The Mu transpositional enhancer can function in trans: requirement of the enhancer for synapsis but not strand cleavage

Transposable Phage Mu

Transposable phage Mu has played a major role in elucidating the mechanism of movement of mobile DNA elements. The high efficiency of Mu transposition has facilitated a detailed biochemical dissection of the reaction mechanism, as well as of protein and DNA elements that regulate transpososome assembly and function. The deduced phosphotransfer mechanism involves in-line orientation of metal ion-activated hydroxyl groups for nucleophilic attack on reactive diester bonds, a mechanism that appears to be used by all transposable elements examined to date. A crystal structure of the Mu transpososome is available. Mu differs from all other transposable elements in encoding unique adaptations that promote its viral lifestyle. These adaptations include multiple DNA (enhancer, SGS) and protein (MuB, HU, IHF) elements that enable efficient Mu end synapsis, efficient target capture, low target specificity, immunity to transposition near or into itself, and efficient mechanisms for recruiting host repair and replication machineries to resolve transposition intermediates. MuB has multiple functions, including target capture and immunity. The SGS element promotes gyrase-mediated Mu end synapsis, and the enhancer, aided by HU and IHF, participates in directing a unique topological architecture of the Mu synapse. The function of these DNA and protein elements is important during both lysogenic and lytic phases. Enhancer properties have been exploited in the design of mini-Mu vectors for genetic engineering. Mu ends assembled into active transpososomes have been delivered directly into bacterial, yeast, and human genomes, where they integrate efficiently, and may prove useful for gene therapy.

Site-specific DNA Inversion by Serine Recombinases

Reversible site-specific DNA inversion reactions are widely distributed in bacteria and their viruses. They control a range of biological reactions that most often involve alterations of molecules on the surface of cells or phage. These programmed DNA rearrangements usually occur at a low frequency, thereby preadapting a small subset of the population to a change in environmental conditions, or in the case of phages, an expanded host range. A dedicated recombinase, sometimes with the aid of additional regulatory or DNA architectural proteins, catalyzes the inversion of DNA. RecA or other components of the general recombination-repair machinery are not involved. This chapter discusses site-specific DNA inversion reactions mediated by the serine recombinase family of enzymes and focuses on the extensively studied serine DNA invertases that are stringently controlled by the Fis-bound enhancer regulatory system. The first section summarizes biological features and general properties of inversion reactions by the Fis/enhancer-dependent serine invertases and the recently described serine DNA invertases in Bacteroides. Mechanistic studies of reactions catalyzed by the Hin and Gin invertases are then discussed in more depth, particularly with regards to recent advances in our understanding of the function of the Fis/enhancer regulatory system, the assembly of the active recombination complex (invertasome) containing the Fis/enhancer, and the process of DNA strand exchange by rotation of synapsed subunit pairs within the invertasome. The role of DNA topological forces that function in concert with the Fis/enhancer controlling element in specifying the overwhelming bias for DNA inversion over deletion and intermolecular recombination is emphasized.

Controlling DNA degradation from a distance: a new role for the Mu transposition enhancer

Phage Mu is unique among transposable elements in employing a transposition enhancer. The enhancer DNA segment is the site where the transposase MuA binds and makes bridging interactions with the two Mu ends, interwrapping the ends with the enhancer in a complex topology essential for assembling a catalytically active transpososome. The enhancer is also the site at which regulatory proteins control divergent transcription of genes that determine the phage lysis-lysogeny decision. Here we report a third function for the enhancer - that of regulating degradation of extraneous DNA attached to both ends of infecting Mu. This DNA is protected from nucleases by a phage protein until Mu integrates into the host chromosome, after which it is rapidly degraded. We find that leftward transcription at the enhancer, expected to disrupt its topology within the transpososome, blocks degradation of this DNA. Disruption of the enhancer would lead to the loss or dislocation of two non-catalytic MuA subunits positioned in the transpososome by the enhancer. We provide several lines of support for this inference, and conclude that these subunits are important for activating degradation of the flanking DNA. This work also reveals a role for enhancer topology in phage development.

The μ transpososome structure sheds light on DDE recombinase evolution

Studies of bacteriophage Mu transposition paved the way for understanding retroviral integration and V(D)J recombination as well as many other DNA transposition reactions. Here we report the structure of the Mu transpososome--Mu transposase (MuA) in complex with bacteriophage DNA ends and target DNA--determined from data that extend anisotropically to 5.2 Å, 5.2 Å and 3.7 Å resolution, in conjunction with previously determined structures of individual domains. The highly intertwined structure illustrates why chemical activity depends on formation of the synaptic complex, and reveals that individual domains have different roles when bound to different sites. The structure also provides explanations for the increased stability of the final product complex and for its preferential recognition by the ATP-dependent unfoldase ClpX. Although MuA and many other recombinases share a structurally conserved 'DDE' catalytic domain, comparisons among the limited set of available complex structures indicate that some conserved features, such as catalysis in trans and target DNA bending, arose through convergent evolution because they are important for function.

Application of the bacteriophage Mu-driven system for the integration/amplification of target genes in the chromosomes of engineered Gram-negative bacteria--mini review

The advantages of phage Mu transposition-based systems for the chromosomal editing of plasmid-less strains are reviewed. The cis and trans requirements for Mu phage-mediated transposition, which include the L/R ends of the Mu DNA, the transposition factors MuA and MuB, and the cis/trans functioning of the E element as an enhancer, are presented. Mini-Mu(LR)/(LER) units are Mu derivatives that lack most of the Mu genes but contain the L/R ends or a properly arranged E element in cis to the L/R ends. The dual-component system, which consists of an integrative plasmid with a mini-Mu and an easily eliminated helper plasmid encoding inducible transposition factors, is described in detail as a tool for the integration/amplification of recombinant DNAs. This chromosomal editing method is based on replicative transposition through the formation of a cointegrate that can be resolved in a recombination-dependent manner. (E-plus)- or (E-minus)-helpers that differ in the presence of the trans-acting E element are used to achieve the proper mini-Mu transposition intensity. The systems that have been developed for the construction of stably maintained mini-Mu multi-integrant strains of Escherichia coli and Methylophilus methylotrophus are described. A novel integration/amplification/fixation strategy is proposed for consecutive independent replicative transpositions of different mini-Mu(LER) units with “excisable” E elements in methylotrophic cells.

DNA repair by the cryptic endonuclease activity of Mu transposase

Phage Mu transposes by two distinct pathways depending on the specific stage of its life cycle. A common strand transfer intermediate is resolved differentially in the two pathways. During lytic growth, the intermediate is resolved by replication of Mu initiated within the flanking target DNA; during integration of infecting Mu, it is resolved without replication, by removal and repair of DNA from a previous host that is still attached to the ends of the incoming Mu genome. We have discovered that the cryptic endonuclease activity reported for the isolated C-terminal domain of the transposase MuA [Wu Z, Chaconas G (1995) A novel DNA binding and nuclease activity in domain III of Mu transposase: Evidence for a catalytic region involved in donor cleavage. EMBO J 14:3835-3843], which is not observed in the full-length protein or in the assembled transpososome in vitro, is required in vivo for removal of the attached host DNA or "5'flap" after the infecting Mu genome has integrated into the E. coli chromosome. Efficient flap removal also requires the host protein ClpX, which is known to interact with the C-terminus of MuA to remodel the transpososome for replication. We hypothesize that ClpX constitutes part of a highly regulated mechanism that unmasks the cryptic nuclease activity of MuA specifically in the repair pathway.

The mu transpososome through a topological lens

Phage Mu is the most efficient transposable element known, its high efficiency being conferred by an enhancer DNA element. Transposition is the end result of a series of well choreographed steps that juxtapose the enhancer and the two Mu ends within a nucleoprotein complex called the 'transpososome.' The particular arrangement of DNA and protein components lends extraordinary stability to the transpososome and regulates the frequency, precision, directionality, and mechanism of transposition. The structure of the transpososome, therefore, holds the key to understanding all of these attributes, and ultimately to explaining the runaway genetic success of transposable elements throughout the biological world. This review focuses on the path of the DNA within the Mu transpososome, as uncovered by recent topological analyses. It discusses why Mu topology cannot be analyzed by standard methods, and how knowledge of the geometry of site alignment during Flp and Cre site-specific recombination was harnessed to design a new methodology called 'difference topology.' This methodology has also revealed the order and dynamics of association of the three interacting DNA sites, as well as the role of the enhancer in assembly of the Mu transpososome.

A unique right end-enhancer complex precedes synapsis of Mu ends: the enhancer is sequestered within the transpososome throughout transposition

Assembly of the Mu transpososome is dependent on interactions of transposase subunits with the left (L) and right (R) ends of Mu and an enhancer (E). We have followed the order and dynamics of association of these sites within a series of transpososomes prior to and during formation of a three-site complex (LER), engagement of Mu ends by the transposase active site (type 0 complex), cleavage of the ends (type I complex) and their transfer to target DNA (type II complex). LER appears to be preceded by a two-site complex (ER) where E and R are interwrapped twice, as in the mature transpososome. At each stage thereafter, the overall topology of five DNA supercoils is retained: two between E and R, one between E and L and two between L and R. However, L-R interactions within LER appear to be flexible. Unexpectedly, the enhancer was seen to persist within the transpososome through cleavage and strand transfer of Mu ends to target DNA.

The Mu three-site synapse: a strained assembly platform in which delivery of the L1 transposase binding site triggers catalytic commitment

The Mu DNA transposition reaction proceeds through a three-site synaptic complex (LER), including the two Mu ends and the transpositional enhancer. We show that the LER contains highly stressed DNA regions in the enhancer and in the L1 transposase binding site. We propose that the L1 site acts as the keystone for assembly of a catalytically competent transpososome. Delivery of L1 through HU-mediated bending completes LER assembly, provides the trigger for necessary conformational transitions in transpososome formation, and allows target capture to occur. Relief of the stress at L1 and the enhancer may help drive Mu A tetramerization and engagement of the Mu ends by the transposase active site.

Path of DNA within the Mu transpososome. Transposase interactions bridging two Mu ends and the enhancer trap five DNA supercoils

The phage Mu transpososome is assembled by interactions of transposase subunits with the left (L) and right (R) ends of Mu and an enhancer (E) located in between. A metastable three-site complex LER progresses into a more stable type 0 complex in which a tetrameric transposase is poised for DNA cleavage. "Difference topology" has revealed five trapped negative supercoils within type 0, three contributed by crossings of E with L and R, and two by crossings of L with R. This is the most complex DNA arrangement seen to date within a recombination synapse. Contrary to the prevailing notion, the enhancer appears not to be released immediately following type 0 assembly. Difference topology provides a simple method for determining the ordered sequestration of DNA segments within nucleoprotein assemblies.

Conformational isomerization in phage Mu transpososome assembly: effects of the transpositional enhancer and of MuB

Initiation of phage Mu DNA transposition requires assembly of higher order protein-DNA complexes called Mu transpososomes containing the two Mu DNA ends and MuA transposase tetramer. Mu transpososome assembly is highly regulated and involves multiple DNA sites for transposase binding, including a transpositional enhancer called the internal activation sequence (IAS). In addition, a number of protein cofactors participate, including the target DNA activator MuB ATPase. We investigated the impact of the assembly cofactors on the kinetics of transpososome assembly with the aim of deciphering the reaction steps that are influenced by the cofactors. The transpositional enhancer IAS appears to have little impact on the initial pairing of the two Mu end segments bound by MuA. Instead, it accelerates the post-synaptic conformational step(s) that converts the reversible complex to the stable transpososome. The transpososome assembly stimulation by MuB does not require its stable DNA binding activity, which appears critical for directing transposition to sites distant from the donor transposon.

Handoff from recombinase to replisome: insights from transposition

Bacteriophage Mu replicates as a transposable element, exploiting host enzymes to promote initiation of DNA synthesis. The phage-encoded transposase MuA, assembled into an oligomeric transpososome, promotes transfer of Mu ends to target DNA, creating a fork at each end, and then remains tightly bound to both forks. In the transition to DNA synthesis, the molecular chaperone ClpX acts first to weaken the transpososome's interaction with DNA, apparently activating its function as a molecular matchmaker. This activated transpososome promotes formation of a new nucleoprotein complex (prereplisome) by yet unidentified host factors [Mu replication factors (MRF alpha 2)], which displace the transpososome in an ATP-dependent reaction. Primosome assembly proteins PriA, PriB, DnaT, and the DnaB--DnaC complex then promote the binding of the replicative helicase DnaB on the lagging strand template of the Mu fork. PriA helicase plays an important role in opening the DNA duplex for DnaB binding, which leads to assembly of DNA polymerase III holoenzyme to form the replisome. The MRF alpha 2 transition factors, assembled into a prereplisome, not only protect the fork from action by nonspecific host enzymes but also appear to aid in replisome assembly by helping to activate PriA's helicase activity. They consist of at least two separable components, one heat stable and the other heat labile. Although the MRF alpha 2 components are apparently not encoded by currently known homologous recombination genes such as recA, recF, recO, and recR, they may fulfill an important function in assembling replisomes on arrested replication forks and products of homologous strand exchange.

DNase protection analysis of retrovirus integrase at the viral DNA ends for full-site integration in vitro

Retrovirus intasomes purified from virus-infected cells contain the linear viral DNA genome and integrase (IN). Intasomes are capable of integrating the DNA termini in a concerted fashion into exogenous target DNA (full site), mimicking integration in vivo. Molecular insights into the organization of avian myeloblastosis virus IN at the viral DNA ends were gained by reconstituting nucleoprotein complexes possessing intasome characteristics. Assembly of IN-4.5-kbp donor complexes capable of efficient full-site integration appears cooperative and is dependent on time, temperature, and protein concentration. DNase I footprint analysis of assembled IN-donor complexes capable of full-site integration shows that wild-type U3 and other donors containing gain-of-function attachment site sequences are specifically protected by IN at low concentrations (<20 nM) with a defined outer boundary mapping ~20 nucleotides from the ends. A donor containing mutations in the attachment site simultaneously eliminated full-site integration and DNase I protection by IN. Coupling of wild-type U5 ends with wild-type U3 ends for full-site integration shows binding by IN at low concentrations probably occurs only at the very terminal nucleotides (<10 bp) on U5. The results suggest that assembly requires a defined number of avian IN subunits at each viral DNA end. Among several possibilities, IN may bind asymmetrically to the U3 and U5 ends for full-site integration in vitro.

The Mu enhancer is functionally asymmetric both in cis and in trans. Topological selectivity of Mu transposition is enhancer-independent

Mu DNA transposition from a negatively supercoiled DNA substrate requires interaction of an enhancer element with the left (attL) and right (attR) ends of Mu. The orientation of the L and R ends with respect to each other (inverted) and with respect to the enhancer is normally inviolate. We show that when the enhancer is provided in trans as a linear fragment, the head to head orientation of the L/R ends is still required. Each functional half of the linear enhancer maintains the same "cross-wise" interaction with the subsites L1 and R1, when present in cis or in trans. In reactions catalyzed by an enhancer-independent variant of the Mu transposase, the need for negative supercoiling of the substrate and the inverted orientation of L and R ends is not relaxed. These results show that the orientation specificity of the enhancer is not determined by its topological linkage to the Mu ends. There is a functional asymmetry inherent to the enhancer. Furthermore, the enhancer does not directly impose topological constraints on the transposition reaction or specify the reactive orientation of the Mu ends.

Differential requirements for cis and trans V(D)J cleavage: effects of substrate length

The assembly of productive synaptic complexes is a critical, but poorly understood, regulatory step in V(D)J recombination. Several lines of evidence suggest that there may be important differences between recombination involving sites situated in cis (on the same DNA molecule) and in trans (on separate molecules). Because biochemical experiments using both purified RAG proteins and crude extracts have failed to detect trans cleavage of plasmid substrates it has been thought that there is a substantial bias against trans synapsis. In conflict with these results are more recent studies showing that purified RAG proteins can catalyze trans cleavage of short oligonucleotide substrates. Furthermore, recent experiments have detected efficient trans cleavage of plasmid substrates in vivo. We sought to investigate why these different systems yield such divergent results. We found that, unexpectedly, the ability of both purified RAG proteins and crude extracts to cleave DNA substrates in trans is a function of substrate length. Our data raise two critical issues: first, oligonucleotides, which are the most commonly used substrates to study V(D)J recombination in vitro, do not mimic the behavior of plasmid substrates; second, in the trans cleavage reaction current purified RAG systems do not accurately reflect the in vivo situation. We propose a unifying model to explain the effects of substrate length and coniguration (cis or trans) on the efficiency of synapsis.

Multiple gene products and sequences required for excision of the mobilizable integrated Bacteroides element NBU1

NBU1 is an integrated 10.3-kbp Bacteroides element, which can excise and transfer to Bacteroides or Escherichia coli recipients, where it integrates into the recipient genome. NBU1 relies on large, >60-kbp, conjugative transposons for factors that trigger excision and for mobilization of the circular form to recipients. Previously, we showed that a single integrase gene, intN1, was necessary and sufficient for integration of NBU1 into its target site on the Bacteroides or E. coli genome. We now show that an unexpectedly large region of NBU1 is required for excision. This region includes, in addition to intN1, four open reading frames plus a large region downstream of the fourth gene, prmN1. This downstream sequence was designated XRS, for "excision-required sequence." XRS contains the oriT of the circular form of NBU1 and about two-thirds of the adjacent mobilization gene, mobN1. This is the first time an oriT, which is involved in conjugal transfer of the circular form, has been implicated in excision. Disruption of the gene immediately downstream of intN1, orf2, completely abolished excision. The next open reading frame, orf2x, was too small to be disrupted, so we still do not know whether it plays a role in the excision reaction. Deletions were made in each of two open reading frames downstream of orf2x, orf3 and prmN1. Both of these deletions abolished excision, indicating that these genes are also essential for excision. Attempts to complement various mutations in the excision region led us to realize that a portion of the excision region carrying prmN1 and part of the XRS (XRS(HIII)) inhibited excision when provided in trans on a multicopy plasmid (8 to 10 copies per cell). However, a fragment carrying prmN1, XRS, and the entire mobilization gene, mobN1, did not have this effect. The smaller fragment may be interfering with excision by attracting proteins made by the intact NBU1 and thus removing them from the excision complex. Our results show clearly that excision is a complex process that involves several proteins and a cis-acting region (XRS) which includes the oriT. We suggest that this complex excision machinery may be necessary to allow NBU1 to coordinate nicking at the ends during excision and nicking at the oriT during conjugal transfer, to prevent premature nicking at the oriT before NBU1 has excised and circularized.

1999 Roche Diagnostics Prize for Biomolecular and Cellular Research / Prix Roche Diagnostics 1999 pour la recherche en biologie moléculaire et cellulaireStudies on a "jumping gene machine": Higher-order nucleoprotein complexes in Mu DNA transposition

Studies in my lab have focused on DNA transposition in the bacterial virus, Mu. In vitro studies have shown that Mu DNA transposition is a three-step process involving DNA breakage, strand transfer and DNA replication. In the first step, a nick is introduced at each end of the transposon. The liberated 3'-OH groups subsequently attack a target DNA molecule resulting in strand transfer. The transposon DNA, now covalently linked to the target, is finally replicated to generate the transposition end-product, referred to as a cointegrate. The DNA cleavage and strand transfer reactions are mediated by a "jumping gene machine" or transpososomes, which we discovered in 1987. They are assembled by bringing together three different DNA regions via a process involving multiple protein-DNA and protein-protein interactions. The action of four different proteins is required in addition to protein-induced DNA bending or wrapping to overcome the intrinsic stiffness of DNA, which would ordinarily prohibit the assembly of such a structure. Transpososome assembly is a gradual process involving multiple steps with an inherent flexibility whereby alternate pathways can be used in the assembly process, biasing the reaction towards completion under different conditions.Key words: DNA transposition, transposons, higher-order nucleoprotein complexes, DNA breakage and reunion, site-specific recombination.

Characterization in vitro and in vivo of a new HU family protein from Streptococcus thermophilus ST11

Streptococcus thermophilus is a thermophilic gram-positive bacterium belonging to the lactic acid group. We report the isolation and characterization of a new 9.6-kDa DNA-binding protein, HSth, belonging to the HU family of nucleoid-associated proteins. The hsth gene was isolated in a 2.5-kb genomic region, upstream of a gene with strong homology to Lactococcus lactis pyrD. It is transcribed from a single E. coli sigma(70)-like promoter. Based on its high level of sequence similarity to B. subtilis and E. coli HU, HSth appears to be an HU homologue. The HSth protein shows biochemical and functional properties typical of HU proteins from gram-positive bacteria, being heat-stable, acid-soluble, and homodimeric. When expressed in HU-deficient E. coli cells, HSth supported the growth of bacteriophage Mu as efficiently as E. coli HU homo- and heterodimeric proteins. It did not, however, display any IHF-specific functions. Finally, we show that HSth binds to linear DNA with no apparent specificity, forming protein-DNA complexes similar but not identical to those observed with E. coli HU proteins.

Multiple DNA binding activities of the novel site-specific recombinase, Piv, from Moraxella lacunata

The recombinase, Piv, is essential for site-specific DNA inversion of the type IV pilin DNA segment in Moraxella lacunata and Moraxella bovis. Piv shows significant homology with the transposases of the IS110/IS492 family of insertion elements, but, surprisingly, Piv contains none of the conserved amino acid motifs of the lambda Int or Hin/Res families of site-specific recombinases. Therefore, Piv may mediate site-specific recombination by a novel mechanism. To begin to determine how Piv may assemble a synaptic nucleoprotein structure for DNA cleavage and strand exchange, we have characterized the interaction of Piv with the DNA inversion region of M. lacunata. Gel shift and nuclease/chemical protection assays, competition and dissociation rate analyses, and cooperativity studies indicate that Piv binds two distinct recognition sequences. One recognition sequence, found at multiple sites within and outside of the invertible segment, is bound by Piv protomers with high affinity. The second recognition sequence is located at the recombination cross-over sites at the ends of the invertible element; Piv interacts with this sequence as an oligomer with apparent low affinity. A model is proposed for the role of the different Piv binding sites of the M. lacunata inversion region in the formation of an active synaptosome.

Dissecting the role of the N-terminal domain of human immunodeficiency virus integrase by trans-complementation analysis

The human immunodeficiency virus (HIV) integrase protein (IN) catalyzes two reactions required to integrate HIV DNA into the human genome: 3' processing of the viral DNA ends and integration. IN has three domains, the N-terminal zinc-binding domain, the catalytic core, and the C-terminal SH3 domain. Previously, it was shown that IN proteins mutated in different domains could complement each other. We now report that this does not require any overlap between the two complementing proteins; an N-terminal domain, provided in trans, can restore IN activity of a mutant lacking this domain. Only the zinc-coordinating form of the N-terminal domain can efficiently restore IN activity of an N-terminal deletion mutant. This suggests that interaction between different domains of IN is needed for functional multimerization. We find that the N-terminal domain of feline immunodeficiency virus IN can support IN activity of an N-terminal deletion mutant of HIV type 2 IN. These cross-complementation experiments indicate that the N-terminal domain contributes to the recognition of specific viral DNA ends.

Drosophila P-element transposase is a novel site-specific endonuclease

We developed in vitro assays to study the first step of the P-element transposition reaction: donor DNA cleavage. We found that P-element transposase required both 5' and 3' P-element termini for efficient DNA cleavage to occur, suggesting that a synaptic complex forms prior to cleavage. Transposase made a staggered cleavage at the P-element termini that is novel for all known site-specific endonucleases: the 3' cleavage site is at the end of the P-element, whereas the 5' cleavage site is 17 bp within the P-element 31-bp inverted repeats. The P-element termini were protected from exonucleolytic degradation following the cleavage reaction, suggesting that a stable protein complex remains bound to the element termini after cleavage. These data are consistent with a cut-and-paste mechanism for P-element transposition and may explain why P elements predominantly excise imprecisely in vivo.

Cruciform structures and functions

In this paper, a structure-function analysis of B-DNA self-fitting is reviewed in the light of recent oligonucleotide crystal structures. Their crystal packings provided a high-resolution view of B-DNA helices closely and specifically fitted by groove-backbone interaction, a natural and biologically relevant manner to assemble B-DNA helices. In revealing that new properties of the DNA molecule emerge during condensation, these crystallographic studies have pointed to the biological importance of DNA—DNA interactions.

Three-site synapsis during Mu DNA transposition: a critical intermediate preceding engagement of the active site

The chemical steps of bacteriophage Mu DNA transposition take place within a higher order nucleoprotein structure. We describe a novel intermediate that precedes the previously characterized transpososomes and directly demonstrates the interaction of a distant enhancer element with recombination regions. The transpositional enhancer interacts with the Mu left and right ends to form a three-site synaptic (LER) complex. Under normal reaction conditions, the LER complex is rapidly converted into the more stable Mu transpososomes. However, mutation of the Mu terminal nucleotides results in accumulation of the LER and a failure to form the type 0 transpososome. During the transition from LER to type 0, the Mu DNA termini and the active site of the transposase engage in a catalytically competent conformation.

The interwoven architecture of the Mu transposase couples DNA synapsis to catalysis

Mu transposition occurs exclusively using a pair of recombination sites found at the ends of the phage genome. To address the mechanistic basis of this specificity, we have determined both where the individual subunits of the tetrameric transposase bind on the DNA and where they catalyze DNA joining. We demonstrate that subunits do not catalyze recombination at the site adjacent to where they are bound, but rather on the opposite end of the phage genome. Furthermore, subunits bound to two different sites contribute to catalysis of one reaction step. This interwoven subunit arrangement suggests a molecular explanation for the precision with which recombination occurs using a pair of DNA signals and provides an example of the way in which the architecture of a protein-DNA complex can define the reaction products.

Kinetic and structural probing of the precleavage synaptic complex (type 0) formed during phage Mu transposition. Action of metal ions and reagents specific to single-stranded DNA

In an earlier kinetic study (Wang, Z., and Harshey, R. M. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 699-703), we showed that supercoiling free energy was utilized during Mu transposition to lower the activation barrier of some rate-limiting step in the formation of the cleaved Mu end synaptic complex (type I complex). We report here results from kinetic studies on the assembled but uncleaved synaptic complex (type 0). Based on the estimated rate constants for the formation of type 0 and type I complexes, as well as their temperature and superhelicity dependence, we infer that the type 0 complex is an authentic intermediate in the pathway to Mu end cleavage. Our results are consistent with type 0 production being the rate-limiting step in the overall type I reaction. The conversion of type 0 to type I complex is a fast reaction, does not show strong temperature dependence, and is apparently independent of substrate superhelicity. We have explored the DNA structure within the type 0 complex using chemical and enzymatic probes. The observed susceptibility of DNA outside the Mu ends to single-strand-specific reagents suggests that a helix opening event is associated with type 0 formation. This structural perturbation could account, at least partly, for the high activation barrier to the reaction. There is a close correlation between the appearance of single strandedness near the Mu ends and the superhelicity of the DNA substrate. It is possible that supercoiling energy is utilized in effecting specific conformational transitions within DNA. We have found that Zn2+ and Co2+ ions, like Mg2+ and Mn2+ ions, can efficiently cleave the type 0 complex. However, unlike Mg2+ and Mn2+ ions, Zn2+ and Co2+ ions cannot support assembly of type 0. We discuss the implications of our findings for the mechanism of Mu transposition.

The wing of the enhancer-binding domain of Mu phage transposase is flexible and is essential for efficient transposition

A tetramer of the Mu transposase (MuA) pairs the recombination sites, cleaves the donor DNA, and joins these ends to a target DNA by strand transfer. Juxtaposition of the recombination sites is accomplished by the assembly of a stable synaptic complex of MuA protein and Mu DNA. This initial critical step is facilitated by the transient binding of the N-terminal domain of MuA to an enhancer DNA element within the Mu genome (called the internal activation sequence, IAS). Recently we solved the three-dimensional solution structure of the enhancer-binding domain of Mu phage transposase (residues 1-76, MuA76) and proposed a model for its interaction with the IAS element. Site-directed mutagenesis coupled with an in vitro transposition assay has been used to assess the validity of the model. We have identified five residues on the surface of MuA that are crucial for stable synaptic complex formation but dispensable for subsequent events in transposition. These mutations are located in the loop (wing) structure and recognition helix of the MuA76 domain of the transposase and do not seriously perturb the structure of the domain. Furthermore, in order to understand the dynamic behavior of the MuA76 domain prior to stable synaptic complex formation, we have measured heteronuclear 15N relaxation rates for the unbound MuA76 domain. In the DNA free state the backbone atoms of the helix-turn-helix motif are generally immobilized whereas the residues in the wing are highly flexible on the pico- to nanosecond time scale. Together these studies define the surface of MuA required for enhancement of transposition in vitro and suggest that a flexible loop in the MuA protein required for DNA recognition may become structurally ordered only upon DNA binding.

Assembly and catalytic properties of retrovirus integrase-DNA complexes capable of efficiently performing concerted integration

The in vitro assembly process for forming nucleoprotein complexes containing linear retrovirus-like DNA and integrase (IN) was investigated. Solution conditions that allowed avian myeloblastosis virus IN to efficiently pair two separate linear DNA fragments (each 487 bp in length) containing 3' OH recessed long terminal repeat termini were established. Pairing of the viral termini by IN during preincubation on ice permitted these nucleoprotein complexes to catalyze the concerted insertion of the two termini into a circular DNA target (full-site reaction), mimicking the in vivo reaction. The three major solution determinants were high concentrations of NaCl (0.33 M), 1,4-dioxane, and polyethylene glycol. The aprotic solvent dioxane (15%) was significantly better (sixfold) than 15% dimethyl sulfoxide for forming complexes capable of full-site rather than half-site integration events. Half-site reactions by IN involved the insertion of a single donor terminus into circular pGEM. Although NaCl was essential for the efficient promotion of the concerted integration reaction, dioxane was necessary to prevent half-site reactions from occurring at high NaCl concentrations. Under optimal solution conditions, the concerted integration reaction was directly proportional to a sixfold range of IN. The complexes appeared not to turn over, and few half-site donor-donor molecules were produced. In the presence of 0.15 or 0.35 M NaCl, dioxane prevented efficient 3' OH trimming of a blunt-ended donor by IN, suggesting that the complexes formed by IN with blunt-ended donors were different from those formed with donors containing 3' OH recessed termini for strand transfer. The results suggest that IN alone was capable of protein-protein and protein-DNA interactions that efficiently promote the in vitro concerted integration reaction.

Assembly of phage Mu transpososomes: cooperative transitions assisted by protein and DNA scaffolds

Transposition of phage Mu takes place within higher order protein-DNA complexes called transpososomes. These complexes contain the two Mu genome ends synapsed by a tetramer of Mu transposase (MuA). Transpososome assembly is tightly controlled by multiple protein and DNA sequence cofactors. We find that assembly can occur through two distinct pathways. One previously described pathway depends on an enhancer-like sequence element, the internal activation sequence (IAS). The second pathway depends on a MuB protein-target DNA complex. For both pathways, all four MuA monomers in the tetramer need to interact with an assembly-assisting element, either the IAS or MuB. However, once assembled, not all MuA monomers within the transpososome need to interact with MuB to capture MuB-bound target DNA. The multiple layers of control likely are used in vivo to ensure efficient rounds of DNA replication when needed, while minimizing unwanted transposition products.

Enhancer-independent variants of phage Mu transposase: enhancer-specific stimulation of catalytic activity by a partner transposase

Assembly of the functional tetrameric form of phage Mu transposase (A protein) requires specific interactions between the Mu A monomer and its cognate sequences at the ends of the Mu genome (attL and attR) as well as those internal to it (the enhancer element). We describe here deletion variants of Mu A that show enhancer-independence in the assembly of the strand cleavage complex. These deletions remove the amino-terminal region of Mu A required for its interactions with the enhancer elements. The basal enhancer-independent activity of the variant proteins can be stimulated by a partner variant harboring an intact enhancer-binding domain. By exploiting the identical att-binding, and nonidentical enhancer-binding specificities of Mu A and D108 A (transposase of the Mu related phage D108), we show that the stimulation of activity is enhancer-specific. Taken together, these results suggest that the domain of Mu A that includes the enhancer-interacting region may exert negative as well as positive modulatory effects on the strand cleavage reaction. We discuss the implications of these results in the framework of a recent model for the assembly of shared active sites within the Mu A tetramer.

Circular structures in retroviral and cellular genomes

A computer program for predicting DNA bending from nucleotide sequence was used to identify circular structures in retroviral and cellular genomes. An 830-base pair circular structure was located in a control region near the center of the genome of the human immunodeficiency virus type I (HIV-I). This unusual structure displayed relatively smooth planar bending throughout its length. The structure is conserved in diverse isolates of HIV-I, HIV-II, and simian immunodeficiency viruses, which implies that it is under selective constraints. A search of all sequences in the GenBank data base was carried out in order to identify similar circular structures in cellular DNA. The results revealed that the structures are associated with a wide range of sequences that undergo recombination, including most known examples of DNA inversion and subtelomeric translocation systems. Circular structures were also associated with replication and transposition systems where DNA looping has been implicated in the generation of large protein-DNA complexes. Experimental evidence for the structures was provided by studies which demonstrated that two sequences detected as circular by computer preferentially formed covalently closed circles during ligation reactions in vitro when compared to nonbent fragments, bent fragments with noncircular shapes, and total genomic DNA. In addition, a single T-->C substitution in one of these sequences rendered it less planar as seen by computer analysis and significantly reduced its rate of ligase-catalyzed cyclization. These results permit us to speculate that intrinsically circular structures facilitate DNA looping during formation of the large protein-DNA complexes that are involved in site- and region-specific recombination and in other genomic processes.

Disassembly of the bacteriophage Mu transposase for the initiation of Mu DNA replication

Upon catalyzing strand transfer, the Mu transposase (MuA) remains tightly bound to the resulting transposition intermediate, the strand transfer complex (STC), and poses an impediment to host replication proteins. Additional host factors, which can be resolved into two fractions (Mu Replication Factor alpha and beta; MRF alpha and MRF beta), are required to disassemble the MuA complex and initiate DNA synthesis. MRF alpha modifies the protein content of the STC, removing MuA from the DNA in the process. The MRF beta promotes initiation of the Mu DNA synthesis on the STC altered by the MRF alpha. These host factors cannot promote initiation of Mu DNA synthesis if the STC is damaged by partial proteolysis. Moreover, the mutant protein MuA211 cannot be removed from the STC by MRF alpha, blocking initiation of DNA synthesis. These results indicate that MuA in the STC plays a critical function in beginning a sequence of events leading to the establishment of a Mu replication fork.

Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration

The crystal structure of the core domain of bacteriophage Mu transposase, MuA, has been determined at 2.4 A resolution. The first of two subdomains contains the active site and, despite very limited sequence homology, exhibits a striking similarity to the core domain of HIV-1 integrase, which carries out a similar set of biochemical reactions. It also exhibits more limited similarity to other nucleases, RNase H and RuvC. The second, a beta barrel, connects to the first subdomain through several contacts. Three independent determinations of the monomer structure from two crystal forms all show the active site held in a similar, apparently inactive configuration. The enzymatic activity of MuA is known to be activated by formation of a DNA-bound tetramer of the protein. We propose that the connections between the two subdomains may be involved in the cross-talk between the active site and the other domains of the transposase that controls the activity of the protein.

Vectors with the fd replicon for in vivo cloning and analysis of genes

We have constructed two new mini-Mu derivatives, pMRfP and pBEf, that combine the properties of known mini-Mu vectors and the advantages of the replication origin (orifd) of filamentous phage fd. Mini-Mu pMRfP consists of the left (850 bp) and the right (216 bp) ends of the Mu genome, orifd, packaging signal of fd, and the gene conferring resistance to chloramphenicol. The second mini-Mu, termed pBEf, carries the left end of Mu (1001 bp), which contains the so-called internal activation sequence (enhancer of transposition), required for a higher frequency of transposition, the right end (116 bp) and the gene conferring resistance to kanamycin. These new mini-Mu vectors are suitable for in vivo cloning with the ability of single-stranded DNA preparation using one of the helper phages (M13K07, rv1, IR1, R408) and with a large cloning capacity (the size of the cloned fragment can be up to 35 kb). They can also be used as the hoppers (a transposable ori that can be turned on or off depending on the presence of the fd gene 2 product). Thus, these mini-Mu derivatives can be employed as vectors for in vivo cloning, and as regulated transposons or mobile replicons.

A novel class of winged helix-turn-helix protein: the DNA-binding domain of Mu transposase

BACKGROUND

Mu transposase (MuA) is a multidomain protein encoded by the bacteriophage Mu genome. It is responsible for translocation of the Mu genome, which is the largest and most efficient transposon known. While the various domains of MuA have been delineated by means of biochemical methods, no data have been obtained to date relating to its tertiary structure.

RESULTS

We have solved the three-dimensional solution structure of the DNA-binding domain (residues 1-76; MuA76) of MuA by multidimensional heteronuclear NMR spectroscopy. The structure consists of a three-membered alpha-helical bundle buttressed by a three-stranded antiparallel beta-sheet. Helices H1 and H2 and the seven-residue turn connecting them comprise a helix-turn-helix (HTH) motif. In addition, there is a long nine-residue flexible loop or wing connecting strands B2 and B3 of the sheet. NMR studies of MuA76 complexed with a consensus DNA site from the internal activation region of the Mu genome indicate that the wing and the second helix of the HTH motif are significantly perturbed upon DNA binding.

CONCLUSIONS

While the general appearance of the DNA-binding domain of MuA76 is similar to that of other winged HTH proteins, the connectivity of the secondary structure elements is permuted. Hence, the fold of MuA76 represents a novel class of winged HTH DNA-binding domain.

Complete transposition requires four active monomers in the mu transposase tetramer

A tetramer of Mu transposase (MuA) cleaves and joins multiple DNA strands to promote transposition. Derivatives of MuA altered at two acidic residues that are conserved among transposases and retroviral integrases form tetramers but are defective in both cleavage and joining. These mutant proteins were used to analyze the contribution of individual monomers to the activity of the tetramer. The performance of different protein combinations demonstrates that not all monomers need to be catalytically competent for the complex to promote an individual cleavage or joining reaction. Furthermore, the results indicate that each pair of essential residues is probably donated to the active complex by a single monomer. Although stable, tetramers composed of a mixture of mutant and wild-type MuA generate products cleaved at only one end and with only one end joined to the target DNA. The abundance of these abortive products and the ratios of the two proteins in complexes stalled at different steps indicate that the complete reaction requires the activity of all four monomers. Thus, each subunit of MuA appears to use the conserved acidic amino acids to promote one DNA cleavage or one DNA joining reaction.

Identification of residues in the Mu transposase essential for catalysis

A tetramer of Mu transposase (MuA) cleaves the phage Mu DNA and joins these ends to a target DNA to catalyze transposition. Substitution mutations at Asp-269 or Glu-392 within MuA destroy both the DNA cleavage and joining activities without blocking tetramer assembly, indicating that the mutations specifically affect catalysis. Although inactive under standard reaction conditions (10 mM Mg2+), the mutant proteins are partially resuscitated by 10-20 mM Mn2+, concentrations 5- to 10-fold higher than optimal for wild-type MuA. Amino acid sequence alignment and the similar effects of mutations suggests that Asp-269 and Glu-392 of MuA may be analogs of the first Asp and final Glu of a conserved triad of acidic amino acids present in many transposases and the retroviral integrases (the D-D-35-E motif). The higher Mn2+ optima observed with MuA derivatives altered at these positions supports a role for the conserved acidic amino acids in coordinating divalent metal ions in the active sites of transposases.

Neighboring plasmid sequences can affect Mini-Mu DNA transposition in the absence of expression of the bacteriophage Mu semi-essential early region

Bacteriophage Mu DNA, like other transposable elements, requires DNA sequences at both extremities to transpose. It has been previously demonstrated that the transposition activity of various transposons can be influenced by sequences outside their ends. We have found that alterations in the neighboring plasmid sequences near the right extremity of a Mini-Mu, inserted in the plasmid pSC101, can exert an influence on the efficiency of Mini-Mu DNA transposition when an induced helper Mu prophage contains a polar insertion in its semi-essential early region (SEER). The SEER of Mu is known to contain several genes that can affect DNA transposition, and our results suggest that some function(s), located in the SEER of Mu, may be required for optimizing transposition (and thus, replication) of Mu genomes from restrictive locations during the lytic cycle.

Transposase A binding sites in the attachment sites of bacteriophage Mu that are essential for the activity of the enhancer and A binding sites that promote transposition towards Fpro-lac

In this paper we determine which of the A binding sites in the attachment sites of phage Mu are required for the stimulatory activity of the transpositional enhancer (IAS). For this purpose the transposition frequencies of mini-Mu's with different truncated attachment sites to an Ftet target were measured both in the presence and the absence of the IAS. The results show that in our in vivo assay the L3 and R3 sites are dispensable for functioning of the IAS. An additional deletion of L2 or R2 however abolishes the stimulating activity of the enhancer suggesting an interaction between A molecules bound to these sites and the IAS. The residual transposition activity of a IAS-containing mini Mu in which R2 (and R3) are deleted is much lower than the activity of the comparable construct without the IAS. This means that in the absence of R2 the IAS is inhibiting transposition. Such an inhibition is not observed when L2 (and L3) are deleted. This suggests that the IAS interacts with the attachment sites in an ordered fashion, first with attL and then with attR. Furthermore we show that mini-Mu transposition is enhanced when Fpro-lac is used as a target instead of Ftet. We show that this elevated transposition is dependent on the Mu A binding sites L2,L3 and R2. These sequences could possibly mediate an interaction between the mini-Mu plasmid and sequences present on Fpro-lac.

Characterization of functionally important sites in the bacteriophage Mu transposase protein

The 663 amino acid Mu transposase protein is absolutely required for Mu DNA transposition. Mutant proteins were constructed in vitro in order to locate regions of transposase that may be important for the catalysis of DNA transposition. Deletions in the A gene, which encodes the transposase, yielded two stable mutant proteins that aid in defining the end-specific DNA-binding domain. Linker insertion mutagenesis at eight sites in the Mu A gene generated two proteins, FF6 and FF14 (resulting from two and four amino acid insertions, respectively, at position 408), which were thermolabile for DNA binding in vitro at 43 degrees C. However, transposition activity in vivo was severely reduced for all mutant proteins at 37 degrees C, except those with insertions at positions 328 and 624. In addition, site-specific mutagenesis was performed to alter tyrosine 414, which is situated in a region that displays amino acid homology to the active sites of a number of nicking/closing enzymes. Tyrosine 414 may reside within an important, yet non-essential, site of transposase, as an aspartate-substituted protein had a drastically reduced frequency of transposition, while the remaining mutants yielded reduced, but substantial, frequencies of microMu transposition in vivo.

Crucial role for DNA supercoiling in Mu transposition: a kinetic study

DNA supercoiling plays an indispensable role in an early step of bacteriophage Mu transposition. This step involves formation of a nucleoprotein complex in which the Mu ends synapse and undergo two concerted single-strand cleavages. We describe a kinetic analysis of the role of supercoiling in the Mu-end synapsis reaction as measured by the cleavage assay. We observe a dependence of the reaction rate on superhelical density as well as on the length of Mu donor plasmid DNA. The reaction has a high activation enthalpy (approximately 67 kcal/mol). These results imply that the free energy of supercoiling is used directly to lower the activation barrier of the rate-limiting step of the reaction. Only the free energy of supercoiling associated with DNA outside the Mu ends appears to be utilized, implying that the Mu ends come together before the supercoiling energy is used. Our results suggest an essential function for the bacterial sequences attached to the ends of Mu virion DNA.

Natural genetic engineering of the bacterial genome

The term 'natural genetic engineering' means viewing genetic change as a coordinated cell biological process, the reorganization of discrete genomic modules, resulting in the formation of new DNA structures. Examples of natural genetic engineering continue to accumulate, and the concept can be used to integrate observations which demonstrate the similarity between in vitro genetic engineering and the action of in vivo agents of genetic change.

Protein-DNA assemblies controlling lytic development of bacteriophage Mu

Recent analysis of the mechanism and regulation of transposition by bacteriophage Mu has emphasized the importance of controlled assembly of specific protein-DNA complexes. Both the Mu transposase and the Mu repressor engage in multiple protein-protein and protein-DNA interactions that modulate the outcome of a phage infection.

Division of labor among monomers within the Mu transposase tetramer

A single tetramer of Mu transposase (MuA) pairs the recombination sites, cleaves the donor DNA, and joins these ends to a target DNA by strand transfer. Analysis of C-terminal deletion derivatives of MuA reveals that a 30 amino acid region between residues 575 and 605 is critical for these three steps. Although inactive on its own, a deletion protein lacking this region assembles with the wild-type protein. These mixed tetramers carry out donor cleavage but do not promote strand transfer, even when the donor cleavage stage is bypassed. These data suggest that the active center of the transposase is composed of the C-terminus of four MuA monomers; one dimer carries out donor cleavage while all four monomers contribute to strand transfer.

Involvement of Escherichia coli FIS protein in maintenance of bacteriophage mu lysogeny by the repressor: control of early transcription and inhibition of transposition

The Escherichia coli FIS (factor for inversion stimulation) protein has been implicated in assisting bacteriophage Mu repressor, c, in maintaining the lysogenic state under certain conditions. In a fis strain, a temperature-inducible Mucts62 prophage is induced at lower temperatures than in a wild-type host (M. Bétermier, V. Lefrère, C. Koch, R. Alazard, and M. Chandler, Mol. Microbiol. 3:459-468, 1989). Increasing the prophage copy number rendered Mucts62 less sensitive to this effect of the fis mutation, which thus seems to depend critically on the level of repressor activity. The present study also provides evidence that FIS affects the control of Mu gene expression and transposition. As judged by the use of lac transcriptional fusions, repression of early transcription was reduced three- to fourfold in a fis background, and this could be compensated by an increase in cts62 gene copy number. c was also shown to inhibit Mu transposition two- to fourfold less strongly in a fis host. These modulatory effects, however, could not be correlated to sequence-specific binding of FIS to the Mu genome, in particular to the strong site previously identified on the left end. We therefore speculate that a more general function of FIS is responsible for the observed modulation of Mu lysogeny.

DNA inversions in phages and bacteria

In certain phages and bacteria, there is a recombination system that specifically promotes the inversion of a DNA fragment. These inversion events appear to act as genetic switches allowing the alternate expression of different sets of genes which in general code for surface proteins. The mechanism of inversion in one class of inversion systems (Gin/Hin) has been studied in detail. It involves the formation of a highly specific nucleoprotein complex in which not only the two recombination sites and the DNA invertase participate but also a recombinational enhancer to which the DNA-bending protein Fis is bound.

DNA-promoted assembly of the active tetramer of the Mu transposase

A stable tetramer of the Mu transposase (MuA) bound to the ends of the Mu DNA promotes recombination. Assembly of this active protein-DNA complex from monomers of MuA requires an intricate array of MuA protein-binding sites on supercoiled DNA, divalent metal ions, and the Escherichia coli HU protein. Under altered reaction conditions, many of these factors stimulate assembly of the MuA tetramer but are not essential, allowing their role in formation of the complex to be analyzed. End-type MuA-binding sites and divalent metal ions are most critical and probably promote a conformational change in MuA that is necessary for multimerization. Multiple MuA-binding sites on the DNA contribute synergistically to tetramer formation. DNA superhelicity assists cooperativity between the sites on the two Mu DNA ends if they are properly oriented. HU specifically promotes assembly involving the left end of the Mu DNA. In addition to dissecting the assembly pathway, these data demonstrate that the tetrameric conformation is intrinsic to MuA and constitutes the form of the protein active in catalysis.