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Zhang J, Wang S, Abee T, van der Veen S. Role of Base Excision Repair in Listeria monocytogenes DNA Stress Survival During Infections. J Infect Dis 2020; 223:721-732. [PMID: 32644146 DOI: 10.1093/infdis/jiaa412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/07/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Base excision repair (BER), consisting mostly of lesion-specific DNA glycosylases and apurinic/apyrimidinic (AP) endonucleases, is one of the most important DNA repair mechanisms for repair of single nucleobase lesions generated by reactive oxygen and nitrogen species as part of an immune response against bacterial infections. However, few studies have addressed the contribution of BER to bacterial virulence and Listeria monocytogenes BER has thus far remained completely uncharacterized. METHODS Analysis of the L. monocytogenes EGDe genome identified 7 DNA glycosylases (MutM, MutY, Nth, Tag, Mpg, Ung, and Ung2) and 2 apurinic/apyrimidinic endonucleases (Xth and Nfo) as part of BER. Markerless in-frame deletion mutants were generated for all 9 genes, and mutants were tested for DNA damage survival, mutagenesis, and the ability to colonize a mouse model of infection. RESULTS Distinct lesion-specific phenotypes were identified for all deletion mutants. Importantly, the Δnth, ΔmutY, and Δnfo mutants were significantly attenuated for virulence in the mouse model and showed much lower colonization of the liver and spleen or were unable to compete with the wild-type strain during in vivo competition assays. CONCLUSIONS Our results highlight the importance of BER for L. monocytogenes virulence and survival of DNA-damaging insults during host colonization.
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Affiliation(s)
- Juan Zhang
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shuyi Wang
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Stijn van der Veen
- Department of Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Dermatology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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2
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Base excision repair pathways of bacteria: new promise for an old problem. Future Med Chem 2020; 12:339-355. [PMID: 32031026 DOI: 10.4155/fmc-2019-0267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Infectious diseases continue to be a major cause of human mortality. With the emergence of drug resistance, diseases that were long thought to have been curable by antibiotics are resurging. There is an urgent clinical need for newer antibiotics that target novel cellular pathways to overcome resistance to currently used therapeutics. The base excision repair (BER) pathways of the pathogen restore altered bases and safeguard the genomic integrity of the pathogen from the host's immune response. Although the BER machinery is of paramount importance to the survival of the pathogens, its potential as a drug target is largely unexplored. In this review, we discuss the importance of BER in different pathogenic organisms and the potential of its inhibition with small molecules.
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Frye SA, Lång E, Beyene GT, Balasingham SV, Homberset H, Rowe AD, Ambur OH, Tønjum T. The Inner Membrane Protein PilG Interacts with DNA and the Secretin PilQ in Transformation. PLoS One 2015; 10:e0134954. [PMID: 26248334 PMCID: PMC4527729 DOI: 10.1371/journal.pone.0134954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/15/2015] [Indexed: 11/19/2022] Open
Abstract
Expression of type IV pili (Tfp), filamentous appendages emanating from the bacterial surface, is indispensable for efficient neisserial transformation. Tfp pass through the secretin pore consisting of the membrane protein PilQ. PilG is a polytopic membrane protein, conserved in Gram-positive and Gram-negative bacteria, that is required for the biogenesis of neisserial Tfp. PilG null mutants are devoid of pili and non-competent for transformation. Here, recombinant full-length, truncated and mutated variants of meningococcal PilG were overexpressed, purified and characterized. We report that meningococcal PilG directly binds DNA in vitro, detected by both an electromobility shift analysis and a solid phase overlay assay. PilG DNA binding activity was independent of the presence of the consensus DNA uptake sequence. PilG-mediated DNA binding affinity was mapped to the N-terminus and was inactivated by mutation of residues 43 to 45. Notably, reduced meningococcal transformation of DNA in vivo was observed when PilG residues 43 to 45 were substituted by alanine in situ, defining a biologically significant DNA binding domain. N-terminal PilG also interacted with the N-terminal region of PilQ, which previously was shown to bind DNA. Collectively, these data suggest that PilG and PilQ in concert bind DNA during Tfp-mediated transformation.
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Affiliation(s)
- Stephan A. Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Emma Lång
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | | | - Ole Herman Ambur
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Department of Microbiology, University of Oslo, Oslo, Norway
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4
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van der Veen S, Tang CM. The BER necessities: the repair of DNA damage in human-adapted bacterial pathogens. Nat Rev Microbiol 2015; 13:83-94. [PMID: 25578955 DOI: 10.1038/nrmicro3391] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During colonization and disease, bacterial pathogens must survive the onslaught of the host immune system. A key component of the innate immune response is the generation of reactive oxygen and nitrogen species by phagocytic cells, which target and disrupt pathogen molecules, particularly DNA, and the base excision repair (BER) pathway is the most important mechanism for the repair of such oxidative DNA damage. In this Review, we discuss how the human-specific pathogens Mycobacterium tuberculosis, Helicobacter pylori and Neisseria meningitidis have evolved specialized mechanisms of DNA repair, particularly their BER pathways, compared with model organisms such as Escherichia coli. This specialization in DNA repair is likely to reflect the distinct niches occupied by these important human pathogens in the host.
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Affiliation(s)
- Stijn van der Veen
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford, OX1 3RE, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford, OX1 3RE, UK
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Alfsnes K, Raynaud X, Tønjum T, Ambur OH. Mathematical and live meningococcal models for simple sequence repeat dynamics - coherent predictions and observations. PLoS One 2014; 9:e101637. [PMID: 24999629 PMCID: PMC4085013 DOI: 10.1371/journal.pone.0101637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/10/2014] [Indexed: 11/18/2022] Open
Abstract
Evolvability by means of simple sequence repeat (SSR) instability is a feature under the constant influence of opposing selective pressures to expand and compress the repeat tract and is mechanistically influenced by factors that affect genetic instability. In addition to direct selection for protein expression and structural integrity, other factors that influence tract length evolution were studied. The genetic instability of SSRs that switch the expression of antibiotic resistance ON and OFF was modelled mathematically and monitored in a panel of live meningococcal strains. The mathematical model showed that the SSR length of a theoretical locus in an evolving population may be shaped by direct selection of expression status (ON or OFF), tract length dependent (α) and tract length independent factors (β). According to the model an increase in α drives the evolution towards shorter tracts. An increase in β drives the evolution towards a normal distribution of tract lengths given that an upper and a lower limit are set. Insertion and deletion biases were shown to skew allelic distributions in both directions. The meningococcal SSR model was tested in vivo by monitoring the frequency of spectinomycin resistance OFF→ON switching in a designed locus. The instability of a comprehensive panel of the homopolymeric SSRs, constituted of a range of 5-13 guanine nucleotides, was monitored in wildtype and mismatch repair deficient backgrounds. Both the repeat length itself and mismatch repair deficiency were shown to influence the genetic instability of the homopolymeric tracts. A possible insertion bias was observed in tracts ≤G10. Finally, an inverse correlation between the number of tract-encoded amino acids and growth in the presence of ON-selection illustrated a limitation to SSR expansion in an essential gene associated with the designed model locus and the protein function mediating antibiotic resistance.
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Affiliation(s)
- Kristian Alfsnes
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Xavier Raynaud
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Ole Herman Ambur
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- * E-mail:
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Nagorska K, Silhan J, Li Y, Pelicic V, Freemont PS, Baldwin GS, Tang CM. A network of enzymes involved in repair of oxidative DNA damage in Neisseria meningitidis. Mol Microbiol 2012; 83:1064-1079. [PMID: 22296581 PMCID: PMC3749813 DOI: 10.1111/j.1365-2958.2012.07989.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although oxidative stress is a key aspect of innate immunity, little is known about how host-restricted pathogens successfully repair DNA damage. Base excision repair is responsible for correcting nucleobases damaged by oxidative stress, and is essential for bloodstream infection caused by the human pathogen, Neisseria meningitidis. We have characterized meningococcal base excision repair enzymes involved in the recognition and removal of damaged nucleobases, and incision of the DNA backbone. We demonstrate that the bi-functional glycosylase/lyases Nth and MutM share several overlapping activities and functional redundancy. However, MutM and other members of the GO system, which deal with 8-oxoG, a common lesion of oxidative damage, are not required for survival of N. meningitidis under oxidative stress. Instead, the mismatch repair pathway provides back-up for the GO system, while the lyase activity of Nth can substitute for the meningococcal AP endonuclease, NApe. Our genetic and biochemical evidence shows that DNA repair is achieved through a robust network of enzymes that provides a flexible system of DNA repair. This network is likely to reflect successful adaptation to the human nasopharynx, and might provide a paradigm for DNA repair in other prokaryotes.
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Affiliation(s)
- Krzysztofa Nagorska
- Centre for Molecular Microbiology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Jan Silhan
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, UK
| | - Yanwen Li
- Centre for Molecular Microbiology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Vladimir Pelicic
- Centre for Molecular Microbiology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Paul S. Freemont
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, UK
| | - Geoff S. Baldwin
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, UK
| | - Christoph M. Tang
- Centre for Molecular Microbiology and Infection, Imperial College London, London, SW7 2AZ, UK
- Sir William Dunn School of Pathology, South Parks Road, University of Oxford, Oxford, OX1 3RE, UK
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Silhan J, Nagorska K, Zhao Q, Jensen K, Freemont PS, Tang CM, Baldwin GS. Specialization of an Exonuclease III family enzyme in the repair of 3' DNA lesions during base excision repair in the human pathogen Neisseria meningitidis. Nucleic Acids Res 2011; 40:2065-75. [PMID: 22067446 PMCID: PMC3300015 DOI: 10.1093/nar/gkr905] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We have previously demonstrated that the two Exonuclease III (Xth) family members present within the obligate human pathogen Neisseria meningitidis, NApe and NExo, are important for survival under conditions of oxidative stress. Of these, only NApe possesses AP endonuclease activity, while the primary function of NExo remained unclear. We now reveal further functional specialization at the level of 3′-PO4 processing for NExo. We demonstrate that the bi-functional meningococcal glycosylases Nth and MutM can perform strand incisions at abasic sites in addition to NApe. However, no such functional redundancy exists for the 3′-phosphatase activity of NExo, and the cytotoxicity of 3′-blocking lesions is reflected in the marked sensitivity of a mutant lacking NExo to oxidative stress, compared to strains deficient in other base excision repair enzymes. A histidine residue within NExo that is responsible for its lack of AP endonuclease activity is also important for its 3′-phosphatase activity, demonstrating an evolutionary trade off in enzyme function at the single amino acid level. This specialization of two Xth enzymes for the 3′-end processing and strand-incision reactions has not previously been observed and provides a new paradigm within the prokaryotic world for separation of these critical functions during base excision repair.
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Affiliation(s)
- Jan Silhan
- Division of Molecular Biosciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
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Benam AV, Lång E, Alfsnes K, Fleckenstein B, Rowe AD, Hovland E, Ambur OH, Frye SA, Tønjum T. Structure-function relationships of the competence lipoprotein ComL and SSB in meningococcal transformation. MICROBIOLOGY (READING, ENGLAND) 2011; 157:1329-1342. [PMID: 21330432 PMCID: PMC3140584 DOI: 10.1099/mic.0.046896-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Neisseria meningitidis, the meningococcus, is naturally competent for transformation throughout its growth cycle. The uptake of exogenous DNA into the meningococcus cell during transformation is a multi-step process. Beyond the requirement for type IV pilus expression for efficient transformation, little is known about the neisserial proteins involved in DNA binding, uptake and genome integration. This study aimed to identify and characterize neisserial DNA binding proteins in order to further elucidate the multi-factorial transformation machinery. The meningococcus inner membrane and soluble cell fractions were searched for DNA binding components by employing 1D and 2D gel electrophoresis approaches in combination with a solid-phase overlay assay with DNA substrates. Proteins that bound DNA were identified by MS analysis. In the membrane fraction, multiple components bound DNA, including the neisserial competence lipoprotein ComL. In the soluble fraction, the meningococcus orthologue of the single-stranded DNA binding protein SSB was predominant. The DNA binding activity of the recombinant ComL and SSB proteins purified to homogeneity was verified by electromobility shift assay, and the ComL-DNA interaction was shown to be Mg²+-dependent. In 3D models of the meningococcus ComL and SSB predicted structures, potential DNA binding sites were suggested. ComL was found to co-purify with the outer membrane, directly interacting with the secretin PilQ. The combined use of 1D/2D solid-phase overlay assays with MS analysis was a useful strategy for identifying DNA binding components. The ComL DNA binding properties and outer membrane localization suggest that this lipoprotein plays a direct role in neisserial transformation, while neisserial SSB is a DNA binding protein that contributes to the terminal part of the transformation process.
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Affiliation(s)
- Afsaneh V Benam
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Emma Lång
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Kristian Alfsnes
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Burkhard Fleckenstein
- Centre for Immune Regulation, Institute of Immunology, University of Oslo, NO-0027 Oslo, Norway
| | - Alexander D Rowe
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
| | - Eirik Hovland
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Ole Herman Ambur
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Stephan A Frye
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
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Unifying themes in microbial associations with animal and plant hosts described using the gene ontology. Microbiol Mol Biol Rev 2011; 74:479-503. [PMID: 21119014 DOI: 10.1128/mmbr.00017-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community.
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Mismatch correction modulates mutation frequency and pilus phase and antigenic variation in Neisseria gonorrhoeae. J Bacteriol 2010; 192:316-25. [PMID: 19854909 DOI: 10.1128/jb.01228-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mismatch correction (MMC) system repairs DNA mismatches and single nucleotide insertions or deletions postreplication. To test the functions of MMC in the obligate human pathogen Neisseria gonorrhoeae, homologues of the core MMC genes mutS and mutL were inactivated in strain FA1090. No mutH homologue was found in the FA1090 genome, suggesting that gonococcal MMC is not methyl directed. MMC mutants were compared to a mutant in uvrD, the helicase that functions with MMC in Escherichia coli. Inactivation of MMC or uvrD increased spontaneous resistance to rifampin and nalidixic acid, and MMC/uvrD double mutants exhibited higher mutation frequencies than any single mutant. Loss of MMC marginally enhanced the transformation efficiency of DNA carrying a single nucleotide mismatch but not that of DNA with a 1-kb insertion. Unlike the exquisite UV sensitivity of the uvrD mutant, inactivating MMC did not affect survival after UV irradiation. MMC and uvrD mutants exhibited increased PilC-dependent pilus phase variation. mutS-deficient gonococci underwent an increased frequency of pilin antigenic variation, whereas uvrD had no effect. Recombination tracts in the mutS pilin variants were longer than in parental gonococci but utilized the same donor pilS loci. These results show that gonococcal MMC repairs mismatches and small insertion/deletions in DNA and also affects the recombination events underlying pilin antigenic variation. The differential effects of MMC and uvrD in gonococci unexpectedly reveal that MMC can function independently of uvrD in this human-specific pathogen.
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