Electron microscopic heteroduplex studies of sequence relations among plasmids of Escherichia coli: structure of F13 and related F-primes

Everyman's Guide to Bacterial Insertion Sequences

The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.

In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.

Bacterial gene amplification: implications for the evolution of antibiotic resistance

Recent data suggest that, in response to the presence of antibiotics, gene duplication and amplification (GDA) constitutes an important adaptive mechanism in bacteria. For example, resistance to sulphonamide, trimethoprim and beta-lactams can be conferred by increased gene dosage through GDA of antibiotic hydrolytic enzymes, target enzymes or efflux pumps. Furthermore, most types of antibiotic resistance mechanism are deleterious in the absence of antibiotics, and these fitness costs can be ameliorated by increased gene dosage of limiting functions. In this Review, we highlight the dynamic properties of gene amplifications and describe how they can facilitate adaptive evolution in response to toxic drugs.

Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes

Molecular interactions define the functional organization of the cell. Epistatic (genetic, or gene-gene) interactions, one of the most informative and commonly encountered forms of functional relationships, are increasingly being used to map process architecture in model eukaryotic organisms. In particular, 'systems-level' screens in yeast and worm aimed at elucidating genetic interaction networks have led to the generation of models describing the global modular organization of gene products and protein complexes within a cell. However, comparable data for prokaryotic organisms have not been available. Given its ease of growth and genetic manipulation, the Gram-negative bacterium Escherichia coli appears to be an ideal model system for performing comprehensive genome-scale examinations of genetic redundancy in bacteria. In this review, we highlight emerging experimental and computational techniques that have been developed recently to examine functional relationships and redundancy in E. coli at a systems-level, and their potential application to prokaryotes in general. Additionally, we have scanned PubMed abstracts and full-text published articles to manually curate a list of approximately 200 previously reported synthetic sick or lethal genetic interactions in E. coli derived from small-scale experimental studies.

Characterization of the cryptic lambdoid prophage DLP12 of Escherichia coli and overlap of the DLP12 integrase gene with the tRNA gene argU

The argU (dnaY) gene of Escherichia coli is located, in clockwise orientation, at 577.5 kilobases (kb) on the chromosome physical map. There was a cryptic prophage spanning the 2 kb immediately downstream of argU that consisted of sequences similar to the phage P22 int gene, a portion of the P22 xis gene, and portions of the exo, P, and ren genes of bacteriophage lambda. This cryptic prophage was designated DLP12, for defective lambdoid prophage at 12 min. Immediately clockwise of DLP12 was the IS3 alpha 4 beta 4 insertion element. The argU and DLP12 int genes overlapped at their 3' ends, and argU contained sequence homologous to a portion of the phage P22 attP site. Additional homologies to lambdoid phages were found in the 25 kb clockwise of argU. These included the cryptic prophage qsr' (P. J. Highton, Y. Chang, W. R. Marcotte, Jr., and C. A. Schnaitman, J. Bacteriol. 162:256-262, 1985), a sequence homologous to a portion of lambda orf-194, and an attR homolog. Inasmuch as the DLP12 att int xis exo P/ren region, the qsr' region, and homologs of orf-194 and attR were arranged in the same order and orientation as the lambdoid prophage counterparts, we propose that the designation DLP12 be applied to all these sequences. This organization of the DLP12 sequences and the presence of the argU/DLP12 int pair in several E. coli strains and closely related species suggest that DLP12 might be an ancestral lambdoid prophage. Moreover, the presence of similar sequences at the junctions of DLP12 segments and their phage counterparts suggests that a common mechanism could have transferred these DLP12 segments to more recent phages.

Mapping of insertion elements IS1, IS2 and IS3 on the Escherichia coli K-12 chromosome. Role of the insertion elements in formation of Hfrs and F' factors and in rearrangement of bacterial chromosomes

The chromosome of an Escherichia coli K-12 strain W3110 contains seven copies of insertion element IS1, 12 copies of IS2 and six copies of IS3. We determined the approximate locations of six copies of IS1 (named is1A to is1F), ten copies of IS2 (named is2A to is2J), and five copies of IS3 (named is3A to is3E) on the W3110 chromosome by plaque hybridization using the "mini-set" of the lambda phage library that includes 476 clones carrying chromosomal segments that cover the W3110 chromosome almost entirely. Cleavage maps of the W3110 chromosome and cleavage analysis of phage DNAs carrying insertion elements allowed us to assign more precise locations to most of the insertion elements and to determine their orientations. Insertion elements were distributed randomly along the W3110 chromosome in one or other orientation. Several of these were located at the same positions on the chromosome of another E. coli K-12 strain, JE5519, and they were assumed to be the original complement of insertion elements in E. coli K-12 wild-type. Locations and orientations of such insertion elements were correlated well with Hfr points of origin and with crossover points for excision of some F' factors derived from several Hfrs. Insertion elements may be involved also in rearrangement of bacterial chromosomes.

Nucleotide sequence of the hemB gene of Escherichia coli K12

The hemB gene of Escherichia coli K12, coding for porphobilinogen synthase (PBG-S; syn., 5-aminolevulinic acid dehydratase, ALA-D), was cloned following insertion of an EcoRI fragment of plasmid F'13 into the mobilizable vector pCR1. The hybrid plasmid carrying the hemB gene was able to complement a hemB mutant of E. coli K12: not only was the PBG-S activity of the mutant restored after the acquisition of the hemB gene, but it was about ten times higher than that of the wild type. Subcloning of the original EcoRI fragment (14.6 kb) enabled us to locate the hemB gene on an NruI-HpaI fragment of about 1.1 kb. The hemB promoter was located toward the NruI end of the fragment, as shown by the use of the pKO promoter-probe series of vectors. Sequencing of the hemB gene indicated the presence of an open reading frame (ORF) of 1051 nucleotides, which should correspond to the HemB protein. Primer extension experiments enabled us to identify the 5' end of the hemB mRNA, and to deduce the -10 and -35 regions of the hemB promoter. Protein synthesis performed by an in vitro coupled transcription-translation system, showed the presence of a protein of about 35 kDa. This is in agreement with the molecular weight of the HemB protein (35.6 kDa), as deduced from the nucleotide sequence of the gene. Comparison of the amino acid sequences of E. coli and human PBG-S allowed the detection of several regions of strong homology between the two proteins. Two of these regions correspond, as expected, to the putative zinc-binding and catalytic sites of the human PBG-S.

Structure of cryptic lambda prophages

When Escherichia coli cells lysogenic for bacteriophage lambda are induced with ultraviolet light, cells carrying cryptic lambda prophages are occasionally found among the apparently cured survivors. The lambda variant crypticogen (lambda crg) carries an insertion of the transposable element IS2, which increases the frequency of cryptic lysogens to about 50% of cured cells: 43 of these cryptic prophages have been characterized. They all contain substitutions that replace the early segment of the prophage genome (from the IS2 to near the cos site) with a duplicate copy of a large segment of the host chromosome. The right end of the substitution always results from recombination between the nin-QSR-cos region of the prophage and the homologous incomplete lambdoid prophage Qsr' at 12.5 minutes in the E. coli chromosome. The left end of the substitution is usually a crossover that recombines the IS2 element in the prophage with an E. coli IS2 at 8.5 minutes, near the lac gene, or with a second IS2 located counterclockwise from leu at 2 minutes, generating duplications of at least 200,000 bases. Five cryptic lysogens derived from cells lysogenic for a reference strain of lambda (which lacks the IS2 present in lambda crg) have been characterized. They contain substitutions whose right termini are generated by a crossover with the Qsr' prophage. The left termini of these substitutions are formed either by a crossover between the lambda exo gene and a short exo-homologous segment of Qsr' (2/5), or by a crossover between sequences to the left of attL and an unmapped distant region of the host chromosome (3/5). The large duplications carried by these cryptic lysogens are stable, unlike tandem duplications, and so may significantly influence the cell's evolutionary potential.

finO sequences on conjugally repressed and derepressed F-like plasmids

DNA-DNA hybridization studies have demonstrated the physical relatedness of the fertility inhibition gene, finO, among both FinO+ and FinO- F-like conjugative plasmids, viz. ColV2-K94, R100-1,R1drd19,R1,R6-5, UCR123, R386, p307, R453, R773, and pIP162-1. Furthermore, the data indicate that finO sequences on the FinO- plasmid ColV2-K94 map downstream of the transfer region, within 93.6-95.3 ColV2-K94.

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).

Inverted repeat sequences flank a Bacillus thuringiensis crystal protein gene

Two sets of inverted repeat DNA sequences, IR2150 and IR1750, were discovered flanking the crystal protein gene on the 75-kilobase plasmid of Bacillus thuringiensis subsp. kurstaki HD73. A restriction map of ca. 40 kilobases around the crystal protein gene was constructed, and the positions of the copies of IR2150 and IR1750 were determined. Three copies of IR2150 were found flanking the crystal protein gene in an inverted orientation, and one partial and three intact copies of IR1750 were found in both inverted and direct orientations around the gene. Hybridization experiments with fragments from within IR2150 and IR1750 demonstrated the presence of multiple copies of these sequences on the chromosome of B. thuringiensis subsp. kurstaki HD73 and also revealed a strong correlation between the presence of these sequences and the presence of the crystal protein gene on plasmids from 14 strains of B. thuringiensis.

Conduction of nonconjugative plasmids by F' lac is not necessarily associated with transposition of the gamma delta sequence

A nonconjugative kanamycin-resistant (Kmr) recombinant plasmid, pNR5311, transferred at a low frequency from an Hfr or F' lac Escherichia coli donor to an F- lac- recipient. Among the transconjugants, two types of Kmr plasmids were found: one was indistinguishable from pNR5311 (type A), and the other was a recombinant between pNR5311 and the gamma delta sequence (type B). When the F' lac strain was used as a donor, 5% of lactose-fermenting (Lac+) and 75% of lactose-nonfermenting (Lac-) transconjugants had type A plasmids. A kinetic study revealed that type A plasmids were transferred more readily in short mating periods than were type B plasmids. Involvement of Tn903, which is present in pNR5311, in transfer of type A plasmids was unlikely since there was no discernible change in the F' lac molecule coexisting with the type A plasmid in the transconjugant cells. The non-gamma delta-associated conduction of pNR5311 by F' lac did not require the recA+ function of the donor. Conduction of pBR322 by F' lac was also carried out, and two types of plasmids with and without gamma delta were found, as with pNR5311. These findings suggest that the transfer of nonconjugative plasmids is conducted by a novel pathway which is not associated with translocation of transposable elements into either plasmid.

A partial restriction map of the proA-purE region of the Escherichia coli K12 chromosome

EcoRI restriction mapping data for fragments larger than 0.7 kb and contained in a 350-kb region of the Escherichia coli K-12 chromosome are presented. 75% of these fragments have been located relative to proA, B, argF, lac, proC, purE, and various insertion sequence elements normally present in this region. BglII and BamHI maps for the regions near argF and purE are also provided.

Gamma delta-mediated deletions of chromosomal segments on F-prime plasmids

Deleted derivatives of F lac+ proC+ tsx+/- purE+ plasmids ORF203 and F13 were isolated and physically characterized. Among 31 deletions, 24 were adjacent to the gamma delta element on F, four were associated with IS2 or IS3 elements normally present on F, and three displayed additional DNA rearrangements. With the genetic selection employed, the deletion endpoints in the chromosomal segment could fall anywhere within a 210 kb (5 min) region between proC and lac. The distribution of endpoints in this region was not random: the endpoints primarily occurred in an extended region near purE, and a 50 kb segment between tsx and purE was devoid of deletion endpoints. Deletion termini for mutants obtained from F13, which contains an additional 48 kb-segment interposed between gamma delta and the target region on ORF203, displayed a distribution similar to that seen for ORF203. Among simple deletions, there was no marked tendency for the chromosomal deletion endpoints to fall at IS1, IS3, or IS5 elements normally present in this chromosomal region. Point mutations and mutations caused by gamma delta or IS transposition into lac appeared in a small proportion of all plasmids studied.

Mapping of chromosomal IS5 elements that mediate type II F-prime plasmid excision in Escherichia coli K-12

Three IS5 elements were mapped in overlapping chromosomal segments on a series of F-prime plasmids by restriction analysis and hybridization. IS5A was located clockwise of proA near 6 min, IS5B was located clockwise of purE near 12 min, and IS5C was tentatively located near 14 min on the Escherichia coli K-12 map. The physical structures of nine type II F-prime plasmids that contain chromosomal DNA from this region indicated that these plasmids were excised from the chromosome by recombination between pairs of IS5 elements.

Isolation of the kanamycin resistance region (Tn2350) of plasmid R1drd-19 as an autonomous replicon

We have isolated a circular form of Tn2350, an IS1-flanked kanamycin resistance transposon forming part of the plasmid R1drd-19. This circle (pTn2350::9.6 kilobases) contains a single IS1 element and probably arises by recombination between the two directly repeated Is1 sequences of Tn2350. It can be used to transform Escherichia coli to kanamycin resistance. It is capable of autonomous replication but is not maintained stably in dividing cells and segregates under nonselective conditions. Cloning of a segment of pTn2350 on a conditional plasmid vector allowed us to assign the replication functions of this plasmid to a 1.6-kilobase restriction fragment. The plasmid R1drd-19 can thus be considered as a cointegrate between two replicons separated by IS1 sequences.

Recombinational instability of F' plasmids in Escherichia coli K-12: localization of fre-sites

The F' plasmids ORF-1 (purE+ tsxs proC+ lac+) and F'14 (argE+ metB+ ilv+) contain active regions of recombination, fre I and fre II correspondingly. The plasmid ORF-1 is stable in recF- cells (i.e., with the RecBC pathway of recombination) and decays in rec+ cells (RecBCF pathway) giving two types of product: F+ and plasmid pCK-1 (tsxs proC+ lac+) containing part of the initial DNA. They are extremely instable in the presence of the RecF pathway, (recBC- sbcB-), yielding F+ and plasmid pCK-2 (proC+ lac+). The instability of plasmids depends on a region of homology between the chromosome and the episome. The instability of ORF-1 shows the participation of IS3 elements (alpha 1 beta 3 and alpha 3 beta 1) in the recA, recF-dependent recombinational decay and allows localization of two active sites on the chromosome: fre I1 between purE and tsx markers and fre I2 between tsx and proC. The plasmid F'14, in accordance with published data, is able to yield F+ cells by recA-independent recombination. But eventually this plasmid may undergo a recA, recF-dependent decay. Genetic analysis of these events allows localization of an active point of recombination, freII1, between argE and metB. Another active point is localized inside the F factor. The recA-dependent decay of plasmid F-14 is also excluded on the RecBC pathway (recF- strains).

Altered stability and integration frequency of a F' factor in RNA polymerase mutants of Escherichia coli

A number of spontaneous rifampicin-resistant (Rifr) mutants were isolated from a strain of E. coli having a deletion in the lac proA proB region of the chromosome. The stability of a F'lac proA proB episome in these mutants was determined by their sensitivity to acridine orange curing and the frequency of spontaneous loss of episomes. The Rifr mutants can be divided into three classes based on their ability to maintain the F'lac pro episome. Class I mutants (25% of the total Rifr mutants) showed high degree of spontaneous episome loss and high sensitivity to acridine orange curing. Class II mutants (55% of the total Rifr mutants), like the parent strains, showed intermediate sensitivity to acridine orange curing. Class III mutants (21% of the total Rifr mutants) showed high resistance to acridine orange curing and low frequency of spontaneous episome loss. Three-fourths of the Class II mutants were found to be Hfr as shown by their lack of the F'lac pro DNA band on agarose gel together with their ability to mobilize chromosomal markers in mating. Representative Rifr mutants from each class were selected and the Rifr mutants from each class were selected and the Rifr mutations were mapped within the proB gene for the beta beta' operon by P1 transduction. These results indicate that RNA polymerase, or the beta subunit of RNA polymerase, plays an important role in maintaining the F' lac pro episome and in the integration of the F' lac pro episome where no extensive sequence homology is involved.

Mapping of IS1 elements flanking the argF gene region on the Escherichia coli K-12 chromosome

Two directly-repeated IS1 elements have been mapped on the Escherichia coli K-12 chromosome at positions 23.2 kb and 34.5 kb counterclockwise of the IS3 element alpha3beta3 by using F-prime plasmids (including the F lac- proAB+ plasmid F128) that carry different portions of the bacterial chromosome in the purE to proA region. Mapping was accomplished in part by construction of EcoRI, BamHI, and BglII restriction enzyme cleavage maps. Electron microscope heteroduplex and hybridization studies indicate that the chromosomal region flanked by these IS1 elements is completely homologous to the IS1-argF-IS1 region (Tn2901) on the P1argF5 transducing phage (York and Stodolsky, 1981), which suggests that the argF gene region in the usual E. coli K-12 strains has a transposon-like structure.

Site-specific integration of an F' lac pro factor in the region of the replication origin (oriC) of E. coli

An episome, F128, which carries approximately 8 x 10(4) base pairs of chromosomal DNA homologous to the lac pro region of the E. coli chromosome, has been found to integrate into the oriC region of the chromosome in a site specific reaction. While the event appears to be recA-dependent, no homology between the episome and this region of the chromosome was detected. The Hfr strains formed result from the integration of intact F128 molecules. The structure of the Hfr strains generated has been determined and their transfer properties analyzed.

Tn2301, a transposon construct carrying the entire transfer region of the F plasmid

The largest R . BamHI fragment of the plasmid F, which carries the entire F conjugation system, has been cloned into the single R . BamHI site of the ampicillin (Ap) resistance transposon TN1. pDS1106 (ColE1 mob::Tn1) was the vector plasmid, and the resultant conjugative plasmid, pED830, was characterized both genetically and by restriction enzyme analysis. The transposon construct, denoted Tn2301, was transposable at frequencies similar to Tn1 to small nonconjugative plasmids or to the Escherichia coli host chromosome. In the former case, Apr conjugative plasmids were obtained, whereas in the latter case, Hfr strains resulted. Representative Hfr strains were characterized by quantitative and interrupted mating experiments. Extension of this technique for Hfvr formation should aid chromosome mapping both in E. coli and in other bacterial genera.

Specificity in the formation of delta tra F-prime plasmids

Twenty-three independent delta tra F-prime plasmids from three different Escherichia coli K-12 sublines were isolated from Hfr strains whose points of origin coincided with the IS3 element alpha 3 beta 3 or alpha 4 beta 4 in the lac-purE region of the E. coli chromosome. Electrophoretic analysis of plasmid deoxyribonucleic acid digested with EcoRI and hybridization analysis of plasmid deoxyribonucleic acid digested with BglII revealed that at least 14 of these plasmids were formed by processes involving specific bacterial and F loci. Two of the specific bacterial loci involved in delta tra F-prime formation were located at approximately 3.3 and 11.7 min on the E. coli chromosomal map. Two of the delta tra F-prime plasmids contained bacterial deoxyribonucleic acid with circularization endpoints that mapped very near the termini of the IS2 element that is normally located between lac and proC.

Plasmids containing insertion elements are potential transposons

We studied in vivo recombination between the plasmid pHS1, a temperature-sensitive replication mutant carrying tetracycline resistance, and pSM1, a small plasmid carrying one copy of the insertion element IS1. Recombinant plasmids were found by selection for tetracycline resistance at 42 degrees C. Their formation was independent of recA function. Analysis of the physical structures of various recombinant DNA molecules with electron microscopy and restriction endonucleases revealed that pSMI was integrated at its IS1 into numerous sites on pHS1, giving rise to a duplication of IS1 in the same orientation at both junctions. Nucleotide sequence analysis of recombinant plasmids and their parental plasmid DNA revealed that nine nucleotides at a target site were duplicated at the junction of each IS1. This phenomenon implies that plasmids containing a translocatable DNA element can be potential transposons.

Deoxyribonucleic acid sequence homologies among bacterial insertion sequence elements and genomes of various organisms

Plasmid and phage deoxyribonucleic acid (DNA) harboring bacterial insertion sequence (IS) elements IS1, IS2, and IS5 were characterized and used as probes to detect homologous sequences in various procaryotic and eucaryotic genomes. The hybridization method used permits the detection of sequences partially homologous to the elements. Hybridization of the IS-containing probes to each other revealed a region of limited homology between IS1 and IS2. Homologous sequences were then detected by computer analysis of the published IS1 and IS2 nucleotide sequences. The homologous sequence contains a tandemly repeated tetranucleotide sequence which resembles the repeated sequence at the hot spot for spontaneous mutations in the lacI gene (P. J. Farabaugh, U. Schmeissner, M. Hofer, and J. Miller, J. Mol. Biol. 126:847-863, 1978). Homology between the IS elements and various genomes was determined by hybridizing labeled DNA containing IS1, IS2, and IS5 sequences to Southern blots of chromosomal DNA cleaved with restriction endonucleases. IS1 and IS5 appear limited to the enteric bacteria, whereas IS2 sequences can also be detected in Pseudomonas putida, Pseudomonas aeruginosa, and Serratia marcescens. Bacteria which appear not to possess extrachromosomal elements, e.g., Caulobacter crescentus, did not show homology with any insertion sequences tested. In addition, sequences homologous to IS1, IS2, or IS5 were not detected in Saccharomyces cerevisiae, Dictyostelium discoideum, or calf thymus DNA.

Inversion in the lactose region of Escherichia coli K-12

A spontaneous mutant of Escherichia coli K-12, strain SY99, with an inversion in the lactose region was isolated and partially characterized. The inversion was detected due to inverse chromosomal conjugational transfer after introduction of an F42 (F'lac) episome. The termini of the inversion are between proAB and lac on one side and lac and proC on the other. The inverse conjugational transfer in SY99 did not appear to be absolute but was always accompanied by a residual "normal" counterclockwise mobilization. This residual transfer was further shown to be caused by the intrinsic instability of this region (at least in the line W3110). The possible involvement of IS3 elements flanking the lactose operon is discussed.

Specificity in formation of type II F' plasmids

Eight new F' plasmids derived from Hfr strains in which F is integrated at the chromosomal element alpha 3 beta 3 have been isolated and subjected to restriction enzyme, hybridization, and electron microscope heteroduplex analysis. Plasmids carrying extensive amounts of bacterial deoxyribonucleic acid were produced even though they were obtained by selection for transfer of lac, which is closely linked to F in the parental Hfr strains. Seven plasmids were type II Flac+ proC+ purE+ plasmids, and one was a type I Flac+ proC+ plasmid. Five of the Flac+ proC+ purE+ plasmids contain approximately 284 kilobases of bacterial deoxyribonucleic acid, which is identical for all five within the resolution of the restriction enzyme analysis. Theses results indicate that type II F' plasmids are the predominant tra+ F' type from this region of the Escherichia coli K-12 chromosome and that the recombination events leading to formation of these plasmids exhibit site specificity.

Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli

Escherichia coli mutants with temperature-sensitive (ts) mutations in dnaX and dnaY genes have been isolated. Based on transduction by phage P1, dnaX and Y have been mapped at minutes 10.4--10.5 and 12.1, respectively, in the sequence dnaX purE dnaY. Both dna Xts36 and Yts10 are recessive to wild-type alleles present on episomes. F13 carries both dnaX+ and Y+; the shorter F210 carries dnaY+, but not X+. Lambda tranducing phages that carry dnaX+ or Y+ have been isolated, and hybrid plasmids of Col E1 and E. coli DNA from the Clarke and Carbon (1976) collection also carry portions of the dnaX purE dnaY region. Results obtained with the lambda transducing phages and the hybrid plasmids suggest that dnaX is a different gene from the previously characterized dnaZ gene, which is also near minute 10.5--The dnaXts36 mutant, after a shift to 42 degrees, stopped DNA synthesis gradually, and the total amount of DNA increased two-fold. When this mutant was shifted to 44 degrees, the rate of DNA synthesis dropped immediately and the final increment of DNA was only 10% of the initial amount. Replicative DNA synthesis in toluene-treated cells was completely inhibited at 42 degrees and was partially inhibited even at 30 degrees.--When the dnaYts10 mutant was shifted to 42 degrees, DNA synthesis gradually stopped, and the amount of DNA increased 3.6-fold. At 44 degrees, residual DNA synthesis amounted to a two-fold increase. Replicative DNA synthesis in vitro in toluene-treated cells was inactivated after 20 minutes at 42 degrees or by "preincubation" of cells at 42 degrees before toluene treatment.--The dnaX and dnaY products probably function in polymerization of DNA, although participation also in initiation cannot be excluded.

IS2-43 and IS2-44: new alleles of the insertion sequence IS2 which have promoter activity

The sequence of two new IS2 alleles with promoter activity (IS2-43 and IS2-44) is reported. The alleles are identical and are formed by a 17 bp tandem duplication in an AT-rich region of IS2. This created a new RNA polymerase binding site. A mutation was found that increased the frequency of formation of these 17 bp duplications but not of another class of duplications, the "mini-insertions". This suggested that the mechanisms of formation of the two classes of duplications are different.

Aromatic amino acid biosynthesis: regulation of shikimate kinase in Escherichia coli K-12

Starvation of cells of Escherichia coli K-12 for the aromatic amino acids results in an increased rate of synthesis of shikimate kinase activity. The two controlling amino acids are tyrosine and tryptophan, and starvation for both results in derepression. The product of the regulator gene tyrR also participates in this control, and shikimate kinase synthesis was depressed in tyrR mutants. Chromatography of cell extracts on diethylaminoethyl-Sephadex allowed partial separation of two shikimate kinase enzymes and demonstrated that only one of these subject to specific repression control involving tyrR. By contrast, chromatography of cell extracts with G-75 or G-200 columns revealed a singl-molecular-weight species of shikimate kinase activity with an apparent molecular weight of 20,000. The levels of shikimate kinase in a series of partial diploid strains indicated that aroL, the structural gene for the tyrR-controlled shikimate kinase enzyme, is located on the E. coli chromosome between the structural genes proC and purE. By means of localized mutagenesis, an aroL mutant of E. coli was isolated. The mutant was an aromatic prototroph and, by the criterion of column chromatography, appeared to have only a single functional species of shikimate kinase enzyme.

Tn10 mediated integration of the plasmid R100.1 into the bacterial chromosome: inverse transposition

Upon integration into the bacterial chromosome the drug resistance plasmid R100.1 often loses its tetracycline resistance character. We have analyzed an Hfr strain formed by such an integration and an R-prime plasmid derived from it. We find that integration took place within the Tn10 transposon, that the two IS10 sequences were retained, but that at least 80% of the transposon segment located between them, and carrying the tetracycline resistance genes, had been lost. We suggest that integration of R100.1 was mediated by an inverse transposition using the IS10 sequences.

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.

Transposon-facilitated recombination in Vibrio cholerae

Improved Vibrio cholerae donors were constructed by introducing the ampicillin transposon, Tn1, into both the conjugative plasmid, P, and the bacterial chromosome to provide "portable regions of homology." The resulting Tfr (Transposon-facilitated recombination) donors transferred genes at high frequency from origins specified by the chromosomally inserted Tn1 copies. Tn1 was transposed into the chromosome from a deleted P::Tn1 vector, which was eliminated from the cells by superinfection with a thermosensitive P::Tn9 (chloramphenicol) mutant plasmid. After eliminating the thermosensitive plasmid, the chromosomally resistant isolates were converted into donors with a P::Tn1 conjugative plasmid. Tfr donors were also obtained by isolating Tn1 insertion mutations in a gene for thymine biosynthesis. Chromosomal sites of Tn1 relative to bacterial genes were determined by measuring gene transfer frequencies and genetic linkage. In one case, linkage of the amp gene to the chromosomal genes that defined its location was demonstrated. Chromosomal transfer by Tfr donors was reversed by isolating P::Tn1 plasmids that contained Tn1 inserted in the opposite orientation.

Genetic and physiological studies on the relationship between colicin B resistance and ferrienterochelin uptake in Escherichia coli K-12

The Escherichia coli gene for the ferrienterochelin uptake and colicins B and D receptor protein is located at approximately 13 min, adjacent to or among genes for enterochelin biosynthetic enzymes. The two receptor functions (colicin and siderophore) are separable by mutation.

Tryptophan genes in Rhizobium--their organization and their transfer to other bacterial genera

R. leguminosarum trp alleles mapped by R68.45-mediated recombination were located in three distinct chromosomal regions. We isolated three derivatives of R68.45 that carried different trp genes of R. meliloti. Each of the plasmids suppressed all of the R. leguminosarum trp alleles in a particular region. The R-primes were transferred to strains of P. aeruginosa carrying mutations in different trp genes. The plasmid pAJ24JI suppressed trpA, B and F mutants, pAJ73JI suppressed trpC and D and pAJ88JI suppressed a trpE mutant. When the R-primes were transferred to E. coli trp strains they failed to suppress any trp mutants. A derivative of pAJ24JI was isolated which was able to suppress trpA and F mutants of E. coli.

Transposition of plasmid DNA segments specifying hydrocarbon degradation and their expression in various microorganisms

The conjugative TOL plasmid (75 Mdal), specifying biodegradation of xylenes, toluene, and trimethylbenzene derivatives, undergoes dissociation in Pseudomonas aeruginosa PAO to a nonconjugative TOL(*) plasmid (28 Mdal) and a transfer plasmid termed TOLDelta (48 Mdal). The TOL(*) plasmid is rendered transmissible through introduction of a number of conjugative plasmids such as factor K, CAM, and TOLDelta but not by the FP2 derivative pR0271. Transfer of TOL(*) via factor K or TOLDelta is mediated by the formation of plasmid cointegrates; no recombination is observed with CAM. A recombinant RP4-TOL plasmid (76 Mdal), which has lost resistance to tetracycline, has been isolated. The TOL(*) segment can be transposed from this RP4-TOL recombinant plasmid to other antibiotic resistance plasmids such as R702. A segment of DNA, specifying salicylate degradation from SAL plasmid, was transposed onto pAC10, the TOL(*-) derivative of RP4-TOL recombinant plasmid, which has lost resistance to tetracycline but retains the transfer genes of RP4. Transposition of the salicylate degradative genes onto pAC10 results in the loss of kanamycin resistance. It has been possible to isolate SAL(+) segregants from pAC10[unk]SAL transposition derivatives that have lost the pAC10 plasmid. Such segregants harbor the salicylate degradative genes in the form of a nonconjugative plasmid (SAL(*)). Transfer of RP4[unk]TOL(*) or pAC10[unk]SAL(*) transposition derivatives to Escherichia coli, Salmonella typhimurium, Agrobacterium tumefaciens, or Azotobacter vinelandii results in the functional expression of the antibiotic resistance genes but not of the hydrocarbon degradative genes. Such genes, however, are fully expressed on being transferred back to Pseudomonas.

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.

Electron microscope heteroduplex studies of sequence relations among plasmids of Escherichia coli: isolation of a new F-prime factor, F80, and its implication for the mechanism of F integration into the chromosome

A new F-prime factor, F80, was isolated from an Escherichia coli strain harboring the F-prime factor F8 by selecting for transfer of the supE marker to a RecA- recipient. Genetic analysis shows that F80 carries a segment of the chromosomal DNA between lip and suc in addition to the tol-gal region normally in F8. Physical analysis by the electron microscope heteroduplex method suggests that the formation of F80 from F8 involves recombination between the alphabeta segment of F, which is present in F8, and the homologous sequence of F present in the E. coli chromosome at the site where F is supposed to integrate to form HfrP3. The implications of this result for the general mechanisms of F integration to form Hfr's are discussed.

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.

Explanations accounting for transduction by bacteriophage lambda in maltose negative bacteriophage lambda resistant mutants of Escherichia coli K-12

Entry of DNA from lambda phages particles into lambdarMAl- mutants of Escherichia coli K-12 is shown to be due to two distinguishable processes. One, residual transduction, results from a low level expression of lamB. The other one, background transduction, is independent of gene lamB. Interpretations are presented for these results. It is propos that residual transduction is due to a weak promoter pB3 located within or near the distal part of the gene preceeding lamB in the same operon. It is proposed that background transduction is due to a secondary receptor structure for phage lambda. Finally a tentative hypothesis relatin pB3 to insertion sequences is presented.

Genetic mapping of the F plasmid gene that promotes degradation of stable ribonucleic acid in Escherichia coli

F+ Escherichi coli cells that contain an srnA mutant allele degrade their stable ribonucleic acid (RNA) extensively after RNA synthesis is blocked at 42 degrees C. The relevant gene promoting degradation of stable RNA, srnB+, or its promoter was mapped between 1.7 and 2.8 kilobases on the F plasmid by using deleted F' plasmids and chimeric plasmids composed of pSC101 and fragments of F plasmid.