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Li M, Wang W, Wu M, Lei J, Lu X, Wang H. Stibnite dissolution and Sb oxidation by Paraccocus versutus XT0.6 via direct and indirect contact. JOURNAL OF HAZARDOUS MATERIALS 2024; 467:133731. [PMID: 38340562 DOI: 10.1016/j.jhazmat.2024.133731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/10/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
In this study Paraccocus versutus XT0.6 was employed to address the mechanism of microbial dissolution and oxidation of stibnite. Results showed that with the growth of XT0.6, pH increased to 9.0 in both microbe-mineral contact (MM) and microbe-mineral non-contact groups (M[M]). Dissolved Sb(III) was released from stibnite, which was subsequently quickly oxidized to Sb(V) completely in MM and partially in M[M] groups. On the contrast, the final pH decreased to 6.5 and 4.9, respectviely, in system amended with extracellular secretion (EM) of XT0.6 and abiotic groups. Dissolution of stibnite and oxidation of Sb(III) were also observed in EM group, suggesting a potential contribution of extracellular enzyme in Sb(III) oxidation. The dissolution and oxidation rates were the highest in MM group, followed by those in M[M], EM and abiotic groups. To be noted, Sb(V) concentration decreased in MM group on the fifth day, which might indicate the formation of Sb(V)-bearing secondary mineral. Genome of XT0.6 consisted of two chromosomes and one plasmid, and most genes responsible for antimony oxidation and antimony resistance were located on the chromosomes. Proteomics analysis of the extracellular secretions indicated the up-regulated proteins were mainly related to electron-transfer, suggesting their potential role in Sb(III) oxidation.
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Affiliation(s)
- Min Li
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Weiqi Wang
- State key Laboratory of Biogeology and Environmental Geology, China
| | - Mengxiaojun Wu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Jingwen Lei
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; State key Laboratory of Biogeology and Environmental Geology, China.
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2
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Palavecino A, Sartorio MG, Carrillo N, Cortez N, Bortolotti A. The extremophilic Andean isolate Acinetobacter sp. Ver3 expresses two ferredoxin-NADP + reductase isoforms with different catalytic properties. FEBS Lett 2024; 598:670-683. [PMID: 38433717 DOI: 10.1002/1873-3468.14826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 03/05/2024]
Abstract
Ferredoxin/flavodoxin-NADPH reductases (FPRs) catalyze the reversible electron transfer between NADPH and ferredoxin/flavodoxin. The Acinetobacter sp. Ver3 isolated from high-altitude Andean lakes contains two isoenzymes, FPR1ver3 and FPR2ver3. Absorption spectra of these FPRs revealed typical features of flavoproteins, consistent with the use of FAD as a prosthetic group. Spectral differences indicate distinct electronic arrangements for the flavin in each enzyme. Steady-state kinetic measurements show that the enzymes display catalytic efficiencies in the order of 1-6 μm-1·s-1, although FPR1ver3 exhibited higher kcat values compared to FPR2ver3. When flavodoxinver3 was used as a substrate, both reductases exhibited dissimilar behavior. Moreover, only FPR1ver3 is induced by oxidative stimuli, indicating that the polyextremophile Ver3 has evolved diverse strategies to cope with oxidative environments.
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Affiliation(s)
- Alejandro Palavecino
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (UNR & CONICET), Universidad Nacional de Rosario, Argentina
| | - Mariana Gabriela Sartorio
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (UNR & CONICET), Universidad Nacional de Rosario, Argentina
| | - Néstor Carrillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (UNR & CONICET), Universidad Nacional de Rosario, Argentina
| | - Néstor Cortez
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (UNR & CONICET), Universidad Nacional de Rosario, Argentina
| | - Ana Bortolotti
- Área Biofísica, Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas., Universidad Nacional de Rosario (UNR & CONICET), Rosario, Argentina
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3
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Willetts A. The Role of Dioxygen in Microbial Bio-Oxygenation: Challenging Biochemistry, Illustrated by a Short History of a Long Misunderstood Enzyme. Microorganisms 2024; 12:389. [PMID: 38399793 PMCID: PMC10891995 DOI: 10.3390/microorganisms12020389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
A Special Issue of Microorganisms devoted to 'Microbial Biocatalysis and Biodegradation' would be incomplete without some form of acknowledgement of the many important roles that dioxygen-dependent enzymes (principally mono- and dioxygenases) play in relevant aspects of bio-oxygenation. This is reflected by the multiple strategic roles that dioxygen -dependent microbial enzymes play both in generating valuable synthons for chemoenzymatic synthesis and in facilitating reactions that help to drive the global geochemical carbon cycle. A useful insight into this can be gained by reviewing the evolution of the current status of 2,5-diketocamphane 1,2-monooxygenase (EC 1.14.14.108) from (+)-camphor-grown Pseudomonas putida ATCC 17453, the key enzyme that promotes the initial ring cleavage of this natural bicyclic terpene. Over the last sixty years, the perceived nature of this monooxygenase has transmogrified significantly. Commencing in the 1960s, extensive initial studies consistently reported that the enzyme was a monomeric true flavoprotein dependent on both FMNH2 and nonheme iron as bound cofactors. However, over the last decade, all those criteria have changed absolutely, and the enzyme is currently acknowledged to be a metal ion-independent homodimeric flavin-dependent two-component mono-oxygenase deploying FMNH2 as a cosubstrate. That transition is a paradigm of the ever evolving nature of scientific knowledge.
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Affiliation(s)
- Andrew Willetts
- 4 Sv Ivan, 21400 Sutivan, Croatia;
- Curnow Consultancies, Helston TR13 9PQ, UK
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4
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Chen L, Wang Y, Miao J, Wang Q, Liu Z, Xie W, Liu X, Feng Z, Cheng S, Chi X, Ge Y. LysR-type transcriptional regulator FinR is required for phenazine and pyrrolnitrin biosynthesis in biocontrol Pseudomonas chlororaphis strain G05. Appl Microbiol Biotechnol 2021; 105:7825-7839. [PMID: 34562115 DOI: 10.1007/s00253-021-11600-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 11/30/2022]
Abstract
Phenazine-1-carboxylic acid and pyrrolnitrin, the two secondary metabolites produced by Pseudomonas chlororaphis G05, serve as biocontrol agents that mainly contribute to the growth repression of several fungal phytopathogens. Although some regulators of phenazine-1-carboxylic acid biosynthesis have been identified, the regulatory pathway involving phenazine-1-carboxylic acid synthesis is not fully understood. We isolated a white conjugant G05W03 on X-Gal-containing LB agar during our screening of novel regulator candidates using transposon mutagenesis with a fusion mutant G05Δphz::lacZ as a recipient. By cloning of DNA adjacent to the site of the transposon insertion, we revealed that a LysR-type transcriptional regulator (LTTR) gene, finR, was disrupted in the conjugant G05W03. To confirm the regulatory function of FinR, we constructed the finR-knockout mutant G05ΔfinR, G05Δphz::lacZΔfinR, and G05Δprn::lacZΔfinR, using the wild-type strain G05 and its fusion mutant derivatives as recipient strains, respectively. We found that the expressions of phz and prn operons were dramatically reduced in the finR-deleted mutant. With quantification of the production of antifungal metabolites biosynthesized by the finR-negative strain G05ΔfinR, it was shown that FinR deficiency also led to decreased yield of phenazine-1-carboxylic acid and pyrrolnitrin. In addition, the pathogen inhibition assay confirmed that the production of phenazine-1-carboxylic acid was severely reduced in the absence of FinR. Transcriptional fusions and qRT-PCR verified that FinR could positively govern the transcription of the phz and prn operons. Taken together, FinR is required for antifungal metabolite biosynthesis and crop protection against some fungal pathogens.Key points• A novel regulator FinR was identified by transposon mutagenesis.• FinR regulates antifungal metabolite production.• FinR regulates the phz and prn expression by binding to their promoter regions.
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Affiliation(s)
- Lijuan Chen
- Affiliated Hospital of Ludong University, Yantai, 264025, China.,The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Yanhua Wang
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Jing Miao
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Qijun Wang
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Zili Liu
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Wenqi Xie
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Xinsheng Liu
- Affiliated Hospital of Ludong University, Yantai, 264025, China.,The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Zhibin Feng
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China.,Biological Fermentation and Separation Engineering Laboratory, School of Life Sciences, Ludong University, Yantai, 264025, China
| | - Shiwei Cheng
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China.,Biological Fermentation and Separation Engineering Laboratory, School of Life Sciences, Ludong University, Yantai, 264025, China
| | - Xiaoyan Chi
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China.
| | - Yihe Ge
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China. .,Biological Fermentation and Separation Engineering Laboratory, School of Life Sciences, Ludong University, Yantai, 264025, China.
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5
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Mohapatra B, Phale PS. Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation. Front Bioeng Biotechnol 2021; 9:602445. [PMID: 33791281 PMCID: PMC8006333 DOI: 10.3389/fbioe.2021.602445] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/09/2021] [Indexed: 12/21/2022] Open
Abstract
Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.
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Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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6
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High c-di-GMP promotes expression of fpr-1 and katE involved in oxidative stress resistance in Pseudomonas putida KT2440. Appl Microbiol Biotechnol 2019; 103:9077-9089. [PMID: 31673742 DOI: 10.1007/s00253-019-10178-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/21/2019] [Accepted: 10/03/2019] [Indexed: 10/25/2022]
Abstract
Oxidative stress is an unavoidable consequence of interactions with various reactive oxygen species (ROS)-inducing agents that would damage cells or even cause cell death. Bacteria have developed defensive systems, including induction of stress-sensing proteins and detoxification enzymes, to handle oxidative stress. Cyclic diguanylate (c-di-GMP) is a ubiquitous intracellular bacterial second messenger that coordinates diverse aspects of bacterial growth and behavior. In this study, we revealed a mechanism by which c-di-GMP regulated bacterial oxidative stress resistance in Pseudomonas putida KT2440. High c-di-GMP level was found to enhance bacterial resistance towards hydrogen peroxide. Transcription assay showed that expression of two oxidative stress resistance genes, fpr-1 and katE, was promoted under high c-di-GMP level. Deletion of fpr-1 and katE both decreased bacterial tolerance to hydrogen peroxide and weakened the effect of c-di-GMP on oxidative stress resistance. The promoted expression of fpr-1 under high c-di-GMP level was caused by increased cellular ROS via a transcriptional regulator FinR. We further demonstrated that the influence of high c-di-GMP on cellular ROS depend on the existence of FleQ, a transcriptional regulatory c-di-GMP effector. Besides, the regulation of katE by c-di-GMP was also FleQ dependent in an indirect way. Our results proved a connection between c-di-GMP and oxidative stress resistance and revealed a mechanism by which c-di-GMP regulated expression of fpr-1 and katE in P. putida KT2440.
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7
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FinR Regulates Expression of nicC and nicX Operons, Involved in Nicotinic Acid Degradation in Pseudomonas putida KT2440. Appl Environ Microbiol 2018; 84:AEM.01210-18. [PMID: 30097438 DOI: 10.1128/aem.01210-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 07/31/2018] [Indexed: 12/24/2022] Open
Abstract
Many proteobacteria harbor FinR homologues in their genomes as putative LysR-type proteins; however, the function of FinR is poorly studied except in the induction of fpr-1 under superoxide stress conditions in Pseudomonas putida and Pseudomonas aeruginosa Here, by analyzing the influence of finR deletion on the transcriptomic profile of P. putida KT2440 through RNA sequencing and real-time quantitative PCR (RT-qPCR), we found 11 operons that are potentially regulated by FinR. Among them, the expression of nicC and nicX operons, which were reported to be responsible for the aerobic degradation of nicotinic acid (NA), was significantly decreased in the finR mutant, and complementation with intact finR restored the expression of the two operons. The results of bacterial NA utilization demonstrated that the deletion of finR impaired bacterial growth in minimal medium supplemented with NA/6HNA (6-hydroxynicotinic acid) as the sole carbon source and that complementation with intact finR restored the growth of the mutant strain. The expression of nicC and nicX operons was previously revealed to be repressed by the NicR repressor and induced by NA/6HNA. Our transcriptional assay revealed that the deletion of finR weakened the induction of nicC and nicX by NA/6HNA. Meanwhile, the deletion of finR largely decreased the effect of nicR deletion on the expression of nicC and nicX operons. These results suggest that finR plays a positive role and cooperates with NicR in the regulation of nicC and nicX operons. In vitro experiments showed that both FinR and NicR bound to nicX and nicC promoter regions directly. The results of this study deepened our knowledge of FinR function and nicotinic acid degradation in P. putida IMPORTANCE This study analyzed the influence of finR deletion on the transcriptomic profile of Pseudomonas putida KT2440. The FinR regulator is widely distributed but poorly studied in diverse proteobacteria. Here, we found 11 operons that potentially are regulated by FinR in KT2440. We further demonstrated that FinR played a positive role and cooperated with the NicR repressor in bacterial nicotinic acid (NA) degradation via regulating the expression of nicC and nicX operons. Furthermore, a transcriptomic analysis also indicated a potentially negative role of FinR in the expression of the hut cluster involved in bacterial histidine utilization. The work deepened our knowledge of FinR function and nicotinic acid degradation in P. putida.
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Zheng Y, Li Y, Long H, Zhao X, Jia K, Li J, Wang L, Wang R, Lu X, Zhang D. bifA Regulates Biofilm Development of Pseudomonas putida MnB1 as a Primary Response to H 2O 2 and Mn 2. Front Microbiol 2018; 9:1490. [PMID: 30042743 PMCID: PMC6048274 DOI: 10.3389/fmicb.2018.01490] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas putida (P. putida) MnB1 is a widely used model strain in environment science and technology for determining microbial manganese oxidation. Numerous studies have demonstrated that the growth and metabolism of P. putida MnB1 are influenced by various environmental factors. In this study, we investigated the effects of hydrogen peroxide (H2O2) and manganese (Mn2+) on proliferation, Mn2+ acquisition, anti-oxidative system, and biofilm formation of P. putida MnB1. The related orthologs of 4 genes, mco, mntABC, sod, and bifA, were amplified from P. putida GB1 and their involvement were assayed, respectively. We found that P. putida MnB1 degraded H2O2, and quickly recovered for proliferation, but its intracellular oxidative stress state was maintained, with rapid biofilm formation after H2O2 depletion. The data from mco, mntABC, sod and bifA expression levels by qRT-PCR, elucidated a sensitivity toward bifA-mediated biofilm formation, in contrary to intracellular anti-oxidative system under H2O2 exposure. Meanwhile, Mn2+ ion supply inhibited biofilm formation of P. putida MnB1. The expression pattern of these genes showed that Mn2+ ion supply likely functioned to modulate biofilm formation rather than only acting as nutrient substrate for P. putida MnB1. Furthermore, blockade of BifA activity by GTP increased the formation and development of biofilms during H2O2 exposure, while converse response to Mn2+ ion supply was evident. These distinct cellular responses to H2O2 and Mn2+ provide insights on the common mechanism by which environmental microorganisms may be protected from exogenous factors. We postulate that BifA-mediated biofilm formation but not intracellular anti-oxidative system may be a primary protective strategy adopted by P. putida MnB1. These findings will highlight the understanding of microbial adaptation mechanisms to distinct environmental stresses.
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Affiliation(s)
- Yanjing Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yumei Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Hongyan Long
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaojuan Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Keke Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Juan Li
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, China
| | - Leyong Wang
- Key Laboratory of Mesoscopic Chemistry of MOE and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing, China
| | - Ruiyong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiancai Lu
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, China
| | - Dongmei Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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Park C, Shin B, Jung J, Lee Y, Park W. Metabolic and stress responses of Acinetobacter oleivorans DR1 during long-chain alkane degradation. Microb Biotechnol 2017; 10:1809-1823. [PMID: 28857443 PMCID: PMC5658608 DOI: 10.1111/1751-7915.12852] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/28/2022] Open
Abstract
Acinetobacter oleivorans DR1 can utilize C12–C30 alkanes as a sole carbon source but not short‐chain alkanes (C6, C10). Two copies of each alkB‐, almA‐ and ladA‐type alkane hydroxylase (AH) are present in the genome of DR1 cells. Expression and mutational analyses of AHs showed that alkB1 and alkB2 are the major AH‐encoding genes under C12–C30, and the roles of other almA‐ and ladA genes are negligible. Our data suggested that AlkB1 is responsible for long‐chain alkane utilization (C24–C26), and AlkB2 is important for medium‐chain alkane (C12–C16) metabolism. Phylogenetic analyses revealed large incongruities between phylogenies of 16S rRNA and each AH gene, which implies that A. oleivorans DR1 has acquired multiple alkane hydroxylases through horizontal gene transfer. Transcriptomic and qRT‐PCR analyses suggested that genes participating in the synthesis of siderophore, trehalose and poly 3‐hydroxybutyrate (PHB) were expressed at much higher levels when cells used C30 than when used succinate as a carbon source. The following biochemical assays supported our gene expression analyses: (i) quantification of siderophore, (ii) measurement of trehalose and (iii) observation of PHB storage. Interestingly, highly induced both ackA gene encoding an acetate kinase A and pta gene encoding a phosphotransacetylase suggested unusual ATP synthesis during C30 alkane degradation, which was demonstrated by ATP measurement using the ΔackA mutant. Impaired growth of the ΔaceA mutant indicated that the glyoxylate shunt pathway is important when C30 alkane is utilized. Our data provide insight into long‐chain alkane degradation in soil microorganisms.
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Korea
| | - Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Korea
| | - Jaejoon Jung
- National Marine Biodiversity Institute of Korea, Chungcheongnam-Do, 33662, Korea
| | - Yunho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Korea
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10
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Boonma S, Romsang A, Duang-Nkern J, Atichartpongkul S, Trinachartvanit W, Vattanaviboon P, Mongkolsuk S. The FinR-regulated essential gene fprA, encoding ferredoxin NADP+ reductase: Roles in superoxide-mediated stress protection and virulence of Pseudomonas aeruginosa. PLoS One 2017; 12:e0172071. [PMID: 28187184 PMCID: PMC5302815 DOI: 10.1371/journal.pone.0172071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/30/2017] [Indexed: 11/23/2022] Open
Abstract
Pseudomonas aeruginosa has two genes encoding ferredoxin NADP(+) reductases, denoted fprA and fprB. We show here that P. aeruginosa fprA is an essential gene. However, the ΔfprA mutant could only be successfully constructed in PAO1 strains containing an extra copy of fprA on a mini-Tn7 vector integrated into the chromosome or carrying it on a temperature-sensitive plasmid. The strain containing an extra copy of the ferredoxin gene (fdx1) could suppress the essentiality of FprA. Other ferredoxin genes could not suppress the requirement for FprA, suggesting that Fdx1 mediates the essentiality of FprA. The expression of fprA was highly induced in response to treatments with a superoxide generator, paraquat, or sodium hypochlorite (NaOCl). The induction of fprA by these treatments depended on FinR, a LysR-family transcription regulator. In vivo and in vitro analysis suggested that oxidized FinR acted as a transcriptional activator of fprA expression by binding to its regulatory box, located 20 bases upstream of the fprA -35 promoter motif. This location of the FinR box also placed it between the -35 and -10 motifs of the finR promoter, where the reduced regulator functions as a repressor. Under uninduced conditions, binding of FinR repressed its own transcription but had no effect on fprA expression. Exposure to paraquat or NaOCl converted FinR to a transcriptional activator, leading to the expression of both fprA and finR. The ΔfinR mutant showed an increased paraquat sensitivity phenotype and attenuated virulence in the Drosophila melanogaster host model. These phenotypes could be complemented by high expression of fprA, indicating that the observed phenotypes of the ΔfinR mutant arose from the inability to up-regulate fprA expression. In addition, increased expression of fprB was unable to rescue essentiality of fprA or the superoxide-sensitive phenotype of the ΔfinR mutant, suggesting distinct mechanisms of the FprA and FprB enzymes.
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Affiliation(s)
- Siriwan Boonma
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Adisak Romsang
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jintana Duang-Nkern
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | | | | | - Paiboon Vattanaviboon
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry Of Education, Bangkok, Thailand.,Program in Applied Biological Sciences: Environmental Health, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry Of Education, Bangkok, Thailand.,Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, Thailand
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11
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Romsang A, Duang-nkern J, Wirathorn W, Vattanaviboon P, Mongkolsuk S. Pseudomonas aeruginosa IscR-Regulated Ferredoxin NADP(+) Reductase Gene (fprB) Functions in Iron-Sulfur Cluster Biogenesis and Multiple Stress Response. PLoS One 2015; 10:e0134374. [PMID: 26230408 PMCID: PMC4521836 DOI: 10.1371/journal.pone.0134374] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 07/08/2015] [Indexed: 12/14/2022] Open
Abstract
P. aeruginosa (PAO1) has two putative genes encoding ferredoxin NADP(+) reductases, denoted fprA and fprB. Here, the regulation of fprB expression and the protein’s physiological roles in [4Fe-4S] cluster biogenesis and stress protection are characterized. The fprB mutant has defects in [4Fe-4S] cluster biogenesis, as shown by reduced activities of [4Fe-4S] cluster-containing enzymes. Inactivation of the gene resulted in increased sensitivity to oxidative, thiol, osmotic and metal stresses compared with the PAO1 wild type. The increased sensitivity could be partially or completely suppressed by high expression of genes from the isc operon, which are involved in [Fe-S] cluster biogenesis, indicating that stress sensitivity in the fprB mutant is partially caused by a reduction in levels of [4Fe-4S] clusters. The pattern and regulation of fprB expression are in agreement with the gene physiological roles; fprB expression was highly induced by redox cycling drugs and diamide and was moderately induced by peroxides, an iron chelator and salt stress. The stress-induced expression of fprB was abolished by a deletion of the iscR gene. An IscR DNA-binding site close to fprB promoter elements was identified and confirmed by specific binding of purified IscR. Analysis of the regulation of fprB expression supports the role of IscR in directly regulating fprB transcription as a transcription activator. The combination of IscR-regulated expression of fprB and the fprB roles in response to multiple stressors emphasizes the importance of [Fe-S] cluster homeostasis in both gene regulation and stress protection.
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Affiliation(s)
- Adisak Romsang
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jintana Duang-nkern
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Wilaiwan Wirathorn
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Paiboon Vattanaviboon
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, Thailand
- Program in Applied Biological Science: Environmental Health, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry Of Education, Bangkok, Thailand
- * E-mail:
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Al-Maleki AR, Mariappan V, Vellasamy KM, Tay ST, Vadivelu J. Altered Proteome of Burkholderia pseudomallei Colony Variants Induced by Exposure to Human Lung Epithelial Cells. PLoS One 2015; 10:e0127398. [PMID: 25996927 PMCID: PMC4440636 DOI: 10.1371/journal.pone.0127398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 04/14/2015] [Indexed: 12/19/2022] Open
Abstract
Burkholderia pseudomallei primary diagnostic cultures demonstrate colony morphology variation associated with expression of virulence and adaptation proteins. This study aims to examine the ability of B. pseudomallei colony variants (wild type [WT] and small colony variant [SCV]) to survive and replicate intracellularly in A549 cells and to identify the alterations in the protein expression of these variants, post-exposure to the A549 cells. Intracellular survival and cytotoxicity assays were performed followed by proteomics analysis using two-dimensional gel electrophoresis. B. pseudomallei SCV survive longer than the WT. During post-exposure, among 259 and 260 protein spots of SCV and WT, respectively, 19 were differentially expressed. Among SCV post-exposure up-regulated proteins, glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase (CbbA) and betaine aldehyde dehydrogenase were associated with adhesion and virulence. Among the down-regulated proteins, enolase (Eno) is implicated in adhesion and virulence. Additionally, post-exposure expression profiles of both variants were compared with pre-exposure. In WT pre- vs post-exposure, 36 proteins were differentially expressed. Of the up-regulated proteins, translocator protein, Eno, nucleoside diphosphate kinase (Ndk), ferritin Dps-family DNA binding protein and peptidyl-prolyl cis-trans isomerase B were implicated in invasion and virulence. In SCV pre- vs post-exposure, 27 proteins were differentially expressed. Among the up-regulated proteins, flagellin, Eno, CbbA, Ndk and phenylacetate-coenzyme A ligase have similarly been implicated in adhesion, invasion. Protein profiles differences post-exposure provide insights into association between morphotypic and phenotypic characteristics of colony variants, strengthening the role of B. pseudomallei morphotypes in pathogenesis of melioidosis.
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Affiliation(s)
- Anis Rageh Al-Maleki
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vanitha Mariappan
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kumutha Malar Vellasamy
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sun Tee Tay
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jamuna Vadivelu
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Mirouze N, Bidnenko E, Noirot P, Auger S. Genome-wide mapping of TnrA-binding sites provides new insights into the TnrA regulon in Bacillus subtilis. Microbiologyopen 2015; 4:423-35. [PMID: 25755103 PMCID: PMC4475385 DOI: 10.1002/mbo3.249] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/22/2015] [Accepted: 02/02/2015] [Indexed: 01/13/2023] Open
Abstract
Under nitrogen limitation conditions, Bacillus subtilis induces a sophisticated network of adaptation responses. More precisely, the B. subtilis TnrA regulator represses or activates directly or indirectly the expression of a hundred genes in response to nitrogen availability. The global TnrA regulon have already been identified among which some directly TnrA-regulated genes have been characterized. However, a genome-wide mapping of in vivo TnrA-binding sites was still needed to clearly define the set of genes directly regulated by TnrA. Using chromatin immunoprecipitation coupled with hybridization to DNA tiling arrays (ChIP-on-chip), we now provide in vivo evidence that TnrA reproducibly binds to 42 regions on the chromosome. Further analysis with real-time in vivo transcriptional profiling, combined with results from previous reports, allowed us to define the TnrA primary regulon. We identified 35 promoter regions fulfilling three criteria necessary to be part of this primary regulon: (i) TnrA binding in ChIP-on-chip experiments and/or in previous in vitro studies; (ii) the presence of a TnrA box; (iii) TnrA-dependent expression regulation. In addition, the TnrA primary regulon delimitation allowed us to improve the TnrA box consensus. Finally, our results reveal new interconnections between the nitrogen regulatory network and other cellular processes.
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Affiliation(s)
- Nicolas Mirouze
- UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.,UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France
| | - Elena Bidnenko
- UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.,UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France
| | - Philippe Noirot
- UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.,UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France
| | - Sandrine Auger
- UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.,UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France
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Kim J, Park W. Oxidative stress response in Pseudomonas putida. Appl Microbiol Biotechnol 2014; 98:6933-46. [PMID: 24957251 DOI: 10.1007/s00253-014-5883-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 11/30/2022]
Abstract
Pseudomonas putida is widely distributed in nature and is capable of degrading various organic compounds due to its high metabolic versatility. The survival capacity of P. putida stems from its frequent exposure to various endogenous and exogenous oxidative stresses. Oxidative stress is an unavoidable consequence of interactions with various reactive oxygen species (ROS)-inducing agents existing in various niches. ROS could facilitate the evolution of bacteria by mutating genomes. Aerobic bacteria maintain defense mechanisms against oxidative stress throughout their evolution. To overcome the detrimental effects of oxidative stress, P. putida has developed defensive cellular systems involving induction of stress-sensing proteins and detoxification enzymes as well as regulation of oxidative stress response networks. Genetic responses to oxidative stress in P. putida differ markedly from those observed in Escherichia coli and Salmonella spp. Two major redox-sensing transcriptional regulators, SoxR and OxyR, are present and functional in the genome of P. putida. However, the novel regulators FinR and HexR control many genes belonging to the E. coli SoxR regulon. Oxidative stress can be generated by exposure to antibiotics, and iron homeostasis in P. putida is crucial for bacterial cell survival during treatment with antibiotics. This review highlights and summarizes current knowledge of oxidative stress in P. putida, as a model soil bacterium, together with recent studies from molecular genetics perspectives.
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Affiliation(s)
- Jisun Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5Ga, Seungbuk-Ku, Seoul, 136-713, Republic of Korea
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Kim J, Park W. Indole inhibits bacterial quorum sensing signal transmission by interfering with quorum sensing regulator folding. MICROBIOLOGY-SGM 2013; 159:2616-2625. [PMID: 24025605 DOI: 10.1099/mic.0.070615-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quorum sensing (QS)-dependent biofilm formation and motility were controlled by AqsR in Acinetobacter oleivorans DR1. QS-controlled phenotypes appeared to be inhibited by indole and the aqsR mutant had the same phenotypes. We demonstrated that the turnover rate of AqsR became more rapid without the N-acylhomoserine lactone (AHL) signal, and that indole could increase the expression of many protease and chaperone proteins. The addition of exogenous indole decreased the expression of two AqsR-targeted genes: AOLE_03905 (putative surface adhesion protein) and AOLE_11355 (L-asparaginase). The overexpression of AqsR in Escherichia coli was impossible with the indole treatment. Surprisingly, our [(35)S]methionine pulse-labelling data demonstrated that the stability and folding of AqsR protein decreased in the presence of indole without changing aqsR mRNA expression in E. coli. Interestingly, indole resulted in a loss of TraR-dependent traG expression in an Agrobacterium tumefaciens indicator strain. However, when indole was added after incubation with exogenous AHL, indole could not inhibit the TraR-dependent expression of the traG promoter. This indicated that AHL-bound TraR could be protective against indole, but TraR without AHL could not be active in the presence of indole. Here, we provided evidence for the first time showing that the indole effect on QS-controlled bacterial phenotypes is due to inhibited QS regulator folding and not a reduced QS signal.
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Affiliation(s)
- Jisun Kim
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Woojun Park
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
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Bortolotti A, Sánchez-Azqueta A, Maya CM, Velázquez-Campoy A, Hermoso JA, Medina M, Cortez N. The C-terminal extension of bacterial flavodoxin-reductases: involvement in the hydride transfer mechanism from the coenzyme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:33-43. [PMID: 24016470 DOI: 10.1016/j.bbabio.2013.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/26/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022]
Abstract
To study the role of the mobile C-terminal extension present in bacterial class of plant type NADP(H):ferredoxin reductases during catalysis, we generated a series of mutants of the Rhodobacter capsulatus enzyme (RcFPR). Deletion of the six C-terminal amino acids beyond alanine 266 was combined with the replacement A266Y, emulating the structure present in plastidic versions of this flavoenzyme. Analysis of absorbance and fluorescence spectra suggests that deletion does not modify the general geometry of FAD itself, but increases exposure of the flavin to the solvent, prevents a productive geometry of FAD:NADP(H) complex and decreases the protein thermal stability. Although the replacement A266Y partially coats the isoalloxazine from solvent and slightly restores protein stability, this single change does not allow formation of active charge-transfer complexes commonly present in the wild-type FPR, probably due to restraints of C-terminus pliability. A proton exchange process is deduced from ITC measurements during coenzyme binding. All studied RcFPR variants display higher affinity for NADP(+) than wild-type, evidencing the contribution of the C-terminus in tempering a non-productive strong (rigid) interaction with the coenzyme. The decreased catalytic rate parameters confirm that the hydride transfer from NADPH to the flavin ring is considerably hampered in the mutants. Although the involvement of the C-terminal extension from bacterial FPRs in stabilizing overall folding and bent-FAD geometry has been stated, the most relevant contributions to catalysis are modulation of coenzyme entrance and affinity, promotion of the optimal geometry of an active complex and supply of a proton acceptor acting during coenzyme binding.
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Affiliation(s)
- Ana Bortolotti
- Instituto de Biología Molecular y Celular de Rosario, Universidad Nacional de Rosario & CONICET, Rosario, Argentina
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Pérez-Pantoja D, Nikel PI, Chavarría M, de Lorenzo V. Endogenous stress caused by faulty oxidation reactions fosters evolution of 2,4-dinitrotoluene-degrading bacteria. PLoS Genet 2013; 9:e1003764. [PMID: 24009532 PMCID: PMC3757077 DOI: 10.1371/journal.pgen.1003764] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/16/2013] [Indexed: 01/13/2023] Open
Abstract
Environmental strain Burkholderia sp. DNT mineralizes the xenobiotic compound 2,4-dinitrotoluene (DNT) owing to the catabolic dnt genes borne by plasmid DNT, but the process fails to promote significant growth. To investigate this lack of physiological return of such an otherwise complete metabolic route, cells were exposed to DNT under various growth conditions and the endogenous formation of reactive oxygen species (ROS) monitored in single bacteria. These tests revealed the buildup of a strong oxidative stress in the population exposed to DNT. By either curing the DNT plasmid or by overproducing the second activity of the biodegradation route (DntB) we could trace a large share of ROS production to the first reaction of the route, which is executed by the multicomponent dioxygenase encoded by the dntA gene cluster. Naphthalene, the ancestral substrate of the dioxygenase from which DntA has evolved, also caused significant ROS formation. That both the old and the new substrate brought about a considerable cellular stress was indicative of a still-evolving DntA enzyme which is neither optimal any longer for naphthalene nor entirely advantageous yet for growth of the host strain on DNT. We could associate endogenous production of ROS with likely error-prone repair mechanisms of DNA damage, and the ensuing stress-induced mutagenesis in cells exposed to DNT. It is thus plausible that the evolutionary roadmap for biodegradation of xenobiotic compounds like DNT was largely elicited by mutagenic oxidative stress caused by faulty reactions of precursor enzymes with novel but structurally related substrates-to-be. Many bacteria have acquired the capacity of metabolizing chemical compounds that have never been in the Biosphere before the onset of contemporary synthetic chemistry. However, the factors that shape the new metabolic properties of such microorganisms remain obscure. We examined the performance of a still-evolving metabolic pathway for biodegradation of 2,4-dinitrotoluene (DNT, an archetypal xenobiotic compound) borne by a Burkholderia strain isolated from soil in an ammunition plant. The biodegradation pathway likely arose from a precursor set of genes for catabolism of naphthalene (although Burkholderia does not degrade this compound any longer), and is now advancing towards the new substrate, DNT. We found that the action of the first enzyme of the biodegradation pathway, a Rieske-type dioxygenase, on the still-suboptimal substrate (DNT) generates a high level of endogenous reactive oxygen species. This, in turn, damages DNA and increases mutagenesis, ultimately resulting in the creation of novelty that may foster evolution of xenobiotic-degrading variants of the strain hosting the biodegradation pathway. The very metabolic problem thus somehow seems to stimulate the exploration of the solution space. Our data is fully consistent with the notion that stress caused by faulty dioxygenation of DNT accelerates the rate of bacterial evolution.
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Affiliation(s)
- Danilo Pérez-Pantoja
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Max Chavarría
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
- * E-mail:
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Role for ferredoxin:NAD(P)H oxidoreductase (FprA) in sulfate assimilation and siderophore biosynthesis in Pseudomonads. J Bacteriol 2013; 195:3876-87. [PMID: 23794620 DOI: 10.1128/jb.00528-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyridine-2,6-bis(thiocarboxylate) (PDTC), produced by certain pseudomonads, is a sulfur-containing siderophore that binds iron, as well as a wide range of transition metals, and it affects the net hydrolysis of the environmental contaminant carbon tetrachloride. The pathway of PDTC biosynthesis has not been defined. Here, we performed a transposon screen of Pseudomonas putida DSM 3601 to identify genes necessary for PDTC production (Pdt phenotype). Transposon insertions within genes for sulfate assimilation (cysD, cysNC, and cysG [cobA2]) dominated the collection of Pdt mutations. In addition, two insertions were within the gene for the LysR-type transcriptional activator FinR (PP1637). Phenotypic characterization indicated that finR mutants were cysteine bradytrophs. The Pdt phenotype of finR mutants could be complemented by the known target of FinR regulation, fprA (encoding ferredoxin:NADP(+) oxidoreductase), or by Escherichia coli cysJI (encoding sulfite reductase). These data indicate that fprA is necessary for effective sulfate assimilation by P. putida and that the effect of finR mutation on PDTC production was due to deficient expression of fprA and sulfite reduction. fprA expression in both P. putida and P. aeruginosa was found to be regulated by FinR, but in a manner dependent upon reduced sulfur sources, implicating FinR in sulfur regulatory physiology. The genes and phenotypes identified in this study indicated a strong dependence upon intracellular reduced sulfur/cysteine for PDTC biosynthesis and that pseudomonads utilize sulfite reduction enzymology distinct from that of E. coli and possibly similar to that of chloroplasts and other proteobacteria.
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Jung J, Seo H, Lee SH, Jeon CO, Park W. The effect of toxic malachite green on the bacterial community in Antarctic soil and the physiology of malachite green-degrading Pseudomonas sp. MGO. Appl Microbiol Biotechnol 2013; 97:4511-21. [PMID: 23296502 DOI: 10.1007/s00253-012-4669-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 12/16/2012] [Accepted: 12/18/2012] [Indexed: 11/28/2022]
Abstract
The effects of malachite green (MG) on the bacterial community in Antarctic soil were assessed. Culture-independent community analysis using 16S rRNA gene pyrosequencing showed that, in the presence of MG, the relative abundance of Pseudomonas dramatically increased from 2.2 % to 36.6 % (16.6-fold), and Pseudomonas became the predominant genus. The reduction in bacterial biodiversity was demonstrated by diversity indices and rarefaction curves. MG-degrading Pseudomonas sp. MGO was isolated from Antarctic soil. MG tolerance and decolorization activity were confirmed by growth, spectrophotometric, high-performance liquid chromatography, and thin-layer chromatography analyses in high MG concentrations. Our data showed that the decolorization process occurred via biodegradation, while biosorption also occurred after some time during the fed-batch decolorization process. Significant inductions in laccase, nicotinamide adenine dinucleotide-2,6 dichlorophenol indophenol reductase, and MG reductase activities suggested their involvement in the decolorization process. We also showed that the high tolerance of strain MGO to toxic MG might be mediated by upregulation of oxidative stress defense systems such as superoxide dismutase and protease. Collectively, these results demonstrated the response of the Antarctic soil bacterial community to MG and provided insight into the molecular mechanism of MG-tolerant Pseudomonas strains isolated from Antarctic soil.
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Affiliation(s)
- Jaejoon Jung
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul 136-713, Republic of Korea
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Yeom J, Park W. Biochemical characterization of ferredoxin-NADP(+) reductase interaction with flavodoxin in Pseudomonas putida. BMB Rep 2012; 45:476-81. [PMID: 22917033 DOI: 10.5483/bmbrep.2012.45.8.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flavodoxin (Fld) has been demonstrated to bind to ferredoxin- NADP(+) reductase A (FprA) in Pseudomonas putida. Two residues (Phe(256), Lys(259)) of FprA are likely to be important for interacting with Fld based on homology modeling. Sitedirected mutagenesis and pH-dependent enzyme kinetics were performed to further examine the role of these residues. The catalytic efficiencies of FprA-Ala(259) and FprA-Asp(259) proteins were two-fold lower than those of the wild-type FprA. Homology modeling also strongly suggested that these two residues are important for electron transfer. Thermodynamic properties such as entropy, enthalpy, and heat capacity changes of FprA-Ala(259) and FprA-Asp(259) were examined by isothermal titration calorimetry. We demonstrated, for the first time, that Phe(256) and Lys(259) are critical residues for the interaction between FprA and Fld. Van der Waals interactions and hydrogen bonding were also more important than ionic interactions for forming the FprA-Fld complex.
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Affiliation(s)
- Jinki Yeom
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Korea
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Yeom J, Lee Y, Park W. Effects of non-ionic solute stresses on biofilm formation and lipopolysaccharide production in Escherichia coli O157:H7. Res Microbiol 2012; 163:258-67. [DOI: 10.1016/j.resmic.2012.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 01/30/2012] [Indexed: 10/14/2022]
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Structural-functional characterization and physiological significance of ferredoxin-NADP reductase from Xanthomonas axonopodis pv. citri. PLoS One 2011; 6:e27124. [PMID: 22096528 PMCID: PMC3212534 DOI: 10.1371/journal.pone.0027124] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 10/11/2011] [Indexed: 11/25/2022] Open
Abstract
Xanthomonas axonopodis pv. citri is a phytopathogen bacterium that causes severe citrus canker disease. Similar to other phytopathogens, after infection by this bacterium, plants trigger a defense mechanism that produces reactive oxygen species. Ferredoxin-NADP+ reductases (FNRs) are redox flavoenzymes that participate in several metabolic functions, including the response to reactive oxygen species. Xanthomonas axonopodis pv. citri has a gene (fpr) that encodes for a FNR (Xac-FNR) that belongs to the subclass I bacterial FNRs. The aim of this work was to search for the physiological role of this enzyme and to characterize its structural and functional properties. The functionality of Xac-FNR was tested by cross-complementation of a FNR knockout Escherichia coli strain, which exhibit high susceptibility to agents that produce an abnormal accumulation of •O2-. Xac-FNR was able to substitute for the FNR in E. coli in its antioxidant role. The expression of fpr in X. axonopodis pv. citri was assessed using semiquantitative RT-PCR and Western blot analysis. A 2.2-fold induction was observed in the presence of the superoxide-generating agents methyl viologen and 2,3-dimethoxy-1,4-naphthoquinone. Structural and functional studies showed that Xac-FNR displayed different functional features from other subclass I bacterial FNRs. Our analyses suggest that these differences may be due to the unusual carboxy-terminal region. We propose a further classification of subclass I bacterial FNRs, which is useful to determine the nature of their ferredoxin redox partners. Using sequence analysis, we identified a ferredoxin (XAC1762) as a potential substrate of Xac-FNR. The purified ferredoxin protein displayed the typical broad UV-visible spectrum of [4Fe-4S] clusters and was able to function as substrate of Xac-FNR in the cytochrome c reductase activity. Our results suggest that Xac-FNR is involved in the oxidative stress response of Xanthomonas axonopodis pv. citri and performs its biological function most likely through the interaction with ferredoxin XAC1762.
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Yeom S, Yeom J, Park W. Molecular characterization of FinR, a novel redox-sensing transcriptional regulator in Pseudomonas putida KT2440. Microbiology (Reading) 2010; 156:1487-1496. [DOI: 10.1099/mic.0.034181-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
FinR is required for the induction of fpr (ferredoxin-NADP+ reductase) under superoxide stress conditions in Pseudomonas putida. Many proteobacteria harbour FinR homologues in their genome as a putative LysR-type protein. Three cysteine residues (at positions 150, 239 and 289 in P. putida FinR) are conserved in all FinR homologues. When these conserved cysteines, along with two other cysteine residues present in FinR, were individually mutated to serines, the FinR remained active, unlike SoxR and OxyR in Escherichia coli. The results of our in vitro DNA-binding assay with cellular extracts showed that FinR binds directly to the fpr promoter region. In order to identify the FinR functional domain for sensing superoxide stress, we employed random and site-directed mutagenesis of FinR. Among 18 single amino acid mutants, three mutants (T39A, R194A and E225A) abolished fpr induction without any alteration of their DNA-binding ability, whereas other mutants also abrogated their DNA-binding abilities. Interestingly, two mutants (L215P and D51A) appeared to be constitutively active, regardless of superoxide stress conditions. Ferrous iron depletion, ferric iron addition and fdxA (ferredoxin) gene deletion also participate in the regulation of fpr. These data indicate that FinR has unusual residues for redox sensing and that the redox-sensing mechanism of FinR differs from the well-known mechanisms of OxyR and SoxR.
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Affiliation(s)
- Sujin Yeom
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5 Ga 136-713, Seoul, Republic of Korea
| | - Jinki Yeom
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5 Ga 136-713, Seoul, Republic of Korea
| | - Woojun Park
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5 Ga 136-713, Seoul, Republic of Korea
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NtrC-sensed nitrogen availability is important for oxidative stress defense in Pseudomonas putida KT2440. J Microbiol 2010; 48:153-9. [DOI: 10.1007/s12275-010-0075-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
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Li C, Wang H, Zhou L, Zhang Y, Song F, Zhang J. Quantitative measurement of pH influence on SalR regulated gene expression in Acinetobacter baylyi ADP1. J Microbiol Methods 2009; 79:8-12. [DOI: 10.1016/j.mimet.2009.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 07/08/2009] [Accepted: 07/08/2009] [Indexed: 10/20/2022]
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Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight. ISME JOURNAL 2009; 3:1402-19. [DOI: 10.1038/ismej.2009.74] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Lee Y, Oh S, Park W. Inactivation of the Pseudomonas putida KT2440 dsbA gene promotes extracellular matrix production and biofilm formation. FEMS Microbiol Lett 2009; 297:38-48. [PMID: 19500143 DOI: 10.1111/j.1574-6968.2009.01650.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
To identify genes essential to biofilm formation in Pseudomonas putida KT2440, 12 mutants defective in oxidative stress-related or metabolic pathway-related genes were evaluated. Of them, only the dsbA mutant lacking the disulfide bond isomerase exhibited significantly increased attachment to the polystyrene surface. Visual evaluation by extracellular matrix staining and scanning electron microscopy indicated that the KT2440-DeltadsbA strain displays enhanced extracellular matrix production, rugose colony morphology on agar plates and floating pellicles in static culture. Accordingly, we propose that deletion of the dsbA gene may stimulate production of the extracellular matrix, resulting in those phenotypes. In addition, the lack of detectable fluorescence in the KT2440-DeltadsbA under UV light as well as in both the wild type and the KT2440-DeltadsbA when grown on Luria-Bertani plates containing ferrous iron suggests that the fluorescent molecule may be a fluorescent siderophore with its synthesis/secretion controlled by DsbA in KT2440. These phenotypic defects observed in the dsbA mutant were complemented by the full-length KT2440 and Escherichia coli dsbA genes. In contrast to the role of DsbA in other bacteria, our results provide the first evidence that disruption of P. putida KT2440 dsbA gene overproduces the extracellular matrix and thus promotes biofilm formation.
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Affiliation(s)
- Yunho Lee
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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Cheng Z, Wei YYC, Sung WWL, Glick BR, McConkey BJ. Proteomic analysis of the response of the plant growth-promoting bacterium Pseudomonas putida UW4 to nickel stress. Proteome Sci 2009; 7:18. [PMID: 19422705 PMCID: PMC2689183 DOI: 10.1186/1477-5956-7-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 05/07/2009] [Indexed: 12/03/2022] Open
Abstract
Background Plant growth-promoting bacteria can alleviate the inhibitory effects of various heavy metals on plant growth, via decreasing levels of stress-induced ethylene. However, little has been done to detect any mechanisms specific for heavy metal resistance of this kind of bacteria. Here, we investigate the response of the wild-type plant growth-promoting bacterium Pseudomonas putida UW4 to nickel stress using proteomic approaches. The mutant strain P. putida UW4/AcdS-, lacking a functional 1-aminocyclopropane-1-carboxylic acid deaminase gene, was also assessed for its response to nickel stress. Results Two dimensional difference in-gel electrophoresis (DIGE) was used to detect significantly up- or down- regulated proteins (p < 0.05, | ratio | > 1.5) in P. putida in response to the presence of 2 mM Ni. Out of a total number of 1,702 proteins detected on the analytical gels for P. putida UW4, the expression levels of 82 (4.82%) proteins increased significantly while the expression of 81 (4.76%) proteins decreased significantly. Of 1,575 proteins detected on the analytical gels for P. putida UW4/AcdS-, the expression levels of 74 (4.70%) proteins increased and 51 (3.24%) proteins decreased significantly. Thirty-five proteins whose expression was altered were successfully identified by mass spectrometry and sequence comparisons with related species. Nineteen of the identified proteins were detected as differentially expressed in both wild-type and mutant expression profiles. Conclusion Functional assessment of proteins with significantly altered expression levels revealed several mechanisms thought to be involved in bacterial heavy metal detoxification, including general stress adaptation, anti-oxidative stress and heavy metal efflux proteins. This information may contribute to the development of plant growth-promoting bacteria mediated phytoremediation processes.
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Affiliation(s)
- Zhenyu Cheng
- Department of Biology, University of Waterloo, Ontario, Canada.
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Kim J, Jeon CO, Park W. Dual regulation of zwf-1 by both 2-keto-3-deoxy-6-phosphogluconate and oxidative stress in Pseudomonas putida. MICROBIOLOGY-SGM 2009; 154:3905-3916. [PMID: 19047757 DOI: 10.1099/mic.0.2008/020362-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Northern blot analysis and a GFP-based reporter assay showed that zwf-1, which encodes glucose-6-phosphate dehydrogenase, was highly induced when Pseudomonas putida KT2440 was cultured in minimal medium containing glucose or gluconate. However, zwf-1 expression was not detected in the presence of pyruvate or succinate. The use of a knockout mutant of HexR, a putative transcription regulator, resulted in constitutively high expression of zwf-1, regardless of the carbon source. An electrophoretic mobility shift assay showed that HexR protein binds to the zwf-1 promoter region and that HexR binding is inhibited by 2-keto-3-deoxy-6-phosphogluconate (KDPG). Despite the presence of gluconate, the edd mutant (non-KDPG producer) was not able to induce the zwf-1 gene. The eda mutant (KDPG overproducer) featured a constitutively high level of zwf-1 expression. Interestingly, zwf-1 was also highly expressed in the presence of oxidative stress-inducing reagents. The level of zwf-1 induction in wild-type cells undergoing oxidative stress did not differ significantly from that observed with the hexR mutant under normal conditions. Interestingly, the hexR mutant was more tolerant of oxidative stress than the wild-type. Expression of zwf-1 was induced by oxidative stress in the edd mutant. Thus, KDPG, a real inducer of zwf-1 gene expression, was not necessary for oxidative-stress induction. In vitro binding of HexR to its cognate promoter region was diminished by menadione and cumene hydroperoxide. The data suggested that HexR might be a dual-sensing regulator of zwf-1 induction that is able to respond to both KDPG and oxidative stress.
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Affiliation(s)
- Juhyun Kim
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5 Ga, Seoul, Republic of South Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 156-756, Republic of South Korea
| | - Woojun Park
- Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, Republic of Korea.,Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5 Ga, Seoul, Republic of South Korea
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Yeom J, Jeon CO, Madsen EL, Park W. In Vitro and In Vivo Interactions of Ferredoxin-NADP+ Reductases in Pseudomonas putida. ACTA ACUST UNITED AC 2009; 145:481-91. [DOI: 10.1093/jb/mvn185] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Ferredoxin-NADP+ reductase from Pseudomonas putida functions as a ferric reductase. J Bacteriol 2008; 191:1472-9. [PMID: 19114475 DOI: 10.1128/jb.01473-08] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas putida harbors two ferredoxin-NADP(+) reductases (Fprs) on its chromosome, and their functions remain largely unknown. Ferric reductase is structurally contained within the Fpr superfamily. Interestingly, ferric reductase is not annotated on the chromosome of P. putida. In an effort to elucidate the function of the Fpr as a ferric reductase, we used a variety of biochemical and physiological methods using the wild-type and mutant strains. In both the ferric reductase and flavin reductase assays, FprA and FprB preferentially used NADPH and NADH as electron donors, respectively. Two Fprs prefer a native ferric chelator to a synthetic ferric chelator and utilize free flavin mononucleotide (FMN) as an electron carrier. FprB has a higher k(cat)/K(m) value for reducing the ferric complex with free FMN. The growth rate of the fprB mutant was reduced more profoundly than that of the fprA mutant, the growth rate of which is also lower than the wild type in ferric iron-containing minimal media. Flavin reductase activity was diminished completely when the cell extracts of the fprB mutant plus NADH were utilized, but not the fprA mutant with NADPH. This indicates that other NADPH-dependent flavin reductases may exist. Interestingly, the structure of the NAD(P) region of FprB, but not of FprA, resembled the ferric reductase (Fre) of Escherichia coli in the homology modeling. This study demonstrates, for the first time, the functions of Fprs in P. putida as flavin and ferric reductases. Furthermore, our results indicated that FprB may perform a crucial role as a NADH-dependent ferric/flavin reductase under iron stress conditions.
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Loh KC, Cao B. Paradigm in biodegradation using Pseudomonas putida—A review of proteomics studies. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kang YS, Lee Y, Jung H, Jeon CO, Madsen EL, Park W. Overexpressing antioxidant enzymes enhances naphthalene biodegradation in Pseudomonas sp. strain As1. Microbiology (Reading) 2007; 153:3246-3254. [PMID: 17906124 DOI: 10.1099/mic.0.2007/008896-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We tested the hypothesis that during metabolism of naphthalene and other substrates by Pseudomonas sp. strain As1 oxidative stress arises and can be reduced by antioxidant enzymes. Our approach was to prepare plasmid constructs that conferred expression of two single antioxidant enzymes [Fpr (ferredoxin-NADP(+) reductase) and SOD (superoxide dismutase)] and the pair of enzymes SOD plus AhpC (alkyl hydroperoxide reductase). The fpr, sodA and ahpC genes were placed under the transcriptional control of both the constitutive lac promoter and their respective native promoters. Both HPLC and growth-rate analyses showed that naphthalene metabolism was enhanced in the recombinant strains. All antioxidant-overexpressing recombinant strains, with the exception of one with an upregulated sodA gene due to the lac promoter [strain As1(sodA)], exhibited resistance to the superoxide generating agent paraquat (PQ). The growth of strain As1(sodA) was inhibited by PQ, but this growth defect was rapidly overcome by the simultaneous overproduction of AhpC, which is a known hydrogen peroxide scavenger. After PQ-induced oxidative damage of the [Fe-S] enzyme aconitase, recovery of enzyme activity was enhanced in the recombinant strains. Reporter strains to monitor oxidative stress in strain As1 were prepared by fusing gfp (encoding green fluorescent protein, GFP) to the fpr promoter. Growth on salicylate and naphthalene boosted the GFP fluorescent signal 21- and 14-fold, respectively. Using these same oxidative stress reporters, overexpression of fpr and sodA was found to considerably reduce PQ-induced stress. Taken together, these data demonstrate that the overproduction of Fpr or SodA contributes to oxidative tolerance during naphthalene degradation; however, elevated SOD activity may trigger the generation of excess hydrogen peroxide, resulting in cell death.
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Affiliation(s)
- Yoon-Suk Kang
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5 Ga, Seoul, South Korea
| | - Yunho Lee
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5 Ga, Seoul, South Korea
| | - Hyungil Jung
- Department of Biotechnology, Yonsei University, Sinchon-Dong, Seoul, South Korea
| | - Che Ok Jeon
- Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, South Korea
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Woojun Park
- Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, South Korea
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5 Ga, Seoul, South Korea
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Park BS, Kwon YM, Pyla R, Boyle JA, Jung YS. E1 component of pyruvate dehydrogenase complex does not regulate the expression of NADPH-ferredoxin reductase inAzotobacter vinelandii. FEMS Microbiol Lett 2007; 273:244-52. [PMID: 17573932 DOI: 10.1111/j.1574-6968.2007.00797.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
In Azotobacter vinelandii, the E1 component of pyruvate dehydrogenase complex (PDHE1) is proposed to be a key regulatory protein in an oxidative stress management system that responds to superoxide. This proposal was tested by constructing an A. vinelandii mutant that had a disruption of aceE gene encoding PDHE1. This mutant exhibited wild-type exponential growth and a normal response to oxidative stress induced by paraquat. Electrophoretic mobility-shift assays revealed that a protein previously shown to bind to a paraquat-activatable DNA promoter was still present in the extract prepared from the mutant, implying that the protein cannot be PDHE1. These observations strongly contradict the previous claim that PDHE1 is a DNA-binding protein that is directly involved in the A. vinelandii oxidative stress-regulatory system.
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Affiliation(s)
- Buem-Seek Park
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi 39762, USA
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Park W, Peña-Llopis S, Lee Y, Demple B. Regulation of superoxide stress in Pseudomonas putida KT2440 is different from the SoxR paradigm in Escherichia coli. Biochem Biophys Res Commun 2006; 341:51-6. [PMID: 16412384 DOI: 10.1016/j.bbrc.2005.12.142] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Accepted: 12/20/2005] [Indexed: 11/20/2022]
Abstract
In Escherichia coli, the SoxR regulon orchestrates genes for defense against certain types of oxidative stress through the SoxR-regulated synthesis of the SoxS transcription activator. The Pseudomonas putida genome did not reveal a clear soxS homolog. The P. putida SoxR protein appears to be functional: its expression in an E. coli DeltasoxR strain restored the paraquat inducibility of soxS. Of nine candidate P. putida oxidative stress genes, which are known to be SoxR regulon in E. coli, tested for response to superoxide or nitric oxide, fumC-1, sodA, zwf-1, and particularly fpr, encoding ferredoxin:NADP(+) reductase, were induced, all independent of P. putida soxR. Disruption of the fpr and finR, a regulatory protein that is required for paraquat-dependent expression of the fpr, resulted in more oxidative stress sensitivity. However, a P. putida soxR-deletion strain had normal resistance to the superoxide-generating agent paraquat. The data presented here show that the genetic responses to superoxide stress in P. putida differ markedly from those seen in E. coli and Salmonella, and the role of P. putida soxR remains to be established.
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Affiliation(s)
- Woojun Park
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5Ga, Seoul.
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