On the nature of sbcA mutations in E. coli K 12

The plasmid vectors, pBS2ndd and pBS3ndd, for versatile cloning with low background in Escherichia coli

For decades, diverse plasmid vectors have been continuously developed for molecular cloning of DNA fragment in the bacterial host cell Escherichia coli. Even with deliberate performances in vector preparation, the cloning approaches still face inevitable background colonies, or false positive clones, that may be arisen from intact or self-ligated plasmid molecules. To assist in such problem, two plasmids, pBS2ndd and pBS3ndd, which resistant to ampicillin and kanamycin respectively, were developed in this study as more advantageous cloning vector. The plasmids carry ndd, a lethal gene from bacteriophage T4 coding for nucleoid disruption protein that binds to the host chromosome and progressively kill the cell. The deadly toxicity of Ndd inhibits host cells that obtain intact or ndd-religated vector from growing, which results in low background and dramatically reduces the effort for selection of recombinants. Moreover, their identical multiple cloning site was designed to support various cloning strategies. Digestion of plasmids with XcmI allows for in vitro T/A ligation, while with EcoRV permits blunt-end ligation, with capability of blue-white colony screening. In vivo homologous recombination cloning is also utilizable by amplification of insert fragments using primers containing homology arms and transformation into capable E. coli strains. To demonstrate their advantages, the plasmids were used to clone PCR product samples for DNA sequencing with low-background and versatile cloning strategies. Such rapid and cost-effective cloning procedures are also proposed here. Finally, the cloning for protein expression with blue-white selection was also possible using egfp as a model regulated by lac and T7 promoters on the plasmid or other build-in promoters with the insert.

The chromosomal nature of LT-II enterotoxins solved: a lambdoid prophage encodes both LT-II and one of two novel pertussis-toxin-like toxin family members in type II enterotoxigenic Escherichia coli

Heat-labile enterotoxins (LT) of enterotoxigenic Escherichia coli (ETEC) are structurally and functionally related to cholera toxin (CT). LT-I toxins are plasmid-encoded and flanked by IS elements, while LT-II toxins of type II ETEC are chromosomally encoded with flanking genes that appear phage related. Here, I determined the complete genomic sequence of the locus for the LT-IIa type strain SA53, and show that the LT-IIa genes are encoded by a 51 239 bp lambdoid prophage integrated at the rac locus, the site of a defective prophage in E. coli K12 strains. Of 50 LT-IIa and LT-IIc, 46 prophages also encode one member of two novel two-gene ADP-ribosyltransferase toxin families that are both related to pertussis toxin, which I named eplBA or ealAB, respectively. The eplBA and ealAB genes are syntenic with the Shiga toxin loci in their lambdoid prophages of the enteric pathogen enterohemorrhagic E. coli. These novel AB₅ toxins show pertussis-toxin-like activity on tissue culture cells, and like pertussis toxin bind to sialic acid containing glycoprotein ligands. Type II ETEC are the first mucosal pathogens known to simultaneously produce two ADP-ribosylating toxins predicted to act on and modulate activity of both stimulatory and inhibitory alpha subunits of host cell heterotrimeric G-proteins.

Two novel pertussis-toxin-like toxins are also present in the genome of the prophage that also encodes the LT-II enterotoxin genes in type II enterotoxigenic Escherichi coli.

The DNA Exonucleases of Escherichia coli

DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB), and III (dnaQ/mutD); Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG), and X (exoX); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.

Bacterial artificial chromosome mutagenesis using recombineering

Gene expression from bacterial artificial chromosome (BAC) clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough to transfer intact genes in their native chromosomal setting together with flanking regulatory elements to provide all the signals for correct spatiotemporal gene expression. Until recently, the use of BACs for functional studies has been limited because their large size has inherently presented a major obstacle for introducing modifications using conventional genetic engineering strategies. The development of in vivo homologous recombination strategies based on recombineering in E. coli has helped resolve this problem by enabling facile engineering of high molecular weight BAC DNA without dependence on suitably placed restriction enzymes or cloning steps. These techniques have considerably expanded the possibilities for studying functional genetics using BACs in vitro and in vivo.

Bacteriophage-encoded functions engaged in initiation of homologous recombination events

Recombination plays a significant role in bacteriophage biology. Functions promoting recombination are involved in key stages of phage multiplication and drive phage evolution. Their biological role is reflected by the great variety of phages existing in the environment. This work presents the role of recombination in the phage life cycle and highlights the discrete character of phage-encoded recombination functions (anti-RecBCD activities, 5' --> 3' DNA exonucleases, single-stranded DNA binding proteins, single-stranded DNA annealing proteins, and recombinases). The focus of this review is on phage proteins that initiate genetic exchange. Importance of recombination is reviewed based on the accepted coli-phages T4 and lambda models, the recombination system of phage P22, and the recently characterized recombination functions of Bacillus subtilis phage SPP1 and mycobacteriophage Che9c. Key steps of the molecular mechanisms involving phage recombination functions and their application in molecular engineering are discussed.

A singular case of prophage complementation in mutational activation of recET orthologs in Salmonella enterica serovar Typhimurium

A class of mutations that suppress the recombination defects of recB mutants in Salmonella enterica serovar Typhimurium strain LT2 activates the normally silent recET module of the Gifsy-1 prophage. Allele sbcE21 is a 794-bp deletion within the immunity region of the prophage. Concomitant with activating recET, sbcE21 stimulates Gifsy-1 excision, resulting in unstable suppression. Early studies found both recB suppression and its instability to depend on the presence of the related Gifsy-2 prophage elsewhere in the chromosome. In cells lacking Gifsy-2, the sbcE21 allele became stable but no longer corrected recB defects. Here, we show that a single Gifsy-2 gene is required for Gifsy-1 recET activation in the sbcE21 background. This gene encodes GtgR, the Gifsy-2 repressor. Significantly, the sbcE21 deletion has one end point within the corresponding gene in the Gifsy-1 genome, gogR, which in strain LT2 is a perfect duplicate of gtgR. The deletion truncates gogR and places the Gifsy-1 left operon, including the recET and xis genes, under the control of the gogR promoter. The ability of GtgR to trans-activate this promoter therefore implies that GtgR and GogR normally activate the transcription of their own genes. Consistent with the symmetry of the system, a similar deletion in Gifsy-2 results in a Gifsy-1-dependent sbc phenotype (sbcF24). Two additional Gifsy-1 deletions (sbcE23 and sbcE25) were characterized, as well. The latter causes all but the last codon of the gogR gene to fuse, in frame, to the second half of recE. The resulting hybrid protein appears to function as both a transcriptional regulator and a recombination enzyme.

MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules

We describe a highly engineered in vivo cloning method, mating-assisted genetically integrated cloning (MAGIC), that facilitates the rapid construction of recombinant DNA molecules. MAGIC uses bacterial mating, in vivo site-specific endonuclease cleavage and homologous recombination to catalyze the transfer of a DNA fragment between a donor vector in one bacterial strain and a recipient plasmid in a separate bacterial strain. Recombination events are genetically selected and result in placement of the gene of interest under the control of new regulatory elements with high efficiency. MAGIC eliminates the need for restriction enzymes, DNA ligases, preparation of DNA and all in vitro manipulations required for subcloning and allows the rapid construction of multiple constructs with minimal effort. We show that MAGIC can generate constructs for expression in multiple organisms. As this new method requires only the simple mixing of bacterial strains, it represents a substantial advance in high-throughput recombinant DNA production that will save time, effort and expense in functional genomics studies.

Chromosomal fragmentation in dUTPase-deficient mutants of Escherichia coli and its recombinational repair

Recent findings suggest that DNA nicks stimulate homologous recombination by being converted into double-strand breaks, which are mended by RecA-catalysed recombinational repair and are lethal if not repaired. Hyper-rec mutants, in which DNA nicks become detectable, are synthetic-lethal with recA inactivation, substantiating the idea. Escherichia coli dut mutants are the only known hyper-recs in which presumed nicks in DNA do not cause inviability with recA, suggesting that nicks stimulate homologous recombination directly. Here, we show that dut recA mutants are synthetic-lethal; specifically, dut mutants depend on the RecBC-RuvABC recombinational repair pathway that mends double-strand DNA breaks. Although induced for SOS, dut mutants are not rescued by full SOS induction if RecA is not available, suggesting that recombinational rather than regulatory functions of RecA are needed for their viability. We also detected chromosomal fragmentation in dut rec mutants, indicating double-strand DNA breaks. Both the synthetic lethality and chromosomal fragmentation of dut rec mutants are suppressed by preventing uracil excision via inactivation of uracil DNA-glycosylase or by preventing dUTP production via inactivation of dCTP deaminase. We suggest that nicks become substrates for recombinational repair after being converted into double-strand DNA breaks.

The diverse and dynamic structure of bacterial genomes

Bacterial genome sizes, which range from 500 to 10,000 kbp, are within the current scope of operation of large-scale nucleotide sequence determination facilities. To date, 8 complete bacterial genomes have been sequenced, and at least 40 more will be completed in the near future. Such projects give wonderfully detailed information concerning the structure of the organism's genes and the overall organization of the sequenced genomes. It will be very important to put this incredible wealth of detail into a larger biological picture: How does this information apply to the genomes of related genera, related species, or even other individuals from the same species? Recent advances in pulsed-field gel electrophoretic technology have facilitated the construction of complete and accurate physical maps of bacterial chromosomes, and the many maps constructed in the past decade have revealed unexpected and substantial differences in genome size and organization even among closely related bacteria. This review focuses on this recently appreciated plasticity in structure of bacterial genomes, and diversity in genome size, replicon geometry, and chromosome number are discussed at inter- and intraspecies levels.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Transcription of the Escherichia coli recE gene from a promoter in Tn5 and IS50

Six sbc::Tn5 insertions and one sbc::IS50 insertion, which cause recE expression in Escherichia coli, have been cloned, and their DNA sequences have been determined. The sites of insertion are found at three positions in a 10-bp region: 58, 63, and 68 bp upstream of recE. Primer extension experiments with the cloned Tn5 insertions demonstrate that recE transcripts start adjacent to the insertion elements of five of these mutations and both adjacent and one nucleotide within the insertion element for the sixth mutation. This supports the hypothesis that these mutations have inserted a promoter, and PCR analysis reveals an outward promoter within the distal 69 nucleotides of Tn5. Primer extension analysis of RNA from the uncloned Tn5 and IS50 mutants reveals three additional insertion sites close to the others. Because all the insertions lie in the spacer region between racC and recE, transcribed in sbcA6 and sbc-23 strains, we propose that these insertions be renamed recEs::Tn5 and recEs::IS50.

Subcloning, nucleotide sequence, and expression of trkG, a gene that encodes an integral membrane protein involved in potassium uptake via the Trk system of Escherichia coli

The trkG gene encodes a component of the K+ uptake system Trk and is located at 30.5 min inside the lambdoid prophage region rac of the Escherichia coli chromosome. trkG was subcloned, its nucleotide sequence was determined, and its product was identified in a minicell system. The open reading frame of 1,455 bp encodes a hydrophobic membrane protein with a calculated molecular weight of 53,493 that is predicted to contain up to 12 transmembrane helices. The trkG gene product behaved as a hydrophobic membrane protein; it was found exclusively in the membrane fraction of the minicells and its migration in sodium dodecyl sulfate-polyacrylamide gel electrophoresis was anomalous, indicating an apparent molecular weight of 35,000. The trkG gene contains an exceptionally high proportion of infrequently used codons, raising the question of the origin of this gene. trkG does not appear to be a prophage gene since no similarity was observed between the nucleotide sequence of trkG or the amino acid sequence of its product and the sequences of genes or proteins from bacteriophage lambda.

Suppression of a frameshift mutation in the recE gene of Escherichia coli K-12 occurs by gene fusion

The nucleotide sequences of a small gene, racC, and the adjacent N-terminal half of the wild-type recE gene are presented. A frameshift mutation, recE939, inactivating recE and preventing synthesis of the active recE enzyme, exonuclease VIII, was identified. The endpoints of five deletion mutations suppressing recE939 were sequenced. All five delete the frameshift site. Two are intra-recE deletions and fuse the N- and C-terminal portions of recE in frame. Three of the deletions remove the entire N-terminal portion of recE, fusing the C-terminal portion to N-terminal portions of racC in frame. These data indicate that about 70% of the N-terminal half of recE is not required to encode a hypothesized protein domain with exonuclease VIII activity.

Analysis of the recE locus of Escherichia coli K-12 by use of polyclonal antibodies to exonuclease VIII

Exonuclease VIII (exoVIII) of Escherichia coli has been purified from a strain carrying a plasmid-encoded recE gene by using a new procedure. This procedure yielded 30 times more protein per gram of cells, and the protein had a twofold higher specific activity than the enzyme purified by the previously published procedure (J. W. Joseph and R. Kolodner, J. Biol. Chem. 258:10411-10417, 1983). The sequence of the 12 N-terminal amino acids was also obtained and found to correspond to one of the open reading frames predicted from the nucleic acid sequence of the recE region of Rac (C. Chu, A. Templin, and A. J. Clark, manuscript in preparation). Polyclonal antibodies directed against purified exoVIII were also prepared. Cell-free extracts prepared from strains containing a wide range of chromosomal- or plasmid-encoded point, insertion, and deletion mutations which result in expression of exoVIII were examined by Western blot (immunoblot) analysis. This analysis showed that two point sbcA mutations (sbcA5 and sbcA23) and the sbc insertion mutations led to the synthesis of the 140-kilodalton (kDa) polypeptide of wild-type exoVIII. Plasmid-encoded partial deletion mutations of recE reduced the size of the cross-reacting protein(s) in direct proportion to the size of the deletion, even though exonuclease activity was still present. The analysis suggests that 39 kDa of the 140-kDa exoVIII subunit is all that is essential for exonuclease activity. One of the truncated but functional exonucleases (the pRAC3 exonuclease) has been purified and confirmed to be a 41-kDa polypeptide. The first 18 amino acids from the N terminus of the 41-kDa pRAC3 exonuclease were sequenced and fond to correspond to one of the translational start signals predicted from the nucleotide sequence of radC (Chu et al., in preparation).

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.

RecBC enzyme activity is required for far-UV induced respiration shutoff in Escherichia coli K12

Shutoff of respiration is one of a number of recA+ lexA+ dependent (SOS) responses caused by far ultraviolet (245 nm) radiation (UV) damage of DNA in Escherichia coli cells. Thus far no rec/lex response has been shown to require the recB recC gene product, the RecBC enzyme. We report in this paper that UV-induced respiration shutoff did not occur in either of these radiation-sensitive derivatives of K12 strain AB1157 nor in the recB recC double mutant. The sbcB gene product is exonuclease I and it has been reported that the triple mutant strain recB recC sbcB has near normal recombination efficiency and resistance to UV. The sbcB strain shut off its respiration after UV but the triple mutant did not show UV-induced respiration shutoff; the shutoff and death responses were uncoupled. We concluded that respiration shutoff requires RecBC enzyme activity. The RecBC enzyme has ATP-dependent double-strand exonuclease activity, helicase activity and several other activities. We tested a recBC+ (double dagger) mutant strain (recC 1010) that had normal recombination efficiency and resistance to UV but which possessed no ATP-dependent double-strand exonuclease activity. This strain did not shut off its respiration. The presence or absence of other RecBC enzyme activities in this mutant is not known. These results support the hypothesis that ATP-dependent double-strand exonuclease activity is necessary for UV-induced respiration shutoff.

Rec-dependent and Rec-independent recombination of plasmid-borne duplications in Escherichia coli K12

Plasmidic recombination in E. coli K12 has been previously demonstrated to be dependent on the host rec genotype. The construction of plasmids that carry a duplication within an antibiotic-resistance gene is described. Recombination between the direct repeats recreates an active antibiotic-resistance gene, allowing quantitative analysis of recombination frequencies in a closely related set of E. coli K12 strains carrying various rec mutations. Using this system, intraplasmidic recombination of a duplication within the pBR322 tetracycline-resistance gene is shown to be rec-dependent while recombination of a similar duplication within the kanamycin-resistance gene of Tn903 is shown to be independent of recA, recB, recC, recE, recF and sbcB.

Mutation-dependent suppression of recB21 recC22 by a region cloned from the Rac prophage of Escherichia coli K-12

Using pBR322 as a vector, we cloned a 5.95-kilobase fragment of the Rac prophage together with 1.70 kilobases of a flanking Escherichia coli chromosome sequence. The resulting plasmid (pRAC1) was unable to suppress the mitomycin and UV sensitivity and recombination deficiency of a recB21 recC22 strain. Five spontaneous mitomycin-resistant derivatives contained deletion mutant plasmids. These plasmids also suppressed the UV sensitivity and recombination deficiency of their recB21 recC22 hosts. All five deletions were contained within a 2.45-kilobase EcoRI-to-HindIII segment of the plasmid. By substituting the corresponding 2.45-kilobase EcoRI-toHindIII fragments of Rac prophage isolated from sbcA+, sbcA6, and sbcA23 strains for the shortened segment of one of the deletion mutant plasmids, we were able to show that sbcA mutations map in this region. Also in this region is the site (or closely linked sites) at which previous studies had shown that insertion of Tn5 and IS50 leads to suppression of recB21 recC22. The sequence in this region that must be altered or circumvented to allow suppression is discussed. Also presented are data correlating the expression of nuclease activity with the degree of suppression.

Detection and physical map of a omega tox+-related defective prophage in Corynebacterium diphtheriae Belfanti 1030(-)tox-

A library of chromosomal DNA from Corynebacterium diphtheriae Belfanti 1030(-)tox- was cloned in the lambda phage vector EMBL4 and screened for sequences homologous to corynephage omega tox+ and the attB1-attB2 region of the C7(-)tox- chromosome. Two portions of the 1030(-)tox- chromosome, 35 and 30.5 kilobases long which contain, respectively, the entire region homologous to corynephage omega tox+ and the attB1-attB2 sites, were mapped with the restriction endonucleases BamHI and EcoRI. Chromosomal DNA from 1030(-)tox- was shown to contain a 15.5-kilobase region that was homologous to ca. 42% of the corynephage omega tox+ genome. These sequences were found to hybridize to three regions of the phage genome and do not contain either the diphtheria tox operon or the attP site. These sequences are distant from the chromosomal region that contains the attB1-attB2 sites. Moreover, unlike other known defective prophages, the physical map of this prophage starts at the cos site and is colinear with the vegetative phage map. The 30.5-kilobase region of the 1030(-)tox- chromosome, which contains the attB1-attB2 sites, has a central core region that is almost identical to the corresponding region of the C7(-)tox- chromosome; however, the flanking sequences in these two strains of C. diphtheriae are different.

A phi 80 function inhibitory for growth of lambdoid phage in him mutants of Escherichia coli deficient in integration host factor. I. Genetic analysis of the Rha phenotype

Bacteriophage phi 80 and lambda-phi 80 hybrid phage of the type lambda (QSR)80, in which the rightmost 10% of the lambda genome is replaced by corresponding phi 80 material, are unable to grow lytically in himA and hip/himD mutants of Escherichia coli K12 at 32 degrees. The genetic element responsible for the growth defect, rha, has been mapped to the (QSR)80 region and was located more precisely by restriction enzyme and DNA heteroduplex analysis of mutations that result in loss of the Rha phenotype. Such an Rha mutant carrying a 1.5-kb deletion beginning 0.58 kb from the right end of the chromosome and extending leftward locates the rha locus at least in part within this region of (QSR)80. In addition, a substitution derivative of lambda (QSR)80 was isolated which does not exhibit the Rha phenotype. In this phage, lambda-80hy95, the right half of the (QSR)80 region is replaced by DNA homologous to the 95-100% segment of lambda. In mixed infections in the himA42 host at 32 degrees, lambda + does not complement lambda (QSR)80 for growth and the burst size of the coinfecting lambda + is reduced in comparison to that in a single infection. Deletion mutants of lambda (QSR)80 that grow normally in himA42 at 32 degrees in single infections are inhibited for growth in mixed infections with lambda (QSR)80. These results suggest the existence of a trans-acting function which inhibits phage growth in the absence of HimA or Hip/HimD function. It is likely that the rha gene either encodes that function or indirectly controls its action.

Restriction nuclease and enzymatic analysis of transposon-induced mutations of the Rac prophage which affect expression and function of recE in Escherichia coli K-12

Fourteen Tn5-generated mutations of the Rac prophage, called sbc because they suppress recB21 recC22, were found to fall into two distinct types: type I mutations, which were insertions of Tn5, and type II mutations, which were insertions of IS50. Both orientations of Tn5 and IS50 were represented among the mutants and were arbitrarily labeled A and B. All 14 of the Tn5 and IS50 insertions occurred in the same location (+/- 100 base pairs) approximately 5.6 kilobases from one of the hybrid attachment sites. Eleven of the mutants contained essentially the same amount of exonuclease VIII, the product of recE. The possibility that a promoter for recE was created by the insertion of Tn5 and IS50 was considered. Two IS50 mutants in which such a promoter could not have been created showed three to four times as much exonuclease VIII, and another showed one-half as much as the majority. The possibility was considered that a promoter internal to IS50 is responsible for this heterogeneity. Restriction alleviation was measured in all 14 mutants. An insertion of the transposon Tn10 which reduces expression of exonuclease VIII (recE101::Tn10) was located within the Rac prophage at a position 2.35 kilobases from the left hybrid attachment site. Location and orientation of the Rac prophage on the Escherichia coli genetic map are discussed in light of these results.

Genetic analysis of transposon-induced mutations of the Rac prophage in Escherichia coli K-12 which affect expression and function of recE

Fourteen mitomycin-resistant revertants of a recB21 recC22 strain were isolated after Tn5 mutagenesis. Eight of the mutations (type I) were essentially inseparable from aphA+ (Kanr) of Tn5; six (type II) were not. We hypothesize that the former are Tn5 and that the latter are IS50 insertions. Because of their phenotypic similarity to sbcA and sbcB mutations, which also suppress recB21 recC22, we have called them sbc mutations. sbc-lll::Tn5 was cotransducible with nirR and has thereby been located at position 29.8 on the Escherichia coli map in the vicinity of the Rac prophage and sbcA mutations. A recB21 recC22 sbc-lll::Tn5 strain was subjected to Tn10 mutagenesis, and a mitomycin- and UV-sensitive mutant was isolated. tet+ of Tn10 was 85% cotransducible with aphA+ of Tn5, locating these two transposons 0.1 map unit apart. A three-point cross located the Tn10 mutation at position 29.7. We hypothesize that the Tn10 insertion is located in recE and that the Tn5 and IS50 insertions activate expression of this gene. sbc-lll::Tn5 was found to be cis acting and dominant to its wild-type allele as were two sbcA mutations (sbcA1 and sbcA6). Five other type I and type II insertion mutations were dominant to their wild-type alleles. We hypothesize that the sbc insertion and sbcA mutations affect transcription regulation of recE and discuss the possibility that they do so differently.

Plasmidic recombination in Escherichia coli K-12: the role of recF gene function

Interplasmidic and intraplasmidic recombination proficiencies were determined in E. coli bacterial strains carrying rec mutations. Our results defined the role of recF gene function, recB, recC, and sbcB gene products (exonuclease V and exonuclease I) in plasmidic recombination in wild-type E. coli cells and in cells in which the recE recombination pathway is activated. RecF gene function is required for interplasmidic recombination regardless of the recB recC genotype. Intraplasmidic recombination is recF dependent in cells having a functional exonuclease V, but not in recB recC mutants. Exonuclease V activity inhibits both interplasmidic and intraplasmidic recombination via the recE pathway.

Zygotic induction of the rac locus can cause cell death in E. coli

Conjugational transfer of the rac locus of E. coli K-12 into a Rac- recipient strain (i.e. rac+ X rac-) results in the killing of a majority of the recipient cells. The efficiency of killing depends somewhat on the plating medium, and can be as high as 98%. The killing is not observed in the rac+ X rac+, rac- X rac- or rac- X rac+ configurations. The rac locus, which has the properties of a cryptic prophage, may carry a function analogous to the kil function of bacteriophage lambda, or may instead cause killing by some replication related process.

A gene coding for a periplasmic protein is located near the locus for termination of chromosome replication in Escherichia coli

Hybrid plasmids carrying trg, the genetic locus in closest proximity to terC, coded for several polypeptides in addition to the Trg protein. Polypeptides of 59,000 and 61,000 apparent molecular weight were the most prominent products synthesized in minicells containing the hybrid plasmids. Analysis of the effects of deletions generated by a restriction endonuclease identified a region of DNA immediately adjacent to trg as the putative gene coding for the two polypeptides. Studies with whole cells and minicells showed that the 59,000-dalton polypeptide is a periplasmic protein. Analysis by limited proteolysis indicated that the two polypeptides are related, and a number of observations support the notion that the 61,000-dalton protein is a precursor form of the 59,000-dalton mature exported protein. The identification and characterization of a protein, in addition to Trg, which is produced by a gene in close proximity to terC emphasizes the fact that the region does contain intact and active genes.

Read-through transcription from a derepressed Tn3 promoter affects ColE1 functions on a ColE1::Tn3 composite plasmid

Mutations in the repressor encoded by the transposon Tn3 tnpR gene lead to increased levels of expression of two gene products: the mutant repressor (TnpR-) and the Tn3 encoded transposase, TnpA (Heffron et al. 1978; Chou et al. 1979a). Derivatives of the ColE1::Tn3 composite plasmid, RSF2124, with mutant Tn3 repressor exhibited the expected elevated levels of transposition. Unexpectedly, hosts containing these tnpR- derivatives produced enhanced levels of the ColE1 encoded toxin, colicin E1. The gene for colicin E1 maps far (0.23-0.98 MU) from the Tn3 insertion point (0.73 MU) (Fig. 1). The colicin E1 overproduction phenotype, designated Eop-, was complemented in trans by wild type repressor gene product (TnpR+) to the wild type phenotype, Eop+. Hosts with RSF2124 derivatives which expressed high levels of both mutant repressor and mutant transposase (TnpR-, TnpA-) were Eop-. Hosts containing plasmids deleted for both tnpA and tnpR promoters were Eop+, while hosts with plasmids carrying a lac promoter substitution for the tnpA promoter were Eop-. These data support the idea that a cis-acting effect of increased transcription from the tnpA promoter into adjacent ColE1 DNA was the cause of colicin overproduction. Increased transcription activated a putative colicin augmentation function (caf) whose presence was required for the Eop- phenotype. Deletion mapping established that one boundary of the caf locus lies within 52 bases of the junction of the left end of Tn3 and ColE1 DNA. ColE1 DNA in this area contains an open reading frame which could encode either a 74 or a 63 residue protein (B. Polisky, unpublished DNA sequence data). The presence of increased levels of an mRNA transcript from this region and/or the increased expression of protein(s) from this transcript could result in an Eop- phenotype. Expression of the Eop- phenotype requires the presence of the host recE gene. Evidence is presented which suggests that the recA repressor, lexA protein, controls expression of the recE gene product, ExoVIII.

P1 transduction mapping of the trg locus in rac+ and rac strains of Escherichia coli K-12

The trg locus, which had been located at min 31 in the cotransduction gap in the terminus region of the chromosome of Escherichia coli, has been mapped by transduction with bacteriophage P1. This locus exhibited no cotransduction with fnr when rac+ strains were used. If rac strains were used, which removed approximately 27 kilobase pairs of DNA, trg and fnr exhibited 8.2% cotransduction. Although this mapping of trg at min 31.1 considerably reduces the size of the cotransduction gap, trg exhibited no cotransduction with a Tn10 insertion located on the other side of the gap at min 34.2.

Rac-E. coli K12 strains carry a preferential attachment site for lambda rev

Lambda rev is a hybrid lambdoid phage formed by recombination between lambda and a defective lambdoid prophage (Rac) present in most E. coli K12 derivatives. We show here that three independently derived Rac-E. coli K12 strains are specifically deleted for the entire Rac prophage consistent with loss of Rac by excisive recombination between hybrid attachment sites that flank the prophage (c.f. excision of a lambda prophage). lambda rev, in which int and PP' of lambda have been replaced by integrative recombination genes and an attachment site derived from Rac (Gottesman et al. 1974), integrates site-specifically and in the correct orientation at the preferential attachment site generated by Rac excision.

Isolation and properties of Tn10 insertions in the rac locus of Escherichia coli

Two Tn10 insertions that are in the rac locus of the chromosome of Escherichia coli have been isolated and characterized. The insertions are located at min 29.7 and min 30.0. The insertions are stable when an F123 rac::Tn10 episome is transferred to an F- rac+ recipient, but they are lost at a high frequency when transferred to an F- rac- recipient. This latter condition has been previously demonstrated to cause the excision of the rac locus. The Tn10 insertions are also lost at a high frequency when strains containing them are lysogenized with lambda reverse. If the lysogens that have lost the Tn10 insertion are subsequently cured of lambda reverse, the cells no longer contain sequences homologous with rac locus DNA. These strains were rac- when tested for recombination activation (Low 1973), and this procedure consequently provides a simple means to make isogenic rac+ and rac- strains.