On the molecular mechanisms of transposition

Helitrons, the Eukaryotic Rolling-circle Transposable Elements

Helitrons, the eukaryotic rolling-circle transposable elements, are widespread but most prevalent among plant and animal genomes. Recent studies have identified three additional coding and structural variants of Helitrons called Helentrons, Proto-Helentron, and Helitron2. Helitrons and Helentrons make up a substantial fraction of many genomes where nonautonomous elements frequently outnumber the putative autonomous partner. This includes the previously ambiguously classified DINE-1-like repeats, which are highly abundant in Drosophila and many other animal genomes. The purpose of this review is to summarize what we have learned about Helitrons in the decade since their discovery. First, we describe the history of autonomous Helitrons, and their variants. Second, we explain the common coding features and difference in structure of canonical Helitrons versus the endonuclease-encoding Helentrons. Third, we review how Helitrons and Helentrons are classified and discuss why the system used for other transposable element families is not applicable. We also touch upon how genome-wide identification of candidate Helitrons is carried out and how to validate candidate Helitrons. We then shift our focus to a model of transposition and the report of an excision event. We discuss the different proposed models for the mechanism of gene capture. Finally, we will talk about where Helitrons are found, including discussions of vertical versus horizontal transfer, the propensity of Helitrons and Helentrons to capture and shuffle genes and how they impact the genome. We will end the review with a summary of open questions concerning the biology of this intriguing group of transposable elements.

The Tn3-family of Replicative Transposons

Transposons of the Tn3 family form a widespread and remarkably homogeneous group of bacterial transposable elements in terms of transposition functions and an extremely versatile system for mediating gene reassortment and genomic plasticity owing to their modular organization. They have made major contributions to antimicrobial drug resistance dissemination or to endowing environmental bacteria with novel catabolic capacities. Here, we discuss the dynamic aspects inherent to the diversity and mosaic structure of Tn3-family transposons and their derivatives. We also provide an overview of current knowledge of the replicative transposition mechanism of the family, emphasizing most recent work aimed at understanding this mechanism at the biochemical level. Previous and recent data are put in perspective with those obtained for other transposable elements to build up a tentative model linking the activities of the Tn3-family transposase protein with the cellular process of DNA replication, suggesting new lines for further investigation. Finally, we summarize our current view of the DNA site-specific recombination mechanisms responsible for converting replicative transposition intermediates into final products, comparing paradigm systems using a serine recombinase with more recently characterized systems that use a tyrosine recombinase.

The evolving story of Mycobacterium tuberculosis clade members detected in fish

Advances in molecular analyses have permitted documentation of an increasing spectrum of mycobacteria infecting fish. Although some of these mycobacteria are not closely related, several species belong to the Mycobacterium tuberculosis clade. One member of the clade, M. marinum, is well known as an agent of piscine mycobacteriosis. Three other clade species, M. shottsii, M. pseudoshottsii and M. 'chesapeaki', have recently been identified as predominant disease agents in a widespread, continuing epizootic in wild striped bass of the Chesapeake Bay. A fifth clade member, M. ulcerans, has recently been indirectly detected in wild, African cichlid fish. As M. ulcerans is the third most common human mycobacterial infection worldwide, even such indirect evidence of M. ulcerans in fish must be more thoroughly investigated. Complicating the differentiation of these clade members is the growing recognition of intraspecies and interspecies variation in phenotypes, genes and virulence. Thus, researchers must be aware of the variety of piscine isolates within the M. tuberculosis clade. This review summarizes the methods of detection and differentiation for this important group of mycobacteria.

Human transaldolase-associated repetitive elements are transcribed by RNA polymerase III

Repetitive elements flanked by exons 2 and 3 of the human transaldolase gene, thus termed transaldolase-associated repetitive elements, TARE, were identified in human DNA. Nonpolyadenylated TARE transcripts were detected by Northern blot analysis and cloned by reverse transcriptase-mediated polymerase chain reaction from human T lymphocytes. A dominant 1085-nucleotide long transcript, TARE-6, contained two adjacent Alu elements, a right monomer and a complete dimer, oriented opposite to the direction of transcription of the transaldolase gene. Reverse transcriptase-polymerase chain reaction and in vitro transcription analyses showed that transcription of TARE-6 proceeded in the orientation of the RNA pol III promoter of the Alu dimer and opposite to the orientation of the TAL-H gene. TAREs lacking RNA polymerase III promoter showed no transcriptional activity. In vitro transcription of TARE-6 was resistant to 1 microg/ml alpha-amanitin but sensitive to 100 microg/ml alpha-amanitin and tagetitoxin, suggesting involvement of RNA polymerase III. TAREs in both the transaldolase and HSAG-1 genomic loci were surrounded by TA target site duplications. Homologies between transaldolase and HSAG-1 break off internally at splice donor and acceptor sites. The results suggest RNA polymerase III-mediated transcription of TARE may be a source of repetitive elements, contributing to distinct genes and thus shaping the human genome.

IS1634, a novel insertion element creating long, variable-length direct repeats which is specific for Mycoplasma mycoides subsp. mycoides small-colony type

A new insertion sequence, IS1634, has been identified in Mycoplasma mycoides subsp. mycoides small-colony type (SC). IS1634 shows structural and functional similarities to IS1549 of Mycobacterium smegmatis and with it seems to form a new class or family of insertion sequences. IS1634 has a size of 1,872 bp, including two 13-bp terminal inverted repeats. It contains an open reading frame (ORF) encoding a product of 533 amino acids which shows similarity to the transposase of IS1549 and to a lesser extent to the transposases of IS elements of the IS4 family. IS1634 is present at about 30 copies in the genome of all 22 different field strains of M. mycoides subsp. mycoides SC tested. Characteristic of IS1634 are the long and variable-length direct repeats at the sites of insertion which were found to reach up to about 500 bp. IS1634 is specific to M. mycoides subsp. mycoides SC and is not present in any of the other members of the M. mycoides cluster. Neither was it found in other closely related Mycoplasma species of ruminants.

IS1549 from Mycobacterium smegmatis forms long direct repeats upon insertion

A new insertion element, IS1549, was identified serendipitously from Mycobacterium smegmatis LR222 during experiments using a vector designed to detect the excision of IS6110 from between the promoter region and open reading frame (ORF) of an aminoglycoside phosphotransferase gene. Six of the kanamycin-resistant isolates had a previously unidentified insertion element upstream of the ORF of the aph gene. The 1,634-bp sequence contained a single ORF of 504 amino acids with 85% G+C content in the third codon position. The putative protein sequence showed a distant relationship to the transposase of IS231, which is a member of the IS4 family of insertion elements. IS1549 contains 11-bp terminal inverted repeats and is characterized by the formation of unusually long and variable-length (71- to 246-bp) direct repeats of the target DNA during transposition. Southern blot analysis revealed that five copies of IS1549 are present in LR222, but not all M. smegmatis strains carry this element. Only strains with a 65-kDa antigen gene with a PCR-restriction fragment length polymorphism type identical to that of M. smegmatis 607 contain IS1549. None of 13 other species of Mycobacterium tested by PCR with two sets of primers specific for IS1549 were positive for the expected amplified product.

Differential roles of the transposon termini in IS91 transposition

Insertion sequence 91 (IS91) inserts specifically at GTTC or CTTG target sequences without duplication of the target. After insertion, the right inverted repeat (IRR) lies adjacent to the 3' end of the target sequences (or 5' to the complementary sequence CAAG or GAAC). We have analyzed the effects of alteration of each terminus of IS91 on transposition activity in Escherichia coli. IRR is absolutely required for transposition. Deletion analysis indicates that a 14-bp segment is not sufficient, but an 81-bp sequence within the IRR region is sufficient. Furthermore, the GTTC/CTTG target site is also required. The left inverted repeat (IRL) of IS91 is dispensable. Plasmid fusions originated by one-ended transposition of IS91 derivatives lacking IRL occur at about the same frequency as cointegrate formation observed for the wild-type element. In the one-ended-type fusions, the inserted fragment of donor DNA is flanked at one end (constant end) by IRR and at the other end by a GTTC or CTTG sequence present in the donor (variable end) in a way that usually results in multiple tandem insertions of the donor plasmid in the target site. These results are easily accommodated by a rolling-circle replicative transposition mechanism. This model also draws support from the finding that the IS91 transposase is related in sequence to the superfamily of rolling-circle replication proteins and the observation that IRR shows some conservation in sequence and secondary structure with the origins of replication of some rolling-circle replication plasmids.

Sister chromatid fusion initiates amplification of the dihydrofolate reductase gene in Chinese hamster cells

We have utilized a dihydrofolate reductase (DHFR) probe in combination with selected probes from other positions along the 2q chromosome arm in a two-color fluorescence in situ hybridization analysis of early DHFR gene amplification events in CHO cells. These studies show clearly that the most frequent initiating event is the formation of a giant inverted duplication, resulting from chromosome breakage and terminal fusion or a reverse unequal sister chromatid exchange. The dicentric chromosomes thus formed initiate bridge/breakage/fusion cycles that appear to mediate subsequent amplification steps to higher copy number.

Unusual features of integrated cDNAs generated by infection with genome-free retroviruses

We previously demonstrated that when nonretroviral RNAs are encapsidated in retroviral particles they can be reverse transcribed into cDNAs, which are then integrated into the cellular genome. This transfer of genetic information via retroviral infection has been designated retrofection. Further analyses of three genes transferred in this manner (retrogenes) revealed that each was present in a single copy at a different site in the recipient quail cell genome and included a transcriptional promoter encoded by the encapsidated neo RNA. A unique feature of the retrogenes was a common 16-nucleotide sequence at or near a recombination border, which was not present in either recombination partner. The existence of this sequence suggests a common mechanism of retrogene formation and/or integration mediated by retrofection.

Unusual features of integrated cDNAs generated by infection with genome-free retroviruses

We previously demonstrated that when nonretroviral RNAs are encapsidated in retroviral particles they can be reverse transcribed into cDNAs, which are then integrated into the cellular genome. This transfer of genetic information via retroviral infection has been designated retrofection. Further analyses of three genes transferred in this manner (retrogenes) revealed that each was present in a single copy at a different site in the recipient quail cell genome and included a transcriptional promoter encoded by the encapsidated neo RNA. A unique feature of the retrogenes was a common 16-nucleotide sequence at or near a recombination border, which was not present in either recombination partner. The existence of this sequence suggests a common mechanism of retrogene formation and/or integration mediated by retrofection.

Analysis of the variable endpoints generated by one-ended transposition of Tn21

One-ended transposition of Tn21 generates recombinants usually containing a whole copy of the donor replicon plus a short duplication of it (S. Mötsch, R. Schmitt, P. Avila, F. de la Crue, E. Ward, and J. Grinsted, Nucleic Acids Res. 13:3335-3342, 1985). This work shows that recombinants containing less than a whole copy of the donor replicon (hereafter called short recombinants) could also be detected when plasmid donors which contained two selectable genetic markers were used. Short recombinants were produced at the same frequency from TnpR+ donor molecules as from TnpR- donor molecules in a RecA- background. Therefore, they were not resolution products of larger recombinants. This result invalidates a previous hypothesis to explain one-ended transposition, that is, that one-ended transposition arises from the use of secondary ends by the transposition apparatus. On the other hand, it suggests that one-ended transposition of Tn21 occurs via a simple insertion mechanism.

Role of replication in IS102-mediated deletion formation

Intramolecular transposition produces replicon dissociation in a bireplicon; this reaction is homologous to the well-characterized IS-associated deletions in the case of a monoreplicon. However the frequencies at which these two reactions occur differ by a factor of more than 10(2) in favor of deletion formation. This raises the question of how these deletions occur. We show that the presence of a productive replication on the fragment to be deleted interferes with deletion formation. Our results also suggest that the deleted fragment is not degraded during deletion formation.

Conjugal acquisition and stable maintenance of Ent plasmids in nontoxigenic wild-type strains of Escherichia coli

In spite of the ability of the genetic determinants for enterotoxin production to be conjugally transferred, mobilized or transposed, enterotoxigenic Escherichia coli (ETEC) isolated from diarrheal patients is restricted to certain serotypes. Four conjugative enterotoxigenic plasmids (Ent plasmids) encoding either a heat-labile enterotoxin or a heat-stable enterotoxin or both and belonging to one of three incompatibility groups IncFI, IncHl, or IncX, were examined for their transferability to and stability in 157 nonenterotoxigenic Escherichia coli strains belonging to various serotypes and 89 clinical isolates nonenterotoxigenic but belonging to those serotypes in which ETEC from diarrheal patients are usually found. The serotypes of the strains to which Ent plasmids were efficiently transferred and in which they were maintained stably were not always the serotypes in which ETEC had usually been found and vice versa. The frequencies of transfer of four Ent and two R plasmids to each of the 157 recipients were correlated with each other, indicating that the frequency of transfer of the plasmid is not determined by a resident plasmid, if there is one, but by a recipient factor which commonly affects transferability to all donors. These results have led to the conclusion that the reason why only certain serotypes are found among ETEC isolated from diarrheal patients is not the ability of these strains specifically and preferentially to acquire and maintain the Ent plasmids.

Mutants of Escherichia coli defective for replicative transposition of bacteriophage Mu

We isolated 142 Hir- (host inhibition of replication) mutants of an Escherichia coli K-12 Mu cts Kil- lysogen that survived heat induction and the killing effect of Mu replicative transposition. All the 86 mutations induced by insertion of Tn5 or a kanamycin-resistant derivative of Tn10 and approximately one-third of the spontaneous mutations were found by P1 transduction to be linked to either zdh-201::Tn10 or Tn10-1230, indicating their location in or near himA or hip, respectively. For a representative group of these mutations, complementation by a plasmid carrying the himA+ gene or by a lambda hip+ transducing phage confirmed their identification as himA or hip mutations, respectively. Some of the remaining spontaneously occurring mutations were located in gyrA or gyrB, the genes encoding DNA gyrase. Mutations in gyrA were identified by P1 linkage to zei::Tn10 and a Nalr gyrA allele; those in gyrB were defined by linkage to tna::Tn10 and to a gyrB(Ts) allele. In strains carrying these gyrA or gyrB mutations, pBR322 plasmid DNA exhibited altered levels of supercoiling. The extent of growth of Mu cts differed in the various gyrase mutants tested. Phage production in one gyrA mutant was severely reduced, but it was only delayed and slightly reduced in other gyrA and gyrB mutants. In contrast, growth of a Kil- Mu was greatly reduced in all gyrase mutant hosts tested.

Tn4400, a compound transposon isolated from Bacteroides fragilis, functions in Escherichia coli

Transfer factor pBFTM10, isolated from the obligate anaerobic bacterium Bacteroides fragilis, carries a clindamycin resistance determinant which we have suggested is part of a transposable element. DNA homologous to this determinant is found in many Clnr Bacteroides isolates, either in the chromosome or on plasmids. We have now established that Ccr resides on a transposon, Tn4400. In addition to the Ccr determinant that functions under anaerobic conditions in B. fragilis, Tn4400 also carries a determinant for tetracycline resistance (Tcr) which only functions in Escherichia coli under aerobic conditions. The presence of Tn4400 on pBFTM10 does not confer tetracycline resistance on B. fragilis cells containing it. DNA from pBFTM10 was cloned in E. coli, with pDG5 as the cloning vector, to form pGAT500. Using a mobilization assay involving pGAT500 and an F factor derivative, pOX38, we determined that a 5.6-kilobase region of pBFTM10 DNA was capable of mediating replicon fusion and transposition. Most of the mobilization products resulted from inverse transposition reactions, while some were the result of true cointegrate formation. Analysis of the cointegrate molecules showed that three were formed by the action of one of the ends of Tn4400 (IS4400), and one was formed by the action of the whole element (Tn4400). The cointegrate molecule carrying intact copies of Tn4400 at the junction of the two plasmids could resolve to yield an unaltered donor plasmid (pGAT500) and a conjugal plasmid containing a copy of Tn4400 or a copy of one insertion sequence element (pOX38::Tn4400 or pOX38::IS4400). Thus, Tn4400 is a compound transposon containing active insertion sequence elements as directly repeated sequences at its ends.

Junction sequences generated by 'one-ended transposition'

In the presence of the cognate transposase, plasmids containing a single inverted repeat (IR) sequence of Tn21 or of Tn1721 can fuse efficiently with other plasmids ('one-ended transposition'). The junctions across the sequences of donor and recipient DNA in recombinants generated by this process have been determined. These show that the segment of donor DNA starts precisely at the IR sequence (it is variable at the other end), and is flanked by a direct repeat of host DNA (usually 5bp) that was present only once in the original host sequence. These are characteristics of recombinants generated by transposition of Tn21 and Tn1721 themselves, suggesting that the mechanism of one-ended transposition is very similar to that of the corresponding entire elements.

ATP-dependent specific binding of Tn3 transposase to Tn3 inverted repeats

Transposons are discrete segments of DNA which are capable of moving from one site in a genome to many different sites. Tn3 is a prokaryotic transposon which is 4,957 base pairs (bp) long and encodes a transposase protein which is essential for transposition. We report here a simple method for purifying Tn3 transposase and demonstrate that the transposase protein binds specifically to the ends of the Tn3 transposon in an ATP-dependent manner. The transposase protein binds to linear double-stranded DNA both nonspecifically and specifically; the nonspecific DNA binding activity is sensitive to challenge with heparin. Site-specific DNA binding to the ends (inverted repeats) of Tn3 is observed only when binding is performed in the presence of ATP; this ATP-dependent site-specific DNA binding activity is resistant to heparin challenge. Our results indicate that ATP qualitatively alters the DNA binding activity of the transposase protein so that the protein is able to bind specifically to the ends of the Tn3 transposon.

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.

Spontaneous deletion of citrate-utilizing ability promoted by insertion sequences

The citrate utilization (Cit+) transposon Tn3411 was shown to be flanked by directly repeated sequences (IS3411L and IS3411R) by restriction enzyme analysis and electron microscope observation. Cit- deletion mutants were frequently found to be generated in pBR322::Tn3411 by intramolecular recombination between the two copies of IS3411. The flanking IS3411 elements of Tn3411 were shown to be functional insertion sequences by Tn3411-mediated direct and inverse transposition. Tn3411-mediated inverse transposition from pBR322::Tn3411 to the F-plasmid derivative pED100 occurred more efficiently than that of direct transposition of the Cit+ determinant. This was thought to be due to the differential transposability of IS3411L and IS3411R in the transposition process. The frequency of transposition of IS3411 marked with a chloramphenicol resistance determinant was much higher than IS3411-mediated cointegrate formation, suggesting that replicon fusions are not essential intermediates in the transposition process of Tn3411 or IS3411. Spontaneous deletions occurred with high frequency in recA hosts. The spontaneous deletion promoted by homologous recombination between two IS3411 elements in Tn3411 was examined with deletion mutants.

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.

Characterization of IS46, an insertion sequence found on two IncN plasmids

The IncN plasmids R46 and N3 each contain two copies of an insertion sequence which we denote IS46. This insertion sequence has single PstI and SalI restriction sites and is 0.81 kilobases long. All four copies of IS46 were capable of forming cointegrates, although the DNA between the insertion sequences, which in each case carries a tetracycline resistance gene, was not transposable in the form of a compound transposon. IS46-mediated cointegrates resolved in Rec+ but not in RecA- cells. Recombination between two copies of IS46, causing an inversion, accounts for the existence of two distinct forms of R46. IS46-mediated deletions were probably responsible for the formation of the plasmid pKM101 from R46. IS46 was not homologous to IS1 but did show homology with IS15.

Atypical deletions generated by mutated IS102 elements

The element IS102 potentially codes for two polypeptide chains. We have introduced several mutations in the larger one near the COOH terminus and determined the residual ability of the mutated elements to generate deletions in order to assign a role to this polypeptide chain. We show that in these elements, deletions still occur, although at a reduced level, but that in all cases examined so far the ends of the element are no longer recognized as the fixed endpoint of IS-mediated deletions, even though some other structural features of normal deletions formation are still present.

Plasmids containing one inverted repeat of Tn21 can fuse with other plasmids in the presence of Tn21 transposase

In the presence of the Tn21 transposase, plasmids that contain a single Tn21 inverted repeat sequence fuse efficiently with other plasmids. This reaction occurs in recA strains, is independent of the transposon-encoded resolution system, and results in insertions into different sites in the recipient plasmid. All fusion products studied contained at least one complete copy of the donor plasmid; most also contained some duplication of it as well. The data are consistent with processive models of transposition.

Replicon fusion mediated by a single-ended derivative of transposon Tn1721

Tn1722 delta 1K, a derivative of transposon Tn1721 lacking one terminal inverted repeat (IR) and conferring kanamycin resistance, promotes transposition of the resistance marker to a target replicon at about 100-fold lower frequency than the wild-type element. A study involving restriction analysis of 16 independent Tn1722 delta 1K-mediated events led to the following results: (i) Tn1722 delta 1K mediates fusions of the donor (pRU506) and target (RSF1010) replicons; the fused entities are non-permuted. (ii) Tn1722 delta 1K promotes insertions of donor DNA at many different sites in the target replicon. (iii) The analyzed fusion plasmids contain the entire target and various lengths of donor DNA. Eleven products contain the entire donor plasmid plus a duplication of the IR (class A), whereas five products contain only portions adjacent to the single IR (class B). (iv) In each case the two replicons are joined at (or very close to) the single IR. The second junction is located shortly beyond the duplicated IR in class A and at different sites within the donor plasmid in class B. These results are interpreted in terms of asymmetric replicative transposition.

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)

Insertions of transposable elements in the promoter proximal region of the gene cluster for Escherichia coli H+-ATPase: 8 base pair repeat generated by insertion of IS1

A plasmid pKY159 (Yamaguchi and Yamaguchi 1983) carrying a promoter proximal portion of the gene cluster of the proton-translocating ATPase (H+-ATPase) of Escherichia coli causes growth inhibition of wild-type cells. Insertion of a transposable element in this plasmid released this inhibitory effect. In analyzing this inhibitory effect, we determined the insertion points at the nucleotide-sequence level of transposable elements on 30 independent derivatives of pKY159 . Insertions of IS1, IS5, and gamma delta were found between the promoter and the gene for a possible component of 14,000 daltons of the H+-ATPase. Of 31 insertions, 26 were of IS1 and were located at the same site, indicating that this site is a hotspot for IS1 insertion and that IS1 insertion is much more frequent than that of IS5 or gamma delta in this region. Four different sites for IS1 insertion were found; in two of these an 8 base pair (bp) duplicate of the target sequence ( AAAAACGT and AAACGTTG ) was generated, while in the other two a 9 bp duplicate was found. In all cases in this study the nucleotide sequence of IS1 was the same as that of IS1-K. In the two cases with an 8 bp duplicate in different sites, a common 6 bp sequence ( AAACGT ) was found. These results suggested that generation of the 8 bp duplicate is related to the common sequence rather than a mutation in IS1 suggested by Iida et al. (1981) and also suggested that the essential length of the duplicate is 8 bp or less than 8 bp. A 6 bp sequence ( GTGATG ) homologous to the end portion of IS1 was found at the hotspot , but not at other sites, suggesting that this homology contributed to the high frequency of IS1 insertion.(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.

Plasmid R46 provides a function that promotes recA-independent deletion, fusion and resolution of replicon

We report that plasmid R46 provides a function which promotes recA-independent deletion, replicon fusion, and resolution of the fusion. R46 belongs to the incompatibility group N and specifies resistance to ampicillin, tetracycline, streptomycin and sulfonamide. Four kinds of deletion derivatives were observed by selection for susceptability to tetracycline from ampicillin-resistant clones. A common region, will be called alpha region thereafter, was postulated to be involved in these deletions. The replicon fusion occurred by a conjugative mobilization of each derivative with plasmid R388. The fusion was suggested to contain both replicons linked at each junction by the sequence in the alpha region in direct orientation. The resolution of the replicon fusion was found between two alpha regions and a consequently generated, parental deletion derivative and an R388 derivative which gained one alpha region. It is possible that the alpha region contains one potential Insertion Sequence (IS) element. These events were also speculated to occur as a consequence of insertion of the potential IS onto the intramolecular or intermolecular target sequence, or reciprocal recombination between two potential IS elements.

The L1Md long interspersed repeat family in the mouse: almost all examples are truncated at one end

We have characterized a large repetitive element which has been found at seven different locations within the beta globin locus of the BALB/c mouse. This repeat has an unusual structure in that each of the different members has the same end of the element conserved while the other end terminates at a different point in each repeat member. The sequences within the repeats from the beta globin locus have homology with other repetitive families such as the MIF-1, Bam-5, R, and the BamH1 families. These were recently proposed (T. Fanning, (1983) Nucleic Acids Res. 11, 5073-5091) to be part of a structure with the same organization which we found in the globin locus. Probing plaques from a BALB/c genomic library with sequences derived from the repeats in the globin locus shows that virtually all of the repeats from this family are organized in a manner consistent with the proposed structure.

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.

Involvement of Escherichia coli K-12 DNA polymerase I in the growth of bacteriophage Mu

We examined several aspects of bacteriophage Mu development in Escherichia coli strains that carry mutations in the polA structural gene for DNA polymerase I (PolI). We found that polA mutants were markedly less efficient than PolI wild-type (PolI+) strains in their capacity to form stable Mu lysogens and to support normal lytic growth of phage Mu. The frequency of lysogenization was determined for polA mutants and their isogenic PolI+ derivatives, with the result that mutants were lysogenized 3 to 8 times less frequently than were PolI+ cells. In one-step growth experiments, we found that phage Mu grew less efficiently in polA cells than in PolI+ cells, as evidenced by a 50 to 100% increase in the latent period and a 20 to 40% decrease in mean burst size in mutant cells. A further difference noted in infected polA strains was a 10-fold reduction in the frequency of Mu-mediated transposition of chromosomal genes to an F plasmid. Pulse labeling and DNA-DNA hybridization assays to measure the rate of phage Mu DNA synthesis after the induction of thermosensitive prophages indicated that phage Mu replication began at about the same time in both polA and PolI+ strains, but proceeded at a slower rate in polA cells. We conclude that PolI is normally involved in the replication and integration of phage Mu. However, since phage Mu does not exhibit an absolute requirement for normal levels of PolI, it appears that residual PolI activity in the mutant strains, other cellular enzymes, or both can partially compensate for the absence of normal PolI activity.

Pseudomonas streptomycin resistance transposon associated with R-plasmid mobilization

Plasmid pMG1 encodes resistance to gentamicin, streptomycin, sulfonamides, and mercuric ions and also mobilizes pRO161, a transfer-deficient plasmid derived from RP1. Upon mobilization, pRO161 acquires streptomycin resistance (Smr) and can subsequently be remobilized by pMG1 at significantly higher frequencies than pRO161 itself. Both the initial acquisition of Smr and the subsequent mobilization of the transfer-deficient plasmid are recA independent: thus, the Smr determinant appears to be located on a transposon, disignated Tn904. Tn904 transposes to a variety of other plasmids, including RP1, FP2, R388, K, pRO1600, and pBR322, and in some cases the acquisition of this transposon accompanied deletions in the target plasmid. When no deletion occurred, target plasmids gained 5.2 kilobase pairs of DNA and new restriction endonuclease cleavage sites for AvaI, BglII, PstI, SmaI, and SstI. Physical analysis of such plasmids showed that the Tn904 termini are inverted repeat DNA sequences of approximately 124 base pairs. After cloning into vector pRO1723, a single site for restriction endonuclease AvaI was identified within the Smr determinant of Tn904. In Escherichia coli, but not in Pseudomonas aeruginosa. Tn904 shows a gene dosage-dependent expression of streptomycin resistance.

Recombination involving transposable elements: role of target molecule replication in Tn1 delta Ap-mediated replicon fusion

Donor DNA molecules carrying Tn1 or Tn3 deletion mutants do not need to replicate in order to participate in replicon fusion recombination events during which the Tn1/Tn3 element is duplicated. We have assayed Tn1 delta Ap-mediated replicon fusion events involving plasmid R388 and the bacteriophage lambda-derived plasmid p lambda CM, and we find that the role of the recipient molecule is distinct. When p lambda CM carries Tn1 delta Ap, replicon fusion occurs in more than 1% of all cells assayed, whether or not p lambda CM::Tn1 delta Ap can replicate. In contrast, when R388 carries Tn1 delta Ap, replicon fusion occurs only when the p lambda CM target can replicate. Blocks to p lambda CM replication by prophage repressor or amber mutations of the O and P cistrons reduce replicon fusion so that it occurs in less than 1 out of 10(5) cells assayed.

Structural requirement for IS50-mediated gene transposition

Replicative transposition is signaled by the formation of cointegrates in which donor and target replicons are joined by direct repeats of a transposable element. Elements not generating such cointegrates may move by a conservative breaking and joining process. The IS50 elements forming the terminal repeats of Tn5 [which carries the determinant for kanamycin resistance (Kanr)] contain genes and sites necessary for transposition and mediate the movement of any DNA segment they bracket. To determine if IS50 generates cointegrates, the products of transposition from pBR322::Tn5 plasmids to an F factor in recA-Escherichia coli were examined. With monomeric pBR322::Tn5 plasmids, transposition of Kanr (from Tn5) was generally not accompanied by movement of the determinant for ampicillin resistance (Ampr) (from the pBR322 vector). With dimeric pBR322::Tn5 plasmids, by contrast, half of the transpositions of kanr were accompanied by transposition of ampr. Restriction endonuclease analyses indicated that these F-Kanr Ampr chimeras contained inserts of a single copy of the pBR322 vector sequence bracketed by one Tn5 element and one IS50 element or by a pair of Tn5 elements. None of 79 chimeras tested was a true cointegrate. Because IS50 seems to move only a segment of the donor replicon it is proposed that IS50 transposition is conservative.

Early intermediates in bacteriophage T4 DNA replication and recombination

We investigated, by density gradients and subsequent electron microscopy, vegetative T4 DNA after single or multiple infection of Escherichia coli with wild-type T4. Our results can be summarized as follows. (i) After single infection (i.e., when early intermolecular recombination could not occur), most, if not all, T4 DNA molecules initiated the first round of replication with a single loop. (ii) After multiple infection, recombinational intermediates containing label from both parents first appeared as early as 1 min after the onset of replication, long before all parental DNA molecules had finished their first round and before secondary replication was detectable. (iii) At the same time, in multiple infections only, complex, highly branched concatemeric T4 DNA first appeared. (iv) Molecules in which two loops or several branches were arranged in tandem were only found after multiple infections. (v) Secondary loops within primary loops were seen after both single and multiple infections, but they were rare and many appeared off center. Thus, recombination in wild-type T4-infected cells occurred very early, and the generation of multiple tandem loops or branches in vegetative T4 DNA depended on recombination. These results are consistent with the previous finding (A. Luder and G. Mosig, Proc. Natl. Acad. Sci. U.S.A. 79:1101-1105, 1982) that most secondary growing points of T4 are not initiated from origin sequences but from recombinational intermediates. By these and previous results, the various DNA molecules that we observed are most readily explained as intermediates in DNA replication and recombination according to a model proposed earlier to explain various other aspects of T4 DNA metabolism (Mosig et al., p. 277-295, in D. Ray, ed., The Initiation of DNA Replication, Academic Press, Inc., New York, 1981).

Fine structure of transposition genes on Tn2603 and complementation of its tnpA and tnpR mutations by related transposons

The fine structure of the genes tnpA, tnpR and res of Tn2603 required for its own transposition, was determined. The order of the genes was tnpA-tnpR-res from the right end of the right hand side region in Tn2603, the tnpA and tnpR encoded gene products having molecular weights of 110,000 and 21,000, respectively. The 110,000 molecular weight polypeptides was absolutely required for replicon fusion as the first stage of transposition, and named transposase. On the other hand, the 21,000 molecular weight polypeptide was necessary for resolution of the cointegrate as the second stage of transposition, and named resolvase. We also examined the ability of various transposons, assumed to be closely related, to complement the tnpA and tnpR mutations of Tn2603. The results indicated that the mercury resistance transposon, Tn2613, and Tn501, can complement both genes, but TnAs and gamma delta cannot at all. Tn501 had much less efficiency of complementation for tnpA than Tn2613. We have also discovered that the transposition frequency of transposons in the tn2613 family systematically depend on their size of transposon.