Mutagenesis by insertion of a drug-resistance element carrying an inverted repetition

Osmoregulation of gene expression in Salmonella typhimurium: proU encodes an osmotically induced betaine transport system

Previous evidence has indicated that a gene, proU, is involved in the response of bacterial cells to growth at high osmolarity. Using Mu-mediated lacZ operon fusions we found that transcription of the proU gene of Salmonella typhimurium is stimulated over 100-fold in response to increases in external osmolarity. Our evidence suggests that changes in turgor pressure are responsible for these alterations in gene expression. Expression of proU is independent of the ompR gene, known to be involved in osmoregulation of porin expression. Thus, there must be at least two distinct mechanisms by which external osmolarity can influence gene expression. We show that there are relatively few genes in the cell which are under such osmotic control. The proU gene is shown to encode a high-affinity transport system (Km = 1.3 microM) for the osmoprotectant betaine, which is accumulated to high concentrations in response to osmotic stress. Even when fully induced, this transport system is only able to function in medium of high osmolarity. Thus, betaine transport is regulated by osmotic pressure at two levels: the induction of expression and by modulation of activity of the transport proteins. We have previously shown that the proP gene encodes a lower-affinity betaine transport system (J. Cairney, I. R. Booth, and C. F. Higgins, J. Bacteriol., 164:1218-1223, 1985). In proP proU strains, no saturable betaine uptake could be detected although there was a low-level nonsaturable component at high substrate concentrations. Thus, S. typhimurium has two genetically distinct pathways for betaine uptake, a constitutive low-affinity system (proP) and an osmotically induced high-affinity system (proU).

Characterization of the in vivo RNA product of the pOUT promoter of IS10R

We characterized a single RNA species (RNAout1) which was the major in vivo RNA made from pOUT of IS10R. RNAout1 was 70 nucleotides long; its 5' end corresponded exactly to the in vitro start of pOUT transcription. The concentration of RNAout1 was estimated at 5 to 10 molecules per cell containing the single-copy plasmid NR1. RNA sequences from pOUT of IS10L were detected at a much lower (less than one molecule per cell) steady-state concentration and may be preferentially degraded in vivo. We suggest that the low level of the IS10L transcript led to the inability of IS10L sequences to translationally inhibit Tn10 transposition.

Direct cloning of the trxB gene that encodes thioredoxin reductase

A strain was constructed which contains mutations in the genes encoding thioredoxin (trxA) and thioredoxin reductase (trxB) such that filamentous phage f1 cannot grow. The complementation of either mutation with its wild-type allele permits phage growth. We used this strain to select f1 phage which contain a cloned trxB gene. The location of the gene on the cloned fragment was determined, and its protein product was identified. Plasmid subclones that contain this gene overproduce thioredoxin reductase.

Mutations that improve the ant promoter of Salmonella phage P22

Mutations that increase the activity of the promoter for the antirepressor gene of phage P22 were isolated by pseudoreversion of four severe promoter-down mutations. The sequence changes in these pseudorevertants include single base pair substitutions, single base pair deletions, tandem double base pair deletions and multisite mutations. The single base pair substitutions change nonconsensus base pairs to consensus base pairs at positions -14 and -8. The other mutations provide support for the idea that the length of the spacer region between the conserved -35 and -10 hexamers is an important determinant of promoter strength. Deletions of one or two base pairs in the spacer region apparently activate an alternate -10 hexamer by shifting it from a spacing of 19 base pairs to a spacing of 18 or 17 base pairs, respectively.

New Tn10 derivatives for transposon mutagenesis and for construction of lacZ operon fusions by transposition

We describe below several new variants of the tetracycline-resistance transposon Tn10 which are more useful than the wild-type transposon for many types of genetic and physical analysis of bacteria. These derivatives have one or more of the following new properties: (i) new drug resistance markers; (ii) high transposition frequencies; (iii) removal of the transposase gene to a position outside of the transposing segment; (iv) internal deletions which eliminate the ability of Tn10 to make adjacent deletion/inversions; or (v) addition of a trp-lac operon fusion segment just inside one terminus such that insertion can automatically generate a transcriptional fusion to the interrupted operon. Phage and plasmid vehicles carrying these new elements are described.

Transposon Tn10 contains two structural genes with opposite polarity between tetA and IS10R

The nucleotide sequence of the central part of Tn10 has been determined from the rightmost HindIII site to IS10R. This sequence contains two open reading frames with opposite polarity. The in vivo transcription start points in this sequence have been determined by S1 mapping. These results define one minor and two major promoters. The transcription starts of the two major promoters are only 18 base pairs apart, and the transcripts show different polarity and overlap by 18 base pairs. The nucleotide sequence reveals two regions with palindromic symmetry which may serve as operators. Their possible involvement in the regulation of transcription of both genes is discussed. Taken together these results allow for a maximal coding capacity of 138 amino acids directed toward IS10R and 197 amino acids directed toward tetA. The possible function of these gene products is discussed. The accompanying article (Braus et al., J. Bacteriol. 160:504-509, 1984) presents evidence that these genes are expressed.

Mapping of markers in the gyrA-his region of Escherichia coli

Discrepancies between our mapping data concerning the cdd and gat marker of Escherichia coli and data obtained by Josephsen et al. (1983) as well as with the current linkage map of Escherichia coli (Bachmann 1983) led us to reinvestigate the mapping of markers in the gyrA-his region by P1 transduction. In addition, we isolated Hfr strains by integrating the temperature-sensitive F'ts114lac+ episome via lac homology of cir'lacZ and mgl'lacZ fusions into the chromosome. From the results of the P1 transductions and using these Hfr strains as donors in crosses it became clear that the transcription of cir and mgl is the same and counterclockwise on the chromosome, with cdd and gat as the counterclockwise markers to mgl and cir. We conclude that our previously published sequence of markers was incorrect and is in fact inverted. The present data indicate the following sequence of markers in clockwise order: his gat cdd mgl cir fpk gyrA.

Genetic characterization and molecular cloning of the tripeptide permease (tpp) genes of Salmonella typhimurium

Of the three bacterial peptide transport systems only one, the oligopeptide permease, has been characterized in any detail. We have now isolated Salmonella typhimurium mutants deficient in a second transport system, the tripeptide permease (Tpp), using the toxic peptide alafosfalin. Alafosfalin resistance mutations map at three loci, the gene encoding peptidase A (pepA) and two transport-defective loci, tppA and tppB. Locus tppA has been mapped to 74 min on the S. typhimurium chromosome, cotransducible with aroB, and is a positive regulator of tppB. Locus tppB maps at 27 min in the cotransduction gap between purB and pyrF. We cloned tppB, the structural locus for the tripeptide permease. Two simple methods are described for mapping the location of cloned DNA fragments on the chromosome of S. typhimurium.

Nucleotide sequence of the repressor gene of the TN10 tetracycline resistance determinant

The Tn10 tetR gene encodes the repressor that regulates transcription of the Tn10 tetracycline resistance determinant. We have determined the DNA sequence of the tetR gene and a 905 base pair region immediately 3' to tetR. The tetR gene is located on a 701 base pair HincII restriction fragment. Deletions at either end of this region eliminate synthesis of the wild-type TetR protein in E. coli minicells, and eliminate TetR activity as measured by repression of beta-galactosidase synthesis in tetA-lacZ operon fusion strains. Taken together, the DNA sequence and the genetic data indicate that tetR encodes a 207 amino acid protein with a calculated molecular weight of 23,328. This value is in good agreement with estimates of 23,000-25,000 based on electrophoretic mobility in SDS-polyacrylamide gels. There is 47% amino acid sequence homology between the deduced sequences of the Tn10 and RP1/Tn1721 TetR proteins. There is, in addition, significant amino acid sequence homology between an NH2-terminal region of the Tn10 TetR repressor and the DNA recognition regions of other DNA-binding proteins.

Genetic analysis of the erf region of the bacteriophage P22 chromosome

Derivatives of P22 with deletions of DNA sequences around and including the erf gene were obtained by crossing phages with plasmids containing fragments of the P22 chromosome. In some cases, the parent phages carried a large insertion in sequences not borne by the plasmids. In these cases, deletion of DNA from the phage chromosome to restore terminal repetition (a selectable trait) could be accomplished by recombination between phage and plasmid DNA in chosen sequences flanking the insertion on both sides and borne by the plasmid. In other cases, the parent phages had deletions of a selectable gene, which could be acquired from the plasmid parents only by acquisition of an overlapping deletion. Deletion-bearing P22 strains were tested for growth and homologous genetic recombination in wild-type, recA-, and rec(B or C)- hosts. This analysis indicated the existence of a gene, mapping to the left of erf, that is helpful (but not completely essential) for growth of P22 in a wild-type host. Because P22 lacking this gene grows as well as wild-type P22 on a recBC- host, it has been designated abc (anti-recBC). The abc gene does not appear to be essential for homologous genetic recombination in any host. A plasmid bearing a 1900 base pair fragment of P22 DNA, that expresses erf and abc under the control of the E. coli lac promoter, was constructed. It supports growth and recombination in a recA- host by a phage that lacks all of the genes known to lie between 24 and 9.

Isolation of F' plasmids carrying a portion of the Salmonella typhimurium histidine transport operon

The transposable drug resistance element Tn10 was employed as a region of homology to direct the insertion of Tn10-containing derivatives of F'ts114 lac into the chromosome of a Salmonella typhimurium strain that carries a Tn10 insertion in the histidine transport operon. Based on the direction of transfer of the resulting Hfr strains, the chromosomal Tn10 insertion was determined to be in orientation "A." New F' plasmids were selectively generated from one of the Hfr strains. The F' factors carry an intact dhuA hisJ portion of the histidine transport operon. A Southern hybridization revealed that one of the F' plasmids was formed by a type II excision event.

Bacteriophage chi sensitivity and motility of Escherichia coli K-12 and Salmonella typhimurium Fla- mutants possessing the hook structure

The production of hook protein and flagellin in 29 Fla- mutants of Escherichia coli K-12 was determined by the complement fixation assay. Six mutants produced hook protein, and four of them also produced flagellin. A flaE mutation was introduced into these fla mutants carrying the hook structure. All of these mutants made polyhooks and were used as hosts for a newly isolated host-range mutant of chi phage that has a high affinity for the hook structure. All except one mutant produced significant amounts of progeny phages. A flaD flaE double mutant was that exception which did not yield significant amounts of progeny by the phage propagation method. All of the flaE double mutants produced comparable amounts of polyhooks, and no qualitative difference was detected between chi-sensitive and chi-insensitive mutants by the complement fixation assay. Accordingly, it was thought that the polyhook of the flaD flaE mutant had a mechanical defect for chi phage infection. This assumption was confirmed by tethered-cell experiments; the flaD flaE mutant did not rotate. These results are well explained by a proposed regulation pathway of flagellar genes. flaE mutants can express other genes which govern the final step of the flagellar morphogenesis, whereas flaD mutants cannot rotate, possibly because the mocha operon is not expressed. The results obtained in E. coli were also found to be applicable to Salmonella typhimurium.

The use of transposon Tn5 mutagenesis in the rapid generation of correlated physical and genetic maps of DNA segments cloned into multicopy plasmids--a review

The properties of transposon Tn5 that render it useful for in vivo mutagenesis of cloned DNA sequences are reviewed. Transposition frequency, insertional specificity, polarity and stability of Tn5 insertion mutations are among the topics discussed. Examples are cited from the published literature which illustrate the applications of Tn5 mutagenesis to the analysis of cloned prokaryotic and eukaryotic genes. A methods section is included which outlines precisely how to carry out transposon Tn5 mutagenesis analysis of cloned DNA segments.

Generation of a Tn5 promoter probe and its use in the study of gene expression in Caulobacter crescentus

A promoter probe, Tn5-VB32, was constructed and placed in a P group R plasmid containing bacteriophage Mu sequences, allowing transfer of the transposon to bacteria such as Caulobacter, Rhizobium, and Agrobacterium without retention of the plasmid. The probe carries an altered Tn5 transposon that allows detection of chromosomal promoter regions by virtue of acquired kanamycin resistance. A fragment of DNA containing the neomycin phosphotransferase II (NPT II) gene from Tn5, lacking its promoter region but retaining its translation initiation signal, was inserted into a Tn5 derivative that lacked the entire NPT II gene and a large portion of the IS50L sequence while retaining its ability to transpose. This Tn5 derivative also contained the intact tetracycline resistance-encoding region of the transposon Tn10. Transposition of the Tn5-VB32 promoter probe into the Caulobacter crescentus chromosome generated auxotrophic and motility mutants and Southern blot analysis of DNA from these mutants showed Tn5-VB32 sequences in random-sized chromosomal restriction fragments. Transcriptional regulation by exogenous cysteine of NPT II gene expression was demonstrated in a cysteine auxotroph generated by Tn5-VB32 insertional inactivation. NPT II synthesis, measured by agar plate assays of kanamycin resistance and by immunoprecipitation of the NPT II protein, was repressed in the presence of cysteine and derepressed in its absence. Several fla- mutants were also isolated by Tn5-VB32 mutagenesis and shown to confer kanamycin resistance. Insertions within temporally regulated genes, such as those involved in flagellar biosynthesis and chemotaxis functions, can now be used directly to monitor transcriptional regulation from Caulobacter promoter sequences.

Characterization of the cloned fip gene and its product

A DNA fragment encoding the fip (filamentous phage production) gene from Escherichia coli, when cloned in a filamentous phage vector, restored to the phage ability to assemble progeny in fip mutant hosts. The fip gene was located just upstream of and transcribed in the same direction as the rho gene. Minicells containing fip+ phage or plasmids synthesized a 12,500-dalton protein that was missing or truncated when the Fip+ phenotype was inactivated by insertion of Tn5. The fip protein was cytoplasmic and was partially purified.

Control of expression of the Tn10-encoded tetracycline resistance operon. II. Interaction of RNA polymerase and TET repressor with the tet operon regulatory region

The promoter and operator sequences of the Tn10-encoded tetracycline resistance operon are determined in vitro by transcription studies of purified DNA restriction fragments, protection of guanosine from methylation by dimethylsulphate, and DNase I footprinting employing the purified TET repressor protein. In vitro transcription reveals three promoters with overlapping consensus sequences. Two of them, designated PR1 and PR2, are directed towards the tet repressor gene and the third, called PA, initiates transcription of the tet resistance gene. All three promoters are regulated simultaneously by the TET repressor protein, as demonstrated by in vitro transcription. Tetracycline functions as an inducer in these experiments. Two palindromic operator sequences in the tet operon control region, called O1 and O2, are occupied simultaneously by the TET repressor. Four guanosine residues in symmetric positions close to the centre of the palindromic operator sequences are protected from methylation in the repressor-operator complex. However, only one guanosine residue exhibits an enhanced reaction with dimethylsulphate under these conditions. Footprinting experiments reveal protection of phosphodiester bonds against DNase I slightly further than the palindromic sequence arrangement. Several phosphodiester bonds between the two operators are accessible for cleavage by DNase I in the repressor-operator complex. Two phosphodiester bonds within each operator sequence are cleaved by DNase I. This feature shows a clear assymmetry with the two inside cleavage positions of O1 and O2 being much less accessible for DNase I as compared to the two outside positions. A molecular mechanism of regulation of the Tn10-encoded tetracycline resistance operon is presented based on these and previous results.

The identification and cloning of genes encoding haloaromatic catabolic enzymes and the construction of hybrid pathways for substrate mineralization

This paper reviews the genetic basis of haloaromatic biodegradation by bacteria, with a focus on the genetic analysis of Alcaligenes eutrophus JMP134, an organism which can utilize 3-chlorobenzoate, 2,4-dichlorophenoxyacetate (2,4-D) and related compounds as sole carbon and energy sources, and Pseudomonas sp. B13, a chlorobenzoate degrader. The involvement of transmissible plasmids pJP4 and pWR1, isolated from strains JMP134 and B13, respectively, in chloroaromatic mineralization has been examined, and restriction fragments of both plasmids have been cloned on the broad host range plasmid vector pKT231. Transposon Tn5 mutagenesis of these and other soil isolates enriched in and purified from mixed cultures utilizing 2,4,5-trichlorophenoxyacetate (2,4,5-T) as sole carbon and energy source, has been carried out using a "suicide" transposon donor, pLG221 (Co1Ibdrd-1::Tn5). Mapping of Tn5 insertions in mutants which accumulate pathway intermediates has facilitated the identification and cloning of genes encoding chlorocatechol 1,2-dioxygenase, and other key enzymes in haloaromatic catabolism. There are good prospects for the genetic construction of hybrid haloaromatic catabolic pathways by combining genes encoding broad specificity enzymes, capable of transforming halogenated analogues of their natural substrates, with genes for halocatechol degradation.

Identification of repressor binding sites controlling expression of tetracycline resistance encoded by Tn10

The regulatory region controlling the expression of tetracycline resistance and repressor genes contains two nearly identical regions of dyad symmetry. Deletions of this control region were isolated by digestion with S1 nuclease. The ability of these deletions to bind the tet repressor was determined by an in vivo repressor titration assay. The results indicate that repressor specifically binds both regions of dyad symmetry.

Sequence homology between the tetracycline-resistance determinants of Tn10 and pBR322

The Tn10 tetracycline resistance gene, tetA, encodes a tetracycline-inducible protein with an apparent Mr of 36 X 10(3). We have determined the nucleotide sequence of the Tn10 tetA gene. The extent of the tetA gene was determined by analysis of amino-terminal and carboxy-terminal deletion mutants. We conclude that a single Tn10 gene, the tetA gene, is sufficient to confer tetracycline resistance. The predicted Mr of the tetA protein is 43.2 X 10(3). The sequence homology between the Tn10 tetA gene and the pBR322 tetracycline resistance determinant (49% nucleotide homology, 44% amino acid homology) indicates that these phenotypically distinct tetracycline-resistance determinants must have evolved from a common ancestral sequence. The markedly hydrophobic character of the predicted amino acid sequences of the Tn10 tetA and pBR322 tet-coded proteins suggests that a substantial portion of these proteins may be embedded within the cytoplasmic membrane.

Mapping of the pin locus coding for a site-specific recombinase that causes flagellar-phase variation in Escherichia coli K-12

Although the vh2 mutation almost entirely prevents phase variation in Salmonella spp., an Escherichia coli strain that carried the Salmonella H1 and H2 region, including the vh2 mutation, showed phase variation. From this strain, EJ1076, a number of mutants defective in phase variation were isolated, and the symbol pin was assigned to their mutant gene. The pin locus was mapped between purB and trp near purB by interrupted matings using Tn10 sites inserted near pin. The locus was cotransduced with purB by P1 vir at a frequency of around 0.33. All the mutations tested were clustered at this locus. Three E. coli K-12 strains probably derived via different lines from the wild type have been tested for the presence of pin+ by introducing the two Salmonella H regions; two were pin+, and one was a pin mutant.

Control of expression of the Tn10-encoded tetracycline resistance genes. Equilibrium and kinetic investigation of the regulatory reactions

The transposon Tn10-encoded TET repressor controls the expression of tetracycline resistance as well as its own synthesis. The antibiotic tetracycline functions as an inducer for both genes, which are transcribed in divergent directions from a common start area. The interaction of the TET repressor with the regulatory sequence of the tetracycline resistance operon is investigated by equilibrium and kinetic methods. The wild-type control sequence contains two nearly identical operators separated by only ten base-pairs. A deletion mutant lacking one of the operators is constructed by controlled digestion with exonuclease Bal31. It serves to prove that the two TET operators are each occupied by a TET repressor dimer in the wild-type tet operon regulatory sequence. The association constants are approximately identical for both operators between 10(12) and 10(13) M-1 as derived from kinetic data. The half-life of the TET repressor--tet operator complex is 12 minutes when competed with tet operator DNA and two minutes when competed with the inducer tetracycline. The dissociation of the repressor--operator complex has no apparent activation enthalpy but has an activation entropy of -320 J/mol K, indicating the involvement of solvent or counterion condensation. The dissociation rate constant of the tetracycline--TET repressor complex depends strongly on temperature. The activation enthalpy is 160 kJ/mol, indicating extremely strong binding of the drug. This result is discussed with respect to the necessary sensitivity of a regulated resistance gene. The native structure of the TET repressor is a dimer, as demonstrated by molecular exclusion chromatography. The elution behavior of the TET repressor--tetracycline complex indicates clearly that the repressor--inducer complex remains a dimer. The results are discussed with respect to the regulatory functions of the components.

Translational control of IS10 transposition

We present genetic evidence that insertion sequence IS10, the active element in transposon Tn10, can negatively control expression of its own transposase protein at the translational level. This control process is manifested in trans in a phenomenon called "multicopy inhibition": the presence of a multicopy plasmid containing IS10 inhibits transposition of a single copy chromosomal Tn10 element by reducing its ability to express transposition functions. Fusion analysis suggests that expression is reduced at the translational and not the transcriptional level. Only the outer 180 bp of IS10-Right are required on the plasmid for full inhibition. Plasmid-encoded transposase protein is not involved. The genetic structure of the essential plasmid region and the effects of point and deletion mutations on multicopy inhibition lead us to propose that inhibition of transposase translation occurs by direct pairing between the transposase messenger RNA and a small, complementary, regulatory RNA specified by the IS10-encoded pOUT promoter.

Overlapping divergent promoters control expression of Tn10 tetracycline resistance

We have previously examined the genetic organization and regulation of the Tn10 tetracycline-resistance determinant in Escherichia coli K-12. The structural genes for tetA, the Tn10 tetracycline-resistance function, and for tetR, the Tn10 tet repressor, are transcribed in opposite directions from promoters in a regulatory region located between the two structural genes. Expression of both tetA and tetR is induced by tetracycline. Here we report the DNA sequence of the Tn10 tet regulatory region. The locations of the tetA and tetR promoters within this region were defined by S1 nuclease mapping of the 5' ends of in vivo tet RNA. The tetA and tetR promoters overlap; the transcription start points are separated by 36 bp. We propose that two similar regions of dyad symmetry within the Tn10 tet regulatory region are operator sites at which tet repressor binds to tet DNA, thereby inhibiting transcription initiation at the tetA and tetR promoters. The Tn10 tet regulatory region and the pBR322 tet regulatory region show significant DNA sequence homology (53%).

Motility development of Salmonella typhimurium cells with flaV mutations after addition of exogenous flagellin

Cells of Salmonella typhimurium with flaV mutations developed motility after exogenous addition of flagellin, similar to what is observed with flbC mutants of Escherichia coli K-12.

A bacterial gene, fip, required for filamentous bacteriophage fl assembly

An Escherichia coli mutant which does not support the growth of filamentous bacteriophage fl allows phage fl DNA synthesis and gene expression in mutant cells, but progeny particles are not assembled. The mutant cells have no other obvious phenotype. On the basis of experiments with phage containing nonlethal gene I mutations and with mutant fl selected for the ability to grow on mutant bacteria, we propose an interaction between the morphogenetic function encoded by gene I of the phage and the bacterial function altered in this mutant. The bacterial mutation defines a new gene, fip (for filamentous phage production), located near 84.2 min on the E coli chromosome.

Genetic transposition and insertional mutagenesis in Bacillus subtilis with Streptococcus faecalis transposon Tn917

The Streptococcus faecalis transposon Tn917 was introduced into Bacillus subtilis by transformation of competent cells with the plasmid pAM alpha 1::Tn917 and was tested for transposition activity by selection for insertions into the temperate phage SP beta. Insertions were obtained at a frequency indicating relatively efficient movement of the element, and Southern hybridization analysis of a particular insertion confirmed it to be the result of a genuine transposition event. A restriction fragment from pAM alpha 1::Tn917 containing the transposon sequences was ligated into a temperature-sensitive plasmid (pBD95), and transpositions into the B. subtilis chromosome were selected by requiring the transposon drug resistance to be maintained at temperatures nonpermissive for plasmid replication. Insertions have been recovered at many chromosomal sites, including ones that produced auxotrophy of different kinds and ones that produced various different sporulation-defective phenotypes, indicating good prospects for the use of Tn917 as a tool for insertional mutagenesis in B. subtilis.

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

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

Physical analysis of the genomes of hybrid phages between phage P1 and plasmid p15B

The genomes of three plaque-forming recombinant phages between phage P1 and plasmid p15B were characterized by restriction cleavage analysis and electron microscopic heteroduplex studies. The structure of all three P1-15 hybrid genomes differs from that of P1 DNA in the res mod region coding for restriction and modification systems EcoP15 and EcoP1, respectively. P1-15 hybrid 2 shows an additional major difference to P1 around the site of the residential IS1 element of P1 and it does not carry an IS1 in its genome.

DNA restriction--modification genes of phage P1 and plasmid p15B. Structure and in vitro transcription

The EcoP1 and EcoP15 DNA restriction-modification systems are coded by the related P1 prophage and p15B plasmid. We have examined the organization of the genes for these systems using P1 itself, "P1-P15" hybrid phages expressing the EcoP15 restriction specificity of p15B and cloned restriction fragments derived from these phage DNAs. The results of transposon mutagenesis, restriction cleavage analysis. DNA heteroduplex analysis and in vitro transcription mapping allow the following conclusions to be drawn concerning the structural genes. (1) All of the genetic information necessary to specify either system is contained within a contiguous DNA segment of 5 x 10(3) bases which encodes two genes. One of them, necessary for both restriction and modification, we call mod and the other, required only for restriction (together with mod), we call res. (2) The res gene is about 2.8 x 10(3) bases long and at the heteroduplex level is largely identical for P1 and P15: it shows a small region of partial nonhomology and some restriction cleavage site differences. The mod gene is about 2.2 x 10(3) bases long and contains a 1.2 x 10(3) base long region of non-homology between P1 and P15 toward the N-terminus of the gene. The rest of the gene at this level of analysis is identical for the two systems. (3) Each of the genes is transcribed in vitro from its own promoter. It is possible that the res gene is also transcribed by readthrough from the mod promoter.

Control of arg gene expression in Salmonella typhimurium by the arginine repressor from Escherichia coli K-12

The regulation of synthesis of arg enzymes in Salmonella typhimurium by the arginine repressor of Escherichia coli K-12 has been reevaluated using a strain of S. typhimurium in which the argR gene was rendered nonfunctional by inserting the translocatable tetracycline-resistance element Tn10 into the argR gene. In contrast to previous studies, the introduction of the argR+ allelle of E. coli on an F-prime factor to the argR::Tn10 S. typhimurium strain reduced the synthesis of arg enzymes to essentially wild-type levels. The elevated levels of arg enzymes observed in other hybrid merodiploids may have been the consequence of the formation of hybrid repressor molecules. The readily scoreable phenotype of tetracycline resistance facilitated establishing linkage of cod and argR (0.6% cotransduction) by P22 phage-mediated transduction.

Construction and use of pyr::lac fusion strains to study regulation of pyrimidine biosynthesis in Salmonella typhimurium

The technique developed by Rosenfeld and Brenchley [J Bacteriol 144, 848-851 (1980)] has been used to introduce Mu d1 (Apr lac) into Salmonella typhimurium for purposes of constructing pyr::lac fusion strains. A stable pyrB::lac fusion mutant was subsequently derived and used for the genetic characterization of the pyrB gene. The direction of transcription of pyrB was determined to be counterclockwise on the S. typhimurium linkage map and argI was shown to be located clockwise of pyrB. Mutants altered in the regulation of expression of pyrB were isolated and two of the isolates chosen for further study were tentatively categorized as promoter or operator mutants.

Tn10 transposase acts preferentially on nearby transposon ends in vivo

Transposition of Tn10 requires sites at the termini of the element and one essential transposon-encoded function, "transposase", which acts at those termini. Genetic complementation experiments reveal that this "transposase" function works much more efficiently on transposon ends located near the gene from which they are expressed than on transposon ends located at a distance. This property accounts for the failure of mutant Tn10 elements to be efficiently complemented in trans. The failure of transposase protein to move freely in three dimensions could be explained by one-dimensional diffusion, energy-dependent translocation and/or extreme protein lability. Additional genetic analyses demonstrate that the rate of Tn10 transposition in vivo depends upon the length of the transposon and the amount of transposase protein. Function dependence and length dependence are independent aspects of the transposition process that could correspond to the break/join and replication aspects into which transposition has been separated conceptually.

Internal promoters of the his operon in Salmonella typhimurium

Two internal promoters in the his operon of Salmonella typhimurium have been precisely mapped genetically. The internal promoters are found in, or very close to, gene border regions in the his operon. The his operon was examined for the presence of additional internal promoters whose transcripts were sensitive to rho-mediated transcription termination and therefore had escaped detection. No new internal promoters were found. It is argued that the internal promoters described here are not likely to be fortuitous message start sites, but may play a physiologically important role in operon expression.

Genetic map of the opp (Oligopeptide permease) locus of Salmonella typhimurium

The uptake of peptides by Salmonella typhimurium is mediated by three apparently independent transport systems. One of these systems, the oligopeptide permease, is encoded by a genetic locus (opp) which has been mapped at 34 min on the S. typhimurium chromosomal map. We accurately mapped the location of opp by cotransduction frequencies and by deletion analysis and show that the gene order for this region of the chromosome is cysB-trp-tonB-opp-galU-tdk. All opp mutants, independently isolated by a variety of means, mapped at this one locus, between tonB and galU. Spontaneous and transposon Tn10-generated deletions were used to construct a fine-structure genetic map of opp. Evidence is presented which indicates that opp covers a 5- to 6-kb segment of DNA and is therefore likely to consist of more than one gene.

Efficient read-through of Tn9 and IS1 by RNA polymerase molecules that initiate at rRNA promoters

Transcription and translation are coupled in most Escherichia coli operons. As a consequence, ribosomes must be present on an mRNA molecule while transcription of the mRNA is in progress or else premature termination of transcription may result. This requirement is most clearly manifested when premature nonsense codons result in polarity in multicistronic operons. Polarity can also result from insertions of transposons and insertion sequences. However, since rRNA operons are not translated, some property of these operons must allow transcription to be uncoupled from translation. In this paper we demonstrate that transposon Tn9 and insertion sequence IS1 are nonpolar or incompletely polar in rRNA operons during normal growth. We also show that essentially all expression of rrn sequences distal to IS1 and Tn9 results from transcripts that originate at rRNA promoters. These results suggest either that rRNA operons possess some mechanism which reduces or prevents termination within rRNA operons or that Tn9 and IS1 can be very inefficient at blocking normal transcription. Insertions of Tn10 in rRNA operons are substantially but incompletely polar. We could not determine whether the residual downstream transcription observed results from promoters within Tn10 or from read-through of Tn10. We discuss the meaning of read-through of Tn9 and IS1 and the residual expression of genes downstream from Tn10 with regard to rRNA operon structure and previous experiments in which polarity of transposons or insertion sequences was observed in protein-encoding operons.

Location on the Salmonella typhimurium chromosome of the gene encoding nucleoside diphosphokinase (ndk)

The gene encoding nucleosidediphosphate kinase (ndk) was located at 55 units on the Salmonella typhimurium chromosome. The ndk locus was 83% cotransducible with hisS and 2% cotransducible with glyA in phage P22-mediated crosses. A nucleosidediphosphate kinase mutant that produced only 10% of the wild-type enzyme activity (ndk-1) grew normally and produced a heat-labile enzyme.

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

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

New class of mutations in Escherichia coli (uup) that affect precise excision of insertion elements and bacteriophage Mu growth

We have used a papillation screening technique to isolate mutations that increase the precise excision of insertion elements. The three mutations isolated stimulated precise excision of Tn5, Tn10, and the IS elements. They had a large, 20- to 600-fold, effect on excision of Tn5 at various chromosomal sites. The varied stimulation for different Tn5 insertions showed that the mutations altered the relationship between a precise excision activity and the chromosomal sequence flanking an inserted Tn5. A much smaller stimulation was observed for insertions on the plasmid F'128. The stimulation was recA independent. The mutations also reduced the rate of production of bacteriophage Mu progeny. The mutations were mapped by two- and three-factor crosses with closely linked Tn10 insertions. They defined the uup locus, located at 21.3 min on the Escherichia coli map, next to pyrD.

Transposon Tn10 provides a promoter for transcription of adjacent sequences

Promoters located within the Tn10 insertion element cause transcription of "host" sequences adjacent to both ends of the inserted Tn10 element. These promoters are usually not observed in genetic experiments because their transcripts are efficiently terminated at nearby rho-dependent termination sites. The observations presented here provide an explanation for several confusing aspects of transposon behavior and suggest the possibility that many transposons possess promoters that have escaped detection for similar reasons.

Transcriptional activity of the transposable element Tn10 in the Salmonella typhimurium ilvGEDA operon

Polarity of Tn10 insertion mutations in the Salmonella typhimurium ilvGEDA operon depends on both the location and the orientation of the Tn10 element. One orientation of Tn10 insertions in ilvG and ilvE permits low-level expression of the downstream ilvEDA and ilvDA genes, respectively. Our analysis of Salmonella ilv recombinant plasmids shows that this residual ilv expression must result from Tn10-directed transcription and does not reflect the presence of internal promoters in the ilvGEDA operon, as was previously suggested. The opposite orientation of Tn10 insertion in ilvE prevents ilvDA expression, indicating that only one end of Tn10 is normally active in transcribing adjacent genes. Both orientations of Tn10 insertion in ilvD exert absolute polarity on ilvA expression. Expression of ilvA is known to be dependent on effective translation of ilvD, perhaps reflecting the lack of a ribosome binding site proximal to the ilvA sequence. Therefore, recognition of the ability of Tn10 to promote transcription of contiguous genes in the ilvGEDA operon apparently requires the presence of associated ribosome binding sites.

DNA sequence organization of IS10-right of Tn10 and comparison with IS10-left

Tn10 is 9,300 base pairs long and has inverted repeats of an insertion sequence (IS)-like sequence (IS10) at its ends. IS10-right provides all of the Tn10-encoded functions used for normal Tn10 transposition. IS10-left can also provide these functions but at a much reduced level. We report here the complete nucleotide sequence of IS10-right and a partial sequence of IS10-left. From our analysis of this information, we draw the following conclusions. (i) IS10-right is 1,329 base pairs long. Like most IS elements, it has short (23-base pair) nearly perfect inverted repeats at its termini. We can divide these 23-base pair segments into at least two functionally distinct parts. IS10-right also shares with other elements the presence of a single long coding region that extends the entire length of the element. Genetic evidence suggests that this coding region specifies an essential IS10 transposition function. A second, overlapping, coding region may or may not be important. (ii) The "outside" end of IS10-right contains three suggestively positioned internal symmetries. Two of these (A1 and A2) are nearly identical in sequence. Symmetry A1 overlaps the terminal inverted repeat; symmetry A2 overlaps the promoter shown elsewhere to be responsible for expression of IS10 functions and lies very near a second characterized promoter that directs transcription outward across the end of IS10. Symmetries A1 and A2 may play a role in modulation of Tn10 activity and are likely to function at least in part as protein recognition sites. We propose that the third symmetry (B) acts to prevent fortuitous expression of IS10 functions from external promoters. The transcripts from such promoters can assume a stable secondary structure in which the AUG start codon of the long coding region is sequestered in a region of double-stranded mRNA formed by pairing between the two halves of symmetry B. (iii) IS10-left differs from IS10-right at many nucleotide positions in both the presumptive regulatory region and the long coding region. The available evidence suggests that Tn10 may be older than other analyzed drug-resistance transposons and thus have had more time to accumulate mutational changes.

A symmetrical six-base-pair target site sequence determines Tn10 insertion specificity

Transposon Tn10 inserts at many sites in the bacterial chromosome, but preferentially inserts at particular hotspots. We believe we have identified the target DNA signal responsible for this specificity. We have determined the DNA sequences of 11 Tn10 insertion sites and identified a particular 6 base pair (bp) symmetrical consensus sequence (GCTNAGC) common to those sites. The sequences at some sites differ from the consensus sequence but only in limited and well defined ways. The sequences at some sites differ from the consensus sequence than do sequences at other sites, and the consensus sequence and closely related sequences are generally absent from potential target regions where Tn10 is known not to insert. Other aspects of the target DNA can significantly influence the efficiency with which a particular target site sequence is used. The 6 bp consensus sequence is symmetrically located within the 9 bp target DNA sequence that is cleaved and duplicated during Tn10 insertion. This juxtaposition of recognition and cleavage sites plus the symmetry of the perfect consensus sequence suggest that the target DNA may be both recognized and cleaved by the symmetrically disposed subunits of a single protein, as suggested for type II restriction endonucleases. There is plausible homology between the consensus sequence and the very ends of Tn10, compatible with recognition of transposon ends and target DNA by the same protein. The sequences of actual insertion sites deviate from the perfect consensus sequence in a way which suggests that the 6 bp specificity determinant may be recognized through protein-DNA contacts along the major groove of the DNA double helix.