IS elements and transposons

How Do Transposable Elements Activate Expression of Transcriptionally Silent Antibiotic Resistance Genes?

The rapidly emerging phenomenon of antibiotic resistance threatens to substantially reduce the efficacy of available antibacterial therapies. Dissemination of resistance, even between phylogenetically distant bacterial species, is mediated mainly by mobile genetic elements, considered to be natural vectors of horizontal gene transfer. Transposable elements (TEs) play a major role in this process-due to their highly recombinogenic nature they can mobilize adjacent genes and can introduce them into the pool of mobile DNA. Studies investigating this phenomenon usually focus on the genetic load of transposons and the molecular basis of their mobility. However, genes introduced into evolutionarily distant hosts are not necessarily expressed. As a result, bacterial genomes contain a reservoir of transcriptionally silent genetic information that can be activated by various transposon-related recombination events. The TEs themselves along with processes associated with their transposition can introduce promoters into random genomic locations. Thus, similarly to integrons, they have the potential to convert dormant genes into fully functional antibiotic resistance determinants. In this review, we describe the genetic basis of such events and by extension the mechanisms promoting the emergence of new drug-resistant bacterial strains.

Extensive and widespread homologies between mitochondrial DNA and chloroplast DNA in plants

We used hybridization techniques to demonstrate that numerous sequence homologies exist between cloned mung bean and spinach chloroplast DNA (ctDNA) restriction fragments and mtDNAs from corn, mung bean, spinach, and pea. The strongest cross-homologies are between clones derived from the ctDNA inverted repeat and mtDNA from corn and pea, although all the ctDNA clones tested hybridized to at least one mtDNA restriction fragment. Known chloroplast genes showing strong mtDNA homologies include those for the large subunit of ribulosebisphosphate carboxylase, which hybridizes to corn mtDNA, and the beta subunit of the chloroplast ATPase, which hybridizes to mung bean mtDNA. Certain of these homologies were confirmed by using cloned spinach mtDNA restriction fragments as probes in reciprocal hybridizations to ctDNA. Several of these ctDNA-homologous mtDNA sequences were shown to be much more closely related to ctDNA from the same species than to that of a distantly related species. We interpret these differential homologies as evidence for relatively recent DNA sequence transfer events, suggesting that transpostion between the two genomes is an ongoing evolutionary process.

Translation of Zea mays endosperm sucrose-synthase mRNA in vitro

mRNA of 23-day-old maize endosperm was translated both in wheat germ extracts and rabbit reticulocyte lysates. A protein with an apparent molecular weight of 88,000 comigrates in dodecylsulfate/polyacrylamide electrophoresis with sucrose synthase. This protein is precipitated with an antiserum against sucrose synthase and shows the same protease digestion pattern as the enzyme. It is not synthesized with mRNA extracted from sh/sh mutant kernels lacking sucrose synthase. By these criteria, the protein is the translation product in vitro of sucrose synthase mRNA. The separation of mRNA in methylmercury-hydroxide--agarose gels and subsequent translation indicates a length of sucrose synthase mRNA of 2800 nucleotides which is compatible with the coding length necessary for a protein with a molecular weight of 88,000 plus untranslated sequences.

Transposable elements in Lactococci: a review

Genetic studies have identified the presence of transposable elements within the genus Lactococcus, which includes industrially important microorganisms used in the production of fermented dairy products. Three insertion sequences have been fully characterized in addition to several reports of transpositionlike events. The three insertion sequence elements, ISS1, IS904, and IS981, exhibit the physical and genetic properties characteristic of known insertion sequences. They are closely related to insertion sequences isolated from a wide variety of microorganisms. In lactococci, insertion sequence elements are associated with lactose and sucrose metabolism, proteinase activity, nisin production and immunity, conjugal transfer determinants, and bacteriophage resistance, which are attributes significant for growth in a milk environment. The characteristics, involvement in lactococcal evolution, and recent developments as tools for genetic engineering of the lactococcal elements are discussed.

Completion of the IS map in E. coli: IS186 positions on the E. coli K12 chromosome

Insertion sites of the transposable element IS186 were physically mapped in the genome of E. coli K12 strain BHB2600. This strain maintains four IS186 copies of which three, assigned to 0.3, 14.1 and 51.8 map min., share common map positions with the three IS186 copies in strains W3110 and HB101. The fourth, unique IS copy in BHB2600 maps at 49.3 min. The IS186 data complete the BHB2600 map for all chromosomal sites of known K12-associated IS types.

Cloning and analysis of s-triazine catabolic genes from Pseudomonas sp. strain NRRLB-12227

Pseudomonas sp. strain NRRLB-12227 degrades the s-triazine melamine by a six-step pathway which allows it to use melamine and pathway intermediates as nitrogen sources. With the plasmid pLG221, mutants defective in five of the six steps of the pathway were generated. Tn5-containing-EcoRI fragments from these mutants were cloned and identified by selection for Tn5-encoded kanamycin resistance in transformants. A restriction fragment from ammelide-negative mutant RE411 was used as a probe in colony hybridization experiments to identify cloned wild-type s-triazine catabolic genes encoding ammeline aminohydrolase, ammelide aminohydrolase, and cyanuric acid amidohydrolase. These genes were cloned from total cellular DNA on several similar, but not identical, HindIII fragments, as well as on a PstI fragment and a BglII fragment. Restriction mapping and Southern hybridization analyses of these cloned DNA fragments suggested that these s-triazine catabolic genes may be located on a transposable element, the ends of which are identical 2.2-kb insertion sequences.

Genetic analysis of the enterobactin gene cluster in Shigella flexneri

The genes for transport and synthesis of the phenolate siderophore enterobactin are present on the chromosomes of both Ent+ and Ent- clinical isolates of Shigella flexneri. To determine why Ent- S. flexneri isolates fail to express a functional enterobactin system, the structure and expression of enterobactin genes were examined. Several alterations may be responsible for the inability of S. flexneri to express enterobactin. (i) The mRNA levels produced from the entC and fepB genes were not derepressed in low-iron media. (ii) DNA sequence analysis of the entC-fepB intergenic region revealed an 83-bp noncontiguous deletion in the putative fepB leader sequence. The deleted sequences are in a region which would be capable of forming extensive stem-and-loop structures. (iii) An amber codon in the 5' portion of the entC gene was also detected. (iv) An IS1 element, previously mapped to the Ent- S. flexneri enterobactin gene cluster, was found to lie within a potential transcriptional termination sequence in the entF-fepE intergenic region. (v) A mutation responsible for the inactivation of the entF gene was mapped to the entF coding region by using entF hybrid gene fusions. (vi) A comparison of outer membrane profiles from an E. coli strain harboring the cloned fepA gene from either an Ent+ or Ent- Shigella isolate revealed that the Ent- FepA protein is present in the outer membrane but at greatly reduced levels than that of the Ent+ FepA protein. This observation, along with additional studies, suggests that the Ent- FepA may be defective in translation and/or translocation.

Behavior of the hybrid plasmid pNSW301 in Zymomonas mobilis grown in continuous culture

The stability of the plasmid pNSW301 which was formed by cointegration of the Inc W R plasmid Sa and the 14.5-kb pNSW1 plasmid of Zymomonas mobilis ZM6100 was investigated in ZM6100(pNSW301) grown in continuous culture without antibiotic selection. The cointegrate plasmid, pNSW301, was found to be structurally unstable and a total reduction in the size of pNSW301 of approximately 21 kb occurred during growth in continuous culture. Following a systematic study, a number of deletion derivatives of pNSW301 were isolated and used to transform Escherichia coli HB101, with the exception of pNSW312. The plasmid pNSW312 was 100% stable in ZM6100(pNSW312) in continuous culture but was unable to replicate in E. coli.

Phase variants of Bordetella bronchiseptica arise by spontaneous deletions in the vir locus

Bordetella bronchiseptica is a common respiratory tract pathogen of many mammalian species. Nucleotide sequences from the locus involved in coordinate regulation of B. pertussis virulence factors, vir, were shown to have a high degree of homology to chromosomal DNA from virulent (Vir+) and avirulent (Vir-) strains of B. bronchiseptica. Small deletions, 50 bp to 500 bp, within the vir locus were found in some of the Vir- phase variants. The vir locus and the adjacent 5' portion of the fhaB structural gene were cloned from the parental Vir+ B. bronchiseptica strain on a 23.5 kb BamHI fragment. Restriction enzyme mapping of the cloned B. bronchiseptica vir locus revealed similarities with and differences from the previously cloned B. pertussis vir locus. The cloned B. bronchiseptica vir locus complemented spontaneous Vir- variants of Bordetella pertussis and B. bronchiseptica as well as vir::Tn5 mutants of B. pertussis. Comparison of various functions of the vir loci of B. bronchiseptica and B. pertussis revealed some interesting differences in the coordinate regulation of virulence factors.

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.

Constitutive activation of the fucAO operon and silencing of the divergently transcribed fucPIK operon by an IS5 element in Escherichia coli mutants selected for growth on L-1,2-propanediol

L-1,2-Propanediol is an irretrievable end product of L-fucose fermentation by Escherichia coli. Selection for increased aerobic growth rate on propanediol results in the escalation of basal synthesis of the NAD+-linked oxidoreductase encoded by fucO, a member of the fuc regulon for the utilization of L-fucose. In general, when fucO becomes constitutively expressed, two other simultaneous changes occur: the fucA gene encoding fuculose-1-phosphate aldolase becomes constitutively expressed and the fucPIK operon encoding fucose permease, fucose isomerase, and fuculose kinase becomes noninducible. In the present study, we show that fucO and fucA form an operon which is divergently transcribed from the adjacent fucPIK operon. In propanediol-positive and fucose-negative mutants the cis-controlling region shared by the operons fucAO and fucPIK is lengthened by 1.2 kilobases. DNA hybridization identified the insertion element to be IS5. This element, always oriented in the same direction with the left end (the BglII end) proximal to fucA, apparently causes constitutive expression of fucAO and noninducibility of fucPIK. The DNA of the fucAO operon and a part of the adjacent fucP was sequenced.

Characterization of the types of mutational events that spontaneously occur in a plasmid system

The immunity region from a cI857 derivative of bacteriophage lambda has been cloned into the EcoRI site of pBR322 to produce a plasmid that can be used to analyze spontaneous mutagenesis. Cells containing this plasmid are temperature-sensitive for growth unless mutations have occurred that somehow prevent the expression of the kil gene in the lambda fragment at non-permissive temperature. 678 such temperature-resistant mutants from 10 independent subcultures each of 2 different recA- E. coli strains have been collected, and the nature of the plasmid mutations obtained has been analyzed. All of the subcultures contained mutants that allowed growth at the restrictive temperature without showing a detectable change in plasmid size. 75% of the total mutants fell in this class. More than half of these mutations involved the lambda leftward promoter, pL, and such mutants were found in all 20 subcultures. The remaining 25% of the mutations involved a change in plasmid size and mutations of this class were found in 18 of 20 subcultures. 12% of the total mutants (found in 16 of 20 subcultures) had an insertion of IS1 in the region between pL and the lambda kil gene. 6% of the total mutants had undergone an IS1-mediated deletion, while 1% were mixed colonies in which multiple IS1-mediated events had occurred. About 1% of the total mutants had undergone complex IS1-mediated DNA rearrangement(s) that have not yet been characterized. In total, 11 of 20 subcultures yielded isolates where IS1-mediated rearrangements had occurred. The remaining 4% of the mutations included insertions of IS5, IS30, and an IS1 family member that appears to be IS1T as well as IS1T-mediated deletions and deletions that do not appear to have been mediated by any insertion sequence. A mutant with both an IS1 insertion and an alteration involving pL has also been isolated.

Spontaneous deletion mutants of bacteriophage Pf3: mapping of signals involved in replication and assembly

Defective deletion mutants (miniphages) arise spontaneously during serial propagation of the filamentous bacteriophage Pf3. They contain a circular single-stranded (ss) DNA molecule which is up to 80% smaller than the wild-type single-stranded genome. Analysis of the genomic structure of three of these miniphages revealed that they consist of sequences that in the wild-type genome are flanked by direct repeats 5-8 nucleotides long; only one copy of these repeats was found again in the miniphage genome. One miniphage genome contained a tandemly duplicated sequence, and from its structure we concluded that the duplication had occurred after a primary deletion event. Also, short direct repeats must have been involved in the duplication process. We conclude that the deletion and duplication events have occurred by an identical recombination process, probably the "slipped mispairing" mechanism. In the presence of helper functions, the three miniphage genomes are replicated and assembled into ssDNA containing virus-like particles. Hence, the assembly signal and the replication origins for viral and complementary strand synthesis are located within the region shared by all three miniphage genomes, i.e., nucleotides 4092-4678 of the wild-type genome (Luiten et al., 1985).

A transcriptional terminator sequence in the prokaryotic transposable element IS1

The prokaryotic transposable element IS1 is known to exert a strong polar effect upon integration into an operon. To elucidate this polar effect, we constructed a plasmid which has an IS1 integrated between the 5' half of the tet gene for tetracycline resistance and the cat structural gene for chloramphenicol resistance. The cat gene is expressed by the tet promoter and the presence of IS1 in orientation I, in which the IS1 transposase genes insA and insB are in the same orientation as the cat gene, reduced the cat expression. By introducing deletions or insertions within the IS1 sequence, we were able to map a rho-dependent terminator TIS1A between the insA and insB genes. Translational interruption between these ins genes is important for TIS1A to be an active terminator.

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.

Structural and functional studies of insertion element IS200

The nucleotide sequence of the insertion element IS200 has been determined partially, including the junctions between the element and the host chromosome at the insertion site. At most, two bases (A-A) are found repeated at the junctions and could be duplications of host sequences generated by the insertion of the element. No obvious sequence repeats, either direct or inverted, have been detected between the sequences just within the two ends of the element. The element is an extremely strong block to host transcription across the insertion site. A sequence similar to known transcription termination signals was found just within the element near the right end. Removal of less than 50 base-pairs at the right end of the element abolishes the transcription block. The putative terminator sequence is located within this 50 base-pair region. Genetic studies suggest that the element contains a promoter located more than 93 base-pairs from its left end. The proposed promoter and terminator are in proper orientation to form an internal transcription unit.

Intramolecular transposition of IS102

It has been postulated that deletions mediated by transposable elements are intramolecular transposition events. An implication of this hypothesis is that the deleted fragment may be recovered if it is capable of autonomous replication. We report here the characterization of the products of intramolecular transposition of the element IS102 in bireplicons. We show that when two origins (ori's) (of pSC101 and R6-5) generate the same copy numbers, two dissociated replicons are recovered as well as the inversions. On the contrary, when two ori's (of pSC101 and pBR322) have different copy numbers, intramolecular transposition results essentially in inversions. However, the very low frequency (5 X 10(-8)) at which intramolecular transpositions in the bireplicons occurs, as compared to the single replicon (10(-4)), suggests that a complete transposition reaction may not be necessary to generate deletions.

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.

Cytochrome oxidase subunit II gene of rice has an insertion sequence within the intron

We have isolated and sequenced the cytochrome oxidase subunit II gene from rice (Oryza sativa L. var Labelle). The overall structural organization of this gene is very similar to that of the maize gene. This gene contains an intron in a position identical to the intron in the maize gene. However, the intron in the rice gene is longer than that of the maize gene largely due to a 461 bp insertion sequence, which has inverted repeats at its termini and is flanked by direct repeats, characteristic of transposable elements. Apart from this insertion sequence, the remainder of the intron sequence is strikingly homologous to that of maize (98.6% homology), suggesting a possible functional or structural role. The coding regions of the two genes exhibit 99.5% nucleotide sequence homology and their deduced amino acid sequences are identical. Similarly, the 3'-noncoding regions, except for several small insertions and deletions, show complete sequence homology. On the contrary, no sequence homology is detected in the 5'-noncoding regions.

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.

Evolutionary relationship between Tn21-like elements and pBP201, a plasmid from Klebsiella pneumoniae mediating resistance to gentamicin and eight other drugs

We have characterized pBP201 one of the plasmids from a collection of 46 strains producing adenylyltransferase ANT(2") (Schmidt 1984). It confers resistance to sulphonamides and produces aminoglycoside adenylyltransferases AAD(3") and ANT(2") and beta-lactamase TEM-1. Plasmid pBP201 has a size of 24.8 kilobases (kb) and contains TnA and a Tn21-related element, Tn4000 delta, with deletions in mer and the termini and a substitution at tnpR. In complementation assays with transposition-deficient mutants of Tn21 the element in pBP201 appears to be TnpA+ but TnpR-. It represents a naturally occurring defective transposon. The sequence organization of pBP201 has been compared with that of Tn21-related elements such as Tn2410, Tn2603, Tn2424, Tn1696, and Tn4000. In these transposons the integration sites of resistance genes cat, bla, aacA, aacC or aadB have been identified at two preferential locations; these are at the termini of the streptomycin resistance gene aadA. Two additional sites have been localized in the Tn21 backbone to the right of the mer operon and at res (internal resolution site) and are probably involved in the evolution of these elements. Based on these results a model for the possible genealogy of class II transposons is presented.

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.

The role of insertions, deletions, and substitutions in the evolution of R6 related plasmids encoding aminoglycoside transferase ANT-(2")

In 7% of gram-negative bacteria resistance to gentamicin is mainly mediated by plasmid-encoded aminoglycoside transferase ANT-(2"). The genome organization of 15 aadB plasmids (42-110 kb) was analyzed by restriction and hybridization techniques. They appeared to be IncFII-like replicons but were distinct from R6 by virtue of small substitutions in the transfer region. Aminoglycoside resistance genes aadB and aadA were located on Tn21 related elements. Only one of them was able to transpose its resistance genes mer sul aadA and aadB ( Tn4000 ), the other elements were naturally occurring defective transposons. In some of these structures deletions were identified at the termini, at sul, aadA , mer or transposition function--insertions adjacent to aadA or mer. The mode of these rearrangements and their site-specificity were considered with respect to the evolution of the Tn21 transposon family.

Genetic structure and stability of a copy number mutant of IncFI group plasmid ColV-K94 in Escherichia coli K-12

Mutants pWS10, pWS11 and pWS12 were derived from an IncFI group plasmid ColV-K94 by the insertion of a transposon Tn903 (Kmr). These plasmids were all approximately 130 kb in length. The plasmid pWS12 resembled the wild type ColV-K94 in transmissibility, incompatibility and stable maintenance. Cells harboring pWS11 were poor conjugal donors but resistant to the same level of kanamycin as pWS12 containing hosts. In contrast, pWS10 conferred a higher resistance to kanamycin and exhibited reduced incompatibility properties in comparison with pWS12. The higher drug resistance associated with pWS10 appeared to be a consequence of an increase in its copy number and the generation of miniplasmids of varying sizes. Electron microscope analysis of the copy mutant pWS10 revealed that Tn903 was located at a site adjacent to a region 32.6F to 35.3F. The latter region appears to be the primary replicon of ColV-K94 and is homologous with the secondary replicon of F. The insertional mutagenesis with Tn903 brought about an extensive DNA rearrangement including the duplication and translocation of the stems of two inverted repeat structures. The DNA alterations of pWS10 were distinguishable through comparison of its EcoRI digestion patterns with those of pWS11 and pWS12.

Escherichia coli K-12 gyrB gene product is involved in the lethal effect of the ligts2 mutant of bacteriophage Mu

Mu ligts2 mutants, defective for development and integration, show a high killing effect on the infected host. A number of survivors to Mu ligts2 infection were analyzed; they are characterized by nonpermissivity for both development and lysogenization of bacteriophage Mu. Bacteriophages D108 and P1 are also inhibited in these strains as is transposon Tn9. The corresponding mutation site was mapped at 82 min and identified with the Escherichia coli gyrB site.

Suicide plasmid vehicles for insertion mutagenesis in Rhizobium meliloti and related bacteria

We describe the construction and use of a set of plasmid vectors of the transposons Tn1, Tn5, and Tn9 that are suicidal in Rhizobium species and therefore suitable for mutagenesis with these three transposons. The vectors are composed of the p15A replicon which functions in Escherichia coli but not in Rhizobium species and a region encoding the N type of bacterial conjugation system which is very efficient in matings between E. coli and Rhizobium species. The usefulness of the vectors has been most extensively assessed in Rhizobium meliloti. It is likely that they will be useful for mutagenesis and genome manipulation in other bacteria as well.

Occurrence of deletion plasmids at high rates after conjugative transfer of the plasmids RP4 and RK2 from Escherichia coli to Alcaligenes eutrophus H16

The broad host-range IncP-1 plasmids RP4 and RK2 were transferred by conjugation from Escherichia coli to Alcaligenes eutrophus H16. Among the transconjugants selected on media containing tetracycline, a considerable number did not express kanamycin resistance. By comparing restriction patterns of plasmids isolated from a large number of transconjugants a variety of different deletion derivatives were found. All of these possess more or less extended deletions always including parts of the tra 1-region. The plasmids RP4 and RK2, once established in A. eutrophus H16 showed a high stability and it can be concluded that deletion formation is connected with the conjugation process. Evidence is given that degradation of DNA entering an A. eutrophus recipient cell during the conjugative transfer process may be involved in deletion formation. Furthermore, the finding of a small deletion derivative of RP4 lacking the transacting replication function trfB and the entire kil-kor-system may allow the assumption that these gene functions are not essential for replication and maintenance of RP4 in A. eutrophus hosts.

IS200: a Salmonella-specific insertion sequence

A new IS element (IS200) has been identified in Salmonella. The sequence was identified as an IS element by the following criteria: its insertion caused the mutation hisD984; six copies of the sequence are present in strain LT2 of S. typhimurium; and transposition of the sequence has been observed on several occasions. IS200 is found in almost all Salmonella species examined but is absent from most other enteric bacteria. The specificity of this element for Salmonella (and the absence of IS1-IS4 from Salmonella) suggest that transfer of insertion sequences between bacterial groups may be less extensive than is commonly believed. Alternatively, the distribution may suggest that these elements play a selectively important role in bacteria.

Specific in vitro transcription of the insertion sequence IS2

The insertion sequence IS2 is a small transposable element of Escherichia coli that lacks any known genetic markers. Insertion of this element in one orientation (I) within bacterial operons blocks expression of downstream genes. In the other orientation (II), IS2 has been associated with the constitutive expression of genes distal to its insertion, suggesting that IS2 might contain promoters directing transcription of IS2(II) into other genes. To test the transcription potential of IS2, we have transcribed in vitro DNA templates from gal3, a Gal- allele in which an IS2(I) is inserted between the gal promoter and the gal genes. We have detected two IS2-specific RNAs which initiate from promoters within IS2 and are transcribed in orientation II (away from the galETK genes). Though the presence and orientation of these promoters suggests that they could be responsible for the constitutive expression of genes adjacent to an IS2(II) element, an alternative role could be for transcription of IS2-encoded genes. Although IS2(I) insertions normally block expression of adjacent genes, certain altered (e.g. mutant) IS2(I) sequences lead to the constitutive expression of downstream genes. We have transcribed DNA templates from galwc5 and galc331, which are Galc alleles that contain altered IS2(I) insertions within the gal operon. For each allele, we have detected two gal-directed transcripts initiating within the IS2 sequence. These RNAs are not detected upon transcription of the unaltered IS2(I) DNA and the promoters arise as a direct consequence of the IS2(I) alterations. This result suggests that these promoters detected in vitro are responsible for the Galc phenotype of these alleles.

Transposable element that causes mutations in a plant pathogenic Pseudomonas sp

A 1.3-kilobase-pair DNA element, IS51, causes a loss of virulence in the plant pathogen Pseudomonas syringae pv. savastanoi. This sequence, IS51, was first discovered in a plasmid-borne iaaM locus, which together with iaaH directs the synthesis of a virulence factor, indoleacetic acid. The spontaneous insertion of IS51 in iaaM resulted in the loss of indoleacetic acid production, attenuation of virulence, and the loss of both enzyme activities coded by iaaM and iaaH. Using a cloned IS51 element as a probe, we found that numerous homologous sequences are present in different strains of this bacterium, on both chromosomal and plasmid DNAs. By artificially positioning IS51 between a tetracycline resistance gene and a promoter region, we showed that IS51 terminated transcription in Escherichia coli.

Superunstable alleles at the cut locus in Drosophila melanogaster

This is a detailed study of the reversions of the ctMR2 allele putatively carrying á mobile element (MR-transposon) in the cut locus. Stable, unstable and superunstable revertants have been identified. Besides, a series of multiple unstable visible and lethal ct mutations derived from the ctMR2 allele have been obtained. They are shown to include supermutable alleles. The results suggest that the MR-transposon is connected with at least three functions: excision; change of orientation; and change of position within the cut locus, these functions being disturbed in different ways in different unstable ct+ and ct alleles. In some cases the mutant transitions are somehow strongly stimulated leading to superinstability, reaching the rate of 0.5.

Switch in the transposition products of Mu DNA mediated by proteins: Cointegrates versus simple insertions

Bacteriophage Mu is a self-contained mobile unit encoding functions that mediate its movement. There appear to be two alternate pathways for Mu DNA transposition that differ with respect to the end products they generate. During the lytic cycle of phage Mu growth the end products of transposition are predominantly cointegrates in an experimental system in which the induced Mu prophage is located on pSC101, a low-copy-number plasmid. On the other hand, Mu insertions into the host genome during lysogenization contain Mu DNA as simple insertions. Two Mu functions, encoded by the A and B genes, are required for Mu DNA transposition during its lytic growth. However, during lysogeny the product of gene B is not required for integration of Mu DNA. Evidence is presented here which shows that in the absence of the B gene product the majority of transposition events are simple insertions. This is in striking contrast to the situation in which the majority of the products are cointegrates in the presence of both A and B gene products. Additional evidence also suggests that these simple insertions do not arise through the resolution of cointegrate structures.

Virus-induced gene mutations of eukaryotic cells

Most animal viruses studied so far induce chromosomal aberrations. In addition, adenoviruses, papovaviruses, and retroviruses are known to induce gene mutations like mutagenic bacteriophages. At least in one case studied retrovirus induced mutagenesis involves gene and/or scripton splitting analogous to the mutagenic mechanism of action of mutatorphage Mu and other movable DNA elements. On the contrary, several results obtained by independent means indicate that Simian virus 40, a papovavirus, does not act by splitting the affected gene but presumably by generation of base pair substitutions or of other minor DNA damages leading to amino acid substitutions. The mechanisms involved are still unknown. There a some hints, however, that these mechanisms might have some step(s) in common with processes leading to malignancy. In fact those viruses proved unequivocally so far to be capable of inducing gene mutations are oncogenic viruses.

Characterization by molecular cloning of insertion mutants in TOL catabolic functions

A physical and genetic map of the Tol catabolic region of pWWO (TOL) was obtained by restriction endonuclease analysis of several DNA insertion mutants (xylA, xylA xylS, xylS, and xylR) of R plasmid--TOL derivatives. In two cases, the inserted DNA was shown from restriction, DNA hybridization, or heteroduplex analysis of cloned Hind III fragments to originate from within pWWO fragment Hind III-E. The effect of these DNA insertions on Tol catabolic activity and on structural alterations to the TOL plasmid is discussed.

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.

Sequence of the site-specific recombinase gene cin and of its substrates serving in the inversion of the C segment of bacteriophage P1

Inversion of the 4.2-kb C segment flanked by 0.6-kb inverted repeats on the bacteriophage P1 genome is mediated by the P1-encoded site-specific cin recombinase. The cin gene lies adjacent to the C segment and the C inversion cross-over sites cixL and cixR are at the external ends of the inverted repeats. We have sequenced the DNA containing the cin gene and these cix sites. The cin structural gene consists of 561 nucleotides and terminates at the inverted repeat end where the cixL site is located. Only two nucleotides in the cixL region differ from those in the cixR and they are within the cin TAA stop codon. The cin promoter was localized by transposon mutagenesis within a 0.1-kb segment, which contains probable promoter sequences overlapping with a 'pseudo-cix' sequence cixPp. In a particular mutant, integration of an IS1-flanked transposon into the cin control region promoted weak expression of the cin gene. The cin and cix sequences show homology with corresponding, functionally related sequences for H inversion in Salmonella and with cross-over sites for G inversion in phage Mu. Based on a comparison of the DNA sequences and of the gene organizations, a possible evolutionary relationship between these three inversion systems and the possible significance of the cixPp sequence in the cin promoter are discussed.

Chloramphenicol acetyltransferase: enzymology and molecular biology

Naturally occurring chloramphenicol resistance in bacteria is normally due to the presence of the antibiotic inactivating enzyme chloramphenicol acetyltransferase (CAT) which catalyzes the acetyl-S-CoA-dependent acetylation of chloramphenicol at the 3-hydroxyl group. The product 3-acetoxy chloramphenicol does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase. The synthesis of CAT is constitutive in E. coli and other Gram-negative bacteria which harbor plasmids bearing the structural gene for the enzyme, whereas Gram-positive bacteria such as staphylococci and streptococci synthesize CAT only in the presence of chloramphenicol and related compounds, especially those with the same stereochemistry of the parent compound and which lack antibiotic activity and a site of acetylation (3-deoxychloramphenicol). Studies of the primary structures of CAT variants suggest a marked degree of heterogeneity but conservation of amino acid sequence at and near the putative active site. All CAT variants are tetramers composed in each case of identical polypeptide subunits consisting of approximately 220 amino acids. The catalytic mechanism does not appear to involve an acyl-enzyme intermediate although one or more cysteine residues are protected from thiol reeagents by substrates. A highly reactive histidine residue has been implicated in the catalytic mechanism.