Identification of Diverse Antimicrobial Resistance Determinants Carried on Bacterial,Plasmid, or Viral Metagenomes from an Activated Sludge Microbial Assemblage

Using both sequence- and function-based metagenomic approaches, multiple antibiotic resistance determinants were identified within metagenomic libraries constructed from DNA extracted from bacterial chromosomes, plasmids, or viruses within an activated sludge microbial assemblage. Metagenomic clones and a plasmid that in Escherichia coli expressed resistance to chloramphenicol, ampicillin, or kanamycin were isolated, with many cloned DNA sequences lacking any significant homology to known antibiotic resistance determinants.Activated sludge in wastewater treatment plants is an open system with a dynamic and phylogenetically diverse microbial community (2, 3, 6, 7, 10, 11). Since the activated sludge process promotes cellular interactions among diverse microorganisms, there is great potential for the lateral transfer of antibiotic resistance genes between microbes in activated sludge and in downstream environments. Several studies have previously identified antibiotic resistance determinants from wastewater communities that are carried on bacterial chromosomes (1, 4, 14) and plasmids (9, 12, 13), but to our knowledge, a simultaneous metagenomic survey of antibiotic resistance determinants from all three genetic reservoirs (i.e., chromosomes, plasmids, and viruses) has never been performed within the same environment. To achieve a more comprehensive assessment of antibiotic resistance genes in the activated sludge microbial community, this study used both function- and sequence-based metagenomic approaches to identify antibiotic resistance determinants carried on bacterial chromosomes, plasmids, or viruses within an activated sludge microbial assemblage.     

Isolation and Characterization of Metalloproteases with a Novel Domain Structure by Construction and Screening of Metagenomic Libraries

Small-insert metagenomic libraries from four samples were constructed by a topoisomerase-based and a T4 DNA ligase-based approach. Direct comparison of both approaches revealed that application of the topoisomerase-based method resulted in a higher number of insert-containing clones per μg of environmental DNA used for cloning and a larger average insert size. Subsequently, the constructed libraries were partially screened for the presence of genes conferring proteolytic activity. The function-driven screen was based on the ability of the library-containing Escherichia coli clones to form halos on skim milk-containing agar plates. The screening of 80,000 E. coli clones yielded four positive clones. Two of the plasmids (pTW2 and pTW3) recovered from positive clones conferred strong proteolytic activity and were studied further. Analysis of the entire insert sequences of pTW2 (28,113 bp) and pTW3 (19,956 bp) suggested that the DNA fragments were derived from members of the genus Xanthomonas. Each of the plasmids harbored one gene (2,589 bp) encoding a metalloprotease (mprA, pTW2; mprB, pTW3). Sequence and biochemical analyses revealed that MprA and MprB are similar extracellular proteases belonging to the M4 family of metallopeptidases (thermolysin-like family). Both enzymes possessed a unique modular structure and consisted of four regions: the signal sequence, the N-terminal proregion, the protease region, and the C-terminal extension. The architecture of the latter region, which was characterized by the presence of two prepeptidase C-terminal domains and one proprotein convertase P domain, is novel for bacterial metalloproteases. Studies with derivatives of MprA and MprB revealed that the C-terminal extension is not essential for protease activity. The optimum pH and temperature of both proteases were 8.0 and 65°C, respectively, when casein was used as substrate.Proteolytic enzymes catalyze the hydrolytic cleavage of peptide bonds. These enzymes are present in all living organisms and are essential for cell growth and differentiation. Microorganisms produce a variety of intracellular and/or extracellular proteases. Intracellular microbial proteases are highly specific and are involved in several cellular and metabolic processes such as activation of inactive precursors, maintenance of the cellular protein pool, and sporulation. Extracellular proteases degrade proteins in cell-free environments. The resulting hydrolytic products (small peptides and amino acids) can be transported into the cells and utilized as carbon or nitrogen sources (13, 39). Especially, extracellular proteases are of industrial importance and are used as cleaning agents and food and feed additives.Proteases can be divided into various groups with respect to the functional group present at the active site and the pH profile of the activity. Microbial alkaline proteases, which are defined to be active in a neutral to alkaline pH range (13), possess either a serine center (serine proteases) or are of metal-type (metalloproteases). Extracellular serine proteases are one of the most important groups of industrial enzymes (13, 23). In addition, many extracellular metalloproteases play an important role in pathogenesis (36). Both types of proteases have been cloned and sequenced from many different individual microorganisms, i.e., Bacillus subtilis (56), Enterobacter sakazakii (22), Listeria monocytogenes (4), and Alteromonas sp. (33, 34).In the present study, we sought to isolate proteases by a metagenomic approach. Functional metagenomics comprising the isolation of DNA from environmental samples without prior enrichment of individual microorganisms, the construction of libraries from the recovered DNA, and function-driven screening of the generated libraries has led to the identification and characterization of a variety of novel enzymes (7, 14, 43), i.e., amylases (44, 58), oxidoreductases (21), lipolytic enzymes (9, 16, 44), monooxygenases (53), and proteins conferring nickel resistance (32). Despite the wealth of different biotechnologically important enzyme activities derived from metagenomes, little information on the characteristics of metagenome-derived proteases is available. One metagenome-derived fibrinolytic metalloprotease has been recovered (26). In addition, one serine protease has been cited in reviews (13, 29). In other metagenome projects, activity-based screening was unsuccessful (19, 44), or the thereby recovered proteolytic clones were not characterized (47).We report here on the identification and characterization of two metagenome-derived metalloproteases. We constructed metagenomic DNA libraries from environmental samples by a T4 DNA ligase-based and a topoisomerase-based cloning method. The suitability of both approaches for the construction of small-insert metagenomic libraries was compared The resulting library-containing Escherichia coli clones were screened for proteolytic activity. The plasmids were recovered from the positive E. coli strains and the insert sequences of two plasmids (pTW2 and pTW3), which conferred strong proteolytic activity, were sequenced. The targeted protease-encoding genes and the corresponding gene products were characterized.     

Role of the DinB Homologs Rv1537 and Rv3056 in Mycobacterium tuberculosis

The environment encountered by Mycobacterium tuberculosis during infection is genotoxic. Most bacteria tolerate DNA damage by engaging specialized DNA polymerases that catalyze translesion synthesis (TLS) across sites of damage. M. tuberculosis possesses two putative members of the DinB class of Y-family DNA polymerases, DinB1 (Rv1537) and DinB2 (Rv3056); however, their role in damage tolerance, mutagenesis, and survival is unknown. Here, both dinB1 and dinB2 are shown to be expressed in vitro in a growth phase-dependent manner, with dinB2 levels 12- to 40-fold higher than those of dinB1. Yeast two-hybrid analyses revealed that DinB1, but not DinB2, interacts with the β-clamp, consistent with its canonical C-terminal β-binding motif. However, knockout of dinB1, dinB2, or both had no effect on the susceptibility of M. tuberculosis to compounds that form N²-dG adducts and alkylating agents. Similarly, deletion of these genes individually or in combination did not affect the rate of spontaneous mutation to rifampin resistance or the spectrum of resistance-conferring rpoB mutations and had no impact on growth or survival in human or mouse macrophages or in mice. Moreover, neither gene conferred a mutator phenotype when expressed ectopically in Mycobacterium smegmatis. The lack of the effect of altering the complements or expression levels of dinB1 and/or dinB2 under conditions predicted to be phenotypically revealing suggests that the DinB homologs from M. tuberculosis do not behave like their counterparts from other organisms.The emergence and global spread of multi- and extensively drug-resistant strains of Mycobacterium tuberculosis have further complicated the already daunting challenge of controlling tuberculosis (TB) (15). The mechanisms that underlie the evolution of drug resistance in M. tuberculosis by chromosomal mutagenesis and their association with the conditions that tubercle bacilli encounter during the course of infection are poorly understood (6). It has been postulated that hypoxia, low pH, nutrient deprivation, and nitrosative and oxidative stress impose environmental and host immune-mediated DNA-damaging insults on infecting bacilli (64). In addition, the observed importance of excision repair pathways for the growth and survival of M. tuberculosis in murine models of infection (13, 55) and the upregulation of M. tuberculosis genes involved in DNA repair and modification in pulmonary TB in humans provide compelling evidence that the in vivo environment is DNA damaging (51).Damage tolerance constitutes an integral component of an organism''s response to genotoxic stress, preventing collapse of the replication fork at persisting, replication-blocking lesions through the engagement of specialized DNA polymerases that are able to catalyze translesion synthesis (TLS) across the sites of damage (19, 21, 60). Most TLS polymerases belong to the Y family, which comprises a wide range of structurally related proteins present in bacteria, archaea, and eukaryotes (44). Of these, the DinB subfamily of Y family polymerases, whose founder member is Escherichia coli Pol IV (63), is conserved among all domains of life (44). The association of Y family polymerases with inducible mutagenesis has implicated these enzymes in the adaptation of bacteria to environmental stress (17, 20, 39, 54, 58, 59, 66). Their key properties are exemplified in E. coli Pol IV: the polymerase catalyzes efficient and accurate TLS across certain N²-dG adducts (27, 28, 34, 40, 45, 67) and has been implicated in the tolerance of alkylation damage (4); furthermore, overexpression of Pol IV significantly increases mutation rates in E. coli (reviewed in references 21 and 26), and dinB is the only SOS-regulated gene required at induced levels for stress-induced mutagenesis in this organism (20). Furthermore, overproduction of E. coli Pol IV inhibits replication fork progression through replacement of the replicative polymerase to form an alternate replisome in which Pol IV modulates the rate of unwinding of the DnaB helicase (25) and also reduces colony-forming ability (61).The M. tuberculosis genome encodes two Y family polymerase homologs belonging to the DinB subfamily, designated herein as DinB1 (DinX, encoded by Rv1537) and DinB2 (DinP, encoded by Rv3056), as well as a third, distantly related homolog encoded by Rv3394c (see Fig. S1 in the supplemental material) (9). On the basis of sequence similarity with their counterparts from E. coli (63) and Pseudomonas aeruginosa (54), including the complete conservation of key acidic residues essential for catalysis, DinB1 and DinB2 may be functional DNA polymerases (see Fig. S1). In contrast, Rv3394c lacks these residues and as such is unlikely to have polymerase activity (see Fig. S1). Unlike most Y family polymerase-encoding genes investigated with other bacteria (17, 26, 54, 58), dinB1 and dinB2 expression in M. tuberculosis is not dependent on RecA, the SOS response, or the presence of DNA damage (5, 7, 52). That these genes are regulated by other mechanisms and so may serve distinct roles in DNA metabolism in M. tuberculosis is suggested by the observation that dinB1 is differentially expressed in pulmonary TB (51) and is a member of the SigH regulon (30), whereas expression of dinB2 is induced following exposure to novobiocin (5).In this study, we adopted a genetic approach to investigate the function of dinB1 and dinB2 in M. tuberculosis. Mutants with altered complements or expression levels of dinB1 and/or dinB2 were analyzed in vitro and in vivo under conditions predicted to be phenotypically revealing based on DinB function established with other model organisms. The lack of discernible phenotypes in any of the assays employed suggests that the DinB homologs from M. tuberculosis do not behave like their counterparts from other organisms.     

Processing of Lagging-Strand Intermediates In Vitro by Herpes Simplex Virus Type 1 DNA Polymerase

The processing of lagging-strand intermediates has not been demonstrated in vitro for herpes simplex virus type 1 (HSV-1). Human flap endonuclease-1 (Fen-1) was examined for its ability to produce ligatable products with model lagging-strand intermediates in the presence of the wild-type or exonuclease-deficient (exo⁻) HSV-1 DNA polymerase (pol). Primer/templates were composed of a minicircle single-stranded DNA template annealed to primers that contained 5′ DNA flaps or 5′ annealed DNA or RNA sequences. Gapped DNA primer/templates were extended but not significantly strand displaced by the wild-type HSV-1 pol, although significant strand displacement was observed with exo⁻ HSV-1 pol. Nevertheless, the incubation of primer/templates containing 5′ flaps with either wild-type or exo⁻ HSV-1 pol and Fen-1 led to the efficient production of nicks that could be sealed with DNA ligase I. Both polymerases stimulated the nick translation activity of Fen-1 on DNA- or RNA-containing primer/templates, indicating that the activities were coordinated. Further evidence for Fen-1 involvement in HSV-1 DNA synthesis is suggested by the ability of a transiently expressed green fluorescent protein fusion with Fen-1 to accumulate in viral DNA replication compartments in infected cells and by the ability of endogenous Fen-1 to coimmunoprecipitate with an essential viral DNA replication protein in HSV-1-infected cells.Herpes simplex virus type 1 (HSV-1), the prototypic member of the family of Herpesviridae and that of the alphaherpesviridae subfamily, has served as the model for understanding the replication of herpesvirus genomes during lytic virus replication (29). The 152-kbp genome of herpes simplex virus type 1 (HSV-1) possesses approximately 85 genes, 7 of which have been shown to be necessary and sufficient for viral DNA replication within host cells (reviewed in references 5 and 38). These seven genes encode a DNA polymerase (pol) and its processivity factor (UL42), a heterotrimeric complex containing a DNA helicase (UL5), primase (UL52), and noncatalytic accessory protein (UL8), a single-stranded DNA binding protein (infected cell protein 8 [ICP-8]), and an origin binding protein with DNA helicase activity (UL9). There is strong evidence in support of the circularization of the linear virion DNA shortly after entry, and DNA replication then is thought to initiate at one or more of the three redundant origins of replication (29, 38). At least in the earliest stages of viral DNA replication, UL9 protein is required, presumably to bind to and unwind the DNA and to attract the other DNA replication proteins (29, 38). The electron microscopic examination of pulse-labeled replicating HSV-1 DNA indicates the presence of lariats, eye-forms, and D-forms (21), which is consistent with bidirectional theta-like replication from origins. To date, however, no biochemical assay has demonstrated origin-dependent DNA replication in vitro. However, in the absence of UL9, the other six HSV DNA replication proteins can support initiation and replication from a circular single-stranded DNA (ssDNA) template in an origin-independent fashion (15, 26), resembling the rolling-circle mode of replication thought to occur during the later stages of viral replication.Although nicks and small gaps have been observed in isolated replicating and virion DNA (38), the evidence for bidirectional duplex synthesis, the rapid rate of viral DNA replication, and the absence of long stretches of ssDNA in replicating and mature DNA isolated from HSV-1-infected cells suggest that leading- and lagging-strand synthesis are closely coordinated in vivo. Falkenberg et al. (15) used a minicircle DNA template with a strand bias and the six essential HSV-1 DNA replication proteins needed for rolling circle replication to demonstrate lagging-strand synthesis in vitro. However, replication from the parental strand template (leading-strand synthesis) was more efficient than synthesis from the complementary-strand template (lagging-strand synthesis). These results suggest the possibility that one or more host functions required for efficient lagging-strand synthesis or for its close coordination with leading-strand synthesis is missing in such in vitro systems.Although leading- and lagging-strand syntheses share many of the same requirements for bulk DNA synthesis, lagging-strand synthesis is a more complex process. Because the direction of polymerization of lagging-strand intermediates is opposite the direction of replication fork movement, lagging-strand synthesis requires that priming and extension occur many times to produce discontinuous segments called Okazaki fragments (reviewed in reference 25). Okazaki fragments need to be processed to remove the RNA primer, to fill in the area previously occupied by the RNA, and to seal the remaining nick between fragments, all of which must occur efficiently, accurately, and completely. Failure to do so would result in the accumulation of DNA breaks, multiple mutations, delayed DNA replication, and/or cell death (16, 61).In eukaryotes, what is currently known regarding the process of lagging-strand synthesis is based on genetic and biochemical studies with Saccharomyces cerevisiae and on in vitro reconstitution studies to define the mammalian enzymes required for simian virus 40 (SV40) T-antigen-dependent DNA replication (17, 37, 44, 57, 58). These studies have revealed that the extension of a newly synthesized Okazaki fragment DNA with pol δ causes the strand displacement of the preceding fragment to produce a 5′ flap (25). Results suggest that flap endonuclease 1 (Fen-1) is the activity responsible for the removal of the bulk of the 5′ flaps generated (1, 44, 48), although dna2 protein may facilitate the removal of longer flaps coated with the ssDNA binding protein complex (2, 44). In addition, the overexpression of exonuclease I can partially compensate for the loss of Fen-1 function in yeast (24, 51). For the proper processing of lagging-strand intermediates, the entire 5′ flap and all of the RNA primer need to be removed, and the gap must be filled to achieve a ligatable nick. DNA ligase I has been shown to be the enzyme involved in sealing Okazaki fragments in yeast and in humans (3, 31, 50, 56, 57). DNA ligase I requires a nick in which there is a 5′ phosphate on one end and a 3′ hydroxyl linked to a deoxyribose sugar entity on the other, and it works poorly in the presence of mismatches (54). The close coordination of Fen-1 and DNA ligase I activities for Okazaki fragment processing is facilitated by the interactions of these proteins with proliferating cell nuclear antigen (PCNA), the processivity factor for pol δ and ɛ (6, 30, 32, 46, 52, 53).HSV-1 does not appear to encode a protein with DNA ligase activity or one that can specifically cleave 5′ flaps, although it does encode a 5′-to-3′ exonuclease activity (UL12 [10, 20]) and a 3′-to-5′ exonuclease activity that is part of the HSV-1 pol catalytic subunit (27). As for most eukaryotes, RNA primers are essential for HSV-1 DNA synthesis, as demonstrated by the presence of oligoribonucleotides in replicating DNA in vivo (4), by the well-characterized ability of the UL52 protein in complex with the UL5 helicase activity to synthesize oligoribonucleotide primers on ssDNA in vitro (11, 13), and by the requirement of the conserved catalytic residues in the UL52 primase in vitro and in HSV-1-infected cells (14, 26). It is the strand displacement activity of pol δ that produces the 5′ flaps that are key to the removal of RNA primers during Okazaki fragment processing (6, 25). However, we previously demonstrated that wild-type HSV-1 DNA polymerase possesses poor strand displacement activity (62), in contrast to mammalian DNA pol δ (25). Thus, it is not apparent how RNA primers would be removed when encountered by HSV-1 pol during HSV-1 lagging-strand synthesis or how such intermediates would be processed.We wished to test the hypothesis that the nick translation activity of mammalian Fen-1 could function in collaboration with HSV-1 pol to facilitate the proper removal of RNA primers and/or short flaps to produce the ligatable products required for Okazaki fragment processing. In this report, we have examined the ability of wild-type and exonuclease-deficient (exo⁻) HSV-1 pol, which differ in their respective strand displacement activities, to extend model lagging-strand substrates in the presence or absence of mammalian Fen-1. Our results demonstrate that both wild-type and exo⁻ HSV-1 pol can cooperate with and enhance Fen-1 activity to achieve a ligatable nick in vitro. Moreover, colocalization and coimmunoprecipitation studies reveal a physical association of Fen-1 with HSV-1 DNA replication proteins, supporting a model for the involvement of Fen-1 in HSV-1 DNA replication.     

Repeat-Associated Plasticity in the Helicobacter pylori RD Gene Family

The bacterium Helicobacter pylori is remarkable for its ability to persist in the human stomach for decades without provoking sterilizing immunity. Since repetitive DNA can facilitate adaptive genomic flexibility via increased recombination, insertion, and deletion, we searched the genomes of two H. pylori strains for nucleotide repeats. We discovered a family of genes with extensive repetitive DNA that we have termed the H. pylori RD gene family. Each gene of this family is composed of a conserved 3′ region, a variable mid-region encoding 7 and 11 amino acid repeats, and a 5′ region containing one of two possible alleles. Analysis of five complete genome sequences and PCR genotyping of 42 H. pylori strains revealed extensive variation between strains in the number, location, and arrangement of RD genes. Furthermore, examination of multiple strains isolated from a single subject''s stomach revealed intrahost variation in repeat number and composition. Despite prior evidence that the protein products of this gene family are expressed at the bacterial cell surface, enzyme-linked immunosorbent assay and immunoblot studies revealed no consistent seroreactivity to a recombinant RD protein by H. pylori-positive hosts. The pattern of repeats uncovered in the RD gene family appears to reflect slipped-strand mispairing or domain duplication, allowing for redundancy and subsequent diversity in genotype and phenotype. This novel family of hypervariable genes with conserved, repetitive, and allelic domains may represent an important locus for understanding H. pylori persistence in its natural host.Helicobacter pylori, a gram-negative bacterium, is remarkable for its ability to persist in the human stomach for decades. Colonization with H. pylori increases risk for peptic ulcer disease and gastric adenocarcinoma (53, 70) and elicits a vigorous immune response (15). The persistence of H. pylori occurs in a niche in the human body previously considered inhospitable to microbial colonization: the acidic stomach replete with proteolytic enzymes.H. pylori strains exhibit substantial genetic diversity, including extensive variation in the presence, arrangement, order, and identity of genes (2, 4-7, 25, 51, 74). Furthermore, analyses of multiple single-colony H. pylori isolates from separate stomach biopsy specimens of individual patients have demonstrated diversity, both within hosts (27, 65), and over time (36). The mechanisms that generate H. pylori genetic diversity may be among the factors that enable persistence in this environment (3, 28).While the natural ability of H. pylori for transformation and recombination may explain some of the intra- and interhost genetic variation observed in this bacterium (43), point mutations and interspecies recombination alone are not sufficient for explaining the extent of the variation in H. pylori (14, 32). The initial genomic sequencing of H. pylori strains 26695 and J99 (6, 72) revealed large amounts of repetitive DNA (1, 59). DNA repeats in bacteria are associated with mechanisms of plasticity, such as phase variation (49, 67); slipped-strand mispairing (41, 46); and increased rates of recombination, deletion, and insertion (17, 60, 62). Because many of the recombination repair and mismatch repair mechanisms common in bacteria are absent or modified in H. pylori (28-30, 56, 76), this organism may be particularly susceptible to the diversifying effects of repetitive DNA. In fact, loci in the H. pylori genome containing repetitive DNA have been shown to exhibit extensive inter- and intrahost variation (9, 10, 28, 37).We hypothesized that identification of repetitive DNA hotspots in H. pylori would allow the recognition of genes whose variation could aid in persistence. To examine this hypothesis, we conducted in silico analyses to identify open reading frames (ORFs) enriched for DNA repeats and then used a combination of sequence analyses and immunoassays to examine the patterns associated with the specific repetitive DNA observed. Our approach led to the realization that a previously identified H. pylori-specific gene family (19, 52) exhibits extensive genetic variation at multiple levels.     

Roles of ExoI and SbcCD Nucleases in “Reckless” DNA Degradation in recA Mutants of Escherichia coli

Exponentially growing recA mutant cells of Escherichia coli display pronounced DNA degradation that starts at the sites of DNA damage and depends on RecBCD nuclease (ExoV) activity. As a consequence of this “reckless” DNA degradation, populations of recA mutants contain a large proportion of anucleate cells. We have found that both DNA degradation and anucleate-cell production are efficiently suppressed by mutations in the xonA (sbcB) and sbcD genes. The suppressive effects of these mutations were observed in normally grown, as well as in UV-irradiated, recA cells. The products of the xonA and sbcD genes are known to code for the ExoI and SbcCD nucleases, respectively. Since both xonA and sbcD mutations are required for strong suppression of DNA degradation while individual mutations have only a weak suppressive effect, we infer that ExoI and SbcCD play partially redundant roles in regulating DNA degradation in recA cells. We suggest that their roles might be in processing (blunting) DNA ends, thereby producing suitable substrates for RecBCD binding.The RecA protein plays a central role in homologous recombination and recombinational DNA repair in Escherichia coli, as well as in other bacterial species. It catalyzes the key stages of the recombination process—homologous pairing and DNA strand exchange. Cells carrying null mutations in the recA gene are completely deficient for homologous recombination and are extremely sensitive to DNA-damaging agents (for a review, see references 21, 24, and 25). Populations of recA null mutants contain a large proportion (50 to 60%) of nonviable cells, reflecting the inability of these mutants to repair spontaneously occurring DNA damage (31). Also, exponentially growing recA cells display pronounced spontaneous DNA degradation that presumably starts at the sites of DNA damage and that depends on RecBCD nuclease (ExoV) activity (5, 48). This phenotype of recA cells is aggravated after DNA-damaging treatment, such as UV irradiation (48).According to the present data, the majority of RecA-catalyzed DNA transactions in E. coli start with binding of the RecA protein onto single-stranded DNA (ssDNA) substrates. This binding is mediated by the RecBCD and/or RecFOR protein, which helps RecA to overcome hindrance imposed by the SSB protein during competition for the DNA substrate. The RecBCD and RecFOR proteins begin RecA polymerization on ssDNA, giving rise to a nucleoprotein filament that is indispensable for further recombination reactions (3, 33; reviewed in reference 44).The RecBCD enzyme is crucial for initiation of recombinational processes at double-stranded DNA (dsDNA) ends (or breaks [DSBs]) in wild-type E. coli (a set of reactions known as the RecBCD pathway) (9, 43, 44). Upon recognizing a blunt or nearly blunt dsDNA end and binding to it, RecBCD acts as a combination of powerful helicase and nuclease, thus unwinding and simultaneously degrading both strands of the DNA duplex. After encountering a specific octanucleotide sequence designated Chi, the strong 3′-5′ nuclease activity of the enzyme is attenuated and a weaker 5′-3′ nuclease activity is upregulated (1). This Chi-dependent modification allows RecBCD to create a long 3′ ssDNA tail and to direct the loading of RecA protein onto it (2, 3). In vivo data suggest that this transition of RecBCD from a nuclease to a recombinase mode of action requires the presence of the RecA protein, suggesting that the two proteins might interact (27).In wild-type E. coli cells, the RecFOR protein complex works predominantly on DNA gaps, which may arise in chromosomes due to replication forks passing over the noncoding lesions (e.g., UV-induced pyrimidine dimers) or may be present in replication forks stalled at different obstacles in DNA (44). On the other hand, the RecFOR complex has an important role in recBC sbcBC(D) mutant cells, replacing the RecA-loading activity of RecBCD during recombination reactions starting from dsDNA ends. Recombination reactions mediated by RecFOR proteins are termed the RecF (or RecFOR) pathway (44).Cells mutated in the recB and/or recC gene exhibit strong deficiency in conjugational and transductional recombination, as well as in the repair of DSBs (8, 21). These defects can be rectified by extragenic sbcB and sbcC(D) suppressor mutations that inactivate two nucleases, thus enabling full efficiency of the RecF pathway on dsDNA ends (21, 44). The sbcB gene (also designated xonA) encodes exonuclease I (ExoI), the enzyme that digests ssDNA in the 3′-5′ direction (23). The sbcC and sbcD genes encode subunits of the SbcCD nuclease, which acts both as an endonuclease that cleaves hairpin structures and as an exonuclease that degrades linear dsDNA molecules (10, 11). Inactivation of either of the two subunits leads to the loss of SbcCD enzyme activity (18).The exact mechanism of activation of the RecF pathway by sbc mutations is not completely understood. A plausible explanation is that inactivation of ExoI and SbcCD nucleases is necessary to prevent the degradation of recombinogenic 3′ DNA ends created in a RecBCD-independent manner (8, 23, 38, 45, 46). It was recently shown that the sbcB15 mutant allele (encoding a protein without nucleolytic activity) (37) is a better suppressor of the RecBCD⁻ phenotype than an sbcB deletion (50), suggesting that some nonnucleolytic activity of ExoI may also contribute to the efficiency of the RecF pathway (46, 50).ExoI and SbcCD are usually viewed as enzymes with inhibitory roles in recombination due to their deleterious actions on the RecF pathway. However, some results suggest that these enzymes could also have stimulatory roles in recombination reactions proceeding on the RecBCD pathway. Genetic experiments with UV-irradiated E. coli cells indicated that ExoI and SbcCD might be involved in blunting radiation-induced DNA ends prior to RecBC(D) action (38, 45, 46). Such a role of ExoI and SbcCD seems to be particularly critical in recD recF mutants, in which the majority of DSB repair depends on the RecBC enzyme (38). It was also suggested that the blunting roles of the two nucleases may be required during conjugational recombination (16, 46).In this work, we studied the effects of sbcB (xonA) and sbcD mutations on DNA degradation occurring spontaneously in exponentially growing recA mutant cells, as well as on DNA degradation induced in recA mutants by UV irradiation. We have demonstrated that in both cases DNA degradation is strongly reduced in recA mutants that carry in addition a combination of xonA and sbcD null mutations. The results described in this paper suggest that ExoI and SbcCD play partially redundant roles in regulating DNA degradation in recA cells.