Hfr Crosses Research Articles

HrpA, a DEAH-box RNA helicase, is involved in mRNA processing of a fimbrial operon in Escherichia coli.

Endonucleolytic cleavage of mRNA in the daa operon of Escherichia coli is responsible for co-ordinate regulation of genes involved in F1845 fimbrial biogenesis. Cleavage occurs by an unidentified endoribonuclease, is translation dependent and involves a unique recognition mechanism. Here, we present the results of a genetic strategy used to identify factors involved in daa mRNA processing. We used a reporter construct consisting of the daa mRNA processing region fused to the gene encoding green fluorescent protein (GFP). A mutant defective in daa mRNA processing and expressing high levels of GFP was isolated by flow cytometry. To determine the location of mutations, two different genetic approaches, Hfr crosses and P1 transductions, were used. The mutation responsible for the processing defect was subsequently mapped to the 32 min region of the E. coli chromosome. A putative DEAH-box RNA helicase-encoding gene at this position, hrpA, was able to restore the ability of the mutant to cleave daa mRNA. Site-directed mutagenesis of the hrpA regions predicted to encode nucleotide triphosphate binding and hydrolysis functions abolished the ability of the gene to restore the processing defect in the mutant. We propose that HrpA is a novel enzyme involved in mRNA processing in E. coli.

Characterization of a Mutant RecA Protein that Facilitates Homologous Genetic Recombination but not Recombinational DNA Repair: RecA423

A recAmutant ( recA423; Arg 169→ His), with properties that should help clarify the relationship between the biochemical properties of RecA protein and its two major functions, homologous genetic recombination and recombinational DNA repair, has been isolated. The mutant has been characterized in vivoand the purified RecA423 protein has been studied in vitro. The recA423cells are nearly as proficient in conjugational recombination, transductional recombination, and recombination of I red − gam −phage as wild-type cells. At the same time, the mutant cells are deficient for intra-chromosomal recombination and nearly as sensitive to UV irradiation as a recAdeletion strain. The cells are proficient in SOS induction, and results indicate the defect involves the capacity of RecA protein to participate directly in recombinational DNA repair. In vitro, the RecA423 protein binds to single-stranded DNA slowly, with an associated decline in the ATP hydrolytic activity. The RecA423 protein promoted a limited DNA strand exchange reaction when the DNA substrates were homologous, but no bypass of a short heterologous insert in the duplex DNA substrate was observed. These results indicate that poor binding to DNA and low ATP hydrolysis activity can selectively compromise certain functions of RecA protein. The RecA423 protein can promote recombina tion between homologous DNAs during Hfr crosses, indicating that the biochemical requirements for such genetic exchanges are minimal. However, the deficiencies in recombinational DNA repair suggest that the biochemical requirements for this function are more exacting.

Mutation of recF, recJ, recO, recQ, or recR improves Hfr recombination in resolvase-deficient ruv recG strains of Escherichia coli.

The formation of recombinants in Hfr crosses was studied in Escherichia coli strains carrying combinations of genes known to affect recombination and DNA repair. Mutations in ruv and recG eliminate activities that have been shown to process Holliday junction intermediates by nuclease cleavage and/or branch migration. Strains carrying null mutations in both ruv and recG produce few recombinants in Hfr crosses and are extremely sensitive to UV light. The introduction of additional mutations in recF, recJ, recO, recQ, or recR is shown to increase the yield of recombinants by 6- to 20-fold via a mechanism that depends on recBC. The products of these genes have been linked with the initiation of recombination. We propose that mutation of recF, recJ, recO, recQ, or recR redirects recombination to events initiated by the RecBCD enzyme. The strains constructed were also tested for sensitivity to UV light. Addition of recF, recJ, recN, recO, recQ, or recR mutations had no effect on the survival of ruv recG strains. The implications of these findings are discussed in relation to molecular models for recombination and DNA repair that invoke different roles for the branch migration activities of the RuvAB and RecG proteins.

RecP, a new minor pathway of general recombination in Escherichia coli encoded by plasmid R1 drd-19

Plasmid R1 drd-19 markedly improves the recombination deficiency of recB and recB recC mutants of Escherichia coli K12 as measured by Hfr crosses and increases their resistance to uv inactivation. The effect correlates with the production of an ATP-dependent ds DNA exonuclease in recB/R1 drd-19 cells. This paper further investigates the suppressive effect of plasmid R1 drd-19 on the recB mutation of E. coli. The gene(s) responsible for the effect was localized to the 13.1-kb EcoRI-C fragment of the resistance transfer factor (RTF) portion of R1 drd-19. The plasmid-encoded activity does not merely replace the RecBCD enzyme failure but differs in several significant ways. It promotes a hyper-recombinogenic phenotype, as judged by the phenomenon of superoligomerization of the tester pACYC184 plasmid in recB/R1 drd-19 cells and two inter- and intramolecular plasmid recombination test systems. It is probably not inhibited by λ Gam protein and does not restrict plating of T4gp2 mutant. No significant homology between the E. coli chromosomal fragment carrying recB recC recD genes and the EcoRI-C fragment of R1 drd-19 was observed. It is suggested that the plasmid-encoded recombination activity is involved in a new minor recombination pathway (designated RecP, for Plasmid). RecP resembles in some traits the RecBCD-independent pathways RecE and RecF but differs in activity and perhaps substrate specificity from the main RecBCD pathway.

Identification of sbcD mutations as cosuppressors of recBC that allow propagation of DNA palindromes in Escherichia coli K-12.

The function of an open reading frame (orf-45) located upstream of the sbcC gene of Escherichia coli was investigated. Mutations that inactivate sbcC improve the ability to propagate lambda red gam phage that carry a palindromic sequence in their DNA. They also act with sbcB mutations as cosuppressors of the defects in recombination, DNA repair, and cell viability associated with recBC mutations. A 1,282-bp cassette encoding resistance to kanamycin was used to disrupt orf-45. The mutation, which has a polar effect on the expression of sbcC, allowed stable propagation of palindromic lambda phage even when the sbcC gene product was provided in trans. Additional nonpolar mutations in orf-45 were isolated on the basis of their ability to improve the growth of recBC sbcB strains. These mutations also confer resistance to mitomycin C, allow efficient recombination in Hfr crosses, and facilitate stable propagation of palindromic phage. It is concluded that the products of orf-45 and sbcC are functionally related. The orf-45 gene is therefore renamed sbcD.

Cloning and expression in Escherichia coli of a recA homologue from Mycobacterium tuberculosis

A 3.8 kb PstI fragment of Mycobacterium tuberculosis was cloned in a recA-deleted Escherichia coli by selecting transformants with increased EMS resistance. The cloned fragment restored homologous recombination in Hfr crosses and conferred resistance to long wave (302 nm) but not short wave (254 nm) UV light. E. coli containing the 3.8 kb PstI fragment produced a 38-40 kDa protein which cross-reacted with antibodies raised against the E. coli RecA protein. The cloned DNA thus probably encodes a RecA homologue.

Identification of the recR locus of Escherichia coli K-12 and analysis of its role in recombination and DNA repair.

A new recombination gene called recR has been identified and located near dnaZ at minute 11 on the current linkage map of Escherichia coli. The gene was detected after transposon mutagenesis of a recB sbcB strain and screening for insertion mutants that had a reduced efficiency of recombination in Hfr crosses. The recR insertions obtained conferred a recombination deficient and extremely UV sensitive phenotype in both recB recC sbcA and recB recC sbcB sbcC genetic backgrounds. recR derivatives of recBC+ sbc+ strains were proficient in conjugational and transductional recombination but deficient in plasmid recombination and sensitive to UV light. Strains carrying recR insertions combined with mutations in uvrA and other rec genes revealed that the gene is involved in a recombinational process of DNA repair that relies also on recF and recO, and possibly recJ, but which is independent of recB, recC and recD. The properties of two other insertions, one located near pyrE and the other near guaA, are discussed in relation to their proximity to recG and xse (the gene for exonuclease VII), respectively.

Localization of stx, a determinant essential for high-level production of shiga toxin by Shigella dysenteriae serotype 1, near pyrF and generation of stx transposon mutants.

Hfr strains of Shigella dysenteriae serotype 1 were constructed by transient integration of an RP4 plasmid derivative carrying transposon Tn501 into the Shigella chromosome through Tn501-mediated cointegration. The Hfr strains were mated with Escherichia coli K-12 recipients carrying various auxotrophic markers, and E. coli recombinants which had received prototrophic Shigella genes were selected. Some of the E. coli transconjugants produced high levels of a cytotoxin which was neutralized by both polyclonal and monoclonal anti-Shiga toxin sera. The determinant for Shiga toxin production, designated stx, was first transferred to E. coli K-12 and then mapped by Hfr crosses to the trp-pyrF region located at 30 min on the E. coli chromosome. Bacteriophage P1-mediated transduction analysis of stx gave the following gene order: trp-pyrF-stx. The level of Shiga toxin production in E. coli Stx+ transconjugants and transductants was as high as that of the parental S. dysenteriae 1 strain. Stx- mutants of an Stx+ E. coli transductant were generated by random in vivo insertion mutagenesis with a Tn10 derivative transposon, Tn-mini-kan, followed by P1 cotransduction of the kanamycin resistance and PyrF+ markers into a pyrF Stx+ E. coli K-12 recipient. One stx::Tn-mini-kan transposon mutation was transferred by P1 transduction from this E. coli Stx- mutant to an E. coli K-12 Hfr strain and in turn transferred by conjugation to the original S. dysenteriae 1 strain plus two others. All kanamycin-resistant recombinants of S. dysenteriae 1 had lost their ability to produce high levels of Shiga toxin. A gene that specifies high-level Shiga toxin production is thus located near pyrF on the chromosome of S. dysenteriae 1. Stx- mutants of S. dysenteriae 1 exhibited full virulence in the Serény test.

Chromosomal map of Pseudomonas putida PPN, and a comparison of gene order with the Pseudomonas aeruginosa PAO chromosomal map.

The generalized transducing phage Pf16h2 has been used to confirm linkage relationships of chromosomal markers of Pseudomonas putida previously determined from their time-of-entry in Hfr crosses, and to map new auxotrophic mutations. By means of spot matings using Hfr donors of known origin of transfer, catabolic markers forming part of a closely linked group of operons referred to as a superoperonic cluster have been shown to be chromosomally located and their map positions determined. R-prime-mediated interspecific complementation has been used to equate functionally 21 auxotrophic loci in P. putida and P. aeruginosa, and the distribution of these loci on the two genetic maps has been compared. While both maps reveal that auxotrophic markers are largely restricted to about 40% of the chromosome and that auxotrophic markers of similar phenotype are not clustered, there is evidence of at least seven chromosomal rearrangements since divergence from a presumed common ancestor.

A molecular model for conjugational recombination in Escherichia coli K12.

Conjugational recombination in Escherichia coli was investigated by measuring lacZ+ product, beta-galactosidase, in crosses between lacZ mutants. Enzyme production in both Hfr and F-prime crosses was detected very soon after transfer of the donor lacZ allele. The level of enzyme activity was reduced by no more than two-fold when the recipient carried a recB mutation. With an F-prime donor, recombination appeared to be restricted largely to a short period immediately after transfer, with little evidence of recombination during subsequent exponential growth of the transconjugant cells. These observations are interpreted to suggest that recA dependent recombination is able to initiate with high efficiency at gaps present in the donor DNA before synthesis of a complementary strand is completed, and independently of recB function. A molecular model for conjugational recombination based on this idea is presented in terms of the known activities of recA and recBC products. Some of the predictions of the model are tested by analysing the recombinant genotypes produced in Hfr crosses with multiply marked strains.

The effect of plasmid R391 and other IncJ plasmids on the survival of Escherichia coli after UV irradiation.

The presence of the IncJ plasmids R391, R997, R705, R706, R748 and R749 was shown to sensitize Escherichia coli AB1157 and both its uvrA and lexA derivatives to UV irradiation. No alteration in post-irradiation survival was observed in a recA mutant containing these plasmids, compared with the non-plasmid-containing recA strain. Analysis of recombination frequency in Hfr crosses to recA+ cells containing plasmid R391 indicated a reduction in recombination frequency compared with that obtained in similar crosses to a non-plasmid-containing strain. This effect was not due to plasmid-encoded restriction or entry exclusion systems and therefore must be considered as a real block in recombination. When cells containing plasmid R391 were irradiated and allowed to photoreactivate, an increase in survival was observed which was comparable to that observed in the non-plasmid-containing derivative. This indicated that post-irradiation processing of UV-induced damage, or lack of such processing, by mechanisms other than photoreactivation was responsible for the UV sensitivity associated with plasmid R391.

Tn 5 -Induced Mutations in the Enterobacterial Phytopathogen Erwinia chrysanthemi

Escherichia coli (2492/pJB4JI) matings with Erwinia chrysanthemi produced kanamycin resistant (Km) transconjugants, a majority of which were gentamicin sensitive (Gm). A small proportion (about 0.8%) of the Km Gm clones were either auxotrophic or failed to catabolize galacturonate (Gtu). The R plasmid (pJB4JI) DNA was detected in the parent E. coli strain and in a Km Gm transconjugant, but not in Km GmE. chrysanthemi strains carrying Tn5-induced mutations. In Hfr crosses, Km (Tn5) was found linked with most mutations. A majority (>95%) of prototrophic recombinants were Km, except for Leu and Arg recombinants which were 30 to 50% Km. Spontaneous revertants were obtained for all markers except car, gtu, lys, thr, and trp. Prototrophic revertants, with the exception of Met, Leu, or His clones, were Km. We conclude from both genetic and physical data that Tn5 transposed from pJB4JI into different sites on the chromosome of E. chrysanthemi.

Plasmid control of recombination of E. coli K12.

The recombination proficiency of three recipient strains of Escherichia coli K12 carrying different plasmids was investigated by conjugal mating with Hfr Cavalli. Some plasmids (e.g. R1drd 19, R6K) caused a marked reduction in the yield of recombinants formed in crosses with Hfr but did not reduce the ability of host strains to accept plasmid F104. The effect of plasmids on recombination was host-dependent. In Hfr crosses with AB1157 (R1-19) used as a recipient the linkage between selected and unselected proximal markers of the donor was sharply decreased. Plasmid R1-19 also decreased the yield of recombinants formed by recF, recL, and recB recC sbcA mutants, showed no effect on the recombination proficiency of recB recC sbcB mutant, and increased the recombination proficiency of recB, recB recC sbcB recF, and recB recC sbcB recL mutants. An ATP-dependent exonuclease activity was found in all tested recB recC mutants carrying plasmid R1-19, while this plasmid did not affect the activity of exonuclease I in strain AB1157 and its rec- derivatives. The same plasmid was also found to protect different rec- derivatives of the strain AB1157 against the lethal action of UV light. We suppose that a new ATP-dependent exonuclease determined by R1-19 plays a role in both repair and recombination of the host through the substitution of or competition with the exoV coded for by the genes recB and recC.

THE INFLUENCE OF THE PO1A1 MUTATION UPON RECOMBINATION IN ESCHERICHIA COLI K12

Genetic recombination in Escherichia coli is a highly regulated process involving multiple gene products. We have investigated the role of DNA polymerase I in this process by studying the effect of the po1A1 mutation upon DNA transfer and conjugation in otherwise isogenic suppressor-free strains of E. coli K-12. It was found that the po1A1 mutation greatly reduces recombination in Hfr crosses (a factor of 20 in Pol+ x Po1A1 crosses and more than a factor of 100 in Po1A1 X Po1A1 crosses). However, since the po1A1 mutation reduces the strains capacity to act as a recipient for an F-prime and the analysis of recombination transfer gradients revealed no differences between Po1+ and Po1- strains, it is concluded that DNA polymerase I probably affects the transfer and/or stability of donor DNA rather than the recombinational process itself.

Lipopolysaccharide Core Defects in Salmonella typhimurium Mutants Which Are Resistant to Felix O Phage but Retain Smooth Character

FOR mutants of Salmonella typhimurium are resistant to Felix O phage, whose receptor includes the N-acetylglucosamine branch of the lipopolysaccharide (LPS) core, but smooth in cultural properties, antigenic character and phage sensitivity pattern (MacPhee et al., 1975). The rfa(FOR) genes determining the FOR character of nine mutants were transduced into a smooth cysE pyrE recipient: the nine FOR transductants (and a tenth FOR mutant) were then made rfb (i.e. unable to make O chains) by transduction or Hfr crosses. The rfb FOR strains were sensitive to FO phage but nearly all of them showed a somewhat reduced efficiency of plating and diminished rate of adsorption of the phage. This observation and the Ra (complete core) serological activity of their LPS (tested by haemagglutination inhibition) indicate the presence of some, but less than the normal number of, completed core chains in FOR rfb LPS. On the basis of the sensitivities of the FOR transductants and their rfb derivatives to various 'rough-specific' phages, their increased sensitivities to some antibiotics and to deoxycholate and the serological activity of the rfb FOR LPS in various incomplete core systems, the mutants were divided into three groups: (i) five mutants with probable defects in previously undetected rfa gene(s) concerned with formation of both the galactose I and the galactose II units of the LPS core; (ii) two mutants with defects inferred to affect the structure of the inner part of the core and also interfere with addition of the N-acetylglucosamine branch; (iii) three mutants in which no type of incomplete core could be detected, probably affected in formation of the inner part of the core chain. The mutation of one mutant of the last class, unlike those of the other nine mutants tested, lay outside the cysE-pyrE segment, in the 90 to 116 min region of the linkage map.

Hyper-recombination in Escherichia coli K-12 mutants constitutive for protein X synthesis

Genetic recombination was studied in Escherichia coli F- strains in which synthesis of the recA gene product protein X is increased due to mutation in either recA (tif-1) or lexA (spr). When a single donor marker was selected, the recombination proficiency of these strains was not significantly altered in Hfr crosses. However, linkage of unselected, proximal Hfr markers was found to be much reduced among the progeny tested, and more of the progeny showed evidence of multiple exchanges between donor and recipient DNA. These effects were much more apparent when the recipient carried both tif-1 and spr mutations, but in this case recombination proficiency was reduced compared with those strains carrying either mutation alone, particularly in crosses with Hfr Cavalli. A lexA mutation was found to suppress the effect of tif-1 on the recombinant genotype.

Genetic locus (ompB) affecting a major outer-membrane protein in Escherichia coli K-12

Three multiply colicin-tolerant mutants in Escherichia coli K-12 from the TolIV, TolXIV, and TolXV phenotypic groups, all lacking or having only trace amounts of protein 1, a major outer-membrane protein, were mapped by Hfr crosses, and the position on the chromosome was confirmed by cotransduction with nearby markers. The mutations were located near malQP in the 74-min region of the E. coli chromosome. This locus is designated ompB, and analysis of data from two three-point crosses determined the linear sequence of genes to be aroB-ompB-malQP-glpD.

Mapping of rfa Genes in Salmonella typhimurium by ES18 and P22 Transduction and by Conjugation

Loci termed rfa, determining biosynthesis of somatic lipopolysaccharide core, have been mapped in Salmonella typhimurium LT2. The smooth-specific phage P22 co-transduced two leaky rfa alleles with cysE and with pyrE; one of the leaky alleles is perhaps rfaG, and the other is an unidentified gene concerned with synthesis of the heptose-containing part of the core. The lipopolysaccharide-indifferent phage ES18 (or its variant ES18.h1) co-transduced rfaF, rfaG, rfaL, rfa(R-res-1), and rfa(R-res-2) alleles with cysE and with pyrE, at rates indicating the order cysE-rfaF-(rfa[R-res-1], rfa[r-res-2], rfaL)-rfaG-pyrE. One proven (and two suspected) rfaE alleles and five proven rfaH alleles were not co-transduced with cysE or pyrE. Hfr crosses indicated that the proven rfaE allele mapped between serA and strA.

Incompatibility of integrated sex factors in double male strains of Escherichia coli.

Several strains of Escherichia coli K-12 harboring two F factors were isolated from Hfr x Hfr crosses. These strains were transiently capable of initiating chromosome transfer from two separate points of origin, and of transferring two different sex factors as integrated chromosomal markers. Each strain tested invariably reverted to a simple Hfr by loss of one of the inherited F factors. The F factor persisting in the revertant was, in nearly every case, that which had been inherited from the recipient Hfr parent.

Behavior of three colicine factors and an R (drug resistance) factor in Hfr crosses in Salmonella typhimurium.

An LT2 Hfr strain,his metC gal, was crossed to a multiply marked LT2 F−line. Analysis of recombinant yields, segregation of unselected markers and interrupted matings indicated injection of the Hfr chromosome in the sequenceThe introduction into the Hfr of the colicine factorscolI, colE1andcolE2and the R factorR2had little or no effect on its fertility. All four factors were transmitted at low frequency to the F−population, and to recombinants at higher frequencies (colI5–30%,colE130–80%,colE25–30%,R20–9%). Transfer ofcolE1occurred before 20 min., that ofcolE2andcolIlater than 100 min. Segregation data did not reveal close linkage of any factor to any chromosomal locus, but recombinants with a long stretch of donor chromosome were more likely than others to have acquiredcolE2andcolI. Nearly all recombinants andF−cells which acquiredcolIorcolE2acquired both, andcolE1also. Most cells which acquiredR2acquired one or more colicine factors. These plasmid associations can be formally represented by transfer of plasmids, independently of the chromosome, in the sequencecolE1—(colI, colE2)—R2. Phage P22 grown on the Hfr carrying the four plasmids transduced thetet-rtrait ofR2at very low frequency, and thesul-r str-rcharacters, together, at low frequency. Some of each sort of drug-resistance transductant, but no transductants in respect of chromosomal characters, acquiredcolEl or colE2by co-transduction.