INTRODUCTION

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HU is one of the most abundant DNA-binding proteins in Escherichia coli, and it contributes to the compaction of the genome into tight nucleosome-like structures (40). E. coli HU is a small, basic, heat-stable dimeric protein composed of two highly homologous subunits, HU and HU, encoded by the hupA and hupB genes located at 90 and 10 min, respectively, on the E. coli chromosome (21, 22). Strains mutated in both hupA and hupB have reduced viability, perturbed cell division, and a number of other deficiencies (18, 50). The HU protein also participates in a number of cellular mechanisms such as modulating the expression of specific genes (36, 55), DNA melting at the initiation of replication (20, 45), DNA breaking/rejoining in transposition and inversion reactions (13, 25), and homologous recombination (7, 19). In addition, although HU does not recognize a particular DNA sequence, it can act at very precise locations on the chromosomal DNA through specific binding to particular DNA structures such as bulged DNA, four-way DNA junctions (2, 37), and single-strand breaks or gaps (5).

E. coli hup mutants are sensitive to  irradiation, and in vitro studies show that HU protects DNA against cleavage by  rays (3). This finding suggests that HU may play a role in DNA repair or in a mechanism of tolerance to DNA damage. There are several pathways for DNA repair or DNA damage tolerance in E. coli. The pathway(s) in which a specific gene is involved can be inferred by studying the phenotypic consequences of the interactions of the specific mutant gene with other mutant genes whose functions in DNA repair or damage tolerance have been well documented (4).

To determine in which pathway of DNA repair or damage tolerance the hup gene is involved, we examined the interactions between hup and other genes whose functions in DNA repair and/or damage tolerance have been well documented. It appears that a deficiency in homologous recombination renders hup mutants UV sensitive.

	MATERIALS AND METHODS

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Bacterial strains, plasmids, and media. The bacterial strains and plasmids used are listed in Table 1. Standard phage P1 transduction, performed as described by Sternberg and Maurer (47), was used for the construction of different hup mutants. Plasmid transformation was performed by the cold CaCl₂ method as described by Sambrook et al. (42). Bacteria were grown in Luria broth (LB) medium and on LB agar. Tetracycline and chloramphenicol were used at 10 µg/ml. Kanamycin, erythromycin, and ampicillin were used at 50 µg/ml. Isopropyl--D-thiogalactopyranoside (IPTG) was used at 1 mM.

UV survival. Strains were grown in LB to mid-log phase (optical density at 600 nm [OD₆₀₀]  0.5) and serially 10-fold diluted in 1% NaCl; 50 µl of the diluted cell suspension was spread onto each of three LB agar plates per UV dose. To induce overexpression of wild-type or mutated plasmid-borne gyrB, 1 mM IPTG was included in the plates. To test the effect of the gyrase inhibitor novobiocin on UV sensitivity, 0 to 60 µg of novobiocin per ml was included in the plates. Under dimmed yellow light, the plates were irradiated with various doses of 254-nm UV and incubated in the dark for 24 or 48 h before the colonies were counted. The survival values given are the means of two to four independent experiments.

	RESULTS AND DISCUSSION

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UV sensitivity of hup strains. Although HU is not essential to E. coli, cells lacking HU have multiple deficiencies (18, 50). Moreover, it has been shown that hup mutants are sensitive to  irradiation (3). As the types of damages induced by  and UV irradiations are different, and mechanisms for repair of these damages are also different, we tested if hup mutations render cells UV sensitive. As shown in Fig. 1, hup mutations render the cells UV sensitive in rec⁺ sbc⁺, recBC sbcA, and recBC sbcBC backgrounds.

View larger version (15K): [in this window] [in a new window]   FIG. 1.   Effects of hup mutations in different genetic backgrounds on sensitivity to UV. Strains were grown in LB to log phase (OD600  0.5), diluted in 1% NaCl, and irradiated on the surface of LB agar plates. Surviving colonies were scored after 24 h of incubation in the dark. The strains identified by genotype were JR1669, JR1670, JR1671, JR1672, and JR1672 transformed with plasmid pYK20 (a), JC7623, SL1012, SL1013, and SL1014 (b), and JC8679, SL1015, SL1016, and SL1017 (c).

hup and uvrA interact synergistically. HU is involved in the compaction of genomic DNA (40); the lack of HU can cause a topological change of DNA (1, 16, 17, 33, 41, 48). Therefore, it is possible that lack of HU can change the DNA UV photochemistry and the excision repair of UV photoproducts. We analyzed the induction and repair patterns of cyclobutane pyrimidine dimers (CPDs) at the nucleotide level in the replication origin oriC, in the mRNA genes lacI and lacZ, and in the tRNA gene tyrT. Almost identical patterns of CPD induction and removal were observed in wild-type and hupAB strains (references 26 and 27 and data not shown). Using a CPD-specific monoclonal antibody, we measured the induction and removal of CPDs in bulk genomic DNA. Again, no apparent difference was seen between wild-type and hupAB cells (data not shown). These results suggest that the UV sensitivity of hup mutants is not caused by the change of UV photoproduct induction or a deficiency in nucleotide excision repair.

View larger version (24K): [in this window] [in a new window]   FIG. 2.   Interactions in terms of UV sensitivity between hup and other genes. Strains were grown in LB to log phase (OD600  0.5), diluted in 1% NaCl, and irradiated on the surface of LB agar plates. Surviving colonies were scored after 24 h of incubation in the dark. The strains identified by genotype were BH200, SL1022, SL1023, and SL1024 (a), SL1018, SL1019, SL1020, and SL1021 (b), SL1037, SL1038, SL1039, and SL1040 (c), AQ9947, SL1031, SL1032, and SL1033 (d), N2057, SL1034, SL1035, and SL1036 (e), TNM759, SL1041, SL1042, and SL1043 (f), BT125, SL1028, SL1029, and SL1030 (g), and N1234, SL1025, SL1026, and SL1027 (h).

hup mutations markedly enhance the UV sensitivity of umuDC strains. Reduced tolerance to DNA damage renders cells sensitive to the damaging agents. One of the known DNA damage tolerance mechanisms is via translesion synthesis, in which the umuDC operon has an indispensable role (reviewed in reference 11). We tested the interaction between mutations of hup and umuDC. As shown in Fig. 2c, the UV killing of the hupAB umuDC strain is roughly the sum of the killing in the umuDC mutant plus the increased killing by hupAB mutations over the level for wild-type strains. This finding suggests that hup and umuDC genes are involved in independent pathways for DNA damage tolerance or repair. In other words, the UV sensitivity caused by hup mutations is not due to the deficiency in translesion synthesis.

hup mutations do not enhance the UV sensitivity of resolvase-deficient recG ruvA strains. hupAB mutations do not curtail the rapid SOS response (3). The -ray sensitivity of hup mutants may result from the lack of sufficient protection of the chromosomal DNA from radiation, as shown by in vitro experiments (3). Alternatively, this sensitivity may be due to the deficiency in the repair of -ray-induced double-strand breaks, which is achieved by homologous recombination (24). It has been shown that hupAB mutants are deficient in homologous recombination (7, 19). Our results, which are similar to those of Dri et al. (7), showed that hupAB caused a two- to fivefold reduction in P1 transduction and conjugational recombination in the rec⁺ sbc⁺, recBC sbcA, and recBC sbcBC backgrounds (data not shown). As shown above, hupAB interact with uvrA synergistically, as is typical for a mutation that blocks recombinational repair (15, 29, 30). The fact that hupAB mutations do not enhance the -ray sensitivity of recA strains (3) also supports the idea that HU is involved in recombinational repair.

hup mutations confer different phenotypes on recG and ruvA strains. RuvAB with RuvC and RecG with RusA provide two overlapping pathways for processing Holliday junctions (28, 32, 34, 44). To test the role of HU in the two pathways, we analyzed the interaction of hup with recG and ruvA. hupAB recG strains are far more sensitive to UV than hupAB or recG strains (Fig. 2f), while hupAB ruvA strains are slightly more sensitive than ruvA strains (Fig. 2g). This finding indicates that hup mutations mainly hinder the recombinational pathway in which Holliday junctions are processed by RuvABC. To exclude the possibility that the interrupted genes were inserted into the recipient genomes rather than substituted for the normal genes during phage P1 transduction, we constructed the hup ruvA strains by introducing ruvA60::Tn10 into the hup strains and by introducing hupA::Cm and hupB::Km into the ruvA strains. Substitutions of the wild-type genes with the interrupted genes were confirmed by Southern blot analysis (data not shown). The strains constructed showed the same interactions between hup and ruvA. Moreover, the hupAB ruvA strains were just as sensitive to UV as hupA ruvA strains (Fig. 2g). Additional hupB mutations in the hupA ruvA strains did not render the cells more UV sensitive. Presumably the 2 homodimers cannot compensate for the function of the heterodimers in hupA ruvA strains.

In which step(s) of recombinational repair is HU involved? The recombinational repair of UV-induced DNA damages is thought to occur by a mechanism termed postreplication repair. Two major types of postreplication repair processes exist; one repairs daughter strand DNA gaps, and the other repairs double-strand breaks generated from the unrepaired daughter strand gaps (51-53). Daughter strand gap repair depends on RecF (51, 52). Double-strand break repair depends mainly on RecB but to a minor extent on RecF (51-53). The RecBCD enzyme initiates DNA unwinding at double-strand DNA ends, and its nuclease activity is controlled by Chi sites in such a way that the enzyme produces a potent single-stranded DNA substrate for homologous pairing (for a review, see reference 46). However, the repair deficiency of recB recC mutants can be suppressed by secondary mutations in either the sbcA or sbcB locus, and in each case the suppression can be rationalized in terms of an effect on the generation of 3' ends (for reviews, see references 23 and 54). sbcA mutations activate exonuclease VIII, which digests double-stranded DNA ends to produce long 3' tails, and this could provide an alternative means of producing the invasive 3' ends. sbcBC mutations inactivate exonuclease I, which digests single-stranded DNA from the 3' end, so that its inactivation might leave 3' ends available to initiate recombinational repair. The hupAB mutants do not degrade their DNA after UV irradiation any more extensively than wild-type strains (data not shown), although it has been proposed that the specific binding of HU to the DNA single-strand breaks or gaps may have a role in protecting these region from further degradation by endonucleases (5). The findings that hupAB mutations render rec⁺ sbc⁺, recBC sbcA, and recBC sbcBC (in which the recombinational substrates are generated by different mechanisms) strains sensitive to UV (Fig. 1) and that the UV sensitivity of the recD strain is also enhanced by the hup mutations (Fig. 2a) suggest that HU is unlikely to be involved in the substrate processing step of recombinational repair.

The UV sensitivity of hup mutants cannot be suppressed by overexpression of wild-type gyrB or gyrB mutations that confer novobiocin resistance. In prokaryotes, the degree of supercoiling is determined by the relative activities of at least two enzymes, DNA gyrase and topoisomerase I. DNA gyrase activity leads to increased negative supercoiling of the DNA, while topoisomerase I activity relaxes the DNA (for reviews, see references 8 and 31). Although lacking topoisomerase activity, HU may contribute to DNA topology. In vitro, HU bends DNA and wraps it into nucleosome-like structures (40). A small amount of relaxation was seen in DNA extracted from HU-deficient cells (41). hupAB mutants show a growth deficiency (18, 33, 50) and are hypersensitive to the gyrase inhibitor novobiocin. These phenotypes of hupAB strains may result from the relaxation of chromosomal DNA, as they can be suppressed by overexpression of the wild-type gyrB gene or by gyrB mutations that confer novobiocin resistance (33). This notion is supported by the observation that DNA supercoiling increased toward wild-type levels in the presence of gyrB suppressors (33). We wondered whether the UV sensitivity of hup mutants can also be suppressed by overexpression of the wild-type gyrB gene or by the gyrB mutations that confer novobiocin resistance. To test this, plasmid pAG111, which bears the tac promoter-controlled wild-type gyrB gene (12), was used to transform the wild-type and hupAB strains. The hupAB strains transformed with pAG111 formed large, uniform colonies if the cells were cultured on agar plates containing 1 mM IPTG. Variable sizes of colonies formed if the same cells were cultured on plates that did not contain IPTG (data not shown). These results indicate that the heterogeneous colony phenotype of hupAB strains is indeed suppressed by overexpression of the gyrB gene. However, UV sensitivity was virtually unchanged for both the wild-type and hupAB strains by inducing the overexpression of the wild-type gyrB gene borne on plasmid pAG111 (data not shown).

The UV sensitivity of hup mutants cannot be suppressed by different concentrations of gyrase inhibitor that can increase or decrease the supercoiling of the chromosomal DNA. Bensaid et al. (1) showed that a decrease in the intracellular concentration of HU is accompanied by an increase in the relaxing activity of topoisomerase I; the ability to increase relaxing activity, or to decrease an excess of supercoiling, is important for cells to survive in the absence of HU. It is proposed that the absence of HU, like the removal of histones, results first in the excess of DNA supercoiling which must be removed by topoisomerase I activity for the cells to survive. Contrary to the scenario suggested by Malik et al. (33), the relaxation of the chromosomal DNA is proposed to be beneficial to the hupAB cells.

2

View larger version (19K): [in this window] [in a new window]   FIG. 3.   Effects of the DNA gyrase inhibitor novobiocin on the UV sensitivity of wild-type (JR1669; ) and hupAB (JR1672; *) strains. Strains were grown in LB to log phase (OD600  0.5), diluted in 1% NaCl, and spread on the surface of LB agar plates containing 0 to 60 µg of novobiocin per ml. Surviving colonies were scored after 48 h of incubation in the dark. (a) Survival curves of unirradiated cells; (b) survival curves of UV-irradiated cells (the survival fractions are expressed as those obtained from the UV-irradiated plates divided by those obtained from the unirradiated plates containing the corresponding concentrations of novobiocin).