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Cordova A, Niese B, Sweet P, Kamat P, Phillip JM, Gordon V, Contreras LM. Quantitative morphological analysis of Deinococcus radiodurans elucidates complex dose-dependent nucleoid condensation during recovery from ionizing radiation. Appl Environ Microbiol 2024; 90:e0010824. [PMID: 38864629 PMCID: PMC11323932 DOI: 10.1128/aem.00108-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 05/19/2024] [Indexed: 06/13/2024] Open
Abstract
The extremophile Deinococcus radiodurans maintains a highly organized and condensed nucleoid as its default state, possibly contributing to its high tolerance to ionizing radiation (IR). Previous studies of the D. radiodurans nucleoid were limited by reliance on manual image annotation and qualitative metrics. Here, we introduce a high-throughput approach to quantify the geometric properties of cells and nucleoids using confocal microscopy, digital reconstructions of cells, and computational modeling. We utilize this novel approach to investigate the dynamic process of nucleoid condensation in response to IR stress. Our quantitative analysis reveals that at the population level, exposure to IR induced nucleoid compaction and decreased the size of D. radiodurans cells. Morphological analysis and clustering identified six distinct sub-populations across all tested experimental conditions. Results indicate that exposure to IR induced fractional redistributions of cells across sub-populations to exhibit morphologies associated with greater nucleoid condensation and decreased the abundance of sub-populations associated with cell division. Nucleoid-associated proteins (NAPs) may link nucleoid compaction and stress tolerance, but their roles in regulating compaction in D. radiodurans are unknown. Imaging of genomic mutants of known and suspected NAPs that contribute to nucleoid condensation found that deletion of nucleic acid-binding proteins, not previously described as NAPs, can remodel the nucleoid by driving condensation or decondensation in the absence of stress and that IR increased the abundance of these morphological states. Thus, our integrated analysis introduces a new methodology for studying environmental influences on bacterial nucleoids and provides an opportunity to further investigate potential regulators of nucleoid condensation.IMPORTANCEDeinococcus radiodurans, an extremophile known for its stress tolerance, constitutively maintains a highly condensed nucleoid. Qualitative studies have described nucleoid behavior under a variety of conditions. However, a lack of quantitative data regarding nucleoid organization and dynamics has limited our understanding of the regulatory mechanisms controlling nucleoid organization in D. radiodurans. Here, we introduce a quantitative approach that enables high-throughput quantitative measurements of subcellular spatial characteristics in bacterial cells. Applying this to wild-type or single-protein-deficient populations of D. radiodurans subjected to ionizing radiation, we identified significant stress-responsive changes in cell shape, nucleoid organization, and morphology. These findings highlight this methodology's adaptability and capacity for quantitatively analyzing the cellular response to stressors for screening cellular proteins involved in bacterial nucleoid organization.
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Affiliation(s)
- Antonio Cordova
- Interdisciplinary Life
Sciences Graduate Program, Department of Molecular Biosciences, The
University of Texas at Austin,
Austin, Texas, USA
- Interdisciplinary Life
Sciences Graduate Program, The University of Texas at
Austin, Austin,
Texas, USA
| | - Brandon Niese
- Department of Physics,
Center for Nonlinear Dynamics, The University of Texas at
Austin, Austin,
Texas, USA
| | - Philip Sweet
- Interdisciplinary Life
Sciences Graduate Program, Department of Molecular Biosciences, The
University of Texas at Austin,
Austin, Texas, USA
| | - Pratik Kamat
- Department of Chemical
and Biomolecular Engineering, Whiting School of Engineering, Johns
Hopkins University,
Baltimore, Maryland,
USA
| | - Jude M. Phillip
- Department of Chemical
and Biomolecular Engineering, Whiting School of Engineering, Johns
Hopkins University,
Baltimore, Maryland,
USA
- Department of
Biomedical Engineering, Institute for Nanobiotechnology, Whiting School
of Engineering, Johns Hopkins
University, Baltimore,
Maryland, USA
| | - Vernita Gordon
- Interdisciplinary Life
Sciences Graduate Program, The University of Texas at
Austin, Austin,
Texas, USA
- Department of Physics,
Center for Nonlinear Dynamics, The University of Texas at
Austin, Austin,
Texas, USA
- LaMontagne Center for
Infectious Disease, The University of Texas at
Austin, Austin,
Texas, USA
| | - Lydia M. Contreras
- Interdisciplinary Life
Sciences Graduate Program, The University of Texas at
Austin, Austin,
Texas, USA
- McKetta Department of
Chemical Engineering, The University of Texas at
Austin, Austin,
Texas, USA
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2
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Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. Nucleic Acids Res 2024; 52:6347-6359. [PMID: 38661211 PMCID: PMC11194089 DOI: 10.1093/nar/gkae308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.
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Affiliation(s)
- Kelly A Manthei
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lia M Munson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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3
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Carr RA, Tucker T, Newman PM, Jadalla L, Jaludi K, Reid BE, Alpheaus DN, Korrapati A, Pivonka AE, Carabetta VJ. N ε-lysine acetylation of the histone-like protein HBsu influences antibiotic survival and persistence in Bacillus subtilis. Front Microbiol 2024; 15:1356733. [PMID: 38835483 PMCID: PMC11148388 DOI: 10.3389/fmicb.2024.1356733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 04/22/2024] [Indexed: 06/06/2024] Open
Abstract
Nε-lysine acetylation is recognized as a prevalent post-translational modification (PTM) that regulates proteins across all three domains of life. In Bacillus subtilis, the histone-like protein HBsu is acetylated at seven sites, which regulates DNA compaction and the process of sporulation. In Mycobacteria, DNA compaction is a survival strategy in response antibiotic exposure. Acetylation of the HBsu ortholog HupB decondenses the chromosome to escape this drug-induced, non-growing state, and in addition, regulates the formation of drug-tolerant subpopulations by altering gene expression. We hypothesized that the acetylation of HBsu plays similar regulatory roles. First, we measured nucleoid area by fluorescence microscopy and in agreement, we found that wild-type cells compacted their nucleoids upon kanamycin exposure, but not exposure to tetracycline. We analyzed a collection of HBsu mutants that contain lysine substitutions that mimic the acetylated (glutamine) or unacetylated (arginine) forms of the protein. Our findings indicate that some level of acetylation is required at K3 for a proper response and K75 must be deacetylated. Next, we performed time-kill assays of wild-type and mutant strains in the presence of different antibiotics and found that interfering with HBsu acetylation led to faster killing rates. Finally, we examined the persistent subpopulation and found that altering the acetylation status of HBsu led to an increase in persister cell formation. In addition, we found that most of the deacetylation-mimic mutants, which have compacted nucleoids, were delayed in resuming growth following removal of the antibiotic, suggesting that acetylation is required to escape the persistent state. Together, this data adds an additional regulatory role for HBsu acetylation and further supports the existence of a histone-like code in bacteria.
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Affiliation(s)
- Rachel A Carr
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
| | - Trichina Tucker
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
| | - Precious M Newman
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
| | - Lama Jadalla
- Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ, United States
| | - Kamayel Jaludi
- Rowan-Virtua School of Osteopathic Medicine, Stratford, NJ, United States
| | - Briana E Reid
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
| | - Damian N Alpheaus
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
| | - Anish Korrapati
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
| | - April E Pivonka
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, United States
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4
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Li L, Guo B, Dai L, Liu C, Lin Z. Ebselen and TPI-1, as RecG helicase inhibitors, potently enhance the susceptibility of Pseudomonas aeruginosa to DNA damage agents. Biochem Pharmacol 2024; 222:116051. [PMID: 38354956 DOI: 10.1016/j.bcp.2024.116051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
Holliday junction (HJ) is a four-way structured DNA intermediate in processes of homologous recombination and DNA double-stranded break (DSB) repair. In bacteria, HJs are processed via either the RuvABC or RecG-dependent pathways. In addition, RecG also plays a critical role in the reactivation of stalled replication forks, making it an attractive target for antibacterial drug development. Here, we conducted a high-throughput screening targeting the RecG helicase from a common opportunistic pathogen Pseudomonas aeruginosa (Pa). From a library containing 7920 compounds, we identified Ebselen and TPI-1 (2',5'-Dichloro-[1,1'-biphenyl]-2,5-dione) as two potent PaRecG inhibitors, with IC50 values of 0.31 ± 0.02 μM and 1.16 ± 0.06 μM, respectively. Further biochemical analyses suggested that both Ebselen and TPI-1 inhibited the ATPase activity of PaRecG, and hindered its binding to HJ DNA with high selectivity. These compounds, when combined with our previously reported RuvAB inhibitors, resulted in more severe DNA repair defects than the individual treatment, and potently enhanced the susceptibility of P. aeruginosa to the DNA damage agents. This work reports novel small molecule inhibitors of RecG, offering valuable chemical tools for advancing our understanding of RecG's function and mechanism. Additionally, these inhibitors might be further developed as promising antibacterial agents in the fight against P. aeruginosa infections.
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Affiliation(s)
- Longheng Li
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Binbin Guo
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Lin Dai
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Chun Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China.
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou 350108, China.
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5
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Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580553. [PMID: 38405983 PMCID: PMC10889028 DOI: 10.1101/2024.02.15.580553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.
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Affiliation(s)
- Kelly A. Manthei
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lia M. Munson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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6
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Zahradka K, Repar J, Đermić D, Zahradka D. Chromosome Segregation and Cell Division Defects in Escherichia coli Recombination Mutants Exposed to Different DNA-Damaging Treatments. Microorganisms 2023; 11:microorganisms11030701. [PMID: 36985274 PMCID: PMC10051365 DOI: 10.3390/microorganisms11030701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/05/2023] [Indexed: 03/30/2023] Open
Abstract
Homologous recombination repairs potentially lethal DNA lesions such as double-strand DNA breaks (DSBs) and single-strand DNA gaps (SSGs). In Escherichia coli, DSB repair is initiated by the RecBCD enzyme that resects double-strand DNA ends and loads RecA recombinase to the emerging single-strand (ss) DNA tails. SSG repair is mediated by the RecFOR protein complex that loads RecA onto the ssDNA segment of gaped duplex. In both repair pathways, RecA catalyses reactions of homologous DNA pairing and strand exchange, while RuvABC complex and RecG helicase process recombination intermediates. In this work, we have characterised cytological changes in various recombination mutants of E. coli after three different DNA-damaging treatments: (i) expression of I-SceI endonuclease, (ii) γ-irradiation, and (iii) UV-irradiation. All three treatments caused severe chromosome segregation defects and DNA-less cell formation in the ruvABC, recG, and ruvABC recG mutants. After I-SceI expression and γ-irradiation, this phenotype was efficiently suppressed by the recB mutation, indicating that cytological defects result mostly from incomplete DSB repair. In UV-irradiated cells, the recB mutation abolished cytological defects of recG mutants and also partially suppressed the cytological defects of ruvABC recG mutants. However, neither recB nor recO mutation alone could suppress the cytological defects of UV-irradiated ruvABC mutants. The suppression was achieved only by simultaneous inactivation of the recB and recO genes. Cell survival and microscopic analysis suggest that chromosome segregation defects in UV-irradiated ruvABC mutants largely result from defective processing of stalled replication forks. The results of this study show that chromosome morphology is a valuable marker in genetic analyses of recombinational repair in E. coli.
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Affiliation(s)
- Ksenija Zahradka
- Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Jelena Repar
- Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Damir Đermić
- Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Davor Zahradka
- Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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7
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RecA is required for the assembly of RecN into DNA repair complexes on the nucleoid. J Bacteriol 2021; 203:e0024021. [PMID: 34339298 DOI: 10.1128/jb.00240-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Homologous recombination requires the coordinated effort of several proteins to complete break resection, homologous pairing and resolution of DNA crossover structures. RecN is a conserved bacterial protein important of double strand break repair and a member of the Structural Maintenance of Chromosomes (SMC) protein family. Current models in Bacillus subtilis propose that RecN responds to double stranded breaks prior to RecA and end processing suggesting that RecN is among the very first proteins responsible for break detection. Here, we investigate the contribution of RecA and end processing by AddAB to RecN recruitment into repair foci in vivo. Using this approach, we found that recA is required for RecN-GFP focus formation on the nucleoid during normal growth and in response to DNA damage. In the absence of recA function, RecN foci form in a low percentage of cells, RecN localizes away from the nucleoid, and RecN fails to assemble in response to DNA damage. In contrast, we show that the response of RecA-GFP foci to DNA damage is unchanged in the presence or absence of recN. In further support of RecA activity preceding RecN we show that ablation of the double-strand break end processing enzyme addAB results in a failure of RecN to form foci in response to DNA damage. With these results, we conclude that RecA and end processing function prior to RecN establishing a critical step for the recruitment and participation of RecN during DNA break repair in Bacillus subtilis. IMPORTANCE Homologous recombination is important for the repair of DNA double-strand breaks. RecN is a highly conserved protein that has been shown to be important for sister chromatid cohesion and for survival to break-inducing clastogens. Here, we show that the assembly of RecN into repair foci on the bacterial nucleoid requires the end processing enzyme AddAB and the recombinase RecA. In the absence of either recA or end processing RecN-GFP foci are no longer DNA damage inducible and foci form in a subset of cells as large complexes in regions away from the nucleoid. Our results establish the stepwise order of action, where double-strand break end processing and RecA association precede the participation of RecN during break repair in Bacillus subtilis.
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8
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Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open Biol 2020; 10:200293. [PMID: 33259746 PMCID: PMC7776575 DOI: 10.1098/rsob.200293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.
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Affiliation(s)
| | | | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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9
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Springall L, Hughes CD, Simons M, Azinas S, Van Houten B, Kad NM. Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival. Nucleic Acids Res 2019; 46:1256-1265. [PMID: 29240933 PMCID: PMC5814901 DOI: 10.1093/nar/gkx1244] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/01/2017] [Indexed: 02/05/2023] Open
Abstract
Nucleotide excision repair (NER) is the primary mechanism for removal of ultraviolet light (UV)-induced DNA photoproducts and is mechanistically conserved across all kingdoms of life. Bacterial NER involves damage recognition by UvrA2 and UvrB, followed by UvrC-mediated incision either side of the lesion. Here, using a combination of in vitro and in vivo single-molecule studies we show that a UvrBC complex is capable of lesion identification in the absence of UvrA. Single-molecule analysis of eGFP-labelled UvrB and UvrC in living cells showed that UV damage caused these proteins to switch from cytoplasmic diffusion to stable complexes on DNA. Surprisingly, ectopic expression of UvrC in a uvrA deleted strain increased UV survival. These data provide evidence for a previously unrealized mechanism of survival that can occur through direct lesion recognition by a UvrBC complex.
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Affiliation(s)
- Luke Springall
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
| | - Craig D Hughes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Stavros Azinas
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | | | - Neil M Kad
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
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10
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Scutigliani EM, Scholl ER, Grootemaat AE, Khanal S, Kochan JA, Krawczyk PM, Reits EA, Garzan A, Ngo HX, Green KD, Garneau-Tsodikova S, Ruijter JM, van Veen HA, van der Wel NN. Interfering With DNA Decondensation as a Strategy Against Mycobacteria. Front Microbiol 2018; 9:2034. [PMID: 30233521 PMCID: PMC6135046 DOI: 10.3389/fmicb.2018.02034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis is once again a major global threat, leading to more than 1 million deaths each year. Treatment options for tuberculosis patients are limited, expensive and characterized by severe side effects, especially in the case of multidrug-resistant forms. Uncovering novel vulnerabilities of the pathogen is crucial to generate new therapeutic strategies. Using high resolution microscopy techniques, we discovered one such vulnerability of Mycobacterium tuberculosis. We demonstrate that the DNA of M. tuberculosis can condense under stressful conditions such as starvation and antibiotic treatment. The DNA condensation is reversible and specific for viable bacteria. Based on these observations, we hypothesized that blocking the recovery from the condensed state could weaken the bacteria. We showed that after inducing DNA condensation, and subsequent blocking of acetylation of DNA binding proteins, the DNA localization in the bacteria is altered. Importantly under these conditions, Mycobacterium smegmatis did not replicate and its survival was significantly reduced. Our work demonstrates that agents that block recovery from the condensed state of the nucleoid can be exploited as antibiotic. The combination of fusidic acid and inhibition of acetylation of DNA binding proteins, via the Eis enzyme, potentiate the efficacy of fusidic acid by 10 and the Eis inhibitor to 1,000-fold. Hence, we propose that successive treatment with antibiotics and drugs interfering with recovery from DNA condensation constitutes a novel approach for treatment of tuberculosis and related bacterial infections.
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Affiliation(s)
- Enzo M Scutigliani
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Edwin R Scholl
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Anita E Grootemaat
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Sadhana Khanal
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Jakub A Kochan
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | | | - Eric A Reits
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Huy X Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | | | - Jan M Ruijter
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Henk A van Veen
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
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11
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Influence of uvrA, recJ and recN gene mutations on nucleoid reorganization in UV-treated Escherichia coli cells. FEMS Microbiol Lett 2018; 365:4987205. [DOI: 10.1093/femsle/fny110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/24/2018] [Indexed: 01/02/2023] Open
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12
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Burby PE, Simmons LA. MutS2 Promotes Homologous Recombination in Bacillus subtilis. J Bacteriol 2017; 199:e00682-16. [PMID: 27799325 PMCID: PMC5198493 DOI: 10.1128/jb.00682-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/21/2016] [Indexed: 02/07/2023] Open
Abstract
Bacterial MutS proteins are subdivided into two families, MutS1 and MutS2. MutS1 family members recognize DNA replication errors during their participation in the well-characterized mismatch repair (MMR) pathway. In contrast to the well-described function of MutS1, the function of MutS2 in bacteria has remained less clear. In Helicobacter pylori and Thermus thermophilus, MutS2 has been shown to suppress homologous recombination. The role of MutS2 is unknown in the Gram-positive bacterium Bacillus subtilis In this work, we investigated the contribution of MutS2 to maintaining genome integrity in B. subtilis We found that deletion of mutS2 renders B. subtilis sensitive to the natural antibiotic mitomycin C (MMC), which requires homologous recombination for repair. We demonstrate that the C-terminal small MutS-related (Smr) domain is necessary but not sufficient for tolerance to MMC. Further, we developed a CRISPR/Cas9 genome editing system to test if the inducible prophage PBSX was the underlying cause of the observed MMC sensitivity. Genetic analysis revealed that MMC sensitivity was dependent on recombination and not on nucleotide excision repair or a symptom of prophage PBSX replication and cell lysis. We found that deletion of mutS2 resulted in decreased transformation efficiency using both plasmid and chromosomal DNA. Further, deletion of mutS2 in a strain lacking the Holliday junction endonuclease gene recU resulted in increased MMC sensitivity and decreased transformation efficiency, suggesting that MutS2 could function redundantly with RecU. Together, our results support a model where B. subtilis MutS2 helps to promote homologous recombination, demonstrating a new function for bacterial MutS2. IMPORTANCE Cells contain pathways that promote or inhibit recombination. MutS2 homologs are Smr-endonuclease domain-containing proteins that have been shown to function in antirecombination in some bacteria. We present evidence that B. subtilis MutS2 promotes recombination, providing a new function for MutS2. We found that cells lacking mutS2 are sensitive to DNA damage that requires homologous recombination for repair and have reduced transformation efficiency. Further analysis indicates that the C-terminal Smr domain requires the N-terminal portion of MutS2 for function in vivo Moreover, we show that a mutS2 deletion is additive with a recU deletion, suggesting that these proteins have a redundant function in homologous recombination. Together, our study shows that MutS2 proteins have adapted different functions that impact recombination.
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Affiliation(s)
- Peter E Burby
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P. Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli. Nat Commun 2016; 7:12568. [PMID: 27562541 PMCID: PMC5007444 DOI: 10.1038/ncomms12568] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 07/14/2016] [Indexed: 11/19/2022] Open
Abstract
Nucleotide excision repair (NER) removes chemically diverse DNA lesions in all domains of life. In Escherichia coli, UvrA and UvrB initiate NER, although the mechanistic details of how this occurs in vivo remain to be established. Here, we use single-molecule fluorescence imaging to provide a comprehensive characterization of the lesion search, recognition and verification process in living cells. We show that NER initiation involves a two-step mechanism in which UvrA scans the genome and locates DNA damage independently of UvrB. Then UvrA recruits UvrB from solution to the lesion. These steps are coordinated by ATP binding and hydrolysis in the ‘proximal' and ‘distal' UvrA ATP-binding sites. We show that initial UvrB-independent damage recognition by UvrA requires ATPase activity in the distal site only. Subsequent UvrB recruitment requires ATP hydrolysis in the proximal site. Finally, UvrA dissociates from the lesion complex, allowing UvrB to orchestrate the downstream NER reactions. Nucleotide excision repair is able to identify and remove a wide range of DNA helix distorting lesions from the genome. Here the authors use single molecule imaging of UvrA and UvrB molecules and suggest a two-step ‘scan and recruit' model for UvrA function.
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Affiliation(s)
- Mathew Stracy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Marcin Jaciuk
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Ksiecia Trojdena Street, 02-109 Warsaw, Poland
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Ksiecia Trojdena Street, 02-109 Warsaw, Poland
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Pawel Zawadzki
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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14
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Passot FM, Nguyen HH, Dard-Dascot C, Thermes C, Servant P, Espéli O, Sommer S. Nucleoid organization in the radioresistant bacteriumDeinococcus radiodurans. Mol Microbiol 2015; 97:759-74. [DOI: 10.1111/mmi.13064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Fanny Marie Passot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris Sud; Bâtiment 409 Orsay 91405 France
| | - Hong Ha Nguyen
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris Sud; Bâtiment 409 Orsay 91405 France
| | - Cloelia Dard-Dascot
- Plateforme Intégrée IMAGIF - CNRS; Avenue de la Terrasse; Gif sur Yvette 91198 France
| | - Claude Thermes
- Plateforme Intégrée IMAGIF - CNRS; Avenue de la Terrasse; Gif sur Yvette 91198 France
| | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris Sud; Bâtiment 409 Orsay 91405 France
| | - Olivier Espéli
- Center for Interdisciplinary Research In Biology (CIRB); Collège de France; CNRS UMR 7241, INSERM U1050, 11 place Marcelin Berthelot Paris 75005 France
| | - Suzanne Sommer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris Sud; Bâtiment 409 Orsay 91405 France
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15
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Sidorenko J, Ukkivi K, Kivisaar M. NER enzymes maintain genome integrity and suppress homologous recombination in the absence of exogenously induced DNA damage in Pseudomonas putida. DNA Repair (Amst) 2015; 25:15-26. [DOI: 10.1016/j.dnarep.2014.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/29/2014] [Accepted: 11/05/2014] [Indexed: 02/04/2023]
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16
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Odsbu I, Skarstad K. DNA compaction in the early part of the SOS response is dependent on RecN and RecA. MICROBIOLOGY-SGM 2014; 160:872-882. [PMID: 24615185 DOI: 10.1099/mic.0.075051-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The nucleoids of undamaged Escherichia coli cells have a characteristic shape and number, which is dependent on the growth medium. Upon induction of the SOS response by a low dose of UV irradiation an extensive reorganization of the nucleoids occurred. Two distinct phases were observed by fluorescence microscopy. First, the nucleoids were found to change shape and fuse into compact structures at midcell. The compaction of the nucleoids lasted for 10-20 min and was followed by a phase where the DNA was dispersed throughout the cells. This second phase lasted for ~1 h. The compaction was found to be dependent on the recombination proteins RecA, RecO and RecR as well as the SOS-inducible, SMC (structural maintenance of chromosomes)-like protein RecN. RecN protein is produced in high amounts during the first part of the SOS response. It is possible that the RecN-mediated 'compact DNA' stage at the beginning of the SOS response serves to stabilize damaged DNA prior to recombination and repair.
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Affiliation(s)
- Ingvild Odsbu
- Department of Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Kirsten Skarstad
- Department of Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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17
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Abstract
DNA helicases have important roles in genome maintenance. The RecD helicase has been well studied as a component of the heterotrimeric RecBCD helicase-nuclease enzyme important for double-strand break repair in Escherichia coli. Interestingly, many bacteria lack RecBC and instead contain a RecD2 helicase, which is not known to function as part of a larger complex. Depending on the organism studied, RecD2 has been shown to provide resistance to a broad range of DNA-damaging agents while also contributing to mismatch repair (MMR). Here we investigated the importance of Bacillus subtilis RecD2 helicase to genome integrity. We show that deletion of recD2 confers a modest increase in the spontaneous mutation rate and that the mutational signature in ΔrecD2 cells is not consistent with an MMR defect, indicating a new function for RecD2 in B. subtilis. To further characterize the role of RecD2, we tested the deletion strain for sensitivity to DNA-damaging agents. We found that loss of RecD2 in B. subtilis sensitized cells to several DNA-damaging agents that can block or impair replication fork movement. Measurement of replication fork progression in vivo showed that forks collapse more frequently in ΔrecD2 cells, supporting the hypothesis that RecD2 is important for normal replication fork progression. Biochemical characterization of B. subtilis RecD2 showed that it is a 5'-3' helicase and that it directly binds single-stranded DNA binding protein. Together, our results highlight novel roles for RecD2 in DNA replication which help to maintain replication fork integrity during normal growth and when forks encounter DNA damage.
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18
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Ghosh A, Passaris I, Tesfazgi Mebrhatu M, Rocha S, Vanoirbeek K, Hofkens J, Aertsen A. Cellular localization and dynamics of the Mrr type IV restriction endonuclease of Escherichia coli. Nucleic Acids Res 2014; 42:3908-18. [PMID: 24423871 PMCID: PMC3973329 DOI: 10.1093/nar/gkt1370] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In this study, we examined the intracellular whereabouts of Mrr, a cryptic type IV restriction endonuclease of Escherichia coli K12, in response to different conditions. In absence of stimuli triggering its activity, Mrr was found to be strongly associated with the nucleoid as a number of discrete foci, suggesting the presence of Mrr hotspots on the chromosome. Previously established elicitors of Mrr activity, such as exposure to high (hydrostatic) pressure (HP) or expression of the HhaII methyltransferase, both caused nucleoid condensation and an unexpected coalescence of Mrr foci. However, although the resulting Mrr/nucleoid complex was stable when triggered with HhaII, it tended to be only short-lived when elicited with HP. Moreover, HP-mediated activation of Mrr typically led to cellular blebbing, suggesting a link between chromosome and cellular integrity. Interestingly, Mrr variants could be isolated that were specifically compromised in either HhaII- or HP-dependent activation, underscoring a mechanistic difference in the way both triggers activate Mrr. In general, our results reveal that Mrr can take part in complex spatial distributions on the nucleoid and can be engaged in distinct modes of activity.
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Affiliation(s)
- Anirban Ghosh
- Department of Microbial and Molecular Systems (M2S), Laboratory of Food Microbiology, KU Leuven, B-3001 Leuven, Belgium and Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
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19
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Ramírez-Guadiana FH, Del Carmen Barajas-Ornelas R, Ayala-García VM, Yasbin RE, Robleto E, Pedraza-Reyes M. Transcriptional coupling of DNA repair in sporulating Bacillus subtilis cells. Mol Microbiol 2013; 90:1088-99. [PMID: 24118570 DOI: 10.1111/mmi.12417] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2013] [Indexed: 11/28/2022]
Abstract
In conditions of halted or limited genome replication, like those experienced in sporulating cells of Bacillus subtilis, a more immediate detriment caused by DNA damage is altering the transcriptional programme that drives this developmental process. Here, we report that mfd, which encodes a conserved bacterial protein that mediates transcription-coupled DNA repair (TCR), is expressed together with uvrA in both compartments of B. subtilis sporangia. The function of Mfd was found to be important for processing the genetic damage during B. subtilis sporulation. Disruption of mfd sensitized developing spores to mitomycin-C (M-C) treatment and UV-C irradiation. Interestingly, in non-growing sporulating cells, Mfd played an anti-mutagenic role as its absence promoted UV-induced mutagenesis through a pathway involving YqjH/YqjW-mediated translesion synthesis (TLS). Two observations supported the participation of Mfd-dependent TCR in spore morphogenesis: (i) disruption of mfd notoriously affected the efficiency of B. subtilis sporulation and (ii) in comparison with the wild-type strain, a significant proportion of Mfd-deficient sporangia that survived UV-C treatment developed an asporogenous phenotype. We propose that the Mfd-dependent repair pathway operates during B. subtilis sporulation and that its function is required to eliminate genetic damage from transcriptionally active genes.
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20
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Shechter N, Zaltzman L, Weiner A, Brumfeld V, Shimoni E, Fridmann-Sirkis Y, Minsky A. Stress-induced condensation of bacterial genomes results in re-pairing of sister chromosomes: implications for double strand DNA break repair. J Biol Chem 2013; 288:25659-25667. [PMID: 23884460 DOI: 10.1074/jbc.m113.473025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genome condensation is increasingly recognized as a generic stress response in bacteria. To better understand the physiological implications of this response, we used fluorescent markers to locate specific sites on Escherichia coli chromosomes following exposure to cytotoxic stress. We find that stress-induced condensation proceeds through a nonrandom, zipper-like convergence of sister chromosomes, which is proposed to rely on the recently demonstrated intrinsic ability of identical double-stranded DNA molecules to specifically identify each other. We further show that this convergence culminates in spatial proximity of homologous sites throughout chromosome arms. We suggest that the resulting apposition of homologous sites can explain how repair of double strand DNA breaks might occur in a mechanism that is independent of the widely accepted yet physiologically improbable genome-wide search for homologous templates. We claim that by inducing genome condensation and orderly convergence of sister chromosomes, diverse stress conditions prime bacteria to effectively cope with severe DNA lesions such as double strand DNA breaks.
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Affiliation(s)
| | | | | | - Vlad Brumfeld
- Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eyal Shimoni
- Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
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21
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Pereira AR, Reed P, Veiga H, Pinho MG. The Holliday junction resolvase RecU is required for chromosome segregation and DNA damage repair in Staphylococcus aureus. BMC Microbiol 2013; 13:18. [PMID: 23356868 PMCID: PMC3584850 DOI: 10.1186/1471-2180-13-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/17/2013] [Indexed: 11/24/2022] Open
Abstract
Background The Staphylococcus aureus RecU protein is homologous to a Bacillus subtilis Holliday junction resolvase. Interestingly, RecU is encoded in the same operon as PBP2, a penicillin-binding protein required for cell wall synthesis and essential for the full expression of resistance in Methicillin Resistant S. aureus strains. In this work we have studied the role of RecU in the clinical pathogen S. aureus. Results Depletion of RecU in S. aureus results in the appearance of cells with compact nucleoids, septa formed over the DNA and anucleate cells. RecU-depleted cells also show increased septal recruitment of the DNA translocase SpoIIIE, presumably to resolve chromosome segregation defects. Additionally cells are more sensitive to DNA damaging agents such as mitomycin C or UV radiation. Expression of RecU from the ectopic chromosomal spa locus showed that co-expression of RecU and PBP2 was not necessary to ensure correct cell division, a process that requires tight coordination between chromosome segregation and septal cell wall synthesis. Conclusions RecU is required for correct chromosome segregation and DNA damage repair in S. aureus. Co-expression of recU and pbp2 from the same operon is not required for normal cell division.
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Affiliation(s)
- Ana R Pereira
- Laboratory of Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av, da República, Oeiras 2780-157, Portugal
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22
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Abstract
From microbes to multicellular eukaryotic organisms, all cells contain pathways responsible for genome maintenance. DNA replication allows for the faithful duplication of the genome, whereas DNA repair pathways preserve DNA integrity in response to damage originating from endogenous and exogenous sources. The basic pathways important for DNA replication and repair are often conserved throughout biology. In bacteria, high-fidelity repair is balanced with low-fidelity repair and mutagenesis. Such a balance is important for maintaining viability while providing an opportunity for the advantageous selection of mutations when faced with a changing environment. Over the last decade, studies of DNA repair pathways in bacteria have demonstrated considerable differences between Gram-positive and Gram-negative organisms. Here we review and discuss the DNA repair, genome maintenance, and DNA damage checkpoint pathways of the Gram-positive bacterium Bacillus subtilis. We present their molecular mechanisms and compare the functions and regulation of several pathways with known information on other organisms. We also discuss DNA repair during different growth phases and the developmental program of sporulation. In summary, we present a review of the function, regulation, and molecular mechanisms of DNA repair and mutagenesis in Gram-positive bacteria, with a strong emphasis on B. subtilis.
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23
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Delmas S, Duggin IG, Allers T. DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii. Mol Microbiol 2012; 87:168-79. [PMID: 23145964 PMCID: PMC3565448 DOI: 10.1111/mmi.12091] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2012] [Indexed: 11/30/2022]
Abstract
In prokaryotes the genome is organized in a dynamic structure called the nucleoid, which is embedded in the cytoplasm. We show here that in the archaeon Haloferax volcanii, compaction and reorganization of the nucleoid is induced by stresses that damage the genome or interfere with its replication. The fraction of cells exhibiting nucleoid compaction was proportional to the dose of the DNA damaging agent, and results obtained in cells defective for nucleotide excision repair suggest that breakage of DNA strands triggers reorganization of the nucleoid. We observed that compaction depends on the Mre11-Rad50 complex, suggesting a link to DNA double-strand break repair. However, compaction was observed in a radA mutant, indicating that the role of Mre11-Rad50 in nucleoid reorganisation is independent of homologous recombination. We therefore propose that nucleoid compaction is part of a DNA damage response that accelerates cell recovery by helping DNA repair proteins to locate their targets, and facilitating the search for intact DNA sequences during homologous recombination.
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Affiliation(s)
- Stéphane Delmas
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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24
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Sambir M, Ivanova LB, Bryksin AV, Godfrey HP, Cabello FC. Functional analysis of Borrelia burgdorferi uvrA in DNA damage protection. FEMS Microbiol Lett 2011; 317:172-80. [PMID: 21272060 DOI: 10.1111/j.1574-6968.2011.02226.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Bacterial pathogens face constant challenges from DNA-damaging agents generated by host phagocytes. Although Borrelia burgdorferi appears to have much fewer DNA repair enzymes than pathogens with larger genomes, it does contain homologues of uvrA and uvrB (subunits A and B of excinuclease ABC). As a first step to exploring the physiologic function of uvrA(Bbu) and its possible role in survival in the host in the face of DNA-damaging agents, a partially deleted uvrA mutant was isolated by targeted inactivation. While growth of this mutant was markedly inhibited by UV irradiation, mitomycin C (MMC) and hydrogen peroxide at doses that lacked effect on wild-type B. burgdorferi, its response to pH 6.0-6.8 and reactive nitrogen intermediates was similar to that of the wild-type parental strain. The sensitivity of the inactivation mutant to UV irradiation, MMC and peroxide was complemented by an extrachromosomal copy of uvrA(Bbu). We conclude that uvrA(Bbu) is functional in B. burgdorferi.
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Affiliation(s)
- Mariya Sambir
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
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25
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Clp and Lon proteases occupy distinct subcellular positions in Bacillus subtilis. J Bacteriol 2008; 190:6758-68. [PMID: 18689473 DOI: 10.1128/jb.00590-08] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among other functions, ATP-dependent proteases degrade misfolded proteins and remove several key regulatory proteins necessary to activate stress responses. In Bacillus subtilis, ClpX, ClpE, and ClpC form homohexameric ATPases that couple to the ClpP peptidase. To understand where these peptidases and ATPases localize in living cells, each protein was fused to a fluorescent moiety. We found that ClpX-GFP (green fluorescent protein) and ClpP-GFP localized as focal assemblies in areas that were not occupied by the nucleoid. We found that the percentage of cells with ClpP-GFP foci increased following heat shock independently of protein synthesis. We determined that ClpE-YFP (yellow fluorescent protein) and ClpC-YFP formed foci coincident with nucleoid edges, usually near cell poles. Furthermore, we found that ClpQ-YFP (HslV) localized as small foci, usually positioned near the cell membrane. We found that ClpQ-YFP foci were dependent on the presence of the cognate hexameric ATPase ClpY (HslU). Moreover, we found that LonA-GFP is coincident with the nucleoid during normal growth and that LonA-GFP also localized to the forespore during development. We also investigated LonB-GFP and found that this protein localized to the forespore membrane early in development, followed by localization throughout the forespore later in development. Our comprehensive study has shown that in B. subtilis several ATP-fueled proteases occupy distinct subcellular locations. With these data, we suggest that substrate specificity could be determined, in part, by the spatial and temporal organization of proteases in vivo.
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26
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Norris V, den Blaauwen T, Cabin-Flaman A, Doi RH, Harshey R, Janniere L, Jimenez-Sanchez A, Jin DJ, Levin PA, Mileykovskaya E, Minsky A, Saier M, Skarstad K. Functional taxonomy of bacterial hyperstructures. Microbiol Mol Biol Rev 2007; 71:230-53. [PMID: 17347523 PMCID: PMC1847379 DOI: 10.1128/mmbr.00035-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The levels of organization that exist in bacteria extend from macromolecules to populations. Evidence that there is also a level of organization intermediate between the macromolecule and the bacterial cell is accumulating. This is the level of hyperstructures. Here, we review a variety of spatially extended structures, complexes, and assemblies that might be termed hyperstructures. These include ribosomal or "nucleolar" hyperstructures; transertion hyperstructures; putative phosphotransferase system and glycolytic hyperstructures; chemosignaling and flagellar hyperstructures; DNA repair hyperstructures; cytoskeletal hyperstructures based on EF-Tu, FtsZ, and MreB; and cell cycle hyperstructures responsible for DNA replication, sequestration of newly replicated origins, segregation, compaction, and division. We propose principles for classifying these hyperstructures and finally illustrate how thinking in terms of hyperstructures may lead to a different vision of the bacterial cell.
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Affiliation(s)
- Vic Norris
- Department of Science, University of Rouen, 76821 Mont Saint Aignan Cedex, France.
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27
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Moeller R, Stackebrandt E, Douki T, Cadet J, Rettberg P, Mollenkopf HJ, Reitz G, Horneck G. DNA bipyrimidine photoproduct repair and transcriptional response of UV-C irradiated Bacillus subtilis. Arch Microbiol 2007; 188:421-31. [PMID: 17551712 DOI: 10.1007/s00203-007-0263-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 03/08/2007] [Accepted: 05/16/2007] [Indexed: 11/24/2022]
Abstract
Vegetative wild-type and DNA repair-deficient (homologous recombination, recA and nucleotide excision repair, uvrB) Bacillus subtilis cells were exposed to UV-C radiation. Colony formation, DNA bipyrimidine photoproducts and gene expression were measured during cell recovery. Gene expression was measured after 60 min cell recovery where 50% (wild-type), 30% (recA) and 8% (uvrB), respectively, of the UV-C induced DNA photoproducts were repaired. We examined changes in the gene expression following UV exposure in wild-type and both repair-deficient strains. A set of known and unknown genes were found to be significantly up-regulated in wild-type B. subtilis cells, whereas no or lower gene induction was determined for both mutant strains. In addition, the possible roles of newly identified UV-responsive genes are discussed with respect to cellular recovery following exposure to UV irradiation.
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Affiliation(s)
- Ralf Moeller
- German Aerospace Center (DLR), Radiation Biology Division, Institute of Aerospace Medicine, Linder Hoehe, 51147 Cologne, Germany.
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28
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Zeibell K, Aguila S, Yan Shi V, Chan A, Yang H, Miller JH. Mutagenesis and repair in Bacillus anthracis: the effect of mutators. J Bacteriol 2007; 189:2331-8. [PMID: 17220233 PMCID: PMC1899402 DOI: 10.1128/jb.01656-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have generated mutator strains of Bacillus anthracis Sterne by using directed gene knockouts to investigate the effect of deleting genes involved in mismatch repair, oxidative repair, and maintaining triphosphate pools. The single-knockout strains are deleted for mutS, mutY, mutM, or ndk. We also made double-knockout strains that are mutS ndk or mutY mutM. We have measured the levels of mutations in the rpoB gene that lead to the Rif(r) phenotype and have examined the mutational specificity. In addition, we examined the mutational specificity of two mutagens, 5-azacytidine and N-methyl-N'-nitro-N-nitroso-guanidine. The mutY and mutM single knockouts are weak mutators by themselves, but the combination of mutY mutM results in very high mutation rates, all due to G:C --> T:A transversions. The situation parallels that seen in Escherichia coli. Also, mutS knockouts are strong mutators and even stronger in the presence of a deletion of ndk. The number of sites in rpoB that can result in the Rif(r) phenotype by single-base substitution is more limited than in certain other bacteria, such as E. coli and Deinococcus radiodurans, although the average mutation rate per mutational site is roughly comparable. Hotspots at sites with virtually identical surrounding sequences are organism specific.
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Affiliation(s)
- Krystle Zeibell
- Department of Microbiology, University of California, Los Angeles, CA 90095, USA
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29
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Abstract
Bacteria, like eukaryotic organisms, must compact the DNA molecule comprising their genome and form a functional chromosome. Yet, bacteria do it differently. A number of factors contribute to genome compaction and organization in bacteria, including entropic effects, supercoiling and DNA-protein interactions. A gamut of new experimental techniques have allowed new advances in the investigation of these factors, and spurred much interest in the dynamic response of the chromosome to environmental cues, segregation, and architecture, during both exponential and stationary phases. We review these recent developments with emphasis on the multifaceted roles that DNA-protein interactions play.
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Affiliation(s)
- Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
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30
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Shen CH, Chiang YC, Hsu CH, Yang MK. Identification and characterization of two uvrA genes of Xanthomonas axonopodis pathovar citri. Mol Genet Genomics 2006; 277:149-60. [PMID: 17146667 DOI: 10.1007/s00438-006-0180-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2006] [Accepted: 10/04/2006] [Indexed: 11/25/2022]
Abstract
Two uvrA-like genes, designated uvrA1 and uvrA2, that may be involved in nucleotide excision repair in Xanthomonas axonopodis pv. citri (X. a. pv. citri) strain XW47 were characterized. The uvrA1 gene was found to be 2,964 bp in length capable of encoding a protein of 987 amino acids. The uvrA2 gene was determined to be 2,529 bp with a coding potential of 842 amino acids. These two proteins share 71 and 39% identity, respectively, in amino acid sequence with the UvrA protein of Escherichia coli. Analyses of the deduced amino acid sequence revealed that UvrA1 and UvrA2 have structures characteristic of UvrA proteins, including the Walker A and Walker B motifs, zinc finger DNA binding domains, and helix-turn-helix motif with a polyglycine hinge region. The uvrA1 or uvrA2 mutant, constructed by gene replacement, was more sensitive to DNA-damaging agents methylmethane sulfonate (MMS), mitomycin C (MMC), or ultraviolet (UV) than the wild type. The uvrA1 mutant was four orders of magnitude more sensitive to UV irradiation and two orders of magnitude more sensitive to MMS than the uvrA2 mutant. The uvrA1uvrA2 double mutant was one order of magnitude more sensitive to MMS, MMC, or UV than the uvrA1 single mutant. These results suggest that UvrA1 plays a more important role than UvrA2 in DNA repair in X. a. pv. citri. Both uvrA1 and uvrA2 genes were found to be constitutively expressed in the wild type and lexA1 or lexA2 mutant of X. a. pv. citri, and treatment of these cells with sublethal dose of MMC did not alter the expression of these two genes. Results of electrophoresis mobility shift assays revealed that LexA1 or LexA2 does not bind to either the uvrA1 or the uvrA2 promoter. These results suggest that uvrA expression in X. a. pv. citri is not regulated by the SOS response system.
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Affiliation(s)
- Che-Hung Shen
- Department of Life Science, Fu Jen University, 510 Chun-Chen Road, Taipei, 242, Taiwan, ROC
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31
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Kim SH, Gorski L, Reynolds J, Orozco E, Fielding S, Park YH, Borucki MK. Role of uvrA in the growth and survival of Listeria monocytogenes under UV radiation and acid and bile stress. J Food Prot 2006; 69:3031-6. [PMID: 17186676 DOI: 10.4315/0362-028x-69.12.3031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Listeria monocytogenes encounters numerous stresses both in the food environment and during infection of the host. The ability to survive and tolerate bile and low pH conditions, which are two major stresses, is of particular importance for survival within the host. The uvrA gene in other bacteria is involved in the repair of acid-induced DNA damage and in adaptation to low pH. Thus, a uvrA in-frame deletion mutant was constructed to identify the role of uvrA in the growth and survival of L. monocytogenes under various environmental conditions. The uvrA mutant was highly sensitive to UV radiation. Growth under normal laboratory conditions was impaired during the exponential phase, and the time to reach the exponential phase of growth, TV(max), was significantly delayed (P < 0.05). Growth of the uvrA mutant in acidic medium (pH 5) was slightly impaired, and the TV(max) was significantly delayed (P < 0.05). Growth and the TV(max) of the mutant in the presence of 0.3% bile salts also were significantly impaired (P < 0.05). These results suggest that uvrA is needed for optimal growth and survival of L. monocytogenes under various stressful environmental conditions.
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Affiliation(s)
- So Hyun Kim
- KRF Zoonotic Disease Priority Research Institute and Department of Microbiology, Seoul National University, Seoul 151-742, Korea
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32
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Waldeck J, Meyer-Rammes H, Nahrstedt H, Eichstädt R, Wieland S, Meinhardt F. Targeted deletion of the uvrBA operon and biological containment in the industrially important Bacillus licheniformis. Appl Microbiol Biotechnol 2006; 73:1340-7. [PMID: 17004053 DOI: 10.1007/s00253-006-0602-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 07/20/2006] [Accepted: 08/07/2006] [Indexed: 10/24/2022]
Abstract
From a Bacillus licheniformis wild type as well as a defined asporogenous derivative, stable UV hypersensitive mutants were generated by targeted deletion of the uvrBA operon, encoding highly conserved key components of the nucleotide excision repair. Comparative studies, which included the respective parental strains, revealed no negative side effects of the deletion, neither on enzyme secretion nor on vegetative propagation. Thus, the uvrBA locus proved to be a useful deletion target for achieving biological containment in this industrially exploited bacterium. In contrast to recA mutants, which also display UV hypersensitivity, further strain development via homologous recombination techniques will be still possible in such uvr mutants.
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Affiliation(s)
- Jens Waldeck
- Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Corrensstrasse 3, 48149, Münster, Germany
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33
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Truglio JJ, Croteau DL, Van Houten B, Kisker C. Prokaryotic nucleotide excision repair: the UvrABC system. Chem Rev 2006; 106:233-52. [PMID: 16464004 DOI: 10.1021/cr040471u] [Citation(s) in RCA: 238] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James J Truglio
- Department of Pharmacological Sciences, State University of New York at Stony Brook, 11794-5115, USA
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Van Houten B, Croteau DL, DellaVecchia MJ, Wang H, Kisker C. 'Close-fitting sleeves': DNA damage recognition by the UvrABC nuclease system. Mutat Res 2005; 577:92-117. [PMID: 15927210 DOI: 10.1016/j.mrfmmm.2005.03.013] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Revised: 03/11/2005] [Accepted: 03/11/2005] [Indexed: 05/02/2023]
Abstract
DNA damage recognition represents a long-standing problem in the field of protein-DNA interactions. This article reviews our current knowledge of how damage recognition is achieved in bacterial nucleotide excision repair through the concerted action of the UvrA, UvrB, and UvrC proteins.
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Affiliation(s)
- Bennett Van Houten
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, 111 Alexander Drive, MD D3-01, Research Triangle Park, NC 27709, USA
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35
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Cappa F, Cattivelli D, Cocconcelli PS. The uvrA gene is involved in oxidative and acid stress responses in Lactobacillus helveticus CNBL1156. Res Microbiol 2005; 156:1039-47. [PMID: 16125908 DOI: 10.1016/j.resmic.2005.06.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 06/01/2005] [Accepted: 06/03/2005] [Indexed: 10/25/2022]
Abstract
The uvrA gene of Lactobacillus helveticus CNBL1156 coding for subunit A of the excinuclease ABC complex involved in the nucleotide excision repair mechanism was identified. Analysis of the uvrA locus revealed the presence of three open reading frames, merR, sat and uvrA, which coded respectively for a MerR-like regulatory protein, a putative protein with homology to streptothricin acetyl transferase and for a UvrA protein. RNA analysis by northern blotting and RT-PCR showed that sat and uvrA were transcriptionally coupled. UvrA from L. helveticus contained the conserved domains of bacterial excinuclease A, as well as the two ATP binding sites and the zinc binding domains. The transcriptional activity of uvrA indicated that this gene was activated by exposure to UV radiation and oxidative stress. In addition, we observed that the expression of uvrA was inducible by pH; moreover, the role of UvrA in protection against stress was confirmed by acid adaptation experiments. Pretreatment of cells at pH 5 conferred resistance to H2O2, suggesting a specific adaptive response to pH-induced DNA damage. The results from this study indicate that UvrA contributes to acid and oxidative tolerance in L. helveticus, and suggest that it plays a role in survival at low pH under normal conditions.
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Affiliation(s)
- Fabrizio Cappa
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29100 Piacenza, Italy
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Erill I, Jara M, Salvador N, Escribano M, Campoy S, Barbé J. Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics. Nucleic Acids Res 2004; 32:6617-26. [PMID: 15604457 PMCID: PMC545464 DOI: 10.1093/nar/gkh996] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The LexA regulon encompasses an ensemble of genes involved in preserving cell viability under massive DNA damage and is present in most bacterial phyla. Up to date, however, the scope of this network had only been assessed in the Gamma Proteobacteria. Here, we report the structure of the LexA regulon in the Alpha Proteobacteria, using a combined approach that makes use of in vitro and in vivo techniques to assist and validate the comparative genomics in silico methodology. This leads to the first experimentally validated description of the LexA regulon in the Alpha Proteobacteria, and comparison of regulon core structures in both classes suggests that a least common multiple set of genes (recA, ssb, uvrA and ruvCAB) might be a defining property of the Proteobacteria LexA network.
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Affiliation(s)
- Ivan Erill
- Biomedical Applications Group, Centro Nacional de Microelectrónica, 08193 Bellaterra, Spain
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37
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Abstract
Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.
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Affiliation(s)
- Abraham Minsky
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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38
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Abstract
DNA repair and protection processes impose arduous demands upon cellular systems. The high-fidelity recombinational repair pathway entails a rapid genome-wide search for sequence homology. The efficiency of this transaction is intriguing in light of the uniquely adverse diffusion traits of the involved species. DNA protection in cells exposed to continuous stress or prolonged starvation is equally enigmatic, because the ability of such cells to deploy energy-dependent enzymatic repair processes is hampered as a result of progressive perturbation of the intracellular energy balance. DNA repair in radio-resistant bacteria, which involves accurate chromosome reconstruction from multiple fragments, is similarly associated with apparently insurmountable logistical obstacles. The studies reviewed here imply that the mechanisms deployed to overcome these intrinsic hurdles have a basic common denominator. In all these cases, condensed and ordered chromatin assemblies are formed, within which molecular diffusion is restricted and confined. Restricted diffusion thus appears as a general strategy that is exploited by nature to facilitate homologous search, to promote energy-independent DNA protection through physical DNA sequestration and attenuated accessibility to damaging agents, and to enable error-free repair of multiple double-strand DNA breaks.
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Affiliation(s)
- Abraham Minsky
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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