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Wu Y, Li J, Zhu L, Wang D, Song J, Yu X, Li Y, Tang BZ. Photosensitive AIEgens sensitize bacteria to oxidative damage and modulate the inflammatory responses of macrophages to salvage the photodynamic therapy against MRSA. Biomaterials 2024; 309:122583. [PMID: 38692148 DOI: 10.1016/j.biomaterials.2024.122583] [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: 01/17/2024] [Revised: 04/07/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
The urgent need for antimicrobial agents to combat infections caused by multidrug-resistant bacteria facilitates the exploration of alternative strategies such as photosensitizer (PS)-mediated photoinactivation. However, increasing studies have discovered uncorrelated bactericidal activities among PSs possessing similar photodynamic and pathogen-targeted properties. To optimize the photodynamic therapy (PDT) against infections, we investigated three type-I PSs of D-π-A AIEgens TI, TBI, and TTI. The capacities of reactive oxygen species (ROS) generation of TI, TBI, and TTI did not align with their bactericidal activities. Despite exhibiting the lowest photodynamic efficiency, TI exhibited the highest activities against methicillin-resistant Staphylococcus aureus (MRSA) by impairing the anti-oxidative responses of bacteria. By comparison, TTI, characterized by the strongest ROS production, inactivated intracellular MRSA by potentiating the inflammatory response of macrophages. Unlike TI and TTI, TBI, despite possessing moderate photodynamic activities and inducing ROS accumulation in both MRSA and macrophages, did not exhibit any antibacterial activity. Therefore, relying on the disturbed anti-oxidative metabolism of pathogens or potentiated host immune responses, transient ROS bursts can effectively control bacterial infections. Our study reevaluates the contribution of photodynamic activities of PSs to bacterial elimination and provides new insights into discovering novel antibacterial targets and agents.
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Affiliation(s)
- Yifan Wu
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China; Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Jiangao Li
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China; Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Liwei Zhu
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Deliang Wang
- Department of Materials Chemistry, Huzhou University, Huzhou, Zhejiang, 313000, China
| | - Jiayi Song
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Xiyong Yu
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Ying Li
- Innovation Research Center for AIE Pharmaceutical Biology, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China.
| | - Ben Zhong Tang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong, 518172, China.
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2
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Abstract
Wide-bandgap semiconductors modified with nanostructures of noble metals for photocatalytic activity under vis irradiation due to localized surface plasmon resonance (LSPR), known as plasmonic photocatalysts, have been intensively investigated over the last decade. Most literature reports discuss the properties and activities of plasmonic photocatalysts for the decomposition of organic compounds and solar energy conversion. Although noble metals, especially silver and copper, have been known since ancient times as excellent antimicrobial agents, there are only limited studies on plasmonic photocatalysts for the inactivation of microorganisms (considering vis-excitation). Accordingly, this review has discussed the available literature reports on microbiological applications of plasmonic photocatalysis, including antibacterial, antiviral and antifungal properties, and also a novel study on other microbiological purposes, such as cancer treatment and drug delivery. Although some reports indicate high antimicrobial properties of these photocatalysts and their potential for medical/pharmaceutical applications, there is still a lack of comprehensive studies on the mechanism of their interactions with microbiological samples. Moreover, contradictory data have also been published, and thus more study is necessary for the final conclusions on the key-factor properties and the mechanisms of inactivation of microorganisms and the treatment of cancer cells.
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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: 1.0] [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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4
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Faridounnia M, Folkers GE, Boelens R. Function and Interactions of ERCC1-XPF in DNA Damage Response. Molecules 2018; 23:E3205. [PMID: 30563071 PMCID: PMC6320978 DOI: 10.3390/molecules23123205] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/27/2018] [Accepted: 12/01/2018] [Indexed: 12/28/2022] Open
Abstract
Numerous proteins are involved in the multiple pathways of the DNA damage response network and play a key role to protect the genome from the wide variety of damages that can occur to DNA. An example of this is the structure-specific endonuclease ERCC1-XPF. This heterodimeric complex is in particular involved in nucleotide excision repair (NER), but also in double strand break repair and interstrand cross-link repair pathways. Here we review the function of ERCC1-XPF in various DNA repair pathways and discuss human disorders associated with ERCC1-XPF deficiency. We also overview our molecular and structural understanding of XPF-ERCC1.
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Affiliation(s)
- Maryam Faridounnia
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Gert E Folkers
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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5
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Butzin NC, Mather WH. Crosstalk between Diverse Synthetic Protein Degradation Tags in Escherichia coli. ACS Synth Biol 2018; 7:54-62. [PMID: 29193958 DOI: 10.1021/acssynbio.7b00122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, a synthetic circuit in E. coli demonstrated that two proteins engineered with LAA tags targeted to the native protease ClpXP are susceptible to crosstalk due to competition for degradation between proteins. To understand proteolytic crosstalk beyond the single protease regime, we investigated in E. coli a set of synthetic circuits designed to probe the dynamics of existing and novel degradation tags fused to fluorescent proteins. These circuits were tested using both microplate reader and single-cell assays. We first quantified the degradation rates of each tag in isolation. We then tested if there was crosstalk between two distinguishable fluorescent proteins engineered with identical or different degradation tags. We demonstrated that proteolytic crosstalk was indeed not limited to the LAA degradation tag, but was also apparent between other diverse tags, supporting the complexity of the E. coli protein degradation system.
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Affiliation(s)
- Nicholas C. Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota 57007, United States
| | - William H. Mather
- Quantitative Biosciences, Inc., Solana Beach, California 92075, United States
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6
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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: 1.2] [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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7
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Shah AA, Wang C, Yoon SH, Kim JY, Choi ES, Kim SW. RecA-mediated SOS response provides a geraniol tolerance in Escherichia coli. J Biotechnol 2013; 167:357-64. [DOI: 10.1016/j.jbiotec.2013.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/13/2013] [Accepted: 07/17/2013] [Indexed: 10/26/2022]
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8
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Rippa V, Duilio A, di Pasquale P, Amoresano A, Landini P, Volkert MR. Preferential DNA damage prevention by the E. coli AidB gene: A new mechanism for the protection of specific genes. DNA Repair (Amst) 2011; 10:934-41. [PMID: 21788159 DOI: 10.1016/j.dnarep.2011.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 06/01/2011] [Accepted: 06/07/2011] [Indexed: 11/19/2022]
Abstract
aidB is one of the four genes of E. coli that is induced by alkylating agents and regulated by Ada protein. Three genes (ada, alkA, and alkB) encode DNA repair proteins that remove or repair alkylated bases. However, the role of AidB remains unclear despite extensive efforts to determine its function in cells exposed to alkylating agents. The E. coli AidB protein was identified as a component of the protein complex that assembles at strong promoters. We demonstrate that AidB protein preferentially binds to UP elements, AT rich transcription enhancer sequences found upstream of many highly expressed genes, several DNA repair genes, and housekeeping genes. AidB allows efficient transcription from promoters containing an UP element upon exposure to a DNA methylating agent and protects downstream genes from DNA damage. The DNA binding domain is required to target AidB to specific genes preferentially protecting them from alkylation damage. However, deletion of AidB's DNA binding domain does not prevent its antimutagenic activity, instead this deletion appears to allow AidB to function as a cytoplasmic alkylation resistance protein. Our studies identify the role of AidB in alkylating agent exposed cells and suggest a new cellular strategy in which a subset of the genome is preferentially protected from damage by alkylating agents.
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Affiliation(s)
- Valentina Rippa
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
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9
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Kuboniwa M, Hendrickson EL, Xia Q, Wang T, Xie H, Hackett M, Lamont RJ. Proteomics of Porphyromonas gingivalis within a model oral microbial community. BMC Microbiol 2009; 9:98. [PMID: 19454014 PMCID: PMC2689231 DOI: 10.1186/1471-2180-9-98] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 05/19/2009] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Porphyromonas gingivalis is a periodontal pathogen that resides in a complex multispecies microbial biofilm community known as dental plaque. Confocal laser scanning microscopy showed that P. gingivalis can assemble into communities in vitro with Streptococcus gordonii and Fusobacterium nucleatum, common constituents of dental plaque. Whole cell quantitative proteomics, along with mutant construction and analysis, were conducted to investigate how P. gingivalis adapts to this three species community. RESULTS 1156 P. gingivalis proteins were detected qualitatively during comparison of the three species model community with P. gingivalis incubated alone under the same conditions. Integration of spectral counting and summed signal intensity analyses of the dataset showed that 403 proteins were down-regulated and 89 proteins up-regulated. The proteomics results were inspected manually and an ontology analysis conducted using DAVID. Significant decreases were seen in proteins involved in cell shape and the formation of the cell envelope, as well as thiamine, cobalamin, and pyrimidine synthesis and DNA repair. An overall increase was seen in proteins involved in protein synthesis. HmuR, a TonB dependent outer membrane receptor, was up-regulated in the community and an hmuR deficient mutant was deficient in three species community formation, but was unimpaired in its ability to form mono- or dual-species biofilms. CONCLUSION Collectively, these results indicate that P. gingivalis can assemble into a heterotypic community with F. nucleatum and S. gordonii, and that a community lifestyle provides physiologic support for P. gingivalis. Proteins such as HmuR, that are up-regulated, can be necessary for community structure.
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Affiliation(s)
- Masae Kuboniwa
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan.
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10
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Fu Y, Pastushok L, Xiao W. DNA damage-induced gene expression inSaccharomyces cerevisiae. FEMS Microbiol Rev 2008; 32:908-26. [DOI: 10.1111/j.1574-6976.2008.00126.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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11
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Abstract
When challenged with unfavorable conditions, microorganisms can develop a stress response that allows them to adapt to or survive in the new environment. A common feature of the numerous specific stress response pathways that have been described in a wide range of bacteria is that they are energy demanding and therefore often transient. In addition, stress responses may come too late or be insufficient to protect the cell or the population against very sudden or severe stresses. However, it seems that microorganisms can also enhance their chances of survival under stress by increasing the generation of diversity at the population level. This can be achieved either by creating genetic diversity by a variety of mechanisms involving for example constitutive or transient mutators and contingency loci, or by revealing phenotypic diversity that remained dormant due to a mechanism called genetic buffering. This review gives an overview of these emerging diversity-generating mechanisms, which seem to play an important role in the ability of microbial populations to overcome stress challenges.
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Affiliation(s)
- Abram Aertsen
- Laboratory of Food Microbiology, Katholieke Universiteit Leuven, Leuven, Belgium.
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12
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Saint-Ruf C, Pesut J, Sopta M, Matic I. Causes and consequences of DNA repair activity modulation during stationary phase in Escherichia coli. Crit Rev Biochem Mol Biol 2007; 42:259-70. [PMID: 17687668 DOI: 10.1080/10409230701495599] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Escherichia coli responds to nutrient exhaustion by entering a state commonly referred to as the stationary phase. Cells entering the stationary phase redirect metabolic circuits to scavenge any available nutrients and become resistant to different stresses. However, many DNA repair pathways are downregulated in stationary-phase cells, which results in increased mutation rates. DNA repair activity generally depends on consumption of energy and often requires de novo proteins synthesis. Consequently, unless stringently regulated during stationary phase, DNA repair activities may lead to an irreversible depletion of energy sources and, therefore to cell death. Most stationary phase morphological and physiological modifications are regulated by an alternative RNA polymerase sigma factor RpoS. However, nutrient availability, and the frequency and nature of stresses, are different in distinct environmental niches, which impose conflicting choices that result in selection of the loss or of the modification of RpoS function. Consequently, DNA repair activity, which is partially controlled by RpoS, is differently modulated in different environments. This results in the variable mutation rates among different E. coli ecotypes. Hence, the polymorphism of mutation rates in natural E. coli populations can be viewed as a byproduct of the selection for improved fitness.
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Affiliation(s)
- Claude Saint-Ruf
- INSERM, U571, Faculté de Médicine, Université Paris 5, Paris, France
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13
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Bjedov I, Dasgupta CN, Slade D, Le Blastier S, Selva M, Matic I. Involvement of Escherichia coli DNA polymerase IV in tolerance of cytotoxic alkylating DNA lesions in vivo. Genetics 2007; 176:1431-40. [PMID: 17483416 PMCID: PMC1931539 DOI: 10.1534/genetics.107.072405] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 05/03/2007] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli PolIV, a DNA polymerase capable of catalyzing synthesis past replication-blocking DNA lesions, belongs to the most ubiquitous branch of Y-family DNA polymerases. The goal of this study is to identify spontaneous DNA damage that is bypassed specifically and accurately by PolIV in vivo. We increased the amount of spontaneous DNA lesions using mutants deficient for different DNA repair pathways and measured mutation frequency in PolIV-proficient and -deficient backgrounds. We found that PolIV performs an error-free bypass of DNA damage that accumulates in the alkA tag genetic background. This result indicates that PolIV is involved in the error-free bypass of cytotoxic alkylating DNA lesions. When the amount of cytotoxic alkylating DNA lesions is increased by the treatment with chemical alkylating agents, PolIV is required for survival in an alkA tag-proficient genetic background as well. Our study, together with the reported involvement of the mammalian PolIV homolog, Polkappa, in similar activity, indicates that Y-family DNA polymerases from the DinB branch can be added to the list of evolutionarily conserved molecular mechanisms that counteract cytotoxic effects of DNA alkylation. This activity is of major biological relevance because alkylating agents are continuously produced endogenously in all living cells and are also present in the environment.
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Affiliation(s)
- Ivana Bjedov
- INSERM U571, Faculté de Médecine, Université Paris 5, 75730 Paris Cedex 15, France
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14
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Prieto AI, Ramos-Morales F, Casadesús J. Repair of DNA damage induced by bile salts in Salmonella enterica. Genetics 2006; 174:575-84. [PMID: 16888329 PMCID: PMC1602091 DOI: 10.1534/genetics.106.060889] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Exposure of Salmonella enterica to sodium cholate, sodium deoxycholate, sodium chenodeoxycholate, sodium glycocholate, sodium taurocholate, or sodium glycochenodeoxycholate induces the SOS response, indicating that the DNA-damaging activity of bile resides in bile salts. Bile increases the frequency of GC --> AT transitions and induces the expression of genes belonging to the OxyR and SoxRS regulons, suggesting that bile salts may cause oxidative DNA damage. S. enterica mutants lacking both exonuclease III (XthA) and endonuclease IV (Nfo) are bile sensitive, indicating that S. enterica requires base excision repair (BER) to overcome DNA damage caused by bile salts. Bile resistance also requires DinB polymerase, suggesting the need of SOS-associated translesion DNA synthesis. Certain recombination functions are also required for bile resistance, and a key factor is the RecBCD enzyme. The extreme bile sensitivity of RecB-, RecC-, and RecA- RecD- mutants provides evidence that bile-induced damage may impair DNA replication.
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Affiliation(s)
- Ana I Prieto
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville 41080, Spain
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15
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Gon S, Camara JE, Klungsøyr HK, Crooke E, Skarstad K, Beckwith J. A novel regulatory mechanism couples deoxyribonucleotide synthesis and DNA replication in Escherichia coli. EMBO J 2006; 25:1137-47. [PMID: 16482221 PMCID: PMC1409723 DOI: 10.1038/sj.emboj.7600990] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Accepted: 01/17/2006] [Indexed: 11/08/2022] Open
Abstract
We present evidence for a complex regulatory interplay between the initiation of DNA replication and deoxyribonucleotide synthesis. In Escherichia coli, the ATP-bound DnaA protein initiates chromosomal replication. Upon loading of the beta-clamp subunit (DnaN) of the replicase, DnaA is inactivated as its intrinsic ATPase activity is stimulated by the protein Hda. The beta-subunit acts as a matchmaker between Hda and DnaA. Chain elongation of DNA requires a sufficient supply of deoxyribonucleotides (dNTPs), which are produced by ribonucleotide reductase (RNR). We present evidence suggesting that the molecular switch from ATP-DnaA to ADP-DnaA is a critical step coordinating DNA replication with increased deoxyribonucleotide synthesis. Characterization of dnaA and dnaN mutations that result in a constitutively high expression of RNR reveal this mechanism. We propose that the nucleotide bound state of DnaA regulates the transcription of the genes encoding ribonucleotide reductase (nrdAB). Accordingly, the conversion of ATP-DnaA to ADP-DnaA after initiation and loading of the beta-subunit DnaN would allow increased nrdAB expression, and consequently, coordinated RNR synthesis and DNA replication during the cell cycle.
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Affiliation(s)
- Stéphanie Gon
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
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16
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Gunderson CW, Segall AM. DNA repair, a novel antibacterial target: Holliday junction-trapping peptides induce DNA damage and chromosome segregation defects. Mol Microbiol 2006; 59:1129-48. [PMID: 16430689 DOI: 10.1111/j.1365-2958.2005.05009.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Holliday junction intermediates arise in several central pathways of DNA repair, replication fork restart, and site-specific recombination catalysed by tyrosine recombinases. Previously identified hexapeptide inhibitors of phage lambda integrase-mediated recombination block the resolution of Holliday junction intermediates in vitro and thereby inhibit recombination, but have no DNA cleavage activity themselves. The most potent peptides are specific for the branched DNA structure itself, as opposed to the integrase complex. Based on this activity, the peptides inhibit several unrelated Holliday junction-processing enzymes in vitro, including the RecG helicase and RuvABC junction resolvase complex. We have found that some of these hexapeptides are potent bactericidal antimicrobials, effective against both Gm+ and Gm- bacteria. Using epifluorescence microscopy and flow cytometry, we have characterized extensively the physiology of bacterial cells treated with these peptides. The hexapeptides cause DNA segregation abnormalities, filamentation and DNA damage. Damage caused by the peptides induces the SOS response, and is synergistic with damage caused by UV and mitomycin C. Our results are consistent with the model that the hexapeptides affect DNA targets that arise during recombination-dependent repair. We propose that the peptides trap intermediates in the repair of collapsed replication forks, preventing repair and resulting in bacterial death. Inhibition of DNA repair constitutes a novel target of antibiotic therapy. The peptides affect targets that arise in multiple pathways, and as expected, are quite resistant to the development of spontaneous antibiotic resistance.
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Affiliation(s)
- Carl W Gunderson
- Center for Microbial Sciences and Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
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17
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Zeller T, Moskvin OV, Li K, Klug G, Gomelsky M. Transcriptome and physiological responses to hydrogen peroxide of the facultatively phototrophic bacterium Rhodobacter sphaeroides. J Bacteriol 2005; 187:7232-42. [PMID: 16237007 PMCID: PMC1272974 DOI: 10.1128/jb.187.21.7232-7242.2005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcriptome responses to hydrogen peroxide, H2O2, of the facultatively phototrophic bacterium Rhodobacter sphaeroides grown under semiaerobic conditions were investigated. At 7 min after the addition of 1 mM H2O2, the expression of approximately 9% of all genes (total, 394) was changed reliably by at least twofold. At 30 min, the number of genes (total, 88) and the magnitude of expression changes were much lower, indicating rapid recovery from stress. Two types of responses were observed: (i) an H2O2 stress response per se and (ii) a shift to high-oxygen metabolism. The former response involved the upregulation of genes for H2O2 detoxification, protein folding and proteolysis, DNA damage repair, iron transport and storage, iron-sulfur cluster repair, and the downregulation of genes for protein translation, motility, and cell wall and lipopolysaccharide synthesis. The shift to high-oxygen metabolism was evident from the differential regulation of genes for aerobic electron transport chain components and the downregulation of tetrapyrrole biosynthesis and photosystem genes. The abundance of photosynthetic complexes was decreased upon prolonged exposure of R. sphaeroides to H2O2, thus confirming the physiological significance of the transcriptome data. The regulatory pathways mediating the shift to high-oxygen metabolism were investigated. They involved the anaerobic activator FnrL and the antirepressor-repressor AppA-PpsR system. The transcription of FnrL-dependent genes was down at 7 min, apparently due to the transient inactivation by H2O2 of the iron-sulfur cluster of FnrL. The transcription of the AppA-PpsR-dependent genes was down at 30 min, apparently due to the significant decrease in appA mRNA.
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Affiliation(s)
- Tanja Zeller
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Germany
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Rathsam C, Eaton RE, Simpson CL, Browne GV, Berg T, Harty DWS, Jacques NA. Up-regulation of competence- but not stress-responsive proteins accompanies an altered metabolic phenotype in Streptococcus mutans biofilms. MICROBIOLOGY-SGM 2005; 151:1823-1837. [PMID: 15941991 DOI: 10.1099/mic.0.27830-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mature biofilm and planktonic cells of Streptococcus mutans cultured in a neutral pH environment were subjected to comparative proteome analysis. Of the 242 protein spots identified, 48 were significantly altered in their level of expression (P<0.050) or were unique to planktonic or biofilm-grown cells. Among these were four hypothetical proteins as well as proteins known to be associated with the maintenance of competence or found to possess a cin-box-like element upstream of their coding gene. Most notable among the non-responsive genes were those encoding the molecular chaperones DnaK, GroEL and GroES, which are considered to be up-regulated by sessile growth. Analysis of the rest of the proteome indicated that a number of cellular functions associated with carbon uptake and cell division were down-regulated. The data obtained were consistent with the hypothesis that a reduction in the general growth rate of mature biofilms of S. mutans in a neutral pH environment is associated with the maintenance of transformation without the concomitant stress response observed during the transient state of competence in bacterial batch cultures.
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Affiliation(s)
- Catherine Rathsam
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO Box 533, Wentworthville, NSW 2145, Australia
| | - Ruth E Eaton
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO Box 533, Wentworthville, NSW 2145, Australia
| | - Christine L Simpson
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO Box 533, Wentworthville, NSW 2145, Australia
| | - Gina V Browne
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO Box 533, Wentworthville, NSW 2145, Australia
| | - Tracey Berg
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO Box 533, Wentworthville, NSW 2145, Australia
| | - Derek W S Harty
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO Box 533, Wentworthville, NSW 2145, Australia
| | - N A Jacques
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO Box 533, Wentworthville, NSW 2145, Australia
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19
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Kyng KJ, May A, Stevnsner T, Becker KG, Kølvrå S, Bohr VA. Gene expression responses to DNA damage are altered in human aging and in Werner Syndrome. Oncogene 2005; 24:5026-42. [PMID: 15897889 DOI: 10.1038/sj.onc.1208692] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The accumulation of DNA damage and mutations is considered a major cause of cancer and aging. While it is known that DNA damage can affect changes in gene expression, transcriptional regulation after DNA damage is poorly understood. We characterized the expression of 6912 genes in human primary fibroblasts after exposure to three different kinds of cellular stress that introduces DNA damage: 4-nitroquinoline-1-oxide (4NQO), gamma-irradiation, or UV-irradiation. Each type of stress elicited damage specific gene expression changes of up to 10-fold. A total of 85 genes had similar changes in expression of 3-40-fold after all three kinds of stress. We examined transcription in cells from young and old individuals and from patients with Werner syndrome (WS), a segmental progeroid condition with a high incidence of cancer, and found various age-associated transcriptional changes depending upon the type of cellular stress. Compared to young individuals, both WS and old individuals had similarly aberrant transcriptional responses to gamma- and UV-irradiation, suggesting a role for Werner protein in stress-induced gene expression. Our results suggest that aberrant DNA damage-induced gene regulation may contribute to the aging process and the premature aging in WS.
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Affiliation(s)
- Kasper J Kyng
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
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20
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Abstract
Genome-wide analysis of temporal gene expression profiles in Escherichia coli following exposure to cadmium revealed a shift to anaerobic metabolism and induction of several stress response systems. Disruption in the transcription of genes encoding ribosomal proteins and zinc-binding proteins may partially explain the molecular mechanisms of cadmium toxicity.
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Affiliation(s)
- Anyou Wang
- Department of Environmental Sciences, University of Caliifornia, Riverside, CA 92521, USA
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21
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Kobayashi H, Miyamoto T, Hashimoto Y, Kiriki M, Motomatsu A, Honjoh KI, Iio M. Identification of factors involved in recovery of heat-injured Salmonella Enteritidis. J Food Prot 2005; 68:932-41. [PMID: 15895724 DOI: 10.4315/0362-028x-68.5.932] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Proteins and genes involved in the recovery of heat-injured Salmonella Enteritidis were investigated. Salmonella Enteritidis cells cultured overnight in tryptic soy broth (TSB; nonselective medium) were suspended in citric acid-disodium hydrogen phosphate buffer (pH 6). After heat treatment at 55 degrees C for 15 min, the culturable counts measured by tryptic soy agar (TSA; nonselective medium) decreased from 10(8) to 10(7) CFU/ml. On the other hand, culturable counts measured by desoxycholate-hydrogen sulfite-lactose (DHL) agar (selective medium) were decreased from 10(8) to 10(4) CFU/ml by the same treatment. The results suggest that 99.9% of Salmonella Enteritidis detected on TSA were injured but recoverable. When injured Salmonella Enteritidis was incubated in TSB, the culturable count measured by TSA did not increase for 2 h, whereas that by DHL agar increased after incubation for 30 min. After incubation for 2 h, the culturable count measured by DHL agar reached a similar level with that by TSA, indicating that Salmonella Enteritidis had recovered. The two-dimensional polyacrylamide gel electrophoresis analysis revealed that elongation factor G (FusA) and pyruvate kinase (PykF) specifically increased in the cells just after heat treatment and in the recovery cells. The levels of transcription of 86 stress-inducible genes were also investigated by reverse transcription PCR. Nineteen heat-inducible (clpB, clpX, degP, dnaJ, fkpA, ftsJ, gapA, hflB, hslJ, hslU, hslV, htpG, htrA, lon, mopA, mopB, mreB, rpoE, and ppiD), and 12 oxidative-stress and DNA damage-inducible (ahpC, ahpF, fldB, fur, grxA, dinF, katG, mutM, recA, soxR, trxC, and zwf) genes were transcribed extensively during recovery in TSB. The results obtained in this study will be used to develop the media or culture conditions that will promote recovery for the detection of food poisoning bacteria, including injured cells from food products.
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Affiliation(s)
- Hiroshi Kobayashi
- Laboratory of Food Hygienic Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
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22
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Len ACL, Harty DWS, Jacques NA. Stress-responsive proteins are upregulated in Streptococcus mutans during acid tolerance. Microbiology (Reading) 2004; 150:1339-1351. [PMID: 15133096 DOI: 10.1099/mic.0.27008-0] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus mutansis an important pathogen in the initiation of dental caries as the bacterium remains metabolically active when the environment becomes acidic. The mechanisms underlying this ability to survive and proliferate at low pH remain an area of intense investigation. Differential two-dimensional electrophoretic proteome analysis ofS. mutansgrown at steady state in continuous culture at pH 7·0 or pH 5·0 enabled the resolution of 199 cellular and extracellular protein spots with altered levels of expression. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry identified 167 of these protein spots. Sixty-one were associated with stress-responsive pathways involved in DNA replication, transcription, translation, protein folding and proteolysis. The 61 protein spots represented isoforms or cleavage products of 30 different proteins, of which 25 were either upregulated or uniquely expressed during acid-tolerant growth at pH 5·0. Among the unique and upregulated proteins were five that have not been previously identified as being associated with acid tolerance inS. mutansand/or which have not been studied in any detail in oral streptococci. These were the single-stranded DNA-binding protein, Ssb, the transcription elongation factor, GreA, the RNA exonuclease, polyribonucleotide nucleotidyltransferase (PnpA), and two proteinases, the ATP-binding subunit, ClpL, of the Clp family of proteinases and a proteinase encoded by thepepgene family with properties similar to the dipeptidase, PepD, ofLactobacillus helveticus. The identification of these and other differentially expressed proteins associated with an acid-tolerant-growth phenotype provides new information on targets for mutagenic studies that will allow the future assessment of their physiological significance in the survival and proliferation ofS. mutansin low pH environments.
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Affiliation(s)
- Alice C L Len
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO BOX 533, Wentworthville, NSW 2145, Australia
| | - Derek W S Harty
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO BOX 533, Wentworthville, NSW 2145, Australia
| | - Nicholas A Jacques
- Institute of Dental Research, Westmead Millennium Institute and Westmead Centre for Oral Health, PO BOX 533, Wentworthville, NSW 2145, Australia
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Lacour S, Kolb A, Landini P. Nucleotides from -16 to -12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase. J Biol Chem 2003; 278:37160-8. [PMID: 12853450 DOI: 10.1074/jbc.m305281200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The alternative sigma factor sigmaS, mainly active in stationary phase of growth, recognizes in vitro a -10 promoter sequence almost identical to the one for the main sigma factor, sigma70, thus raising the problem of how specific promoter recognition by sigmaS-RNA polymerase (EsigmaS) is achieved in vivo. We investigated the promoter features involved in selective recognition by EsigmaS at the strictly sigmaS-dependent aidB promoter. We show that the presence of a C nucleotide as first residue of the aidB -10 sequence (-12C), instead of the T nucleotide canonical for sigma70-dependent promoters, is the major determinant for selective recognition by EsigmaS. The presence of the -12C does not allow formation of an open complex fully proficient in transcription initiation by Esigma70. The role of -12C as specific determinant for promoter recognition by EsigmaS was confirmed by sequence analysis of known EsigmaS-dependent promoters as well as site-directed mutagenesis at the promoters of the csgB and sprE genes. We propose that EsigmaS, unlike Esigma70, can recognize both C and T as the first nucleotide in the -10 sequence. Additional promoter features such as the presence of a C nucleotide at position -13, contributing to open complex formation by EsigmaS, and a TG motif found at the unusual -16/-15 location, possibly contributing to initial binding to the promoter, also represent important factors for sigmaS-dependent transcription. We propose a new sequence, TG(N)0-2CCATA(c/a)T, as consensus -10 sequence for promoters exclusively recognized by EsigmaS.
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Affiliation(s)
- Stephan Lacour
- Swiss Federal Institute of Environmental Technology (EAWAG), Uberlandstrasse 133, CH-8600 Dübendorf, Switzerland
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Woynarowska BA, Woynarowski JM. Preferential targeting of apoptosis in tumor versus normal cells. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1587:309-17. [PMID: 12084473 DOI: 10.1016/s0925-4439(02)00094-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Elimination of cancer cells by early apoptosis is preferred over other forms of cell growth inhibition. Apoptosis directly leads to tumor regression and reduces risks of selecting more aggressive and/or drug-resistant phenotypes that are often responsible for tumor regrowth and treatment failure. Although DNA damage by anticancer drugs is commonly recognized as an apoptotic stimulus, there is enormous variability in the magnitude and timing of such effects. Especially potent and rapid apoptosis seems to be a hallmark of various alkylating anticancer drugs that are regarded as DNA-reactive agents but are observed to react mainly with cellular proteins. Our studies with such dual-action drugs (irofulven, oxaliplatin) suggest that not only DNA damage, but also protein damage, contributes to apoptosis induction. DNA damage is well known to initiate death-signaling pathways leading to mitochondrial dysfunction. Protein damage, in turn, can distort cell redox homeostasis, which facilitates apoptosis execution. Such dual effects can be particularly lethal to tumor cells, which tend to function under pro-oxidative conditions. In contrast to tumor cells that are highly susceptible, normal cells show marginal apoptotic responses to the dual action drugs. This protection of normal cells might reflect their greater ability to buffer pro-oxidative changes and quickly restore redox homeostasis, despite substantial drug uptake and macromolecular binding. Importantly, by targeting the death process at multiple points, DNA- and protein-damaging drugs can be less vulnerable to various bypass mechanisms possible with single targets. The reviewed studies provide a proof of concept that differential apoptosis targeting in cancer versus normal cells can be a basis for tumor selectivity of anticancer drugs.
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Affiliation(s)
- Barbara A Woynarowska
- Department of Radiation Oncology, The University of Texas Health Science Center, 14960 Omicron Drive, San Antonio, TX 78245, USA.
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