/21/2022]
Abstract
The integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires within higher-order nucleoprotein complexes that form when its amino-terminal domain binds to arm-type DNA sequences that are located distal to the site of strand exchange. Arm-site binding by Int is essential for catalysis, as it promotes Int-mediated bridge structures that stabilize the recombination machinery. We have elucidated how Int is able to sequence specifically recognize the arm-type site sequence by determining the solution structure of its amino-terminal domain (Int(N), residues Met1 to Leu64) in complex with its P'2 DNA binding site. Previous studies have shown that Int(N) adopts a rare monomeric DNA binding fold that consists of a three-stranded antiparallel beta-sheet that is packed against a carboxy-terminal alpha helix. A low-resolution crystal structure of the full-length protein also revealed that the sheet is inserted into the major groove of the arm-type site. The solution structure presented here reveals how Int(N) specifically recognizes the arm-type site sequence. A novel feature of the new solution structure is the use of an 11-residue tail that is located at the amino terminus. DNA binding induces the folding of a 3(10) helix in the tail that projects the amino terminus of the protein deep into the minor groove for stabilizing DNA contacts. This finding reveals the structural basis for the observation that the "unstructured" amino terminus is required for recombination.
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Affiliation(s)
- Evgeny A Fadeev
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA
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12
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Lee SY. Amino-terminal domain interactions of lambda integrase on arm-type DNA. Biochem Biophys Res Commun 2008; 376:139-142. [PMID: 18765228 DOI: 10.1016/j.bbrc.2008.08.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 08/25/2008] [Indexed: 05/26/2023]
Abstract
In contrast to the other tyrosine recombinase family members, integrase protein (Int) of bacteriophage lambda has an additional amino-terminal domain that binds to "arm-type" DNA sequences distant from those involved in strand exchange. The homomeric interaction between neighboring amino-terminal domains of Int is contributed by R30-D71 salt-bridge in a non-equivalent manner on Holliday-junction intermediates. In this report, R30 and D71 residues were investigated in regard to Int's cooperative binding to "arm-type" DNA and the attenuating function of "arm-type" DNA. The results suggest the electrostatic interaction between residues 30 and 71 is dependent on "arm-type" DNA and contributes the "selective" inhibition of catalytic activity of lambda Int by "arm-type" DNA.
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Affiliation(s)
- Sang Yeol Lee
- Department of Life Science, Kyungwon University, San 65, Bokjeong-Dong, Sujeong-Gu, Seongnam-Si, Kyeonggi-Do 461-701, Republic of Korea.
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13
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Kolot M, Gorovits R, Silberstein N, Fichtman B, Yagil E. Phosphorylation of the integrase protein of coliphage HK022. Virology 2008; 375:383-90. [DOI: 10.1016/j.virol.2008.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 02/07/2008] [Accepted: 02/13/2008] [Indexed: 10/22/2022]
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14
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Hazelbaker D, Azaro MA, Landy A. A biotin interference assay highlights two different asymmetric interaction profiles for lambda integrase arm-type binding sites in integrative versus excisive recombination. J Biol Chem 2008; 283:12402-14. [PMID: 18319248 DOI: 10.1074/jbc.m800544200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The site-specific recombinase integrase encoded by bacteriophage lambda promotes integration and excision of the viral chromosome into and out of its Escherichia coli host chromosome through a Holliday junction recombination intermediate. This intermediate contains an integrase tetramer bound via its catalytic carboxyl-terminal domains to the four "core-type" sites of the Holliday junction DNA and via its amino-terminal domains to distal "arm-type" sites. The two classes of integrase binding sites are brought into close proximity by an ensemble of accessory proteins that bind and bend the intervening DNA. We have used a biotin interference assay that probes the requirement for major groove protein binding at specified DNA loci in conjunction with DNA protection, gel mobility shift, and genetic experiments to test several predictions of the models derived from the x-ray crystal structures of minimized and symmetrized surrogates of recombination intermediates lacking the accessory proteins and their cognate DNA targets. Our data do not support the predictions of "non-canonical" DNA targets for the N-domain of integrase, and they indicate that the complexes used for x-ray crystallography are more appropriate for modeling excisive rather than integrative recombination intermediates. We suggest that the difference in the asymmetric interaction profiles of the N-domains and arm-type sites in integrative versus excisive recombinogenic complexes reflects the regulation of recombination, whereas the asymmetry of these patterns within each reaction contributes to directionality.
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Affiliation(s)
- Dane Hazelbaker
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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15
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Subramaniam S, Kamadurai HB, Foster MP. Trans cooperativity by a split DNA recombinase: the central and catalytic domains of bacteriophage lambda integrase cooperate in cleaving DNA substrates when the two domains are not covalently linked. J Mol Biol 2007; 370:303-14. [PMID: 17531268 PMCID: PMC2034338 DOI: 10.1016/j.jmb.2007.04.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 04/05/2007] [Accepted: 04/10/2007] [Indexed: 10/23/2022]
Abstract
Site-specific recombinases of the lambda-integrase family recognize and cleave their cognate DNA sites through cooperative binding to opposite sides of the DNA substrate by a C-terminal catalytic domain and a flexibly linked "core-binding" domain; regulation of this cleavage is achieved via the formation of higher-order complexes. We report that the core-binding domain of lambda-integrase is able to stimulate the activity of the catalytic domain even when the two domains are not linked. This trans stimulation is accomplished without significantly increasing the affinity of the catalytic domain for its DNA substrate. Moreover, we show that mutations in the DNA substrate can abrogate this effect while retaining specificity determinants for cleavage. Since the domains do not significantly interact directly, this finding implies that trans activation is achieved via the DNA substrate in a manner that may be mechanistically important in this and similar DNA binding and cleaving enzymes.
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Affiliation(s)
| | | | - Mark P. Foster
- * Corresponding author contact: (614) 292-1377, FAX: (614) 292-6773,
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16
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Abbani MA, Papagiannis CV, Sam MD, Cascio D, Johnson RC, Clubb RT. Structure of the cooperative Xis-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly. Proc Natl Acad Sci U S A 2007; 104:2109-14. [PMID: 17287355 PMCID: PMC1893000 DOI: 10.1073/pnas.0607820104] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DNA architectural protein Xis regulates the construction of higher-order nucleoprotein intasomes that integrate and excise the genome of phage lambda from the Escherichia coli chromosome. Xis modulates the directionality of site-specific recombination by stimulating phage excision 10(6)-fold, while simultaneously inhibiting phage reintegration. Control is exerted by cooperatively assembling onto a approximately 35-bp DNA regulatory element, which it distorts to preferentially stabilize an excisive intasome. Here, we report the 2.6-A crystal structure of the complex between three cooperatively bound Xis proteins and a 33-bp DNA containing the regulatory element. Xis binds DNA in a head-to-tail orientation to generate a micronucleoprotein filament. Although each protomer is anchored to the duplex by a similar set of nonbase specific contacts, malleable protein-DNA interactions enable binding to sites that differ in nucleotide sequence. Proteins at the ends of the duplex sequence specifically recognize similar binding sites and participate in cooperative binding via protein-protein interactions with a bridging Xis protomer that is bound in a less specific manner. Formation of this polymer introduces approximately 72 degrees of curvature into the DNA with slight positive writhe, which functions to connect disparate segments of DNA bridged by integrase within the excisive intasome.
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Affiliation(s)
- Mohamad A. Abbani
- *Department of Chemistry and Biochemistry and University of California–Department of Energy Institute of Genomics and Proteomics, and
| | - Christie V. Papagiannis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Los Angeles, CA 90095-1737
| | - My D. Sam
- *Department of Chemistry and Biochemistry and University of California–Department of Energy Institute of Genomics and Proteomics, and
| | - Duilio Cascio
- *Department of Chemistry and Biochemistry and University of California–Department of Energy Institute of Genomics and Proteomics, and
| | - Reid C. Johnson
- Molecular Biology Institute, University of California, 611 Charles Young Drive East, Los Angeles, CA 90095-1570; and
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Los Angeles, CA 90095-1737
- To whom correspondence may be addressed. E-mail:
or
| | - Robert T. Clubb
- *Department of Chemistry and Biochemistry and University of California–Department of Energy Institute of Genomics and Proteomics, and
- Molecular Biology Institute, University of California, 611 Charles Young Drive East, Los Angeles, CA 90095-1570; and
- To whom correspondence may be addressed. E-mail:
or
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17
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Sun X, Mierke DF, Biswas T, Lee SY, Landy A, Radman-Livaja M. Architecture of the 99 bp DNA-six-protein regulatory complex of the lambda att site. Mol Cell 2007; 24:569-80. [PMID: 17114059 PMCID: PMC1866956 DOI: 10.1016/j.molcel.2006.10.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 09/13/2006] [Accepted: 10/04/2006] [Indexed: 11/28/2022]
Abstract
The highly directional and tightly regulated recombination reaction used to site-specifically excise the bacteriophage lambda chromosome out of its E. coli host chromosome requires the binding of six sequence-specific proteins to a 99 bp segment of the phage att site. To gain structural insights into this recombination pathway, we measured 27 FRET distances between eight points on the 99 bp regulatory DNA bound with all six proteins. Triangulation of these distances using a metric matrix distance-geometry algorithm provided coordinates for these eight points. The resulting path for the protein-bound regulatory DNA, which fits well with the genetics, biochemistry, and X-ray crystal structures describing the individual proteins and their interactions with DNA, provides a new structural perspective into the molecular mechanism and regulation of the recombination reaction and illustrates a design by which different families of higher-order complexes can be assembled from different numbers and combinations of the same few proteins.
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Affiliation(s)
- Xingmin Sun
- Division of Biology and Medicine Brown University Providence, Rhode Island 02912
| | - Dale F. Mierke
- Division of Biology and Medicine Brown University Providence, Rhode Island 02912
| | - Tapan Biswas
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston, Massachusetts 02115
| | - Sang Yeol Lee
- Division of Biology and Medicine Brown University Providence, Rhode Island 02912
| | - Arthur Landy
- Division of Biology and Medicine Brown University Providence, Rhode Island 02912
- *Correspondence: (A.L.), (M.R.-L.)
| | - Marta Radman-Livaja
- Division of Biology and Medicine Brown University Providence, Rhode Island 02912
- *Correspondence: (A.L.), (M.R.-L.)
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18
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Papagiannis CV, Sam MD, Abbani MA, Yoo D, Cascio D, Clubb RT, Johnson RC. Fis targets assembly of the Xis nucleoprotein filament to promote excisive recombination by phage lambda. J Mol Biol 2007; 367:328-43. [PMID: 17275024 PMCID: PMC1852488 DOI: 10.1016/j.jmb.2006.12.071] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2006] [Revised: 12/05/2006] [Accepted: 12/12/2006] [Indexed: 10/23/2022]
Abstract
The phage-encoded Xis protein is the major determinant controlling the direction of recombination in phage lambda. Xis is a winged-helix DNA binding protein that cooperatively binds to the attR recombination site to generate a curved microfilament, which promotes assembly of the excisive intasome but inhibits formation of an integrative intasome. We find that lambda synthesizes surprisingly high levels of Xis immediately upon prophage induction when excision rates are maximal. However, because of its low sequence-specific binding activity, exemplified by a 1.9 A co-crystal structure of a non-specifically bound DNA complex, Xis is relatively ineffective at promoting excision in vivo in the absence of the host Fis protein. Fis binds to a segment in attR that almost entirely overlaps one of the Xis binding sites. Instead of sterically excluding Xis binding from this site, as has been previously believed, we show that Fis enhances binding of all three Xis protomers to generate the microfilament. A specific Fis-Xis interface is supported by the effects of mutations within each protein, and relaxed, but not completely sequence-neutral, binding by the central Xis protomer is supported by the effects of DNA mutations. We present a structural model for the 50 bp curved Fis-Xis cooperative complex that is assembled between the arm and core Int binding sites whose trajectory places constraints on models for the excisive intasome structure.
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Affiliation(s)
- Christie V. Papagiannis
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave., Los Angeles, CA 90095-1737
| | - My D. Sam
- Department of Chemistry and Biochemistry and UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 405 Hilgard Ave., Los Angeles, CA, 90095-1570
| | - Mohamad A. Abbani
- Department of Chemistry and Biochemistry and UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 405 Hilgard Ave., Los Angeles, CA, 90095-1570
| | - Daniel Yoo
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave., Los Angeles, CA 90095-1737
| | - Duilio Cascio
- Department of Chemistry and Biochemistry and UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 405 Hilgard Ave., Los Angeles, CA, 90095-1570
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry and UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 405 Hilgard Ave., Los Angeles, CA, 90095-1570
- Molecular Biology Institute, University of California, Los Angeles, 405 Hilgard Ave., Los Angeles, CA 90095
| | - Reid C. Johnson
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave., Los Angeles, CA 90095-1737
- Molecular Biology Institute, University of California, Los Angeles, 405 Hilgard Ave., Los Angeles, CA 90095
- Corresponding author: Department of Biological Chemistry, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave., Los Angeles, CA 90095-1737. Tel# 310-825-7800; Fax# 310-206-5272; email
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19
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Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger T. A structural basis for allosteric control of DNA recombination by lambda integrase. Nature 2005; 435:1059-66. [PMID: 15973401 PMCID: PMC1809751 DOI: 10.1038/nature03657] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Accepted: 04/15/2005] [Indexed: 11/09/2022]
Abstract
Site-specific DNA recombination is important for basic cellular functions including viral integration, control of gene expression, production of genetic diversity and segregation of newly replicated chromosomes, and is used by bacteriophage lambda to integrate or excise its genome into and out of the host chromosome. lambda recombination is carried out by the bacteriophage-encoded integrase protein (lambda-int) together with accessory DNA sites and associated bending proteins that allow regulation in response to cell physiology. Here we report the crystal structures of lambda-int in higher-order complexes with substrates and regulatory DNAs representing different intermediates along the reaction pathway. The structures show how the simultaneous binding of two separate domains of lambda-int to DNA facilitates synapsis and can specify the order of DNA strand cleavage and exchange. An intertwined layer of amino-terminal domains bound to accessory (arm) DNAs shapes the recombination complex in a way that suggests how arm binding shifts the reaction equilibrium in favour of recombinant products.
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Affiliation(s)
- Tapan Biswas
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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20
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Warren D, Lee SY, Landy A. Mutations in the amino-terminal domain of lambda-integrase have differential effects on integrative and excisive recombination. Mol Microbiol 2005; 55:1104-12. [PMID: 15686557 PMCID: PMC1808434 DOI: 10.1111/j.1365-2958.2004.04447.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Lambda integrase (Int) forms higher-order protein-DNA complexes necessary for site-specific recombination. The carboxy-terminal domain of Int (75-356) is responsible for catalysis at specific core-type binding sites whereas the amino-terminal domain (1-70) is responsible for cooperative arm-type DNA binding. Alanine scanning mutagenesis of residues 64-70, within full-length integrase, has revealed differential effects on cooperative arm binding interactions that are required for integrative and excisive recombination. Interestingly, while these residues are required for cooperative arm-type binding on both P'1,2 and P'2,3 substrates, cooperative binding at the arm-type sites P'2,3 was more severely compromised than binding at arm-type sites P'1,2 for L64A. Concomitantly, L64A had a much stronger effect on integrative than on excisive recombination. The arm-binding properties of Int appear to be intrinsic to the amino-terminal domain because the phenotype of L64A was the same in an amino-terminal fragment (Int 1-75) as it was in the full-length protein.
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Affiliation(s)
| | | | - Arthur Landy
- *For correspondence. E-mail ; Tel. (+1) 401 863 2571; Fax: (+1) 401 863 1348
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21
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Radman-Livaja M, Biswas T, Mierke D, Landy A. Architecture of recombination intermediates visualized by in-gel FRET of lambda integrase-Holliday junction-arm DNA complexes. Proc Natl Acad Sci U S A 2005; 102:3913-20. [PMID: 15753294 PMCID: PMC554831 DOI: 10.1073/pnas.0500844102] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lambda integrase (Int) mediates recombination between attachment sites on phage and Escherichia coli DNA. Int is assisted by accessory protein-induced DNA loops in bridging pairs of distinct "arm-type" and "core-type" DNA sites to form synapsed recombination complexes that subsequently recombine by means of a Holliday junction (HJ) intermediate. An in-gel FRET assay was developed and used to measure 15 distances between six points in two Int-HJ complexes containing arm-DNA oligonucleotides, and 3D maps of these complexes were derived by distance-geometry calculations. The maps reveal unexpected positions for the arm-type DNAs relative to core sites on the HJ and a new Int conformation in the HJ tetramer. The results show how the position of arm DNAs determines the bias of catalytic activities responsible for directional resolution, provide insights into the organization of Int higher-order complexes, and lead to models of the structure of the full HJ recombination intermediates.
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Affiliation(s)
- Marta Radman-Livaja
- Division of Biology and Medicine, Brown University, Providence, RI 02912, USA
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22
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Lee SY, Radman-Livaja M, Warren D, Aihara H, Ellenberger T, Landy A. Non-equivalent interactions between amino-terminal domains of neighboring lambda integrase protomers direct Holliday junction resolution. J Mol Biol 2005; 345:475-85. [PMID: 15581892 DOI: 10.1016/j.jmb.2004.10.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Accepted: 10/21/2004] [Indexed: 11/28/2022]
Abstract
The bacteriophage lambda site-specific recombinase (Int), in contrast to other family members such as Cre and Flp, has an amino-terminal domain that binds "arm-type" DNA sequences different and distant from those involved in strand exchange. This defining feature of the heterobivalent recombinases confers a directionality and regulation that is unique among all recombination pathways. We show that the amino-terminal domain is not a simple "accessory" element, as originally thought, but rather is incorporated into the core of the recombination mechanism, where it is well positioned to exert its profound effects. The results reveal an unexpected pattern of intermolecular interactions between the amino-terminal domain of one protomer and the linker region of its neighbor within the tetrameric Int complex and provide insights into those features distinguishing an "active" from an "inactive" pair of Ints during Holliday junction resolution.
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Affiliation(s)
- Sang Yeol Lee
- Division of Biology and Medicine, Brown University, 69 Brown Street, Providence, RI 02912, USA
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23
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Abbani M, Iwahara M, Clubb RT. The Structure of the Excisionase (Xis) Protein from Conjugative Transposon Tn916 Provides Insights into the Regulation of Heterobivalent Tyrosine Recombinases. J Mol Biol 2005; 347:11-25. [PMID: 15733914 DOI: 10.1016/j.jmb.2005.01.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 12/21/2004] [Accepted: 01/04/2005] [Indexed: 11/16/2022]
Abstract
Heterobivalent tyrosine recombinases play a prominent role in numerous bacteriophage and transposon recombination systems. Their enzymatic activities are frequently regulated at a structural level by excisionase factors, which alter the ability of the recombinase to assemble into higher-order recombinogenic nucleoprotein structures. The Tn916 conjugative transposon spreads antibiotic resistance in pathogenic bacteria and is mobilized by a heterobivalent recombinase (Tn916Int), whose activity is regulated by an excisionase factor (Tn916Xis). Unlike the well-characterized (lambda)Xis excisionase from bacteriophage lambda, Tn916Xis stimulates excision in vitro and in Escherichia coli only modestly. To gain insights into this functional difference, we have performed in vitro DNA-binding studies of Tn916Xis and Tn916Int, and we have solved the solution structure of Tn916Xis. We show that the heterobivalent Tn916Int protein is capable of bridging the DR2-type and core-type sites on the left arm of the tranpsoson. Consistent with the notion that Tn916Int is regulated only loosely, we find that Tn916Xis binding does not alter the stability of DR2-Tn916Int-core bridges or the ability of Tn916Int to recognize the arms of the transposon in vitro. Despite a high degree of divergence at the primary sequence level, we show that Tn916Xis and (lambda)Xis adopt related prokaryotic winged-helix structures. However, they differ at their C termini, with Tn916Xis replacing the flexible integrase contacting tail found in (lambda)Xis with a positively charged alpha-helix. This difference provides a structural explanation for why Tn916Xis does not interact cooperatively with its cognate integrase in vitro, and reveals how subtle changes in the winged-helix fold can modulate the functional properties of excisionase factors.
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Affiliation(s)
- Mohamad Abbani
- Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, and the Molecular Biology Institute, University of California, Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095-1570, USA
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24
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Swalla BM, Cho EH, Gumport RI, Gardner JF. The molecular basis of co-operative DNA binding between lambda integrase and excisionase. Mol Microbiol 2003; 50:89-99. [PMID: 14507366 DOI: 10.1046/j.1365-2958.2003.03687.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Higher-order nucleoprotein complexes often stabilize catalytic proteins in appropriate conformations for optimal activity and contribute to regulation during reactions requiring association of proteins and DNA. Formation of such complexes, known as intasomes, is required for site-specific recombination catalysed by bacteriophage Lambda Integrase protein (Int). Int-catalysed recombination is regulated by a second bacteriophage-encoded protein, Excisionase (Xis), which both stimulates excision and inhibits integration. To exert its effect, Xis binds co-operatively with Int, thereby inducing and stabilizing a DNA bend that alters the intasome structures formed during recombination. A rare int mutant, int 2268 ts, was reported (Enquist, L.W. and Weisberg, R.A. (1984) Mol Gen Genet 195: 62-69) to be more defective for excision than integration. Here, we have determined that this mutant Int protein contains an E47K substitution, and that the resultant excision-specific defect is due, at least in part, to destabilized interactions between Int and Xis. Analysis of several engineered substitutions at Int position 47 showed that a negatively charged residue is required for co-operative DNA binding between Int and Xis, and suggest that the Int-E47 residue may contact Xis directly. Substitutions at Int position 47 also affect co-operative binding among Int proteins at arm-type DNA sites, and thereby reduce the efficiency of both integration and excision. Collectively, these results suggest that a single surface of the Int amino-terminal domain mediates two alternate types of co-operative binding interactions.
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25
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Warren D, Sam MD, Manley K, Sarkar D, Lee SY, Abbani M, Wojciak JM, Clubb RT, Landy A. Identification of the lambda integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation. Proc Natl Acad Sci U S A 2003; 100:8176-81. [PMID: 12832614 PMCID: PMC166202 DOI: 10.1073/pnas.1033041100] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lambda integrase (Int) is a heterobivalent DNA-binding protein that together with the accessory DNA-bending proteins IHF, Fis, and Xis, forms the higher-order protein-DNA complexes that execute integrative and excisive recombination at specific loci on the chromosomes of phage lambda and its Escherichia coli host. The large carboxyl-terminal domain of Int is responsible for binding to core-type DNA sites and catalysis of DNA cleavage and ligation reactions. The small amino-terminal domain (residues 1-70), which specifies binding to arm-type DNA sites distant from the regions of strand exchange, consists of a three-stranded beta-sheet, proposed to recognize the cognate DNA site, and an alpha-helix. We report here that a site on this alpha-helix is critical for both homomeric interactions between Int protomers and heteromeric interactions with Xis. The mutant E47A, which was identified by alanine-scanning mutagenesis, abolishes interactions between Int and Xis bound at adjacent binding sites and reduces interactions between Int protomers bound at adjacent arm-type sites. Concomitantly, this residue is essential for excisive recombination and contributes to the efficiency of the integrative reaction. NMR titration data with a peptide corresponding to Xis residues 57-69 strongly suggest that the carboxyl-terminal tail of Xis and the alpha-helix of the aminoterminal domain of Int comprise the primary interaction surface for these two proteins. The use of a common site on lambda Int for both homotypic and heterotypic interactions fits well with the complex regulatory patterns associated with this site-specific recombination reaction.
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Affiliation(s)
- David Warren
- Division of Biology and Medicine, Brown
University, Providence, RI 02912; Department
of Chemistry and Biochemistry, Molecular Biology Institute, University of
California, and UCLA–DOE Institute for Genomics and Proteomics, 405
Hilgard Avenue, Los Angeles, CA 90095; and
Institute of Microbial Technology, Sector 39A,
Chandigarh 160036, India
| | - My D. Sam
- Division of Biology and Medicine, Brown
University, Providence, RI 02912; Department
of Chemistry and Biochemistry, Molecular Biology Institute, University of
California, and UCLA–DOE Institute for Genomics and Proteomics, 405
Hilgard Avenue, Los Angeles, CA 90095; and
Institute of Microbial Technology, Sector 39A,
Chandigarh 160036, India
| | - Kate Manley
- Division of Biology and Medicine, Brown
University, Providence, RI 02912; Department
of Chemistry and Biochemistry, Molecular Biology Institute, University of
California, and UCLA–DOE Institute for Genomics and Proteomics, 405
Hilgard Avenue, Los Angeles, CA 90095; and
Institute of Microbial Technology, Sector 39A,
Chandigarh 160036, India
| | - Dibyendu Sarkar
- Division of Biology and Medicine, Brown
University, Providence, RI 02912; Department
of Chemistry and Biochemistry, Molecular Biology Institute, University of
California, and UCLA–DOE Institute for Genomics and Proteomics, 405
Hilgard Avenue, Los Angeles, CA 90095; and
Institute of Microbial Technology, Sector 39A,
Chandigarh 160036, India
| | - Sang Yeol Lee
- Division of Biology and Medicine, Brown
University, Providence, RI 02912; Department
of Chemistry and Biochemistry, Molecular Biology Institute, University of
California, and UCLA–DOE Institute for Genomics and Proteomics, 405
Hilgard Avenue, Los Angeles, CA 90095; and
Institute of Microbial Technology, Sector 39A,
Chandigarh 160036, India
| | - Mohamad Abbani
- Division of Biology and Medicine, Brown
University, Providence, RI 02912; Department
of Chemistry and Biochemistry, Molecular Biology Institute, University of
California, and UCLA–DOE Institute for Genomics and Proteomics, 405
Hilgard Avenue, Los Angeles, CA 90095; and
Institute of Microbial Technology, Sector 39A,
Chandigarh 160036, India
| | - Jonathan M. Wojciak
- Division of Biology and Medicine, Brown
University, Providence, RI 02912; Department
of Chemistry and Biochemistry, Molecular Biology Institute, University of
California, and UCLA–DOE Institute for Genomics and Proteomics, 405
Hilgard Avenue, Los Angeles, CA 90095; and
Institute of Microbial Technology, Sector 39A,
Chandigarh 160036, India
| | - Robert T. Clubb
- Division of Biology and Medicine, Brown
University, Providence, RI 02912; Department
of Chemistry and Biochemistry, Molecular Biology Institute, University of
California, and UCLA–DOE Institute for Genomics and Proteomics, 405
Hilgard Avenue, Los Angeles, CA 90095; and
Institute of Microbial Technology, Sector 39A,
Chandigarh 160036, India
- To whom correspondence may be addressed. E-mail:
or
| | - Arthur Landy
- Division of Biology and Medicine, Brown
University, Providence, RI 02912; Department
of Chemistry and Biochemistry, Molecular Biology Institute, University of
California, and UCLA–DOE Institute for Genomics and Proteomics, 405
Hilgard Avenue, Los Angeles, CA 90095; and
Institute of Microbial Technology, Sector 39A,
Chandigarh 160036, India
- To whom correspondence may be addressed. E-mail:
or
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26
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Gottfried P, Silberstein N, Yagil E, Kolot M. Activity of coliphage HK022 excisionase (Xis) in the absence of DNA binding. FEBS Lett 2003; 545:133-8. [PMID: 12804763 DOI: 10.1016/s0014-5793(03)00512-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A mutated excisionase (Xis) protein of coliphage HK022 whose single Cys residue was replaced by Ser does not bind to its two tandem binding sites (X1, X2) on the P arm of attR. Despite its DNA-binding inability the protein showed 30% excision activity of the wild type Xis both in vitro and in vivo. This partial activity is attributed to the interaction of Xis with integrase that is retained in the mutant protein. This protein-protein interaction occurs in the absence of DNA binding.
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Affiliation(s)
- Pnina Gottfried
- Department of Biochemistry, Tel-Aviv University, Tel-Aviv 69978, Israel
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27
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Radman-Livaja M, Shaw C, Azaro M, Biswas T, Ellenberger T, Landy A. Arm sequences contribute to the architecture and catalytic function of a lambda integrase-Holliday junction complex. Mol Cell 2003; 11:783-94. [PMID: 12667459 DOI: 10.1016/s1097-2765(03)00111-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
lambda integrase (Int) mediates recombination between attachment sites on lambda phage and E. coli DNAs. With the assistance of accessory proteins that induce DNA loops, Int bridges pairs of distinct arm- and core-type DNA binding sites to form synapsed recombination complexes, which then recombine via a Holliday junction (HJ) intermediate. We show that, in addition to promoting the proper positioning of Int protomers, the arm sequences facilitate the catalytic activities of the Int tetramer, independent of accessory proteins or physical continuity between the arm and core sites. We have determined the architecture of ternary complexes containing a HJ, Int, and P'1,2 arm-type DNA. These structures accommodate simultaneous binding of Int to direct-repeat arm sites and indirect-repeat core sites and afford a new view of the higher-order recombinogenic complexes.
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Affiliation(s)
- Marta Radman-Livaja
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Box G-J360, Providence, RI 02912, USA
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Sam MD, Papagiannis CV, Connolly KM, Corselli L, Iwahara J, Lee J, Phillips M, Wojciak JM, Johnson RC, Clubb RT. Regulation of directionality in bacteriophage lambda site-specific recombination: structure of the Xis protein. J Mol Biol 2002; 324:791-805. [PMID: 12460578 DOI: 10.1016/s0022-2836(02)01150-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Upon induction of a bacteriophage lambda lysogen, a site-specific recombination reaction excises the phage genome from the chromosome of its bacterial host. A critical regulator of this process is the phage-encoded excisionase (Xis) protein, which functions both as a DNA architectural factor and by cooperatively recruiting integrase to an adjacent binding site specifically required for excision. Here we present the three-dimensional structure of Xis and the results of a structure-based mutagenesis study to define the molecular basis of its function. Xis adopts an unusual "winged"-helix motif that is modeled to interact with the major- and minor-grooves of its binding site through a single alpha-helix and loop structure ("wing"), respectively. The C-terminal tail of Xis, which is required for cooperative binding with integrase, is unstructured in the absence of DNA. We propose that asymmetric bending of DNA by Xis positions its unstructured C-terminal tail for direct contacts with the N-terminal DNA-binding domain of integrase and that an ensuing disordered to ordered transition of the tail may act to stabilize the formation of the tripartite integrase-Xis-DNA complex required for phage excision.
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Affiliation(s)
- My D Sam
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095-1570, USA
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Tekle M, Warren DJ, Biswas T, Ellenberger T, Landy A, Nunes-Düby SE. Attenuating functions of the C terminus of lambda integrase. J Mol Biol 2002; 324:649-65. [PMID: 12460568 DOI: 10.1016/s0022-2836(02)01108-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The tyrosine family site-specific recombinases, in contrast to the related type I topoisomerases, which act as monomers on a single DNA molecule, rely on multi-protein complexes to synapse partner DNAs and coordinate two sequential strand exchanges involving four nicking-closing reactions. Here, we analyze three mutants of the catalytic domain of lambda integrase (Int), A241V, I353M and W350ter that are defective for normal recombination, but possess increased topoisomerase activity. The mutant enzymes can carry out individual DNA strand exchanges using truncated substrates or Holliday junctions, and they show more DNA-cleavage activity than wild-type Int on isolated att sites. Structural modeling predicts that the substituted residues may destabilize interactions between the C-terminal beta-strand (beta7) of Int and the core of the protein. The cleavage-competent state of Int requires the repositioning of the nucleophile (Y342) located on beta6 and the catalyst K235 located on the flexible beta2-beta3 loop, relative to their positions in a crystal structure of the inactive conformation. We propose that the anchoring of beta7 against the protein core restrains the movement of Tyr342 and/or Lys235, causing an attenuation of cleavage activity in most contexts. Within a bona fide recombination complex, the release of strand beta7 would allow Tyr342 and Lys235 to assume catalytically active conformations in coordination with other Int protomers in the complex. The loss of beta7 packing by misalignment or truncation in the mutant proteins described here causes a loss of regulated activity, thereby favoring DNA cleavage activity in monomeric complexes and forfeiting the coordination of strand-exchange necessary for efficient recombination.
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Affiliation(s)
- Michael Tekle
- Division of Pathology, Department of Microbiology, Pathology and Immunology, Karolinska Institutet, Huddinge University Hospital, F46, SE-141 86 Stockholm, Sweden
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