alphabeta sequence of F is IS31

Evidence for past integration of IncP-1 plasmids into bacterial chromosomes

Plasmids of the IncP-1 incompatibility group are self-transmissible between and stably maintained in a very broad range of Gram-negative bacteria. A characteristic feature of IncP-1 genomes is the existence of multiple binding sites (OB) for the KorB protein which plays a dual role in active partitioning of plasmid and coordinate regulation of expression of genes for replication, maintenance and transfer. A search of the available bacterial genome sequences revealed a significant number (70 out of 322) with one or more putative KorB binding sites. Binding of KorB to such a site was demonstrated by chromatin immunoprecipitation (ChIP) for Pseudomonas putida KT2440. While such a site may arise by chance, this is unlikely for Pseudomonas aeruginosa UCBPP-PA14 whose genome sequence contains four clustered OB sites and several regions have more than 80% nucleotide identity to traJ, trbJ and trbL of IncP-1 plasmids. A number of other bacterial genomes also contain integrated partial IncP-1 genomes or their remnants. These data provide evidence for multiple past integration events of IncP-1 plasmids into bacterial chromosomes and provide new evidence for IncP-1 plasmids being important elements in gene mobility.

Insertion element IS3-based PCR method for subtyping Escherichia coli O157:H7

An Escherichia coli O157:H7 subtyping method based on PCR amplification of variable DNA sequences between the repetitive element IS3 was developed. Template DNA was prepared by boiling cells in Chelex. Two separate IS3 PCR amplifications were performed for each isolate: one with a single primer (primer IS3A) and one with two primers (primers IS3A and IS3B). The IS3 PCR subtyping method was applied to 35 epidemiologically related and unrelated E. coli O157:H7 isolates that had been previously characterized by pulsed-field gel electrophoresis (PFGE). PFGE identified 25 different subtypes (difference of one or more bands). PCR with single primer IS3A and primer pair IS3A-IS3B identified 6 and 14 different subtypes, respectively. By combining the results of the two PCR amplifications, 15 different IS3 PCR subtypes were identified. While not as sensitive as PFGE, IS3 PCR subtyping grouped all outbreak-related isolates. IS3 PCR banding patterns were reproducible between amplifications and between subcultures. IS3 PCR could serve as a simple, rapid screening method for the identification of unrelated E. coli O157:H7 isolates.

Identification and characterization of the linear IS3 molecules generated by staggered breaks

Insertion sequences IS3 encodes two, out-of-phase, overlapping open reading frames, orfA and orfB. The OrfAB transframe protein that is IS3 transposase is produced by -1 translational frameshifting between orfA and orfB. Efficient production of the IS3 transposase in the cells harboring the IS3-carrying plasmid has been shown to generate miniplasmids as well as characteristic minicircles, called IS3 circles, consisting of the entire IS3 sequence and one of the 3-base pair sequences flanking IS3 in the parental plasmid. Here, we show that the IS3 transposase also generates the linear molecules of IS3 with 3-nucleotide overhangs at the 5'-ends. The nucleotide sequences of the overhangs are the same as those flanking IS3 in the parental plasmid, suggesting that the linear IS3 molecules are generated from the parental plasmid DNA by staggered double strand breaks at the end regions of IS3. The linear IS3 molecules are likely to be the early intermediates in the transposition reaction, which proceeds in a non-replicative manner.

Large inversion in Escherichia coli K-12 1485IN between inversely oriented IS3 elements near lac and cdd

A companion study has shown that the inversion carried by strain 1485IN has one terminus between lac and proC and the other between his and cdd of the normal strain. Starting with this mapping data, we have done molecular work demonstrating that the inversion occurred by recombination between inversely oriented two IS3 elements, one present near lac and the other near the cdd locus; i.e., the inversion is IN(is3B-is3E). Evidence supporting this conclusion includes: (i) Normal and inversion strains share two short regions with identical restriction maps. One of these regions is near lac and the other near cdd. (ii) IS3 homology was detected in each of the terminus regions of both the normal and inversion strains. (iii) The sequence on one side of the original IS3 element near lac has been exchanged with the sequence on one side of the IS3 near cdd. Whether the inversion has occurred by one event of homologous recombination between the two IS3 elements or has been caused by involvement of IS3 elements on an F factor is discussed. Another rearrangement, probably related to inversion and deletion, was detected between the IS3 and cdd of the inversion strain.

Complete maps of IS1, IS2, IS3, IS4, IS5, IS30 and IS150 locations in Escherichia coli K12

In this paper complete distribution maps are presented of the seven IS elements 1, 2, 3, 4, 5, 30 and 150. These maps were obtained during the construction of an almost complete restriction map of the Escherichia coli genome of K12 strain BHB2600. The positions of IS elements were correlated to this map. The distribution of integration sites of all IS types is nonrandom. Besides a large gap from 79 min to 96 min, there is a pronounced IS cluster at 6 min and another at 97 min, map locations that have low gene incidences on the classical map. One cluster coincides with a region of IS induced rearrangements. The IS distribution pattern was compared to patterns of strains W3110 and HB101.

A naturally occurring large chromosomal inversion in Escherichia coli K12

Strain 1485IN and its derivatives were found to have a large inversion extending to about 35% of the chromosome. Because of this, the question arose as to whether 1485IN had arisen from an Escherichia coli strain other than K12. However, 1485IN had a flagellar antigen and a restriction-modification system indistinguishable from those of W3110, a major line of K12, and had retained an amber suppressor and lambda sensitivity that are characteristics of W1485 from which this strain seems to have arisen. Strain 1485IN had acquired proline auxotrophy, but showed the same growth rate as W1485 in nutrient broth at 37 degrees C. Interrupted matings with Hfr strains of 1485IN revealed a gene arrangement of nalA-gal-trp-his-lac-proA-thrleu-ilv, in which gal, trp, and his were on the inverted segment. The termini of the inversion were inferred to be situated between tsx (9.5 min) and purE (12 min) and between his (44 min) and cdd (46.5 min).

Complete sequence of IS3

We have determined the nucleotide sequence of IS3. Our IS3 isolate has 39 bp inverted repeats (IR's) with 6 mismatches, and is 1258 bp long. IS3 contains a large open reading frame (ORF) of 288 codons with a smaller, partially overlapping ORF of 91 codons on the opposite strand in codon-codon register. The large ORF is preceded by and has a 4 bp overlap with a 99 codon ORF that has potential transcriptional and translational start signals. Thus, IS3 could encode a bicistronic mRNA. The Shine-Dalgarno sequence for this 99 codon ORF could be sequestered in a stem-loop structure, but only if the transcript began outside IS3, as was first seen with IS10. This could be a means for preventing fortuitous activation of IS3 by outside promoters. No DNA sequence homology was found between IS3 and other prokaryotic IS elements, but there is slight amino acid sequence homology and significant conservation of hydropathicity patterns between the putative transposases of IS3 and IS2.

Discontinuity of homology of Escherichia coli and Salmonella typhimurium DNA in the lac region

Partial homology of Salmonella typhimurium DNA to Escherichia coli DNA was demonstrated by Southern hybridization blots to exist on either side of the lac operon of E. coli but no homology was detected between S. typhimurium DNA and about 12 kb of E. coli DNA including the lac genes as well as about 5 kb of E. coli DNA between lac and proC. Thus portions of DNA seem to have been either added to the E.coli genome or deleted from the S. typhimurium genome since their divergence from a common ancestor. Although an IS1 element was located near the lac operon of E. coli, the insertional element was shown not to be near any of the junctures of discontinuity of E. coli--S. typhimurium homology near lac.

pED100, a conjugative F plasmid derivative without insertion sequences

The largest HindIII fragment of F includes the entire replication and transfer regions, and its circularisation with ligase gave the conjugative plasmid pED100. This plasmid, which contains none of the F insertion sequences, was essentially unable to mobilise the E. coli chromosome or to give integrative suppression of a dnaA strain.

Integration of IS3 into IS2 generates a short sequence duplication

The Gal+ allele IS2-43 is known to segregate Gal- clones. Among 11 Gal- segregants, one was shown to be due to the integration of IS3 into IS2-43. Precise excision of the integrated IS3 element occurred at a rate of 5 x 10(-9)/cell/generation. DNA sequence analysis revealed that the termini of the IS3 element have the relation of imperfect inverted repeats and it is now flanked by a 3bp or 4bp duplication, a size which has not been seen before with other elements.

The ends of Tn10 are not IS3

By heteroduplex and hybridization analysis we showed that the inverted repetition (here called IS10) at the ends of the translocatable tetracycline resistance element Tn10 is not IS3, as had previously been reported by Ptashne and Cohen (J. Bacteriol. 122:776--781, 1975). Further analysis confirmed the homology between IS3 and the alpha beta sequence of F and demonstrated that IS10 was not present in the genomes of Salmonella typhimurium LT2 or Escherichia coli K-12.

Enumeration and identification of IS3 elements in Escherichia coli strains

Escherichia coli K-12 strains ordinarily contain five IS3 elements. Three of these correspond to previously mapped IS3 elements (R. C. Deonier, G. R. Oh, and M. Hu, J. Bacteriol. 129:1129--1140, 1977; S. Hu, E. Ohtsubo, and N. Davidson, J. Bacteriol. 122:749--763, 1975), and two additional IS3 elements are identified. The distribution of IS3 elements among deoxyribonucleic acid fragments generated by digestion with EcoRI indicates a basic pattern from which deviation is detected.

Investigations of the F conjugation gene traI:traI mutants and lambdatraI transducing phages

A series of traI point and deletion mutants of Flac, and a traM mutant, were characterised. Complementation tests with an amber Flac traI mutant confirmed their genotypes, and in addition all the traI mutants, but not the traM mutant, were complemented by pRS31 (PSC101 traDI) and EDlambda109 (lambdatraI). Judging from the efficiencies of plating of F-specific phages, none of the mutations affected pilus formation. The traI products of F and of the F-like plasmid R1 were interchangeable with each other but not with that of R100, while the traM product of F could not be replaced by those of R1 or of R100. Neither traI nor traM were needed for conjugal transfer of ColE1. Three lambda transducing phages carrying traI were isolated by in vivo or in vitro techniques, and characterised by genetic complementation tests, by analysis of the fragments produced by restriction endonucleases, and by measurement of heteroduplex molecules. The genetic structures together with the sizes and F coordinates, of the transfer regions carried by the phages were thereby determined. Comparison of the proteins synthesised in UV-irradiated cells by one of the lambdatraI phages with those made by a derivative carrying an amber traI mutation, allowed the traI product to be identified as a protein of molecular weight 174,000. In addition, the molecular weights of the traD (84,000), traS (18,000), and traT (25,000) products made by the lambdatraSTD1 phage EDlambda107 were measured. The possible roles of the traI and traM products in conjugation are discussed.

Electron microscope heteroduplex studies of sequence relations among plasmids of Escherichia coli: structure of F100, F152, and F8 and mapping of the Escherichia coli chromosomal region fep-supE-gal-attlambda-uvrB

The genetic and physical structures of commonly used F-prime factors carrying the galactose region of the Escherichia coli chromosome were analyzed. Deletions in the chromosomal DNA sequences in the F-prime factors were found to be frequent events. A genetic method was developed to reconstruct the original F-prime factors from deletion variants. Heteroduplex analysis of the reconstructed F-prime factors confirmed the derivation of the F-prime factors F100 and F152, from the same Hfr, and finally determined the normal E. coli chromosomal sequence in the region between fep and uvrB, containing about 5 min in genetic units and about 246.5 in kilobase units (kb). This sequence could be connected with the DNA sequences of the lac-purE region, which had been physically determined previously. Together they constituted a total of 528.6 kb. From these combined sequences, the distance from lacPO to galK was calculated to be 412.9 kb, which corresponds to 8.8 min in genetic units.

Plasmid cointegrates of Flac and lambda prophage

Fifteen cointegrates of the plasmid Flac and prophage lambda that had suffered no detectable change in plasmid phenotype were isolated and characterized. The locations of the prophage insertions were determined by genetic analysis of deletion mutants obtained from each cointegrate as survivors of growth at 42 degrees C. In 11 cointegrates, the prophage was inserted between traI and lac, although probably in more than one location; in 3 others, it was on one side or the other of lac; and in 1 it was between lac and pif. Deletions covering all or part of the transfer region, as well as of lac and of pif, were obtained in the course of this analysis. Deletion mutants that had lost all known transfer genes were also oriT, but they retained the capacity to recircularize after transfer. Attempts were made to isolate lambda transducing phages for nearby plasmid genes from the cointegrates, and lambdaptraGD, lambdaptraD, lambdaptraI, and lambdadtraDI phages were obtained.

Nucleotide sequence of an insertion element, IS1

PSM2, PSM1, and PSM15 are small plasmids derived from R100 by spontaneous deletions at either end of the insertion sequence IS1. These plasmids were used to identify regions neighboring IS1 as well as the IS1 DNA itself, by cleavage with EcoR1, HindIII, Hae III, Hpa II, Hha I, Hinf, and AIu I. The nucleotide sequencing results demonstrate that IS1 contains 768 bases. About 30 bases at the ends of IS1 were found to be repeated in an inverted order. The deletions occurring at the ends of IS1 were found to be due to illegitimate recombination. The hypothesis that RNA polymerase could play an important role in such recombination phenomena is discussed based on the nucleotide sequences surrounding the recombinational hot spots.

Excision of F plasmid sequences by recombination at directly repeated insertion sequence 2 elements: involvement of recA

The DNA of the F plasmid is joined to bacterial DNA sequences in the F' ORF203 by directly repeated insertion sequence 2 (IS2) elements. The rate of excision of the F plasmid form this F' (presumably by recombination at the directly repeated IS2s) has been estimated in both recA+ and recA- strains. Normal F is produced in the recA+ strain, but is not detected in recA-. The autonomous plasmids produced in the recA- background were F's having deletions. F excision in this particular recA+ case is specific in the sense that the directly repeated IS2s appear to be more active in recombination than similarly disposed IS3 direct repetitions in this F'.

Further mapping of IS2 and IS3 in the lac-purE region of the Escherichia coli K-12 genome: structure of the F-prime ORF203

The sequence organization of the F-prime ORF203 was determined by heteroduplex analysis. This large, type II F-prime (Scaife, 1967) contains lac, proC, and purE genes derived from the W1485 subline of Escherichia coli K-12. The IS3 and IS2 elements previously found in the lac-proC-purE region derived from the 58-161 subline (Hu et al., 1975) are also present in the same locations in the bacterial deoxyribonucleic acid (DNA) from the W1485 subline. Recombination between the IS2 region of F and an IS2 element located between lac and proC on the bacterial DNA apparently led to the formation of the perental Hfr, OR21. IS2 is thus directly repeated, with one copy of each element appearing at each of the two junctions between F and the bacterial sequences on ORF203. The F plasmid is found together with ORF203 in the plasmid DNA, and this probably forms from ORF203 by recombination between the directly repeated IS2 elements. ORF203 appears to have been excised from the Hfr chromosome by recombination between the IS3 sequence alpha3beta3 located counterclockwise of lac and the directly repeated IS3 sequence alpha4beta4 located clockwise of purE.

Transposable genetic elements and plasmid evolution

Transposable elements of DNA that are structurally defined and genetically discrete units seem to have an important role in the evolution of bacterial plasmids. Recombination occurring at the termini of such elements can result in the joining together of unrelated DNA segments that lack extensive nucleotide sequence homology. In addition, transposable elements serve as novel biological switches capable of turning on and off the expression of nearby genes as a consequence of their insertion into or excision from plasmid genomes.

Insertion sequence IS2 near the gene for prophage lambda excision

In this study we characterize a variant of the lambdacI857S7 prophage, designated lambdabi2cI857S7, which carries a DNA insertion. The insertion sequence is IS2, and it resides in the antipolar orientation II just upstream from the gene for prophage excision (xis) at 61.6%lambda. This bi2 insertion mutant could prove valuable for studies on possible recombination functions of IS2 DNA and of its effect on the lambda integration and excision functions.

Electron microscope study of a plasmid chimera containing the replication region of the Escherichia coli F plasmid

pML31, a plasmid chimera constructed to contain the replication genes of an Flac plasmid, has been studied by electron microscope methods. Heteroduplex analysis shows that the only F sequence present in pML31 is that with corrdinates 40.3-49.3F. This region has previously been identified as essential for plasmid maintenance. The sequence of pML31, which was derived originally from R6-5, carries the km gene(s) and an inverted duplication of a 1.0-kilobase sequence. On the basis of length measurements, the repeated sequence is different from IS1, IS2, IS3, and an inverted repeat associated with the km gene(s) of plasmid JR67.

Isolation of inverted repeat sequences, including IS1, IS2, and IS3, in Escherichia coli plasmids

A method is described for isolation of inverted repeat DNA sequences that occur in E. coli plasmids. The procedures of the isolation involved: (a) denaturation of intact plasmid DNA, (b) a rapid, 30 sec, renaturation of inverted-repeat sequences in the genome, (c) digestion of the single-stranded portion by S1 nuclease to recover duplex DNA, and (d) detection and purification of the duplexes using 1.4% agarose gel electrophoresis. If a plasmid DNA carried inverted repeats of either one type or two different types of special DNA sequences, these procedures enabled us to observe either one or two characteristic DNA bands, respectively, in the agarose gels. If a plasmid DNA did not carry any inverted repeats, or if the plasmid DNA only carried direct repeat sequences, no characteristic DNA bands were recovered. Cleavage of the spacer DNA between inverted repeat sequences generated no gel bands. This indicated that the inverted repeat sequences must be in the same strand. Using this method, we isolated and purified several repeated sequences, including IS1, IS2, and IS3, from derivatives of F and R plasmids.

The isolation of IS1 and IS2 DNA

DNA of the IS-elements IS1 and IS2 was prepared by digestion of appropriate heteroduplex molecules with endonuclease S1, followed by sucrose gradient centrifugation or gel electrophoresis. The material obtained is homogeneous with regard to size. The length of IS1 DNA is 820 +/- 65 nucleotides, the length of IS2 DNA is 1,350 +/- 70 nucleotides. IS1 DNA is not cleaved by the restriction endonucleases Eco R1, Hind II or Hind III. IS2 DNA is cleaved once by each of the two latter enzymes. The buoyand density determined by equilibrium centrifugation of Hg-complexes in Cs2so4 corresponds to a GC content of approximately 50%. Labelling with polynucleotide kinase indicates that both IS DNA's have a guanosyl residue at both of their 5'-termini.

Molecular cloning of DNA from F sex factor of Escherichia coli K-12

We describe the molecular cloning of various DNA segments generated by partial EcoRI endonuclease digestion of the sex factor F. These segments have been analyzed by agarose gel electrophoresis of EcoRI digests and were arranged in a series of overlapping fragments using the EcoRI fragment map of F established by H. Ohtsubo and E. Ohtsubo. The clones isolated demonstrate one or more of the following F-specified functions: inhibition of female-specific phage (T7) multiplication, formation of F pili, surface exclusion, or immunity to lethal zygosis. These properties are discussed in terms of the EcoRI fragments of F that specify them.