The kanamycin resistance transposon Tn2680 derived from the R plasmid Rts1 and carried by phage P1Km has flanking 0.8-kb-long direct repeats

IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers

SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.

Understanding the rapid spread of antimicrobial resistance genes mediated by IS26

Insertion sequences (ISs) promote the transmission of antimicrobial resistance genes (ARGs) across bacterial populations. However, their contributions and dynamics during the transmission of resistance remain unclear. In this study, we selected IS26 as a representative transposable element to decipher the relationship between ISs and ARGs and to investigate their transfer features and transmission trends. We retrieved 2656  translocatable  IS 26 -bounded  units with  ARGs (tIS26-bUs-ARGs) in complete bacterial genomes from the NCBI RefSeq database. In total, 124 ARGs spanning 12 classes of antibiotics were detected, and the average contribution rate of IS26 to these genes was 41.2%. We found that  IS 26 -bounded  units (IS26-bUs) mediated extensive ARG dissemination within the bacteria of the Gammaproteobacteria class, showing strong transfer potential between strains, species, and even phyla. The IS26-bUs expanded in bacterial populations over time, and their temporal expansion trend was significantly correlated with antibiotic usage. This wide dissemination could be due to the nonspecific target site preference of IS26. Finally, we experimentally confirmed that the introduction of a single copy of IS26 could lead to the formation of a composite transposon mediating the transmission of "passenger" genes. These observations extend our knowledge of the IS26 and provide new insights into the mediating role of ISs in the dissemination of antibiotic resistance.

Microevolution of Salmonella 4,[5],12:i:- derived from Salmonella enterica serovar Typhimurium through complicated transpositions

Salmonella enterica subsp. enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-), derived from S. Typhimurium, has become the dominant serotype causing human salmonellosis. In this study, we define the genetic mechanism of the generation of Salmonella 4,[5],12:i:- from S. Typhimurium through complicated transpositions and demonstrate that Salmonella 4,[5],12:i:- displays more efficient colonization and survival abilities in mice than its parent S. Typhimurium strain. We identified intermediate strains carrying both resistance regions (RRs) and the fljAB operon for the generation of Salmonella 4,[5],12:i:-. The insertion of RR3 into the chromosomal hin-iroB site of S. Typhimurium produced RR3-S. Typhimurium as a primary intermediate. Salmonella 4,[5],12:i:- was then produced by replacing the fljAB operon and/or its flanking sequences through intramolecular transpositions mediated by IS26 and/or IS1R elements in RR3-S. Typhimurium, which was further confirmed both in vitro and in vivo. Overall, we demonstrate the molecular mechanism underlying the origin, generation, and advantage of RRs-Salmonella 4,[5],12:i:- from S. Typhimurium.

Different threats posed by two major mobilized colistin resistance genes - mcr-1.1 and mcr-3.1 - revealed through comparative genomic analysis

OBJECTIVES

Global spread of mobilized colistin resistance gene (mcr)-carrying Escherichia coli poses serious threats to public health. This study aimed to provide insights into different threats posed by two major mcr variants: mcr-1.1 and mcr-3.1.

METHODS

Genetic backgrounds and characteristics of mobile genetic elements carrying mcr-1.1 or mcr-3.1 in 74 (mcr)-carrying E. coli isolated from swine farms were analysed, and comparative genomic analysis was performed with the public sequence database.

RESULTS

The mcr-1.1 showed high horizontal transferability (6.30 logCFU/ml). Genetic background of mcr-1.1, including genetic cassette/plasmid, was transferred without insertion sequences (ISs) and/or multi-drug resistance (MDR) and highly shared across strains. The major mcr-1.1-cassette was "mcr-1.1-pap2", mainly encoded in IncI2 and IncX4. Mcr-3.1 exhibited relatively lower conjugation frequency (0.97 logCFU/ml). The mcr-3.1-cassette was flanked by IS26 and was highly variable across strains because of the insertion, deletion, or truncation of IS6100, IS4321, or IS5075. Near the mcr-3.1 cassette, MDR regions consisting of antimicrobial/heavy metal resistance genes were identified, which varied across strains. From the MCR3-E13 strain, a mcr-3.1-carrying IncHI2-fragment was integrated into the bacterial chromosome via IS26-mediated co-integration. To our knowledge, this was the first study to describe that a mcr-3.1-carrying plasmid could be inserted into the bacterial chromosome.

CONCLUSIONS

Based on high horizontal transferability, mcr-1.1 could play a major role on colistin resistance propagation. On the other hand, mcr-3.1 could be transmitted with MDR and have dual pathways mediated by plasmid transfer (horizontal transmission) and chromosomal insertion (vertical transmission), enabling it to proliferate stably despite its lower horizontal transferability.

An analysis of the IS6/IS26 family of insertion sequences: is it a single family?

The relationships within a curated set of 112 insertion sequences (ISs) currently assigned to the IS6 family, here re-named the IS6/IS26 family, in the ISFinder database were examined. The encoded DDE transposases include a helix-helix-turn-helix (H-HTH) potential DNA binding domain N-terminal to the catalytic (DDE) domain, but 10 from Clostridia include one or two additional N-terminal domains. The transposase phylogeny clearly separated 75 derived from bacteria from 37 from archaea. The longer bacterial transposases also clustered separately. The 65 shorter bacterial transposases, including Tnp26 from IS26, formed six clades but share significant conservation in the H-HTH domain and in a short extension at the N-terminus, and several amino acids in the catalytic domain are completely or highly conserved. At the outer ends of these ISs, 14 bp were strongly conserved as terminal inverted repeats (TIRs) with the first two bases (GG) and the seventh base (G) present in all except one IS. The longer bacterial transposases are only distantly related to the short bacterial transposases, with only some amino acids conserved. The TIR consensus was longer and only one IS started with GG. The 37 archaeal transposases are only distantly related to either the short or the long bacterial transposases and different residues were conserved. Their TIRs are loosely related to the bacterial TIR consensus but are longer and many do not begin with GG. As they do not fit well with most bacterial ISs, the inclusion of the archaeal ISs and the longer bacterial ISs in the IS6/IS26 family is not appropriate.

Insertion Sequence IS26 Reorganizes Plasmids in Clinically Isolated Multidrug-Resistant Bacteria by Replicative Transposition

Carbapenemase-producing Enterobacteriaceae (CPE), which are resistant to most or all known antibiotics, constitute a global threat to public health. Transposable elements are often associated with antibiotic resistance determinants, suggesting a role in the emergence of resistance. One insertion sequence, IS26, is frequently associated with resistance determinants, but its role remains unclear. We have analyzed the genomic contexts of 70 IS26 copies in several clinical and surveillance CPE isolates from the National Institutes of Health Clinical Center. We used target site duplications and their patterns as guides and found that a large fraction of plasmid reorganizations result from IS26 replicative transpositions, including replicon fusions, DNA inversions, and deletions. Replicative transposition could also be inferred for transposon Tn4401, which harbors the carbapenemase bla_KPC gene. Thus, replicative transposition is important in the ongoing reorganization of plasmids carrying multidrug-resistant determinants, an observation that carries substantial clinical and epidemiological implications for understanding how such extreme drug resistance phenotypes evolve.

Although IS26 is frequently reported to reside in resistance plasmids of clinical isolates, the characteristic hallmark of transposition, target site duplication (TSD), is generally not observed, raising questions about the mode of transposition for IS26. The previous observation of cointegrate formation during transposition implies that IS26 transposes via a replicative mechanism. The other possible outcome of replicative transposition is DNA inversion or deletion, when transposition occurs intramolecularly, and this would also generate a specific TSD pattern that might also serve as supporting evidence for the transposition mechanism. The numerous examples we present here demonstrate that replicative transposition, used by many mobile elements (including IS26 and Tn4401), is prevalent in the plasmids of clinical isolates and results in significant plasmid reorganization. This study also provides a method to trace the evolution of resistance plasmids based on TSD patterns.

Translocation of transposition-deficient (TndPKLH2-like) transposons in the natural environment: mechanistic insights from the study of adjacent DNA sequences

A family of plasmid-borne DNA fragments of different length, apparently inherited from an ancient plasmid, has been identified in the world population of environmental Acinetobacter strains. These fragments, named PPFs (parental plasmid DNA fragments), were >/=99.8 % identical to each other in the common regions, and contained in their central region a variant of an aberrant mercury-resistance transposon (Tn(d)PKLH2) that has lost its transposition genes. As a rule, recombinogenic elements were found at the breakpoints of identity between the different PPFs. Of these recombinogenic elements, a newly identified IS6 family element, a transposon, or a resolvase gene interrupted one end of the PPFs. At the opposite end, the breakpoint of some PPFs was mapped to the recombination point within, in each case, a different variant of a res site (RS2), whilst in other PPFs, this end was eroded by insertion of a newly identified IS6 family element. On the basis of DNA sequence data, possible mechanisms of translocation of defective Tn(d)PKLH2-like elements via recombination events implicating the nearby res (resolution) site and IS element are proposed.

Chloramphenicol resistance transposable element TnSs1 of Streptococcus suis, a transposon flanked by IS6-family elements

A new transposon, designated TnSs1, which contains a chloramphenicol acetyltransferase gene flanked by direct repeats of an IS6-family element was found in a field isolate of Streptococcus suis. Polymerase chain reaction and hybridization analyses indicated that another field isolate carried the same transposon in a different location on the chromosome. A transposition assay done with a thermosensitive suicide vector showed that, among the seven TnSs1 mutants tested in this study, six formed a cointegrate between the S. suis genome and the vector with the generation of the third copy of the insertion sequence element, and one harbored one copy of TnSs1 on the chromosome as a result of a subsequent resolution step. On transposition, TnSs1 duplicated an 8-bp sequence at the target site.

Complete nucleotide sequence of plasmid Rts1: implications for evolution of large plasmid genomes

Rts1, a large conjugative plasmid originally isolated from Proteus vulgaris, is a prototype for the IncT plasmids and exhibits pleiotropic thermosensitive phenotypes. Here we report the complete nucleotide sequence of Rts1. The genome is 217,182 bp in length and contains 300 potential open reading frames (ORFs). Among these, the products of 141 ORFs, including 9 previously identified genes, displayed significant sequence similarity to known proteins. The set of genes responsible for the conjugation function of Rts1 has been identified. A broad array of genes related to diverse processes of DNA metabolism were also identified. Of particular interest was the presence of tus-like genes that could be involved in replication termination. Inspection of the overall genome organization revealed that the Rts1 genome is composed of four large modules, providing an example of modular evolution of plasmid genomes.

Accessory genes in the darA operon of bacteriophage P1 affect antirestriction function, generalized transduction, head morphogenesis, and host cell lysis

Bacteriophage P1 mutants with the 8.86-kb region between the invertible C-segment and the residential IS1 element deleted from their genome are still able to grow vegetatively and to lysogenize stably, but they show several phenotypic changes. These include the formation of minute plaques due to delayed cell lysis, the abundant production of small-headed particles, a lack of specific internal head proteins, sensitivity to type I host restriction systems, and altered properties to mediate generalized transduction. In the wild-type P1 genome, the accessory genes encoding the functions responsible for these characters are localized in the darA operon that is transcribed late during phage production. We determined the relevant DNA sequence that is located between the C-segment and the IS1 element and contains the cin gene for C-inversion and the accessory genes in the darA operon. The darA operon carries eight open reading frames that could encode polypeptides containing >100 amino acids. Genetic studies indicate that some of these open reading frames, in particular those residing in the 5' part of the darA operon, are responsible for the phenotypic traits identified. The study may contribute to a better comprehension of phage morphogenesis, of the mobilization of host DNA into phage particles mediating generalized transduction, of the defense against type I restriction systems, and of the control of host lysis.

Cloning and characterization of an aminoglycoside 6'-N-acetyltransferase gene from Citrobacter freundii which confers an altered resistance profile

A novel gene encoding a 6'-N-aminoglycoside acetyltransferase, aac(6')-In, has been cloned and sequenced from Citrobacter freundii 13996-19, a clinical isolate from Venezuela. This gene mediates resistance to amikacin, 2'-N-ethylnetilmicin, isepamicin, kanamycin, netilmicin, and tobramycin. The aac(6')-In gene is 573 nucleotides in length and encodes a putative protein of 190 amino acids. AAC(6')-In is most closely related to AAC(6')-Im and AAC(6')-Ie, demonstrating 64.4% and 62.3% similarity, respectively, at the protein level, suggesting these proteins share a common ancestor. The aac(6')-In flanking sequences demonstrated homology to integron- and transposon-related elements which are often found associated with resistance determinants. Hybridization studies performed with an intragenic probe specific for aac(6')-In indicate that this gene is prevalent within Venezuela but has not been observed outside of the country. Furthermore, the aac(6)-In gene was found in 10 different species of gram-negative bacteria.

Nucleotide sequence and characterization of erythromycin resistance determinant that encodes macrolide 2'-phosphotransferase I in Escherichia coli

The DNA fragment (3.3 kb) containing the erythromycin resistance determinant was cloned from Escherichia coli Tf481A and sequenced. Deletion and complementation analyses indicated that the expression of high-level resistance to erythromycin requires two genes, mphA and mrx, which encode macrolide 2'-phosphotransferase I and an unidentified hydrophobic protein, respectively.

Sequence identity with type VIII and association with IS176 of type IIIc dihydrofolate reductase from Shigella sonnei

An uncommon dihydrofolate reductase (DHFR), type IIIc, was coded for by Shigella sonnei that harbors plasmid pBH700 and that was isolated in North Carolina. The trimethoprim resistance gene carried on pBH700 was subcloned and sequenced. The nucleotide sequence of the gene encoding type IIIc DHFR was identical to the gene encoding type VIII DHFR. The type IIIc amino acid sequence was approximately 50% similar to those of DHFRs commonly found in enteric bacteria. Furthermore, this gene was flanked by IS176 (IS26), an insertion sequence usually associated with those of aminoglycoside resistance genes. The gene for type IIIc DHFR was located by hybridization within a 1,993-bp PstI fragment in each of eight conjugative plasmids from geographically diverse strains of S. sonnei. Each plasmid also conferred resistance to ampicillin, streptomycin, and sulfamethoxazole and belonged to incompatibility group M. Plasmids carrying this new trimethoprim resistance gene, which is uniquely associated with IS176, have disseminated throughout the United States.

Characterization of transposon Tn1528, which confers amikacin resistance by synthesis of aminoglycoside 3'-O-phosphotransferase type VI

Providencia stuartii BM2667, which was isolated from an abdominal abscess, was resistant to amikacin by synthesis of aminoglycoside 3'-O-phosphotransferase type VI. The corresponding gene, aph(3')-VIa, was carried by a 30-kb self-transferable plasmid of incompatibility group IncN. The resistance gene was cloned into pUC18, and the recombinant plasmid, pAT246, was transformed into Escherichia coli DH1 (recA) harboring pOX38Gm. The resulting clones were mixed with E. coli HB101 (recA), and transconjugants were used to transfer pAT246 by plasmid conduction to E. coli K802N (rec+). Analysis of plasmid DNAs from the transconjugants of K802N by agarose gel electrophoresis and Southern hybridization indicated the presence of a transposon, designated Tn1528, in various sites of pOX38Gm. This 5.2-kb composite element consisted of aph(3')-VIa flanked by two direct copies of IS15-delta and transposed at a frequency of 4 x 10(-5). It therefore appears that IS15-delta, an insertion sequence widely spread in gram-negative bacteria, is likely responsible for dissemination to members of the family Enterobacteriaceae of aph(3')-VIa, a gene previously confined to Acinetobacter spp.

Three short fragments of Rts1 DNA are responsible for the temperature-sensitive growth phenotype (Tsg) of host bacteria

Rts1 is a multiphenotype drug resistance factor, and one of its phenotypes is temperature-sensitive growth (Tsg) of host bacteria. A 3.65-kb fragment from Rts1 DNA was shown to cause the Tsg phenotype in host cells. This tsg fragment was split by a restriction enzyme, HincII, into four fragments. Two of these fragments were called HincII-S (short) and HincII-L (long), respectively. Each of these two fragments conferred the Tsg phenotype, indicating that, in fact, these two independent regions were responsible for the Tsg phenotype. The HincII-S 783-bp and HincII-L 1,479-bp fragments were sequenced. The region in the HincII-S fragment to which the Tsg phenotype was attributed was narrowed to a 146-bp (nucleotides 1 to 146) fragment by various restriction enzyme digestions. Further digestion of the 146-bp fragment with Bal 31 suggested that the 116-bp (nucleotides 9 to 124) fragment is the minimum sequence required for Tsg. On the other hand, in the HincII-L fragment, a fragment of 249 bp (nucleotides 1210 to 1458) and a fragment of 321 bp (nucleotides 1942 to 2262) contained separate temperature-sensitive growth activity. None of three tsg fragments contained open reading frames. The 249-bp fragment had very weak Tsg activity, while the 321-bp fragment had no Tsg activity. On the other hand, when these two fragments were together in the pUC19 vector, they exhibited very strong Tsg activity equivalent to that of the original 1,479-bp fragment. In addition, two of the 249-bp fragments gave similar, strong Tsg activity. The HincII-L 1,479-bp fragment contained an open reading frame for kanamycin resistance which was found between nucleotides 1423 and 2238. This kanamycin resistance gene sequence was different from that of the reported kanamycin resistance gene of Tn903 at 12 positions which were deduced to change seven amino acids.

Nucleotide-sequence of insertion element IS15 delta IV from plasmid pBP11

The nucleotide sequence of an insertion element in R-factor R1767 derivative pBP11 was determined. It is almost overall identical with IS15 delta, IS26 and IS46. Like IS46 it flanks one end of the sul-bla determinant and is involved in amplification of the resistance cassette. The significance for this process of a palindrome comprising part of IS15 delta IV is discussed.

Identification of the Rts 1 DNA fragment responsible for temperature sensitive growth of host cells harboring a drug resistant factor Rts 1

We have placed a kanamycin resistance SalI fragment (3.65 Kb) from the drug resistance factor Rts1 into pUC19 and pBR322. These chimeric plasmids containing the kanamycin resistance fragment from Rts1 cause temperature sensitive growth in E coli. The orientation of the kanamycin resistance fragment in the vector plasmids does not influence this phenotype.

Characterization of the drug resistance plasmid NTP16

A functional and physical analysis of the multicopy plasmid NTP16 is presented. The plasmid-encoded drug resistance determinants are located, as are regions encoding the origin of replication, incompatibility functions, copy number determinants, and mobility functions. It is demonstrated that NTP16 probably arose from the closely related plasmid NTP1 by the acquisition of a novel kanamycin resistance transposon, Tn4352, followed by deletion of some NTP1 sequences. The incompatibility behavior of NTP16 derivatives indicates a system of control rather more complex than that which operates in ColE1. In addition to the RNA I/primer RNA system, the production of a further trans-acting product is demonstrated and its site of action located. A series of derivative plasmids have been created which may prove useful as vectors for genetic engineering.

A pathway for the evolution of the plasmid NTP16 involving the novel kanamycin resistance transposon Tn4352

The kanamycin resistance determinant of the drug resistance plasmid NTP16 has been characterized by DNA sequencing and has been shown to possess all of the structural features of a transposable element. It is made up of a 1040-bp central region encoding a protein identical to the aminoglycoside 3'-phosphotransferase of Tn903, flanked by direct repeats of an element identical to IS26. This novel transposon has been designated Tn4352. Analysis of the host sequences flanking the transposon reveal that they are derived from a Tn3-like element, and contain no 8 base pair target size duplications which are normally created by the insertion of IS26-like elements. Comparison to the Tn3 sequence shows that the flanking sequences are noncontiguous within Tn3, with the clear implication that NTP16 has evolved from a similar plasmid encoding only ampicillin resistance (presumably NTP1) by the insertion of Tn4352 into the Tn3-like element, followed by a substantial deletion. The sequence analysis suggests that the initial insertion was into the tnpR gene of the ampicillin transposon, followed by a deletion extending to a specific site within tnpA.

Tn1721 derivatives for transposon mutagenesis, restriction mapping and nucleotide sequence analysis

New derivatives of the tetracycline-resistance transposon Tn1721 that carry resistances to chloramphenicol, tetracycline, kanamycin and streptomycin are described. These elements are provided on various plasmid vehicles and as chromosomal insertions to extend the range of targets for Tn mutagenesis. Single EcoRI sites at the ends of these transposons proved most useful for physical mapping, for the generation of new EcoRI sites in cloning experiments, for end-labelling and for sequencing of DNA adjacent to an insertion.

Gene organization and target specificity of the prokaryotic mobile genetic element IS26

The 820-bp mobile genetic element IS26 loses its ability to promote transpositional cointegration (1) by short deletions near the middle of the element causing shifts in both reading frames ORFI (left to right) and ORFII (right to left) and (2) by deletions causing substitutions of the C-terminus of ORFI but not affecting ORFII. The 702-bp ORFI is thus likely to code for the IS26 transposase. An 82-bp long sequence from the left end of IS26 contains a promoter-like structure in front of the start of ORFI at coordinate 64. In appropriately constructed plasmids, this sequence promotes the expression of the galK structural gene. The observation provides additional evidence for the functional relevance of ORFI. Neither the presence nor the absence of an intact IS26 element on the same plasmid affects measurably the degree of the galK gene expression by the IS26 promoter. Sequence comparison of 14 independent integration sites of IS26 and its relatives reveals no striking rules for target selection by the element, and the distrubtion of integration sites of IS26 on small multicopy plasmids is nearly random and independent of the local AT-content.

Organization of the Tn6-related kanamycin resistance transposon Tn2680 carrying two copies of IS26 and an IS903 variant, IS903. B

The kanamycin resistance transposon Tn2680, which originates from the R plasmid Rts1, is homologous to Tn6 and carries two directly repeated copies of IS26, one at each end. The kanamycin resistance gene codes for type I aminoglycoside-3'-phosphotransferase. Tn2680 also contains, in the middle of the transposon, an additional IS element homologous to IS903. This element, designated IS903.B, is flanked by a 9-base-pair direct target duplication. A novel kanamycin resistance transposon. Tn2681, can be generated from Tn2680 by IS903.B-mediated cointegration and subsequent reciprocal recombination between the directly repeated IS26 sequences. Tn2681 carries a single IS26 element in the middle of the transposon and is flanked by two directly repeated copies of IS903.B. Possible evolutionary relationships between Tn2680 and other kanamycin resistance transposons such as Tn903 and Tn2350 are discussed, based on the gene organization and DNA sequences.

An active variant of the prokaryotic transposable element IS903 carries an amber stop codon in the middle of an open reading frame

The prokaryotic mobile genetic element IS903.B is an active variant of IS903. It differs from IS903 and IS102 by 34 and 61 nucleotide substitutions, respectively. The large open reading frame (ORFI) which probably encodes the transposase is conserved in all three IS elements, whereas the smaller open reading frame (ORFII), which codes on the opposite DNA strand and entirely overlaps ORFI, contains an amber stop codon past the middle of ORFII in IS903.B. Experiments using Escherichia coli K12 strains permissive or non-permissive for amber mutations revealed no difference in the cointegration frequency mediated by IS903.B. Therefore, a possible peptide encoded by ORFII on the IS903-related element is unlikely to be necessary for transposition.

Identification of an Rts1 DNA fragment conferring temperature-dependent instability to vector plasmids

The multiphenotypic drug resistance factor Rts1 expresses a temperature-dependent instability characteristic. This plasmid was digested with the restriction enzyme BamHI. A DNA fragment with a molecular weight of 5.6 MDa (the H fragment) was inserted into plasmid pBR322 (pFK896) or into pSC105 (pYH156) at the BamHI site. These plasmids were unstable at 42 degrees C but stable at 32 degrees C. A restriction-enzyme map of the H fragment was constructed and the instability phenotype (Tdi) was localized to a DNA fragment with 0.5 MDa molecular weight. The temperature-dependent loss of the unstable plasmid pFK896 is abrupt and no gradual plasmid loss of this multicopy recombinant plasmid is observed. The possibility that the Tdi phenotype is due to overgrowth of R- cells was eliminated.

Functional characterization of the prokaryotic mobile genetic element IS26

IS26L and IS26R are the 820 bp long elements found as direct repeats at both ends of the kanamycin resistance transposon Tn2680. They can mediate cointegration in E. coli K12 which contains no IS26 in its chromosome. Cointegration occurs in rec+ or recA- strains with similar frequency. Upon cointegration mediated by either IS26R or IS26L, the element is duplicated and integrated into one of many different sites. Both IS26L and IS26R carry 14 bp perfect terminal inverted repeats and generate 8 bp direct repeats at their target sequences. Deletion formation mediated by IS26R was also observed. These functional and structural features of IS26 are characteristic of a prokaryotic mobile genetic element.

Nucleotide sequence of the transposable element IS15

We have determined the complete nucleotide sequence of the right (R) copy of the insertion sequence IS15 which flanks, in direct orientation, the composite transposon Tn1525. IS15-R, which is capable of independent transposition, is 1648 bp long and has short (14 bp) perfect inverted repeats at its termini. Analysis of the nucleotide sequence indicates that IS15-R results from the transposition, in direct orientation, of a smaller (820 bp long) IS, designated IS15-delta, into itself. This integration event is accompanied by the duplication of 8 bp in the target DNA. IS15-delta possesses two large overlapping open reading frames (ORF) located on opposite strands. Because of this particular structure, IS15 possesses four large ORFs which, due to the integration event, exhibit some differences with those of the parental IS15-delta.

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.

Bacteriophage P1 carries two related sets of genes determining its host range in the invertible C segment of its genome

The bacteriophage P1 genome carries an invertible C segment consisting of 3-kb unique sequences flanked by 0.6-kb inverted repeats. Host range mutations of P1 have been mapped in the C segment region. P1 derivatives carrying insertions and deletions in the left half of the C segment in one of two orientations termed C(+) do not affect the plaque-forming ability on Escherichia coli K12 and E coli C, whereas those having insertions in the right half of the C segment fail to form plaques on these hosts. An E. coli C mutant which allows the latter insertion mutants with the C segment in the C(-) configuration to form plaques has been isolated. Not only P1 C(-) but also P1 C(+) phages gave plaques on this E. coli C mutant. The results are consistent with the notion that the C segment of P1 carries two sets of genes for host specificity, and that C inversion alters the P1 host range through activation of one set of the genes. Furthermore, extended host range mutants can be isolated by point mutation in either set of the P1 genes. C inversion is a slow process, but it occurs on the phage genome upon its vegetative growth as well as on the prophage in the lysogenic state. The 3-kb invertible G segment of the phage Mu genome is known to be homologous with the central 3-kb part of the C segment of P1 and to carry also two sets of genes for Mu host specificity. While only Mu G(-) grows on E. coli C, both Mu G(+) and Mu G(-) phages form plaques on the E. coli C mutant sensitive to P1 C(-). In the discussion the gene organization of the P1 C segment is compared with that of the Mu G segment.

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.

Genes for gentamicin-(3)-N-acetyltransferases III and IV: I. Nucleotide sequence of the AAC(3)-IV gene and possible involvement of an IS140 element in its expression

Genes for gentamicin-3-acetyltransferases [ACC(3)] of types III and IV have been cloned from various R-plasmids. In two R-plasmids, pWP14a (AAC(3)-III) and pWP7b [AAC(3)-IV], resistance genes have been found directly adjacent to a single copy of an IS element, IS140. Nucleotide sequence determination of the AAC(3)-IV gene from plasmid pWP7b and of part of IS140 from three different sources suggested that the -35 region of the AAC(3)-IV promoter was part of the IS element. A similarly built-up promoter was found in pWP14a. It was found also, that a hygromycin B phosphotransferase was expressed from a locus neighbouring the AAC(3)-IV gene in pWP7b which was under the control of the same promoter. In two other R-plasmids, pWP113a and pWP116a, the AAC(3)-III gene was found in different genetic environments, namely close to Tn3-like structures.

Nucleotide sequence of IS26, a new prokaryotic mobile genetic element

The DNA sequence of a new IS element, the IS26, is 820 bp long and carries 14 bp perfect terminal inverted repeats. Upon integration, IS26 generates an 8 bp duplication of its target sequence. A large open reading frame within IS26 could code for a protein of 234 amino acids. On its reverse strand, IS26 also carries one large open reading frame, 591 bp long, which contains no stop codon within IS26.

Cointegrational transduction and mobilization of gentamicin resistance plasmid pWP14a is mediated by IS140

The structures of two R-plasmids pWP14a and pWP12a (Tra-, Ap, Gm; 21 kb) and of several cointegrates they form with bacteriophages P1Cm and P1-15 were analyzed. In each case, replicon fusion was mediated by the element IS140 (about 0.8 kb), one copy of which resides on both plasmids adjacent to the gentamicin resistance determinant (AAC(3)-III). pWP14a cointegrated preferentially into or near the invertible C-loop structure of the P1 genome. Cointegrational mobilization of pWP14a was observed also with several conjugative R-factors. The process of replicon fusion is independent of the host's rec+ functions. Sequences homologous to IS140 are constituents of many R-factors, including RA1, R40a, R124, R144, Rts1, N3, and pJR255. IS140 also shows homology to two other sequences, IS15 delta and Tn2680, but not to other, well studied transposable elements. The ampicillin resistance determinant of pWP14a is within a Tn3-like transposon, Tn3651.

Genome fusion mediated by the site specific DNA inversion system of bacteriophage P1

The genome of bacteriophage P1 contains a segment which is invertible by site specific recombination between sequences near the outside ends of the inverted repeats which flank it. Immediately adjacent to this C segment is the coding sequence for cin, the enzyme catalyzing inversion. We show that multicopy plasmids carrying cin and the sequences at which it acts (cix) can form dimers in the absence of the host recA function. Further, such plasmids can be cotransduced with P1 markers at high frequency from recA lysogens, indicating cointegration with the P1 genome. It is thus demonstrated that a system whose primary role is the inversion of a specific DNA segment can also mediate intermolecular recombination.

A site-specific, conservative recombination system carried by bacteriophage P1. Mapping the recombinase gene cin and the cross-over sites cix for the inversion of the C segment

The bacteriophage P1 genome carries an invertible C segment consisting of 3-kb unique sequences flanked by 0.6-kb inverted repeats. With insertion and deletion mutants of P1 derivatives the site-specific recombinase gene cin for C inversion) has been mapped adjacent to the C segment and the cix sites (for C inversion cross-over) have been located at the outside ends of the inverted repeats. Inversion of the C segment functions as a biological switch and controls expression of the gene(s) responsible for phage infectivity carried on the C segment. The cin gene product can promote recombination between a 'quasi- cix ' site on plasmid pBR322 and a cix site on P1 DNA. The junctions formed on the resulting co-integrate can also serve as cix sites. This observation implies a potential evolutionary process to bring genes under the control of a biological switch acting by DNA inversion.