Structural requirement for IS50-mediated gene transposition

Julian Davies and the discovery of kanamycin resistance transposon Tn5

This paper recounts some of my fond memories of a collaboration between Julian Davies and myself that started in 1974 in Geneva and that led to our serendipitous discovery of the bacterial kanamycin resistance transposon Tn5, and aspects of the lasting positive impact of our interaction and discovery on me and the community. Tn5 was one of the first antibiotic resistance transposons to be found. Its analysis over the ensuing decades provided valuable insights into mechanisms and control of transposition, and led to its use as a much-valued tool in diverse areas of molecular genetics, as also will be discussed here.

Alternative mechanisms for tn5 transposition

Bacterial transposons are known to move to new genomic sites using either a replicative or a conservative mechanism. The behavior of transposon Tn5 is anomalous. In vitro studies indicate that it uses a conservative mechanism while in vivo results point to a replicative mechanism. To explain this anomaly, a model is presented in which the two mechanisms are not independent--as widely believed--but could represent alternate outcomes of a common transpositional pathway.

Genesis, effects and fates of repeats in prokaryotic genomes

DNA repeats are causes and consequences of genome plasticity. Repeats are created by intrachromosomal recombination or horizontal transfer. They are targeted by recombination processes leading to amplifications, deletions and rearrangements of genetic material. The identification and analysis of repeats in nearly 700 genomes of bacteria and archaea is facilitated by the existence of sequence data and adequate bioinformatic tools. These have revealed the immense diversity of repeats in genomes, from those created by selfish elements to the ones used for protection against selfish elements, from those arising from transient gene amplifications to the ones leading to stable duplications. Experimental works have shown that some repeats do not carry any adaptive value, while others allow functional diversification and increased expression. All repeats carry some potential to disorganize and destabilize genomes. Because recombination and selection for repeats vary between genomes, the number and types of repeats are also quite diverse and in line with ecological variables, such as host-dependent associations or population sizes, and with genetic variables, such as the recombination machinery. From an evolutionary point of view, repeats represent both opportunities and problems. We describe how repeats are created and how they can be found in genomes. We then focus on the functional and genomic consequences of repeats that dictate their fate.

Transposable element ISHp608 of Helicobacter pylori: nonrandom geographic distribution, functional organization, and insertion specificity

A new member of the IS605 transposable element family, designated ISHp608, was found by subtractive hybridization in Helicobacter pylori. Like the three other insertion sequences (ISs) known in this gastric pathogen, it contains two open reading frames (orfA and orfB), each related to putative transposase genes of simpler (one-gene) elements in other prokaryotes; orfB is also related to the Salmonella virulence gene gipA. PCR and hybridization tests showed that ISHp608 is nonrandomly distributed geographically: it was found in 21% of 194 European and African strains, 14% of 175 Bengali strains, 43% of 131 strains from native Peruvians and Alaska natives, but just 1% of 223 East Asian strains. ISHp608 also seemed more abundant in Peruvian gastric cancer strains than gastritis strains (9 of 14 versus 15 of 45, respectively; P = 0.04). Two ISHp608 types differing by approximately 11% in DNA sequence were identified: one was widely distributed geographically, and the other was found only in Peruvian and Alaskan strains. Isolates of a given type differed by < or = 2% in DNA sequence, but several recombinant elements were also found. ISHp608 marked with a resistance gene was found to (i) transpose in Escherichia coli; (ii) generate simple insertions during transposition, not cointegrates; (iii) insert downstream of the motif 5"-TTAC without duplicating target sequences; and (iv) require orfA but not orfB for its transposition. ISHp608 represents a widespread family of novel chimeric mobile DNA elements whose further analysis should provide new insights into transposition mechanisms and into microbial population genetic structure and genome evolution.

Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori

A search by subtractive hybridization for sequences present in only certain strains of Helicobacter pylori led to the discovery of a 2-kb transposable element to be called IS607, which further PCR and hybridization tests indicated was present in about one-fifth of H. pylori strains worldwide. IS607 contained two open reading frames (ORFs) of possibly different phylogenetic origin. One ORF (orfB) exhibited protein-level homology to one of two putative transposase genes found in several other chimeric elements including IS605 (also of H. pylori) and IS1535 (of Mycobacterium tuberculosis). The second IS607 gene (orfA) was unrelated to the second gene of IS605 and might possibly be chimeric itself: it exhibited protein-level homology to merR bacterial regulatory genes in the first approximately 50 codons and homology to the second gene of IS1535 (annotated as "resolvase," apparently due to a weak short recombinase motif) in the remaining three-fourths of its length. IS607 was found to transpose in Escherichia coli, and analyses of sequences of IS607-target DNA junctions in H. pylori and E. coli indicated that it inserted either next to or between adjacent GG nucleotides, and generated either a 2-bp or a 0-bp target sequence duplication, respectively. Mutational tests showed that its transposition in E. coli required orfA but not orfB, suggesting that OrfA protein may represent a new, previously unrecognized, family of bacterial transposases.

The role of tandem IS dimers in IS911 transposition

Using a combined in vivo and in vitro approach, we demonstrated that the transposition products generated by IS911 from a dimeric donor plasmid are different from those generated from a plasmid monomer. When carried by a monomeric plasmid donor, free IS911 transposon circles are generated by intra-IS recombination in which one IS end undergoes attack by the other. These represent transposition intermediates that undergo integration using the abutted left (IRL) and right (IRR) ends of the element, the active IRR-IRL junction, to generate simple insertions. In contrast, the two IS911 copies carried by a dimeric donor plasmid not only underwent intra-IS recombination to generate transposon circles but additionally participated in inter-IS recombination. This also creates an active IRR-IRL junction by generating a head-to-tail IS tandem dimer ([IS]2) in which one of the original plasmid backbone copies is eliminated in the formation of the junction. Both transposon circles and IS tandem dimers are generated from an intermediate in which two transposon ends are retained by a single strand joint to generate a figure 8 molecule. Inter-IS figure 8 molecules generated in vitro could be resolved into the [IS]2 form following introduction into a host strain by transformation. Resolution did not require IS911 transposase. The [IS]2 structure was stable in the absence of transposase but was highly unstable in its presence both in vivo and in vitro. Previous studies had demonstrated that the IRR-IRL junction promotes efficient intermolecular integration and intramolecular deletions both in vivo and in vitro. Integration of the [IS]2 derivative would result in a product that resembles a co-integrate structure. It is also shown here that the IRR-IRL junction of the [IS]2 form and derivative structures can specifically target one of the other ends in an intramolecular transposition reaction to generate transposon circles in vitro. These results not only demonstrate that IS911 (and presumably other members of the IS3 family) is capable of generating a range of transposition products, it also provides a mechanistic framework which explains the formation and activity of such structures previously observed for several other unrelated IS elements. This behaviour is probably characteristic of a large number of IS elements.

IS elements as constituents of bacterial genomes

We provide here an overview of our present understanding of the distribution of different insertion sequences (ISs) within bacterial genomes (both chromosomes and plasmids). This is at present fragmentary and a significant effort is needed in the analysis of the increasing number of genomes whose sequence has been determined. We also consider some of the properties of ISs which are important in their role of assembling, reassorting, and transmitting groups of genes.

The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution

Transposon Tn5 employs a unique means of self-regulation by expressing a truncated version of the transposase enzyme that acts as an inhibitor. The inhibitor protein differs from the full-length transposase only by the absence of the first 55 N-terminal amino acid residues. It contains the catalytic active site of transposase and a C-terminal domain involved in protein-protein interactions. The three-dimensional structure of Tn5 inhibitor determined to 2.9-A resolution is reported here. A portion of the protein fold of the catalytic core domain is similar to the folds of human immunodeficiency virus-1 integrase, avian sarcoma virus integrase, and bacteriophage Mu transposase. The Tn5 inhibitor contains an insertion that extends the beta-sheet of the catalytic core from 5 to 9 strands. All three of the conserved residues that make up the "DDE" motif of the active site are visible in the structure. An arginine residue that is strictly conserved among the IS4 family of bacterial transposases is present at the center of the active site, suggesting a catalytic motif of "DDRE." A novel C-terminal domain forms a dimer interface across a crystallographic 2-fold axis. Although this dimer represents the structure of the inhibited complex, it provides insight into the structure of the synaptic complex.

Novel sequence organization and insertion specificity of IS605 and IS606: chimaeric transposable elements of Helicobacter pylori

IS605, an insertion sequence (IS) that is unusual in containing homologs of genes for the single putative transposases of two other unrelated IS elements (IS200 and IS1341), was found in nearly one-third of a set of 238 independent isolates of the gastric pathogen Helicobacter pylori. Hybridization and PCR tests indicated that any strain carrying one of these ORFs also carried the other, which implies that both ORFs are in the same unit of transposition. The IS605 ends and target sites for insertion were identified by sequencing eight preexisting insertions in strain NCTC11638, corresponding empty sites in other strains, and new transpositions in E. coli of an IS605 derivative marked with a selectable chloramphenicol-resistance gene. These tests showed that IS605 is also unusual in: (1) having unique, not inverted repeat, ends; (2) not duplicating (or deleting) target sequences during transposition; and (3) inserting with its left (IS200-homolog) end next to 5'-TTTAA or 5'-TTTAAC. IS605 was implicated in at least two genome rearrangements in strain NCTC11638. A second member of the IS605 family, called IS606 (25% amino acid identity to IS605 in inferred proteins) was found in one-third of 38 H. pylori strains tested, many of which did not carry IS605. The features of these two chimaeric IS elements are discussed in terms of possible transposition mechanisms, IS element evolution, and effects of IS elements on genome organization and evolution in the microbes that they inhabit.

Insertion sequences

Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available.

IS10/Tn10 transposition efficiently accommodates diverse transposon end configurations

Transposon Tn10 and its component insertion sequence IS10 move by non-replicative transposition. We have studied the array of reaction intermediates and products in a high efficiency in vitro IS10/Tn10 transposition reaction. Synapsis of two transposon ends, followed by cleavage and strand transfer, can occur very efficiently irrespective of the relative locations and orientations of the two ends. The two participating ends can occur in inverted or direct orientation on the same molecule or, most importantly, on two different molecules. This behavior contrasts sharply with that of Mu, in which transposition is strongly biased in favor of inverted repeat synapsis. Mechanistically, the absence of discrimination amongst various end configurations implies that the architecture within the IS10/Tn10 synaptic complex is relatively simple, i.e. lacking any significant intertwining of component DNA strands. Biologically these observations are important because they suggest that the IS10 insertion sequence module has considerable flexibility in the types of DNA rearrangements that it can promote. Most importantly, it now seems highly probable that a single non-replicative IS10 element can promote DNA rearrangements usually attributed to replicative transposition, i.e. adjacent deletions and cointegrates, by utilizing transposon ends on two sister chromosomes. Other events which probably also contribute to the diversity of IS10/Tn10-promoted rearrangements are discussed.

Intermolecular transposition of IS10 causes coupled homologous recombination at the transposition site

Interplasmid and chromosome to plasmid transposition of IS10 were studied by assaying inactivation of the phage 434 cI gene, carried on a low copy number plasmid. This was detected by the activity of the tet gene expressed from the phage 434 PR promoter. Each interplasmid transposition resulted in the fusion of the donor and acceptor plasmids into cointegrate structure, with a 9-bp duplication of the target DNA at the insertion site. Cointegrate formation was abolished in delta recA strains, although simple insertions of IS10 were observed. This suggests a two-stage mechanism involving IS10 conservative transposition, followed by homologous recombination between the donor and the acceptor. Two plasmids carrying inactive IS10 sequences were fused to cointegrates at a 100-fold lower frequency, suggesting that homologous recombination is coupled to and stimulated by the transposition event. Each IS10 transposition from the chromosome to the acceptor plasmid involved replicon fusion, providing a mechanism for IS10-mediated integration of extrachromosomal elements into the chromosome. This was accompanied by the formation of an additional copy of IS10 in the chromosome. Thus, like replicative transposition, conservative transposition of IS10 is accompanied by cointegrate formation and results in duplication of the IS10.

DNA length, bending, and twisting constraints on IS50 transposition

Transposition is a multistep process in which a transposable element DNA sequence moves from its original genetic location to a new site. Early steps in this process include the formation of a transposition complex in which the end sequences of the transposable element are brought together in a structurally precise fashion through the action of the element-encoded transposase protein and the cleavage of the element free from the adjoining DNA. If transposition complex formation must precede DNA cleavage (or nicking), then changing the length of the donor DNA between closely spaced ends should have dramatic effects on the frequency of the transposition. This question has been examined by studying the effects of altering donor DNA length on IS50 transposition. Donor DNA < or = 64 bp severely impaired transposition. Donor DNA > or = 200 bp demonstrated high transposition frequencies with only modest length dependencies. Constructs with donor DNA lengths between 66 and 174 bp demonstrated a dramatic periodic effect on transposition (periodicity approximately 10.5 bp).

One-ended insertion of IS911

An apparently nonreplicative integration reaction mediated by the insertion sequence IS911 has been analyzed. It is shown to involve the right-end inverted repeat (IRR) of the element and sequences in the flanking vector DNA. The flanking sequences appear to behave as a surrogate IS911 end, since integration is greatly reduced when limited similarities with IRR are eliminated by site-directed mutagenesis. Data are presented which suggest that the activity of the IRR junction results from the proximity of the transposase gene and may therefore reflect preferential transposase recognition of IRR in cis.

Formation of the tandem repeat (IS30)2 and its role in IS30-mediated transpositional DNA rearrangements

Plasmids carrying two IS30 elements in the same orientation, as in the composite transposon Tn2706, are structurally unstable in Escherichia coli. A primary segregation product is formed by site-specific deletion of the sequences carried between the two IS30 elements. The resulting covalently closed replicon carries the two IS30 elements as tandem repeats separated by only 2 bp. This (IS30)2 structure is extremely unstable, but it can nevertheless be isolated on its vector plasmid and, after purification, can be reintroduced into host cells by transformation. Among the descendants of transformants of recA- bacteria, replicated copies of the introduced (IS30)2 structure are still present, together with various kinds of segregation products which provide evidence for the efficient generation of DNA rearrangements. Most abundant is the product of another site-specific recombination between two identical ends of the IS30 elements involved, which results in the presence of just one intact IS30 on the plasmid. Apart from this, and depending on the presence of appropriate targets for IS30 transposition, various transposition products of (IS30)2 are also seen. Intramolecular reactions lead to DNA inversions and deletions with breakpoints other than IS30 ends. In intermolecular reactions inverse transposition occurs at high frequency and one also obtains simple transposition and cointegration. A mutational study revealed the requirement in cis of one intact IS30 transposase gene and of both proximal ends of the two IS30 elements concerned not only for the formation of (IS30)2, but also for its further rearrangement reactions, including the efficient formation of site-specific deletions. A model is proposed, which postulates that (IS30)2 intermediates play a key role in IS30 transposition pathways in which the formation of (IS30)2 may be rate-limiting. Once this structure is formed, it gives rise to a burst of transpositional rearrangements in the subclone carrying (IS30)2. Evolutionary implications of these findings are discussed.

Germline excision of the transposable element Tc1 in C. elegans

We have examined eight germline revertants generated by the excision of Tc1 from a site within the unc-22 gene of Caenorhabditis elegans. A rich variety of rearrangements accompanied Tc1 excision at this site, including transposon 'footprints', deletions of sequences flanking the insertion site and direct nontandem duplications of flanking DNA. With only modest modification the double-strand gap repair model for transposition, recently proposed by Engles and coworkers (Cell 62: 515-525 1990), can explain even the most complex of these rearrangements. In light of this model rearrangements of the target site accompanying transposition/excision may not be the end result of imprecise excision of the element. Instead, these rearrangements may be the result of imprecise repair of the double-strand gap by the host replication and repair machinery. Sequences surrounding an insertion site influence the fidelity of gap repair by this machinery. This may lead to a number of possible resolutions of a double-strand gap as documented here for a Tc1 site in unc-22.

Intramolecular transposition by a synthetic IS50 (Tn5) derivative

We report the formation of deletions and inversions by intramolecular transposition of Tn5-derived mobile elements. The synthetic transposons used contained the IS50 O and I end segments and the transposase gene, a contraselectable gene encoding sucrose sensitivity (sacB), antibiotic resistance genes, and a plasmid replication origin. Both deletions and inversions were associated with loss of a 300-bp segment that is designated the vector because it is outside of the transposon. Deletions were severalfold more frequent than inversions, perhaps reflecting constraints on DNA twisting or abortive transposition. Restriction and DNA sequence analyses showed that both types of rearrangements extended from one transposon end to many different sites in target DNA. In the case of inversions, transposition generated 9-bp direct repeats of target sequences.

Site-specific transposition of insertion sequence IS630

IS630 is a 1.15-kilobase sequence in Shigella sonnei that, unlike many mobile elements, seems not to mediate cointegration between different replicons. To assess its transposition, we constructed composite elements containing inverted copies of IS630 flanking a drug resistance gene. We found that these composite elements transposed to plasmid ColE1 in Escherichia coli. DNA sequencing showed that transposition was, in all cases, to the dinucleotide sequence 5'-TA-3'. There were two preferred insertion sites which corresponded to the TA sequences in the inverted repeats of a 13-base-pair stem region of the [rho]-dependent transcription terminator. IS630 is flanked by TA, and nucleotide substitution by in vitro mutagenesis at these ends did not affect transposition activity of a composite element or its ability to insert preferentially into TA within the 13-base-pair inverted repeat sequences or to duplicate the target sequence.

Transposition in Shigella dysenteriae: isolation and analysis of IS911, a new member of the IS3 group of insertion sequences

Twenty-nine clear-plaque mutants of bacteriophage lambda were isolated from a Shigella dysenteriae lysogen. Three were associated with insertions in the cI gene: two were due to insertion of IS600, and the third resulted from insertion of a new element, IS911. IS911 is 1,250 base pairs (bp) long, carries 27-bp imperfect terminal inverted repeats, and generates 3-bp duplications of the target DNA on insertion. It was found in various copy numbers in all four species of Shigella tested and in Escherichia coli K-12 but not in E. coli W. Analysis of IS911-mediated cointegrate molecules indicated that the majority were generated without duplication of IS911. They appeared to result from direct insertion via one end of the element and the neighboring region of DNA, which resembles a terminal inverted repeat of IS911. Nucleotide sequence analysis revealed that IS911 carries two consecutive open reading frames which code for potential proteins showing similarities to those of the IS3 group of elements.

Tn7 inserts in both orientations at a single chromosomal location and apparently forms cointegrates in Pasteurella multocida

Pasteurella multocida transconjugants isolated after mating with Escherichia coli strains that carry one or the other of two Tn7-containing suicide plasmids, pRKTV5 and pUW964 (pRKTV5::Tn5), were analysed. These plasmids have the ColE1 replication origin and were thus expected to deliver transposons but not be maintained as free replicons in Pasteurella. Five out of six transconjugants selected for acquisition of Tn7 from E. coli (pRKTV5) had simple insertions of the transposon, in either orientation, at a single chromosomal location, while the sixth had pRKTV5 integrated at the same location. By contrast, all of 27 transconjugants selected for acquisition of either Tn7 or Tn5 from E. coli (pUW964) maintained pUW964. Of seven subsequently examined at the molecular level, all had pUW964 (in one case, a deletion derivative) integrated at the same location as the Tn7 insertions obtained with pRKTV5. A copy of Tn7 was present at each boundary between the integrated plasmids (pRKTV5 or pUW964) and the chromosome in each strain. The two copies of Tn7 at either end of an integrated plasmid were either in the same (six cases) or in opposite (two cases) orientations with respect to each other. These seem to be products of replicative transposition by Tn7 but can also derive from conservative mechanisms.

Sequence and characteristics of IS900, an insertion element identified in a human Crohn's disease isolate of Mycobacterium paratuberculosis

The complete sequence of an insertion element IS900 in Mycobacterium paratuberculosis is reported. This is the first characterised example of a mycobacterial insertion element. IS900 consists of 1451bp of which 66% is G + C. It lacks terminal inverted and direct repeats, characteristic of Escherichia coli insertion elements but shows a degree of target sequence specificity. A single open reading frame (ORF 1197) coding for 399 amino acids is predicted. This amino acid sequence, and to a lesser extent the nucleotide sequence, show significant homologies to IS110, an insertion element of Streptomyces coelicolor A3(2). It is proposed that IS900, IS110, and similar insertion elements recently identified in disease isolates of Mycobacterium avium are members of a phylogenetically related family. IS900 will provide highly specific markers for the precise identification of Mycobacterium paratuberculosis, useful in defining its relationship to animal and human diseases.

Cointegrate formation by IS50 requires multiple donor molecules

The insertion sequence, IS50R, promotes cointegrate formation between a lambda::IS50R phage and the chromosome of Escherichia coli strain C. We show that formation of cointegrates mediated by IS50R between the non-replicating phage genome and the bacterial chromosome requires multiple donor molecules and depends on homologous recombination functions. We conclude that the two copies of IS50 present in the cointegrate originate in two different molecules. Thus, the existence of the cointegrate structure cannot be used as evidence for replication of IS50 sequences during IS50 transposition.

Identification of base pairs in the outside end of insertion sequence IS50 that are needed for IS50 and Tn5 transposition

Short DNA sequences at ends of transposable elements are needed as sites for transposition. Previous deletion mapping showed that, in Tn5 and its component IS50 elements, these essential sites are about 19 base pairs long. To determine which positions are important in transposition, we made one or more sequence changes at each position in the IS50 outside (O) end and assayed the effects of these changes on transposition. Our results indicate that the specific base pairs at 18 of the 19 positions are important in transposition. A 9-base-pair segment in the O end corresponds to a binding site for the Escherichia coli DnaA protein. Comparisons of effects of mutations at different positions in this site, and also measurements of Tn5 transposition in dnaA- cells, indicate that DnaA protein participates in O-end-mediated transposition.

dnaA, an essential host gene, and Tn5 transposition

Mutations in dnaA, an essential gene in Escherichia coli, decrease the frequency of transposition of Tn5. An insertion mutation in the dnaA gene does not affect Tn5 gene expression. Therefore, the DnaA protein plays a role either in the transposition reaction itself or in some type of cellular regulation of transposition. Analysis of a mutation in the DnaA box, found at the outside end of IS50, is consistent with a direct interaction of the protein through these bases. IS50 transposition, which utilizes only one end containing a DnaA box, is not affected by dnaA mutations. Overproduction of the DnaA protein does not increase transposition frequencies in wild-type cells, even when the transposase is also overproduced.

A temperature-dependent pBR322 copy number mutant resulting from a Tn5 position effect

In the process of randomly mutagenizing a recombinant pBR322 clone with transposon Tn5, a high copy number plasmid mutant, pLO88, has been isolated. The copy number phenotype of pLO88 is observed only at elevated temperatures, greater than or equal to 37 degrees C, and is due to the precise position of a Tn5 insertion. Nucleotide sequence of the Tn5-pBR322 junction reveals that Tn5-88 has inserted into an open reading frame that codes for a 63 amino acid protein previously shown to negatively regulate pBR322 plasmid copy number. By deleting portions of the Tn5 it is shown that the copy number phenotype is due not only to the insertion of Tn5 in pBR322 but also to the requirement that some Tn5 sequences remain intact. It appears that an outwardly directed Tn5 promoter initiates the synthesis of a transcript (RNA X) that interferes with the normal repressor RNA (RNA I)-primer RNA (RNA II) interaction at elevated temperatures.

Recombination between IS5 elements: requirement for homology and recombination functions

Intermolecular recombination between two IS5 elements was measured, using bacteriophage lambda recombination vectors, and was compared to recombination between two copies of an SV40 segment cloned into the same vectors. Experiments were conducted in the presence and in the absence of RecA and Red functions, and with the recombining inserts in the same or in reversed orientation. Under all conditions, IS5 elements recombined in a manner similar to the SV40 inserts, indicating that IS-encoded functions did not confer measurable additional intermolecular recombination ability to IS5 in E. coli K-12. Bacteriophages containing reversed IS5 inserts, for which the 16 base pair (bp) termini are identical in 15 positions and which display 12 bp of uninterrupted homology, recombined at approximately the same low frequency under Rec+ and Rec- conditions, indicating that these short homologies were not good substrates for the Rec system. Bacteriophages having reversed inserts recombined better under Red+ than under Red- conditions, but the crossovers were located in nonhomologous regions flanking the element termini. This suggests that 12-bp homologies are not good substrates for the Red system.

Vector insertion mutagenesis of Rhizobium sp. strain ORS571: direct cloning of mutagenized DNA sequences

When the limited-host-range plasmid pVP2021 carrying Tn5 was mobilized into Rhizobium sp. strain ORS571 and stable acquisition of Tn5 was selected, ORS571 plasmid-genome cointegrates were exclusively obtained; direct Tn5 transposition was never observed. In every case, genomic cointegrates exhibited an additional (third) IS50 element that bordered VP2021 DNA sequences but maintained a single Tn5 element. Genomic cointegrates containing IS50 triplications were stable; neither phenotypic reversion nor resolution was detectable. Auxotrophic mutant strains (vector insertion mutants) were identified at expected frequencies among derivatives carrying ostensibly random genomic pVP2021 insertions; N2 fixation (Nif)-defective vector insertion mutants were observed among these derivatives at a frequency of 10(-3). The presence of integrated pVP2021 in ORS571 nif::VP2021 mutant genomes enabled VP2021 to constitute an endogenous cloning vector. After EcoRI or KpnI digestions, genomic nif::pVP2021 DNA sequences contiguous with integrated pVP2021 were directly cloned as new replicons without addition of an exogenous vector. Recombinant plasmids derived from two such nif::pVP2021 mutants hybridized to previously analyzed ORS571 Nif DNA sequences. Recombinant plasmid DNA and ORS571 Nif region DNA were found to be colinear; pVP2021 insertions could be accurately mapped. pVP2021 insertion-mutagenesis thus allows the direct cloning of ORS571 gene sequences for which mutant phenotypes can be selected or screened.

recA-independent recombination between repeated IS50 elements is not caused by an IS50-encoded function

Certain pBR322-related plasmids containing direct repeats of the insertion element IS50 appear to be unstable in recA Escherichia coli because smaller recombinant derivatives accumulate rapidly in plasmid DNA populations. We show here that (i) this instability is plasmid specific, but not IS50 specific; (ii) it is due to a detrimental effect exerted by these plasmids on bacterial growth; and (iii) the growth impairment is alleviated in cells harboring the smaller recombinant plasmids. Although a recent report had concluded that accumulation of recombinants reflected an IS50-specific recombination function, when correction is made for the relative growth rates of cells containing the parental and recombinant plasmids the evidence for such a recombination function disappears.

Transposable element IS1 intrinsically generates target duplications of variable length

Target duplication during transposition is one of the characteristics of mobile genetic elements. IS1, a resident insertion element of Escherichia coli K-12, was known to generate a 9-base-pair target duplication, while an IS1 variant, characterized by a nucleotide substitution in one of its terminal inverted repeats, was reported to duplicate 8 base pairs of its target during cointegration. We have constructed a series of transposons flanked by copies of either the normal or the variant IS1. The analysis of their transposition products revealed that transposons with normal termini as well as those with variant termini can intrinsically generate either 9- or 8-base-pair target duplications. We also observed that a normal IS1 from the host chromosome generated an 8-base-pair repeat. The possible relevance of the observation for the understanding of transposition processes and models to explain the variable length of target duplications are discussed.

Mechanisms of transposition in bacteria

The transposable elements of bacteria are diverse in size, functional arrangement, DNA sequence, and in their modes of transposition. We review here data suggesting that the kanamycin-resistance transposon Tn5 moves without replicating (conservative transposition), but the ampicillin-resistance transposon Tn3 is duplicated when it transposes, and that both the chloramphenicol-resistance transposon Tn9 and bacteriophage Mu are replicated in some events but not in others. A model is presented in which conservative and replicative transposition are alternative branches of a single pathway.

The E. coli K-12 chromosome flanked by two IS10 sequences transposes

Transposon are commonly found among prokaryotes and usually range up to 20 kilobases. In this study, we were interested to determine whether a larger DNA segment could transpose. We observed that the E. coli K-12 chromosome, 4,000 kilobases in size, when flanked by two IS10 sequences, could transpose to pACYC177 at a frequency of 10(-8) per cell per generation. We suggest that this transposition event occurs independently of the size and without duplication of the entire DNA sequence flanked by the IS10 elements.

Extrachromosomal copies of transposon Tc1 in the nematode Caenorhabditis elegans

Extrachromosomal copies of the 1.6-kilobase transposable element Tc1 are present at the level of between 0.1 and 1.0 copy per cell in Caenorhabditis elegans strain Bergerac. Extrachromosomal elements were detected and studied using Southern hybridizations employing a Tc1-specific probe. The amount of extrachromosomal Tc1 DNA was roughly constant during development in Bergerac, which has approximately 300 integrated chromosomal copies of Tc1 in its haploid genome. Extrachromosomal Tc1 DNA was not detected in strain Bristol, which has 30 chromosomal copies of Tc1. Three forms of extrachromosomal DNA were detected. The predominant form was a 1.6-kilobase linear molecule with ends corresponding to the ends of an integrated Tc1 element. The other two forms were, respectively, relaxed and supercoiled circular copies of the element. Structural assignments were based on electrophoretic mobility, the results of sedimentation velocity and equilibrium density gradient experiments, and on the sizes of the products produced by treatment of purified extrachromosomal DNA with restriction endonucleases. The suggestion is made that these extrachromosomal transposable elements are the products of excision events known to be occurring at high frequency in somatic cells in Bergerac.

Does Tn10 transpose via the cointegrate molecule?

It has been well established that Tn3 and its relatives transpose from one replicon to another by two successive reactions: formation of the cointegrate molecule and resolution from it. Whether or not the 9300 base pair tetracycline resistance transposon Tn10 transposes in the same manner as Tn3 was investigated by two methods. In the first method, lambda 55, a lambda phage carrying Tn10 was lysogenized in an Escherichia coli strain carrying a Tn10 insertion; the phage has a deletion in attP, hence it was lysogenized in a Tn10 sequence in the E. coli chromosome by reciprocal recombination. The chromosomal structure in these lysogens is equivalent to the Tn10-mediated cointegrate molecule of lambda and the E. coli chromosomal DNA. The stability of the cointegrate molecule was examined by measuring the rate of excision of lambda from the host chromosome, and was found to be stable, especially in a Rec- strain. Because of this stability, the cointegrate molecule should be accumulated if Tn10 transposes via the cointegrate molecule. Then, we examined the configuration of products made by transposition of Tn10 from lambda 55 to the E. coli chromosome. The cointegrate molecule was found in products of Tn10 transposition in a Rec+ strain at a frequency of 5% per Tn10 transposition, but this molecule could not be found in a Rec- strain. Since transposition of Tn10 was recA-independent, absence of the cointegrate molecule formed in a RecA- strain strongly suggested that the cointegrate molecule is not an obligatory intermediate of transposition of Tn10.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization of the new insertion sequence IS91 from an alpha-hemolysin plasmid of Escherichia coli

IS91 is a 1.85 kb insertion sequence originally resident in the alpha-hemolytic plasmid pSU233. The element was transposed sequentially from this plasmid to pACYC184, to R388, and to pBR322. Both cointegrates and simple insertions of the element were obtained. A detailed restriction enzyme map of the element is presented. This does not bear any relationship to the maps of previously described insertion sequences. Furthermore, hybridization between these sequences and IS91 could not be demonstrated. Deletion derivatives of IS91 were constructed which are unable to transpose. However, their transposition can be complemented in trans by wild-type elements. One of these deletion derivatives has been genetically labeled with a kanamycin resistance marker from Tn5. When this new element was complemented for transposition, only about 2% of the transposition products were cointegrates. Thus, the behavior of IS91 is better explained by transposition models that allow direct transposition.

Transposition of Tn554 does not generate a target duplication

Transposable elements from prokaryotic and eukaryotic organisms are discrete DNA segments bounded by inverted or directly repeated sequences that insert into non-homologous DNA in a reaction that is independent of the general recombination functions of the host. The mechanisms proposed generally involve a staggered double-stranded scission of the target DNA, ligation to the nicked ends of the transposable element, and replication of the element, resulting in the generation of a directly repeated oligonucleotide target sequence flanking the new copy of the element. Most transposons have a relatively low degree of target site specificity coupled with a low insertion frequency. Tn554, a Staphylococcus aureus transposon which specifies resistances to erythromycin and spectinomycin, displays an unusually high degree of insertion specificity. Tn554 transposes with high efficiency to a unique ('primary') site in the S. aureus chromosome and only rarely (less than 10(-6) per transductant) to other, secondary sites. We report here the nucleotide sequences surrounding the junctions of Tn554 in three independent 'primary' insertions and two 'secondary' insertions of the transposon. Two unusual features are revealed: first, the termini of Tn554 contain neither inverted nor directly repeated sequences. Second, transposition of Tn554 does not generate the short direct repeats of the target DNA that are characteristic of other transposable elements. These results suggest that the mechanism of Tn554 insertion may be significantly different from that of other transposons.

Sequences essential for transposition at the termini of IS50

The DNA sequences found repeated in opposite orientation at the ends of insertion (IS) elements are thought to contain sites at which transposase proteins act during transposition. Many elements have repeats of at least 15 base pairs (bp). Those of IS50 are quite short, however: just 8 of the first 9 bp. Functional tests had indicated that one end of IS50 is more effective in transposition than the other end and suggested that at least one of the recognition sites of IS50 extends beyond the common 8/9 bp. To determine the lengths of recognition sites of IS50 we mutagenized IS50 in vitro and tested the transposition proficiency of the resulting mutants. Our results show that the recognition sites at each end of IS50 are about 19 bp long. These findings suggest models for the evolution of IS elements from simpler immobile gene complexes.

Yeast plasmid 2-micron circle promotes recombination within bacterial transposon Tn5

The site-specific recombination system (FLP) encoded by the yeast plasmid 2-micron circle can also act in yeast on the inverted repeats of the bacterial transposon Tn5. The efficiency of this recombination is dependent on the location of Tn5 within the 2-micron circle genome but can be as high as that observed for 2-micron circle itself. Comparison of the DNA sequences between the Tn5 repeat and the 2-micron circle recombination region reveals certain strikingly similar structural features that might be important in the recombination reaction.

DNA sequences at the ends of transposon Tn5 required for transposition

Transposons are a class of genetic elements that can move from one site in a cell's genome to another independently of the cell's general recombination system. Little is known about the mechanism of transposition of compound transposons such as Tn5, but it is thought that a transposon-encoded protein (a transposase) must recognize the outer ends of the element and, together with host factors, catalyse the transfer of the internal DNA into a new site in a manner that may involve replication. It has previously been shown that the synthesis of an IS50R-encoded protein (protein 1) is an essential requirement for Tn5 transposition. Here we demonstrate that a structure containing only the outer 186 base pairs (bp) of both inverted repeats is capable of being efficiently complemented to transpose in Escherichia coli, provided IS50R is located close by on the same replicon. In addition, Bal31-generated deletions indicate that 16-18 bp of the outer end of IS50L are required for transposition. This 16-18-bp sequence contains the 8-9-bp small inverted repeat present at each end of IS50 plus a 9-bp sequence which is homologous to an interrelated sequence present in four copies in the chromosomal origin of replication in a variety of Gram-negative bacteria. This sequence organization suggests that the ends of Tn5 may function to provide a recognition site for the Tn5 transposase adjacent to a sequence recognized by the host replication system.