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Abstract
Staphylococcus aureus is a common cause of both superficial and invasive infections of humans and animals. Despite a potent host response and apparently appropriate antibiotic therapy, staphylococcal infections frequently become chronic or recurrent, demonstrating a remarkable ability of S. aureus to withstand the hostile host environment. There is growing evidence that staphylococcal DNA repair makes important contributions to the survival of the pathogen in host tissues, as well as promoting the emergence of mutants that resist host defenses and antibiotics. While much of what we know about DNA repair in S. aureus is inferred from studies with model organisms, the roles of specific repair mechanisms in infection are becoming clear and differences with Bacillus subtilis and Escherichia coli have been identified. Furthermore, there is growing interest in staphylococcal DNA repair as a target for novel therapeutics that sensitize the pathogen to host defenses and antibiotics. In this review, we discuss what is known about staphylococcal DNA repair and its role in infection, examine how repair in S. aureus is similar to, or differs from, repair in well-characterized model organisms, and assess the potential of staphylococcal DNA repair as a novel therapeutic target.
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Genome-scale target identification in Escherichia coli for high-titer production of free fatty acids. Nat Commun 2021; 12:4976. [PMID: 34404790 PMCID: PMC8371096 DOI: 10.1038/s41467-021-25243-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/29/2021] [Indexed: 12/17/2022] Open
Abstract
To construct a superior microbial cell factory for chemical synthesis, a major challenge is to fully exploit cellular potential by identifying and engineering beneficial gene targets in sophisticated metabolic networks. Here, we take advantage of CRISPR interference (CRISPRi) and omics analyses to systematically identify beneficial genes that can be engineered to promote free fatty acids (FFAs) production in Escherichia coli. CRISPRi-mediated genetic perturbation enables the identification of 30 beneficial genes from 108 targets related to FFA metabolism. Then, omics analyses of the FFAs-overproducing strains and a control strain enable the identification of another 26 beneficial genes that are seemingly irrelevant to FFA metabolism. Combinatorial perturbation of four beneficial genes involving cellular stress responses results in a recombinant strain ihfAL−-aidB+-ryfAM−-gadAH−, producing 30.0 g L−1 FFAs in fed-batch fermentation, the maximum titer in E. coli reported to date. Our findings are of help in rewiring cellular metabolism and interwoven intracellular processes to facilitate high-titer production of biochemicals. Identification of gene targets is one of the major challenges to construct superior microbial cell factory for chemical synthesis. Here, the authors employ CRISPRi and omics analyses for genome-scale target genes identification for high-titer production of free fatty acids in E. coli.
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Lienard A, Hosny M, Jneid J, Schuldiner S, Cellier N, Sotto A, La Scola B, Lavigne JP, Pantel A. Escherichia coli Isolated from Diabetic Foot Osteomyelitis: Clonal Diversity, Resistance Profile, Virulence Potential, and Genome Adaptation. Microorganisms 2021; 9:microorganisms9020380. [PMID: 33668594 PMCID: PMC7918245 DOI: 10.3390/microorganisms9020380] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 01/22/2023] Open
Abstract
This study assessed the clonal diversity, the resistance profile and the virulence potential of Escherichia coli strains isolated from diabetic foot infection (DFI) and diabetic foot osteomyelitis (DFOM). A retrospective single-centre study was conducted on patients diagnosed with E. coli isolated from deep DFI and DFOM at Clinique du Pied Diabétique Gard-Occitanie (France) over a two-year period. Phylogenetic backgrounds, virulence factors (VFs) and antibiotic resistance profiles were determined. Whole-genome analysis of E. coli strains isolated from same patients at different periods were performed. From the two-years study period, 35 E. coli strains isolated from 33 patients were analysed; 73% were isolated from DFOM. The majority of the strains belonged to the virulent B2 and D phylogenetic groups (82%). These isolates exhibited a significant higher average of VFs number than strains belonging to other groups (p < 0.001). papG2 gene was significantly more detected in strains belonging to B2 phylogroup isolated from DFI compared to DFOM (p = 0.003). The most prevalent antibiotic resistance pattern was observed for ampicillin (82%), cotrimoxazole (45%), and ciprofloxacin (33%). The genome analysis of strains isolated at two periods in DFOM showed a decrease of the genome size, and this decrease was more important for the strain isolated at nine months (vs. four months). A shared mutation on the putative acyl-CoA dehydrogenase-encoding gene aidB was observed on both strains. E. coli isolates from DFOM were highly genetically diverse with different pathogenicity traits. Their adaptation in the bone structure could require genome reduction and some important modifications in the balance virulence/resistance of the bacteria.
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Affiliation(s)
- Alexi Lienard
- VBIC, INSERM U1047, Université de Montpellier, UFR de Médecine, 30908 Nîmes CEDEX 2, France;
| | - Michel Hosny
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France; (M.H.); (J.J.); (B.L.S.)
| | - Joanne Jneid
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France; (M.H.); (J.J.); (B.L.S.)
| | - Sophie Schuldiner
- VBIC, INSERM U1047, Université de Montpellier, Service des Maladies Métaboliques et Endocriniennes, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
| | - Nicolas Cellier
- Service d’Orthopédie, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
| | - Albert Sotto
- VBIC, INSERM U1047, Université de Montpellier, Service des Maladies Infectieuses et Tropicales, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
| | - Bernard La Scola
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France; (M.H.); (J.J.); (B.L.S.)
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
- Correspondence:
| | - Alix Pantel
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
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Di Somma A, Canè C, Moretta A, Cirillo A, Cemič F, Duilio A. Characterization of the Proteins Involved in the DNA Repair Mechanism in M. smegmatis. Int J Mol Sci 2020; 21:ijms21155391. [PMID: 32751237 PMCID: PMC7432924 DOI: 10.3390/ijms21155391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 11/26/2022] Open
Abstract
Several alkylating agents that either occur in the environment or are self-produced can cause DNA-damaging injuries in bacterial cells. Therefore, all microorganisms have developed repair systems that are able to counteract DNA alkylation damage. The adaptive response to alkylation stress in Escherichia coli consists of the Ada operon, which has been widely described; however, the homologous system in Mycobacterium tuberculosis (MTB) has been shown to have a different genetic organization but it is still largely unknown. In order to describe the defense system of MTB, we first investigated the proteins involved in the repair mechanism in the homologous non-pathogenic mycobacterium M. smegmatis. Ogt, Ada-AlkA and FadE8 proteins were recombinantly produced, purified and characterized. The biological role of Ogt was examined using proteomic experiments to identify its protein partners in vivo under stress conditions. Our results suggested the formation of a functional complex between Ogt and Ada-AlkA, which was confirmed both in silico by docking calculations and by gel filtration chromatography. We propose that this stable association allows the complex to fulfill the biological roles exerted by Ada in the homologous E. coli system. Finally, FadE8 was demonstrated to be structurally and functionally related to its E. coli homologous, AidB.
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Affiliation(s)
- Angela Di Somma
- Department of Chemical Sciences, Università Federico II di, 80126 Naples, Italy; (A.D.S.); (C.C.)
- Istituto Nazionale Biostrutture Biostrumentazioni, INBB, 00136 Rome, Italy
| | - Carolina Canè
- Department of Chemical Sciences, Università Federico II di, 80126 Naples, Italy; (A.D.S.); (C.C.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy;
| | - Antonio Moretta
- Department of Science, Università degli Studi della Basilicata, 85100 Potenza, Italy;
| | | | - Franz Cemič
- Department of Mathematics, Natural Sciences and Computer Science, University of Applied Sciences Giessen, Wiesenstr. 14, 35390 Giessen, Germany;
| | - Angela Duilio
- Department of Chemical Sciences, Università Federico II di, 80126 Naples, Italy; (A.D.S.); (C.C.)
- Correspondence:
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5
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Poncin K, Roba A, Jimmidi R, Potemberg G, Fioravanti A, Francis N, Willemart K, Zeippen N, Machelart A, Biondi EG, Muraille E, Vincent SP, De Bolle X. Occurrence and repair of alkylating stress in the intracellular pathogen Brucella abortus. Nat Commun 2019; 10:4847. [PMID: 31649248 PMCID: PMC6813329 DOI: 10.1038/s41467-019-12516-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 09/10/2019] [Indexed: 01/08/2023] Open
Abstract
It is assumed that intracellular pathogenic bacteria have to cope with DNA alkylating stress within host cells. Here we use single-cell reporter systems to show that the pathogen Brucella abortus does encounter alkylating stress during the first hours of macrophage infection. Genes encoding direct repair and base-excision repair pathways are required by B. abortus to face this stress in vitro and in a mouse infection model. Among these genes, ogt is found to be under the control of the conserved cell-cycle transcription factor GcrA. Our results highlight that the control of DNA repair in B. abortus displays distinct features that are not present in model organisms such as Escherichia coli. It is assumed that intracellular pathogenic bacteria must cope with DNA alkylating stress within host cells. Here, Poncin et al. show that the pathogen Brucella abortus does encounter alkylating stress within macrophages, and shed light into the pathways required for DNA repair in this organism.
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Affiliation(s)
- Katy Poncin
- URBM, Narilis, University of Namur, Namur, Belgium.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Agnès Roba
- URBM, Narilis, University of Namur, Namur, Belgium
| | - Ravikumar Jimmidi
- Unité de Chimie Organique, University of Namur, 61 rue de Bruxelles, 5000, Namur, Belgium
| | | | - Antonella Fioravanti
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, Université de Lille, 50 Avenue Halley, Villeneuve d'Ascq, France.,VIB,Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | | | | | | | - Arnaud Machelart
- URBM, Narilis, University of Namur, Namur, Belgium.,Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, Center for Infection and Immunity of Lille, Lille, France
| | - Emanuele G Biondi
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, Université de Lille, 50 Avenue Halley, Villeneuve d'Ascq, France
| | - Eric Muraille
- IMM, 31 Chemin Joseph Aiguier, 13009 Marseille, Aix-Marseille Université, Marseille, France.,Laboratoire de Parasitologie, Faculté de Médecine, Université Libre de Bruxelles, Brussels, Belgium
| | - Stéphane P Vincent
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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Di Somma A, Caterino M, Soni V, Agarwal M, di Pasquale P, Zanetti S, Molicotti P, Cannas S, Nandicoori VK, Duilio A. The bifunctional protein GlmU is a key factor in biofilm formation induced by alkylating stress in Mycobacterium smegmatis. Res Microbiol 2019; 170:171-181. [DOI: 10.1016/j.resmic.2019.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
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7
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Di Pasquale P, Caterino M, Di Somma A, Squillace M, Rossi E, Landini P, Iebba V, Schippa S, Papa R, Selan L, Artini M, Palamara AT, Palamara A, Duilio A. Exposure of E. coli to DNA-Methylating Agents Impairs Biofilm Formation and Invasion of Eukaryotic Cells via Down Regulation of the N-Acetylneuraminate Lyase NanA. Front Microbiol 2016; 7:147. [PMID: 26904018 PMCID: PMC4749703 DOI: 10.3389/fmicb.2016.00147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/26/2016] [Indexed: 12/26/2022] Open
Abstract
DNA methylation damage can be induced by endogenous and exogenous chemical agents, which has led every living organism to develop suitable response strategies. We investigated protein expression profiles of Escherichia coli upon exposure to the alkylating agent methyl-methane sulfonate (MMS) by differential proteomics. Quantitative proteomic data showed a massive downregulation of enzymes belonging to the glycolytic pathway and fatty acids degradation, strongly suggesting a decrease of energy production. A strong reduction in the expression of the N-acetylneuraminate lyases (NanA) involved in the sialic acid metabolism was also observed. Using a null NanA mutant and DANA, a substrate analog acting as competitive inhibitor, we demonstrated that down regulation of NanA affects biofilm formation and adhesion properties of E. coli MV1161. Exposure to alkylating agents also decreased biofilm formation and bacterial adhesion to Caco-2 eukaryotic cell line by the adherent invasive E. coli (AIEC) strain LF82. Our data showed that methylation stress impairs E. coli adhesion properties and suggest a possible role of NanA in biofilm formation and bacteria host interactions.
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Affiliation(s)
- Pamela Di Pasquale
- Department of Chemical Sciences, University of Naples "Federico II" Naples, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II" Naples, Italy
| | - Angela Di Somma
- Department of Chemical Sciences, University of Naples "Federico II" Naples, Italy
| | - Marta Squillace
- Department of Chemical Sciences, University of Naples "Federico II" Naples, Italy
| | - Elio Rossi
- Department of Biosciences, University of Milan Milan, Italy
| | - Paolo Landini
- Department of Biosciences, University of Milan Milan, Italy
| | - Valerio Iebba
- Department of Public Health and Infectious Diseases, Pasteur Institute Cenci, Bolognetti Foundation, Sapienza University of Rome Rome, Italy
| | - Serena Schippa
- Department of Public Health and Infectious Diseases, Sapienza University of Rome Rome, Italy
| | - Rosanna Papa
- Department of Public Health and Infectious Diseases, Sapienza University of Rome Rome, Italy
| | - Laura Selan
- Department of Public Health and Infectious Diseases, Sapienza University of Rome Rome, Italy
| | - Marco Artini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome Rome, Italy
| | - Anna Teresa Palamara
- Department of Public Health and Infectious Diseases, Pasteur Institute Cenci, Bolognetti Foundation, Sapienza University of RomeRome, Italy; IRCCS, San Raffaele Pisana Telematic UniversityRome, Italy
| | | | - Angela Duilio
- Department of Chemical Sciences, University of Naples "Federico II" Naples, Italy
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Mielecki D, Wrzesiński M, Grzesiuk E. Inducible repair of alkylated DNA in microorganisms. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:294-305. [PMID: 25795127 DOI: 10.1016/j.mrrev.2014.12.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 12/15/2022]
Abstract
Alkylating agents, which are widespread in the environment, also occur endogenously as primary and secondary metabolites. Such compounds have intrinsically extremely cytotoxic and frequently mutagenic effects, to which organisms have developed resistance by evolving multiple repair mechanisms to protect cellular DNA. One such defense against alkylation lesions is an inducible Adaptive (Ada) response. In Escherichia coli, the Ada response enhances cell resistance by the biosynthesis of four proteins: Ada, AlkA, AlkB, and AidB. The glycosidic bonds of the most cytotoxic lesion, N3-methyladenine (3meA), together with N3-methylguanine (3meG), O(2)-methylthymine (O(2)-meT), and O(2)-methylcytosine (O(2)-meC), are cleaved by AlkA DNA glycosylase. Lesions such as N1-methyladenine (1meA) and N3-methylcytosine (3meC) are removed from DNA and RNA by AlkB dioxygenase. Cytotoxic and mutagenic O(6)-methylguanine (O(6)meG) is repaired by Ada DNA methyltransferase, which transfers the methyl group onto its own cysteine residue from the methylated oxygen. We review (i) the individual Ada proteins Ada, AlkA, AlkB, AidB, and COG3826, with emphasis on the ubiquitous and versatile AlkB and its prokaryotic and eukaryotic homologs; (ii) the organization of the Ada regulon in several bacterial species; (iii) the mechanisms underlying activation of Ada transcription. In vivo and in silico analysis of various microorganisms shows the widespread existence and versatile organization of Ada regulon genes, including not only ada, alkA, alkB, and aidB but also COG3826, alkD, and other genes whose roles in repair of alkylated DNA remain to be elucidated. This review explores the comparative organization of Ada response and protein functions among bacterial species beyond the classical E. coli model.
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Affiliation(s)
- Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Michał Wrzesiński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland.
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9
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Mielecki D, Grzesiuk E. Ada response - a strategy for repair of alkylated DNA in bacteria. FEMS Microbiol Lett 2014; 355:1-11. [PMID: 24810496 PMCID: PMC4437013 DOI: 10.1111/1574-6968.12462] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/04/2014] [Accepted: 05/05/2014] [Indexed: 11/29/2022] Open
Abstract
Alkylating agents are widespread in the environment and also occur endogenously. They can be cytotoxic or mutagenic to the cells introducing alkylated bases to DNA or RNA. All organisms have evolved multiple DNA repair mechanisms to counteract the effects of DNA alkylation: the most cytotoxic lesion, N3-methyladenine (3meA), is excised by AlkA glycosylase initiating base excision repair (BER); toxic N1-methyladenine (1meA) and N3-methylcytosine (3meC), induced in DNA and RNA, are removed by AlkB dioxygenase; and mutagenic and cytotoxic O6-methylguanine (O6meG) is repaired by Ada methyltransferase. In Escherichia coli, Ada response involves the expression of four genes, ada, alkA, alkB, and aidB, encoding respective proteins Ada, AlkA, AlkB, and AidB. The Ada response is conserved among many bacterial species; however, it can be organized differently, with diverse substrate specificity of the particular proteins. Here, an overview of the organization of the Ada regulon and function of individual proteins is presented. We put special effort into the characterization of AlkB dioxygenases, their substrate specificity, and function in the repair of alkylation lesions in DNA/RNA.
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Affiliation(s)
- Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
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10
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Vijayalaxmi, Cao Y, Scarfi MR. Adaptive response in mammalian cells exposed to non-ionizing radiofrequency fields: A review and gaps in knowledge. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2014; 760:S1383-5742(14)00004-0. [PMID: 24548818 DOI: 10.1016/j.mrrev.2014.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 02/03/2014] [Accepted: 02/06/2014] [Indexed: 11/19/2022]
Abstract
Adaptive response is a phenomenon in which cells which were pre-exposed to extremely low and non-toxic doses of a genotoxic agent became resistant to the damage induced by subsequent exposure to a higher and toxic dose of the same, similar (in action) or another genotoxic agent. Such response has been well documented in scientific literature in cells exposed in vitro and in vivo to low doses of physical (especially, ionizing radiation) and chemical mutagens. The existence of similar phenomenon in mammalian cells exposed in vitro and in vivo to non-ionizing radiofrequency fields has been reported in several research publications. In in vitro studies, human blood lymphocytes exposed to radiofrequency fields and then treated with a genotoxic mutagen or subjected to ionizing radiation showed significantly decreased genetic damage. Similar studies in tumor cells showed significantly increased viability, decreased apoptosis, increased mitochondrial membrane potential, decreased intracellular free Ca2+ and, increased Ca2+-Mg2+-ATPase activity. In in vivo studies, exposure of rodents to radiofrequency fields and then to lethal/sub-lethal doses of γ-radiation showed survival advantage, significantly decreased damage in hematopoietic tissues, decreased genetic damage in blood leukocytes and bone marrow cells, increased numbers of colony forming units in bone marrow, increased levels of colony stimulating factor and interleukin-3 in the serum and increased expression of genes related to cell cycle. These observations suggested the ability of radiofrequency fields to induce adaptive response and also indicated some potential mechanisms for the induction of such response. Several gaps in knowledge that need to be investigated were discussed.
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Kreuzer KN. DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks. Cold Spring Harb Perspect Biol 2013; 5:a012674. [PMID: 24097899 DOI: 10.1101/cshperspect.a012674] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent advances in the area of bacterial DNA damage responses are reviewed here. The SOS pathway is still the major paradigm of bacterial DNA damage response, and recent studies have clarified the mechanisms of SOS induction and key physiological roles of SOS including a very major role in genetic exchange and variation. When considering diverse bacteria, it is clear that SOS is not a uniform pathway with one purpose, but rather a platform that has evolved for differing functions in different bacteria. Relating in part to the SOS response, the field has uncovered multiple apparent cell-cycle checkpoints that assist cell survival after DNA damage and remarkable pathways that induce programmed cell death in bacteria. Bacterial DNA damage responses are also much broader than SOS, and several important examples of LexA-independent regulation will be reviewed. Finally, some recent advances that relate to the replication and repair of damaged DNA will be summarized.
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Affiliation(s)
- Kenneth N Kreuzer
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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12
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Booth JA, Thomassen GOS, Rowe AD, Weel-Sneve R, Lagesen K, Kristiansen KI, Bjørås M, Rognes T, Lindvall JM. Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response. Sci Rep 2013; 3:3053. [PMID: 24157950 PMCID: PMC6505713 DOI: 10.1038/srep03053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/11/2013] [Indexed: 11/25/2022] Open
Abstract
The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB. We have applied custom designed tiling arrays to study transcriptional changes in Escherichia coli following a MNNG challenge. Along with the expected upregulation of the adaptive response genes (ada, alkA and alkB), we identified a number of differentially expressed transcripts, both novel and annotated. This indicates a wider regulatory response than previously documented. There were 250 differentially-expressed and 2275 similarly-expressed unannotated transcripts. We found novel upregulation of several stress-induced transcripts, including the SOS inducible genes recN and tisAB, indicating a novel role for these genes in alkylation repair. Furthermore, the ada-regulon A and B boxes were found to be insufficient to explain the regulation of the adaptive response genes after MNNG exposure, suggesting that additional regulatory elements must be involved.
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Affiliation(s)
- James A Booth
- 1] Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, NO-0424 Oslo, Norway [2] Department of Microbiology, University of Oslo, PO Box 4950 Nydalen, NO-0424 Oslo, Norway [3]
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13
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Mielecki D, Saumaa S, Wrzesiński M, Maciejewska AM, Żuchniewicz K, Sikora A, Piwowarski J, Nieminuszczy J, Kivisaar M, Grzesiuk E. Pseudomonas putida AlkA and AlkB proteins comprise different defense systems for the repair of alkylation damage to DNA - in vivo, in vitro, and in silico studies. PLoS One 2013; 8:e76198. [PMID: 24098441 PMCID: PMC3788762 DOI: 10.1371/journal.pone.0076198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 08/19/2013] [Indexed: 11/18/2022] Open
Abstract
Alkylating agents introduce cytotoxic and/or mutagenic lesions to DNA bases leading to induction of adaptive (Ada) response, a mechanism protecting cells against deleterious effects of environmental chemicals. In Escherichia coli, the Ada response involves expression of four genes: ada, alkA, alkB, and aidB. In Pseudomonas putida, the organization of Ada regulon is different, raising questions regarding regulation of Ada gene expression. The aim of the presented studies was to analyze the role of AlkA glycosylase and AlkB dioxygenase in protecting P. putida cells against damage to DNA caused by alkylating agents. The results of bioinformatic analysis, of survival and mutagenesis of methyl methanesulfonate (MMS) or N-methyl-N’-nitro-N-nitrosoguanidine (MNNG) treated P. putida mutants in ada, alkA and alkB genes as well as assay of promoter activity revealed diverse roles of Ada, AlkA and AlkB proteins in protecting cellular DNA against alkylating agents. We found AlkA protein crucial to abolish the cytotoxic but not the mutagenic effects of alkylans since: (i) the mutation in the alkA gene was the most deleterious for MMS/MNNG treated P. putida cells, (ii) the activity of the alkA promoter was Ada-dependent and the highest among the tested genes. P. putida AlkB (PpAlkB), characterized by optimal conditions for in vitro repair of specific substrates, complementation assay, and M13/MS2 survival test, allowed to establish conservation of enzymatic function of P. putida and E. coli AlkB protein. We found that the organization of P. putida Ada regulon differs from that of E. coli. AlkA protein induced within the Ada response is crucial for protecting P. putida against cytotoxicity, whereas Ada prevents the mutagenic action of alkylating agents. In contrast to E. coli AlkB (EcAlkB), PpAlkB remains beyond the Ada regulon and is expressed constitutively. It probably creates a backup system that protects P. putida strains defective in other DNA repair systems against alkylating agents of exo- and endogenous origin.
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Affiliation(s)
- Damian Mielecki
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Signe Saumaa
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Michał Wrzesiński
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka M. Maciejewska
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Żuchniewicz
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Sikora
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jan Piwowarski
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jadwiga Nieminuszczy
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Maia Kivisaar
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- * E-mail: (EG); (MK)
| | - Elżbieta Grzesiuk
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (EG); (MK)
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14
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Mackie A, Keseler IM, Nolan L, Karp PD, Paulsen IT. Dead end metabolites--defining the known unknowns of the E. coli metabolic network. PLoS One 2013; 8:e75210. [PMID: 24086468 PMCID: PMC3781023 DOI: 10.1371/journal.pone.0075210] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 08/12/2013] [Indexed: 12/19/2022] Open
Abstract
The EcoCyc database is an online scientific database which provides an integrated view of the metabolic and regulatory network of the bacterium Escherichia coli K-12 and facilitates computational exploration of this important model organism. We have analysed the occurrence of dead end metabolites within the database – these are metabolites which lack the requisite reactions (either metabolic or transport) that would account for their production or consumption within the metabolic network. 127 dead end metabolites were identified from the 995 compounds that are contained within the EcoCyc metabolic network. Their presence reflects either a deficit in our representation of the network or in our knowledge of E. coli metabolism. Extensive literature searches resulted in the addition of 38 transport reactions and 3 metabolic reactions to the database and led to an improved representation of the pathway for Vitamin B12 salvage. 39 dead end metabolites were identified as components of reactions that are not physiologically relevant to E. coli K-12 – these reactions are properties of purified enzymes in vitro that would not be expected to occur in vivo. Our analysis led to improvements in the software that underpins the database and to the program that finds dead end metabolites within EcoCyc. The remaining dead end metabolites in the EcoCyc database likely represent deficiencies in our knowledge of E. coli metabolism.
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Affiliation(s)
- Amanda Mackie
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | | | - Laura Nolan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Peter D. Karp
- SRI International, Menlo Park, California, United States of America
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- * E-mail:
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15
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Abstract
Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-, and dioxygenase-mediated repair processes. We present specific examples to describe new findings of known enzymes and appealing discoveries of new proteins. At the end of this article, we also briefly discuss the influence of direct DNA repair on other fields of biology and its implication on the discovery of new biology.
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Affiliation(s)
- Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
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16
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Hamill MJ, Jost M, Wong C, Bene NC, Drennan CL, Elliott SJ. Electrochemical characterization of Escherichia coli adaptive response protein AidB. Int J Mol Sci 2012; 13:16899-915. [PMID: 23443126 PMCID: PMC3546729 DOI: 10.3390/ijms131216899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 11/26/2012] [Accepted: 12/03/2012] [Indexed: 11/16/2022] Open
Abstract
When exposed to known DNA-damaging alkylating agents, Escherichia coli cells increase production of four DNA repair enzymes: Ada, AlkA, AlkB, and AidB. The role of three enzymes (Ada, AlkA, and AlkB) in repairing DNA lesions has been well characterized, while the function of AidB is poorly understood. AidB has a distinct cofactor that is potentially related to the elusive role of AidB in adaptive response: a redox active flavin adenine dinucleotide (FAD). In this study, we report the thermodynamic redox properties of the AidB flavin for the first time, both for free protein and in the presence of potential substrates. We find that the midpoint reduction potential of the AidB flavin is within a biologically relevant window for redox chemistry at -181 mV, that AidB significantly stabilizes the flavin semiquinone, and that small molecule binding perturbs the observed reduction potential. Our electrochemical results combined with structural analysis allow for fresh comparisons between AidB and the homologous acyl-coenzyme A dehydrogenase (ACAD) family of enzymes. AidB exhibits several discrepancies from ACADs that suggest a novel catalytic mechanism distinct from that of the ACAD family enzymes.
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Affiliation(s)
- Michael J. Hamill
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA; E-Mails: (M.J.H.); (N.C.B.)
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA; E-Mails: (M.J.); (C.L.D.)
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA; E-Mails: (M.J.); (C.L.D.)
| | - Cintyu Wong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA; E-Mails: (M.J.); (C.L.D.)
| | - Nicholas C. Bene
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA; E-Mails: (M.J.H.); (N.C.B.)
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA; E-Mails: (M.J.); (C.L.D.)
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Environmental Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sean J. Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA; E-Mails: (M.J.H.); (N.C.B.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-617-358-2816; Fax: +1-617-353-6466
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17
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Dotreppe D, Mullier C, Letesson JJ, De Bolle X. The alkylation response protein AidB is localized at the new poles and constriction sites in Brucella abortus. BMC Microbiol 2011; 11:257. [PMID: 22111948 PMCID: PMC3236019 DOI: 10.1186/1471-2180-11-257] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 11/23/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brucella abortus is the etiological agent of a worldwide zoonosis called brucellosis. This alpha-proteobacterium is dividing asymmetrically, and PdhS, an essential histidine kinase, was reported to be an old pole marker. RESULTS We were interested to identify functions that could be recruited to bacterial poles. The Brucella ORFeome, a collection of cloned predicted coding sequences, was placed in fusion with yellow fluorescent protein (YFP) coding sequence and screened for polar localizations in B. abortus. We report that AidB-YFP was systematically localized to the new poles and at constrictions sites in B. abortus, either in culture or inside infected HeLa cells or RAW264.7 macrophages. AidB is an acyl-CoA dehydrogenase (ACAD) homolog, similar to E. coli AidB, an enzyme putatively involved in destroying alkylating agents. Accordingly, a B. abortus aidB mutant is more sensitive than the wild-type strain to the lethality induced by methanesulphonic acid ethyl ester (EMS). The exposure to EMS led to a very low frequency of constriction events, suggesting that cell cycle is blocked during alkylation damage. The localization of AidB-YFP at the new poles and at constriction sites seems to be specific for this ACAD homolog since two other ACAD homologs fused to YFP did not show specific localization. The overexpression of aidB, but not the two other ACAD coding sequences, leads to multiple morphological defects. CONCLUSIONS Data reported here suggest that AidB is a marker of new poles and constriction sites, that could be considered as sites of preparation of new poles in the sibling cells originating from cell division. The possible role of AidB in the generation or the function of new poles needs further investigation.
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Affiliation(s)
- Delphine Dotreppe
- URBM, University of Namur (FUNDP), 61 rue de Bruxelles, Namur, 5000, Belgium
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18
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Hamill M, Jost M, Wong C, Elliott SJ, Drennan CL. Flavin-induced oligomerization in Escherichia coli adaptive response protein AidB. Biochemistry 2011; 50:10159-69. [PMID: 22004173 PMCID: PMC3217306 DOI: 10.1021/bi201340t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The process known as "adaptive response" allows Escherichia coli to respond to small doses of DNA-methylating agents by upregulating the expression of four proteins. While the role of three of these proteins in mitigating DNA damage is well understood, the function of AidB is less clear. Although AidB is a flavoprotein, no catalytic role has been established for the bound cofactor. Here we investigate the possibility that flavin plays a structural role in the assembly of the AidB tetramer. We report the generation and biophysical characterization of deflavinated AidB and of an AidB mutant that has greatly reduced affinity for flavin adenine dinucleotide (FAD). Using fluorescence quenching and analytical ultracentrifugation, we find that apo AidB has a high affinity for FAD, as indicated by an apparent dissociation constant of 402.1 ± 35.1 nM, and that binding of substoichiometric amounts of FAD triggers a transition in the AidB oligomeric state. In particular, deflavinated AidB is dimeric, whereas the addition of FAD yields a tetramer. We further investigate the dimerization and tetramerization interfaces of AidB by determining a 2.8 Å resolution crystal structure in space group P3(2) that contains three intact tetramers in the asymmetric unit. Taken together, our findings provide strong evidence that FAD plays a structural role in the formation of tetrameric AidB.
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Affiliation(s)
- Michael
J. Hamill
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States,‡Department
of Chemistry, §Department of Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Environmental Health, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States
| | - Marco Jost
- ‡Department
of Chemistry, §Department of Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Environmental Health, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States
| | - Cintyu Wong
- ‡Department
of Chemistry, §Department of Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Environmental Health, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States
| | - Sean J. Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States,S.J.E.:
telephone, (617) 358-2816; fax, (617) 353-6466; e-mail, . C.L.D.: telephone, (617) 253-5622; fax, (617) 258-7847; e-mail,
| | - Catherine L. Drennan
- ‡Department
of Chemistry, §Department of Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Environmental Health, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States,S.J.E.:
telephone, (617) 358-2816; fax, (617) 353-6466; e-mail, . C.L.D.: telephone, (617) 253-5622; fax, (617) 258-7847; e-mail,
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