Genetic functions promoting homologous recombination in Escherichia coli: a study of inversions in phage lambda.

We have studied homologous recombination in a derivative of phage lambda containing two 1.4-kb repeats in inverted orientation. Inversion of the intervening 2.5-kb segment occurred efficiently by the Escherichia coli RecBC pathway but markedly less efficiently by the lambda Red pathway or the E. coli RecE or RecF pathways. Inversion by the RecBCD pathway was stimulated by Chi sites located to the right of the invertible segment; this stimulation decreased exponentially by a factor of about 2 for each 2.2 kb between the invertible segment and the Chi site. In addition to RecA protein and RecBCD enzyme, inversion by the RecBC pathway required single-stranded DNA binding protein, DNA gyrase, DNA polymerase I and DNA ligase. Inversion appeared to occur either intra- or intermolecularly. These results are discussed in the framework of a current molecular model for the RecBC pathway of homologous recombination.

Genetic dissection of the biochemical activities of RecBCD enzyme.

RecBCD enzyme of Escherichia coli is required for the major pathway of homologous recombination following conjugation. The enzyme has an ATP-dependent DNA unwinding activity, ATP-dependent single-stranded (ss) and double-stranded (ds) DNA exonuclease activities, and an activity that makes a ss DNA endonucleolytic cut near Chi sites. We have isolated and characterized ten mutations that reduced recombination proficiency and inactivated some, but not all, activities of RecBCD enzyme. One class of mutants had weak ds DNA exonuclease activity and lacked Chi-dependent DNA cleavage activity, a second class lacked only Chi-dependent DNA cleavage activity, and a third class retained all activities tested. The properties of these mutants indicate that the DNA unwinding and ss DNA exonuclease activities of the RecBCD enzyme are not sufficient for recombination. Furthermore, they suggest that the Chi-dependent DNA cleavage activity or another, as yet unidentified activity or both are required for recombination. The roles of the RecBCD enzymatic activities in recombination and exclusion of foreign DNA are discussed in light of the properties of these and other recBCD mutations.

Detection of herpes simplex virus intertypic recombinant genomes in infected cell DNA.

Intertypic recombination between herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) was detected using DNA from mixedly infected cells. Because HSV-1 and HSV-2 share a 50% base sequence homology along the genome but have markedly different DNA restriction enzyme cleavage patterns, recombination events can be detected and quantified by analysis of restriction endonuclease digests for the presence of novel DNA fragments. We have used this technique to quantify the degree of interference by HSV-2 on HSV-1 replication as well as the effect of limiting the availability of one genome on the frequency of intertypic recombination. Because this technique does not require production of viable progeny virions, it should also be useful for studying early recombination events.

Adherence of Escherichia coli to human urinary tract epithelial cells.

The adherence of Escherichia coli to human uroepithelial cells obtained from midstream urine specimens of healthy women was studied. Bacteria labeled with [(3)H]uridine were used, and unattached organisms were separated from the epithelial cells by vacuum filtration with 5-mum-pore-size Nucleopore membrane filters. These techniques allowed adherence to be measured in large numbers of epithelial cells and overcame the problem of distinguishing experimental bacteria from the indigenous organisms present on uroepithelial cells. Adherence was not appreciably affected by temperature. Adherence was maximal at pH 4 to 5 and at bacterial-to-epithelial-cell ratios of 5,000 or more. The latter observation suggested that there are a limited number of receptors on the epithelial cell surface, an idea which was supported by competition experiments. Adherence occurred within 1 min and then decreased gradually or quickly, depending on the type of bacterial growth medium, to a stationary level of adherence, approximately 50% of that observed initially. The ability of epithelial cells from a single individual to bind E. coli varied in a cyclical and repetitive pattern. Adherence tended to be higher during the early phase of the menstrual cycle and diminished shortly after the time of expected ovulation; adherence frequently correlated with the value obtained on the same day of the menstrual cycle during the preceding months. Adherence was markedly enhanced by bacterial incubation in broth for 72 h and inhibited by alpha-d-mannose. These results suggest that adherence is a complex phenomenon perhaps mediated in part by bacterial pili and mannose residues on uroepithelial cells.

Bacterial effect of hydrogen peroxide on urinary tract pathogens.

Bacterial contamination of urinary drainage bags is a frequent source of bladder bacteriuria in patients with indwelling catheters. Previous work demonstrated that the addition of 30 ml of 3% H2O2 prevented bacterial contamination of urinary drainage bags for up to 8 h in patients with urinary infections (greater than 10(5) colony-forming units per ml). Survival curves of a variety of organisms in filter-sterilized urine with various concentrations of H2O2 (0.6 to 0.01%) were constructed. Organisms with high cellular catalase activity (Staphylococcus aureus, Serratia marcescens, and Proteus mirabilis) required 30 to 60 min of exposure to 0.6% H2O2 for a reduction of 10(8) to less than 1 colony-forming unit per ml, whereas Escherichia coli, Streptococcus sp., and Pseudomonas sp. required only 15 min of exposure. The efficacy of H2O2 in urine was maintained despite exposure to room temperature for 5 days and reinoculation with bacterial suspensions. H2O2 is inexpensive and relatively nontoxic, and these data suggest that periodic instillation of H2O2 into urinary drainage bags may eliminate a source of bladder bacteriuria and environmental contamination.

The RecD subunit of the Escherichia coli RecBCD enzyme inhibits RecA loading, homologous recombination, and DNA repair.

The RecBCD enzyme is required for homologous recombination and DNA repair in Escherichia coli. The structure and function of RecBCD enzyme is altered on its interaction with the recombination hotspot Chi (5'-GCTGGTGG-3'). It has been hypothesized that the RecD subunit plays a role in Chi-dependent regulation of enzyme activity [Thaler, D. S., Sampson, E., Siddiqi, I., Rosenberg, S. M., Stahl, F. W. & Stahl, M. (1988) in Mechanisms and Consequences of DNA Damage Processing, eds. Friedberg, E. & Hanawalt, P. (Liss, New York), pp. 413-422; Churchill, J. J., Anderson, D. G. & Kowalczykowski, S. C. (1999) Genes Dev. 13, 901-911]. We tested the hypothesis that the RecD subunit inhibits recombination by deleting recD from the nuclease- and recombination-deficient mutant recB(D1080A)CD. We report here that the resulting strain, recB(D1080A)C, was proficient for recombination and DNA repair. Recombination proficiency was accompanied by a change in enzyme activity: RecB(D1080A)C enzyme loaded RecA protein onto DNA during DNA unwinding whereas RecB(D1080A)CD enzyme did not. Together, these genetic and biochemical results demonstrate that RecA loading by RecBCD enzyme is required for recombination in E. coli cells and suggest that RecD interferes with the enzyme domain required for its loading. A nuclease-dependent signal appears to be required for a change in RecD that allows RecA loading. Because RecA loading is not observed with wild-type RecBCD enzyme until it acts at a Chi site, our observations support the view that RecD inhibits recombination until the enzyme acts at Chi.

A stimulatory RNA associated with RecBCD enzyme.

RecBCD enzyme acts in the major pathway of homologous recombination of linear DNA in Escherichia coli. The enzyme unwinds DNA and is an ATP-dependent double-strand and single-strand exonuclease and a single-strand endonuclease; it acts at Chi recombination hotspots (5'-GCTGGTGG-3') to produce a recombinogenic single-stranded DNA 3'-end. We found that a small RNA with a unique sequence of approximately 24 nt was tightly bound to RecBCD enzyme and co-purified with it. When added to native enzyme this RNA, but not four others, increased DNA unwinding and Chi nicking activities of the enzyme. In seven similarly active enzyme preparations the molar ratio of RNA molecules to RecBCD enzyme molecules ranged from 0.2 to <0.008. These results suggest that, although this unique RNA is not an essential enzyme subunit, it has a biological role in stimulating RecBCD enzyme activity.

Effect of carbohydrates on adherence of Escherichica coli to human urinary tract epithelial cells.

Adherence of Escherichia coli cells to voided uroepithelial cells from healthy women was measured by use of [3H]uridine-labeled bacteria filtered through a polycarbonate membrane filter (5-micrometer pore size). At a concentration of 2.5% (wt/vol), D-mannose, D-mannitol, alpha-methyl-D-mannoside, and yeast mannan completely inhibited adherence of the bacteria to the epithelial cells. At this same concentration, D-fructose, D-lyxose, D-arabinose, and D-glyceraldehyde partially inhibited adherence. Reducing the concentration of D-mannose, or its derivatives, to between 1.0 and 0.1% resulted in partial inhibition in the adherence of the bacteria; a further reduction in the concentration to between 0.01 and 0.001% caused an enhancement of adherence up to 160% of the control level. Bacterial preincubation in 2.5% D-mannose for 1 min before epithelial cells were added completely inhibited adherence; similar treatment of the epithelial cells had no significant effect on subsequent adherence of the bacteria. Bacteria that were preincubated for 1 h with D-mannose at concentrations between 0.1 and 0.75% showed enhanced adherence. The inhibitory effect of D-mannose was decreased if bacterial adhesive ability, or cell receptivity, increased. A variety of other carbohydrates tested had no effect on the adherence of E. coli to the uroepithelial cells. These results suggest that adherence can be altered by interaction(s) between specific carbohydrate molecules and receptors on the bacterial surface.

The initiation and control of homologous recombination in Escherichia coli.

The chromosome of Escherichia coli recombines at low frequency when it is an intact circle but recombines at high frequency when it is broken, for example by X-rays, or when a linear DNA fragment is introduced into the cell during conjugation or transduction. The high recombinogenicity of double-strand (ds) DNA ends is attributable to RecBCD enzyme, which acts on ds DNA ends and is essential for recombination and ds DNA break repair. RecBCD enzyme initiates DNA unwinding at ds DNA ends, and its nuclease activity is controlled by Chi sites (5' G-C-T-G-G-T-G-G 3') in such a way that the enzyme produces a potent single-stranded DNA substrate for homologous pairing by RecA and single-stranded DNA binding proteins. We discuss a unifying model for recombination and ds DNA break repair, based upon the enzymic activities of these and other proteins and upon the behaviour of E. coli mutants altered in these proteins.

recD: the gene for an essential third subunit of exonuclease V.

Exonuclease V (EC 3.1.11.5) of Escherichia coli, an enzyme with multiple activities promoting genetic recombination, has previously been shown to contain two polypeptides, the products of the recB and recC genes. We report here that the enzyme contains in addition a third polypeptide (alpha) with a molecular mass of about 58 kDa. The alpha polypeptide is not synthesized by a class of mutants (previously designated recB) lacking the nuclease activity of exonuclease V but retaining recombination proficiency. The gene, recD, coding for the alpha polypeptide is located near recB in the order thyA-recC-ptr-recB-recD-argA on the E. coli chromosome. The recB and recD genes appear to be governed by a common promoter to the left of recB; a weaker promoter appears to govern recD alone. In the light of these results we discuss the relation between the structure and function of the three polypeptides of exonuclease V, hereby alternatively designated RecBCD enzyme.

Mannose-sensitive haemagglutination in the absence of piliation in Escherichia coli.

The relationship between type 1 pilus structure and the mannose-sensitive adhesin was investigated by analysing the properties of an 11.2 kb fragment of DNA derived from the chromosomal pil region of a type 1 piliated uropathogenic strain of Escherichia coli. The recombinant plasmids pHA9 and pSJH9, containing the cloned fragment, conferred a mannose-sensitive haemagglutination (MSHA)-positive but non-piliated phenotype on recipient cells of ORN104. Most of the DNA sequences homologous to the pilA and hyp genes were not present in the 11.2 kb insert, and the genetic information necessary for MSHA in the absence of piliation spanned a 6.5 kb region of the cloned fragment. The polypeptides expressed by pSJH9 were examined in minicells and Tn1000 insertions in three genes encoding proteins of molecular weights 90 kD, 29 kD and 17 kD abolished the MSHA phenotype.

Gene replacement with linear DNA in electroporated wild-type Escherichia coli.

Gene replacement using linear double-stranded DNA fragments in wild-type Escherichia coli transformation is generally inefficient due to exonucleolytic degradation of incoming DNA. Recombination-proficient strains, in which the exonucleolytic activity of RecBCD is inactivated, have been used as transformation recipients to overcome this difficulty. Here we report that gene replacements using linear double-stranded donor DNA can be achieved in wild-type E.coli if electrocompetent cells are used. Using a plasmid target, we obtained 10(2)-10(3) gene replacement events/microgram linear DNA. Using an independent chromosomal target, approximately 60 gene replacement events/microgram linear DNA were obtained. The presence of Chi sites on the linear DNA, which are known to block DNA degradation and stimulate recombination in E.coli, had no effect on gene replacement efficiency in either case. RecBCD-mediated exonucleolytic activity was found to be diminished in electroporated cells. Electrotransformation thus provides a simple way to perform gene replacements in many E.coli strains.

Role of Escherichia coli adhesins in urethral colonization of catheterized patients.

Escherichia coli is a major cause of catheter-associated urinary tract infection and frequently colonizes the urethra prior to invading the urinary tract. Bacterial pili, filamentous protein cell surface-associated appendages, have been shown to mediate colonization of epithelial cells. Pili associated adhesins can be detected in vitro by their ability to mediate bacterial hemagglutination of erythrocytes. We have assessed the role of bacterial adhesins in supporting urethral colonization by determining the hemagglutination reactions of 56 E. coli isolates from the urethra of patients with indwelling urethral catheters. The adhesin detected most frequently was the type 1 mannose-sensitive hemagglutinin (43%), and 43% of isolates failed to hemagglutinate guinea pig or human erythrocytes. E. coli hemagglutinins were no more common on urethral isolates from patients that were persistently colonized (E. coli present 70% of the time catheterized), than from those that were transiently colonized (E. coli present 30% of the time catheterized). Analysis of the HA reactions and DNA plasmid profiles of multiple isolates from persistently colonized patients suggested that the E. coli strain colonizing the urethra changed over time. The data suggest that bacterial colonization of the urethra is mediated in part by adhesins and changes over time.

In vivo expression and variation of Escherichia coli type 1 and P pili in the urine of adults with acute urinary tract infections.

In vivo expression of pili by Escherichia coli in the urine of 41 adults with lower urinary tract infections was analyzed by immunostaining with polyclonal antiserum to type 1 and P pili. Type 1 pili were detected in 31 of 41 urine specimens, while P pili were detected in 6 of 18 specimens. The piliation status of bacterial populations in urine was heterogeneous, varying from predominantly piliated to a mixture of piliated and nonpiliated cells. Bacteria frequently adhered to exfoliated uroepithelial cells and leukocytes in urine. Expression of pili in vivo did not always correlate with the hemagglutination phenotype after growth in vitro. Strains isolated from different sites in the urogenital tract of two individuals showed phenotypic variation in the state of piliation. The results demonstrate that E. coli type 1 and P pili are expressed and are subject to variation in vivo during acute urinary tract infections in adults.