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Wray AC, Gorman-Lewis D. Bioenergetics of aerobic and anaerobic growth of Shewanella putrefaciens CN32. Front Microbiol 2023; 14:1234598. [PMID: 37601367 PMCID: PMC10433392 DOI: 10.3389/fmicb.2023.1234598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Shewanella putrefaciens is a model dissimilatory iron-reducing bacterium that can use Fe(III) and O2 as terminal electron acceptors. Consequently, it has the ability to influence both aerobic and anaerobic groundwater systems, making it an ideal microorganism for improving our understanding of facultative anaerobes with iron-based metabolism. In this work, we examine the bioenergetics of O2 and Fe(III) reduction coupled to lactate oxidation in Shewanella putrefaciens CN32. Bioenergetics were measured directly via isothermal calorimetry and by changes to the chemically defined growth medium. We performed these measurements from 25 to 36°C. Modeling metabolism with macrochemical equations allowed us to define a theoretical growth stoichiometry for the catabolic reaction of 1.00 O2:lactate and 1.33 Fe(III):lactate that was consistent with the observed ratios of O2:lactate (1.20 ± 0.23) and Fe(III):lactate (1.46 ± 0.15) consumption. Aerobic growth showed minimal variation with temperature and minimal variation in thermodynamic potentials of incubation. Fe(III)-based growth showed a strong temperature dependence. The Gibbs energy and enthalpy of incubation was minimized at ≥30°C. Energy partitioning modeling of Fe(III)-based calorimetric incubation data predicted that energy consumption for non-growth associate maintenance increases substantially above 30°C. This prediction agrees with the data at 33 and 35°C. These results suggest that the effects of temperature on Shewanella putrefaciens CN32 are metabolism dependent. Gibbs energy of incubation above 30°C was 3-5 times more exergonic with Fe(III)-based growth than with aerobic growth. We compared data gathered in this study with predictions of microbial growth based on standard-state conditions and based on the thermodynamic efficiency of microbial growth. Quantifying the growth requirements of Shewanella putrefaciens CN32 has advanced our understanding of the thermodynamic constraints of this dissimilatory iron-reducing bacterium.
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Affiliation(s)
- Addien C. Wray
- Earth and Space Sciences, University of Washington, Seattle, WA, United States
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2
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Adam-Beyer N, Perner M. Activity-Based Screening of Metagenomic Fosmid Libraries for Hydrogen-Uptake Enzymes. Methods Mol Biol 2023; 2555:91-101. [PMID: 36306080 DOI: 10.1007/978-1-0716-2795-2_6] [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] [Indexed: 06/16/2023]
Abstract
Here, we outline how to identify hydrogenase enzymes from metagenomic fosmid libraries through an activity-based screening approach. A metagenomic fosmid library is constructed in E. coli and the fosmids are transferred into a hydrogenase deletion mutant of Shewanella oneidensis MR-1 (ΔhyaB) via triparental mating. If a fosmid clone exhibits hydrogen-uptake activity, S. oneidensis' phenotype is restored and hydrogenase activity is indicated by a color change of the medium from yellow to colorless. The screen enables screening of 48 metagenomic fosmid clones in parallel.
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Affiliation(s)
- Nicole Adam-Beyer
- Geomicrobiology, Department of Marine Biogeochemistry GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstraße, Kiel, Germany.
| | - Mirjam Perner
- Geomicrobiology, Department of Marine Biogeochemistry GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstraße, Kiel, Germany
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3
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Pal A, Bhattacharjee S, Saha J, Sarkar M, Mandal P. Bacterial survival strategies and responses under heavy metal stress: a comprehensive overview. Crit Rev Microbiol 2021; 48:327-355. [PMID: 34473592 DOI: 10.1080/1040841x.2021.1970512] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Heavy metals bring long-term hazardous consequences and pose a serious threat to all life forms. Being non-biodegradable, they can remain in the food webs for a long period of time. Metal ions are essential for life and indispensable for almost all aspects of metabolism but can be toxic beyond threshold level to all living beings including microbes. Heavy metals are generally present in the environment, but many geogenic and anthropogenic activities has led to excess metal ion accumulation in the environment. To survive in harsh metal contaminated environments, bacteria have certain resistance mechanisms to metabolize and transform heavy metals into less hazardous forms. This also gives rise to different species of heavy metal resistant bacteria. Herein, we have tried to incorporate the different aspects of heavy metal toxicity in bacteria and provide an up-to-date and across-the-board review. The various aspects of heavy metal biology of bacteria encompassed in this review includes the biological notion of heavy metals, toxic effect of heavy metals on bacteria, the factors regulating bacterial heavy metal resistance, the diverse mechanisms governing bacterial heavy metal resistance, bacterial responses to heavy metal stress, and a brief overview of gene regulation under heavy metal stress.
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Affiliation(s)
- Ayon Pal
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Sukanya Bhattacharjee
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Jayanti Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Sarkar
- Mycology and Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
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Using metabolic charge production in the tricarboxylic acid cycle (Q TCA) to evaluate the extracellular-electron-transfer performances of Shewanella spp. Bioelectrochemistry 2018; 124:119-126. [PMID: 30015268 DOI: 10.1016/j.bioelechem.2018.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/24/2018] [Accepted: 07/03/2018] [Indexed: 01/13/2023]
Abstract
Using an electrochemical cell equipped with carbon felt electrodes (poised at +0.63 V vs. SHE), the current production capabilities of two Shewanella strains-NTOU1 and KR-12-were examined under various conditions with lactate as an electron donor. The metabolic charge produced in the tricarboxylic acid cycle (QTCA) was calculated by mass-balance. The data showed a linear relation between the electric coulomb production (QEL) and QTCA with an R2 of 0.65. In addition, a large amount of pyruvate accumulation was observed at pH = 6, rendering QTCA negative. The results indicate an occurrence of an undesired cataplerotic reaction. It was also found that QTCA provides important information showing the oxygen-boosting TCA cycle and anodic-current generation of Shewanella spp. Linear dependence of the change in charge for biomass growth (4.52FΔnCell) on QTCA was also found as expressed by 4.52FΔnCell = 1.0428 QTCA + 0.0442, indicating that these two charge quantities are inherently identical under most of the experimental conditions. In the mediator-spiked experiments, the external addition of the mediators (ferricyanide, anthraquinone-2, 6-disulfonate, and riboflavin) beyond certain concentrations inhibited the activity of the TCA cycle, indicating that the oxidative phosphorylation is deactivated by excessive amounts of mediators, yet Shewanella spp. are constrained with regard to carrying out the substrate-level phosphorylation.
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5
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Adam N, Perner M. Activity-Based Screening of Metagenomic Libraries for Hydrogenase Enzymes. Methods Mol Biol 2018; 1539:261-270. [PMID: 27900696 DOI: 10.1007/978-1-4939-6691-2_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Here we outline how to identify hydrogenase enzymes from metagenomic libraries through an activity-based screening approach. A metagenomic fosmid library is constructed in E. coli and the fosmids are transferred into a hydrogenase deletion mutant of Shewanella oneidensis (ΔhyaB) via triparental mating. If a fosmid exhibits hydrogen uptake activity, S. oneidensis' phenotype is restored and hydrogenase activity is indicated by a color change of the medium from yellow to colorless. This new method enables screening of 48 metagenomic fosmid clones in parallel.
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Affiliation(s)
- Nicole Adam
- Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Mirjam Perner
- Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
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6
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Milewska K, Węgrzyn G, Szalewska-Pałasz A. Transformation of Shewanella baltica with ColE1-like and P1 plasmids and their maintenance during bacterial growth in cultures. Plasmid 2015; 81:42-9. [PMID: 26170108 DOI: 10.1016/j.plasmid.2015.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 07/04/2015] [Accepted: 07/06/2015] [Indexed: 11/28/2022]
Abstract
The presence of natural plasmids has been reported for many Shewanella isolates. However, knowledge about plasmid replication origin and segregation mechanisms is not extensive for this genus. Shewanella baltica is an important species in the marine environment due to its denitrification ability in oxygen-deficient zones and the potential role in bioremediation processes. However, no information about possible use of plasmid vectors in this species has been reported to date. Here we report that plasmids with ColE1-type and plasmid P1 origin can transform S. baltica and replicate in this bacterium. Without the antibiotic selection pressure plasmid maintenance is less efficient than in Escherichia coli. Nevertheless, cultivation of S. baltica in the presence of appropriate antibiotics caused relatively stable maintenance of ColE1-like and P1-derived plasmids. This indicates that plasmid-based genetic manipulations and gene transfer in S. baltica are possible.
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Affiliation(s)
- Klaudia Milewska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdańsk, Poland
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Li SL, Nealson KH. Enriching distinctive microbial communities from marine sediments via an electrochemical-sulfide-oxidizing process on carbon electrodes. Front Microbiol 2015; 6:111. [PMID: 25741331 PMCID: PMC4330880 DOI: 10.3389/fmicb.2015.00111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/29/2015] [Indexed: 11/13/2022] Open
Abstract
Sulfide is a common product of marine anaerobic respiration, and a potent reactant biologically and geochemically. Here we demonstrate the impact on microbial communities with the removal of sulfide via electrochemical methods. The use of differential pulse voltammetry revealed that the oxidation of soluble sulfide was seen at +30 mV (vs. SHE) at all pH ranges tested (from pH = 4 to 8), while non-ionized sulfide, which dominated at pH = 4 was poorly oxidized via this process. Two mixed cultures (CAT and LA) were enriched from two different marine sediments (from Catalina Island, CAT; from the Port of Los Angeles, LA) in serum bottles using a seawater medium supplemented with lactate, sulfate, and yeast extract, to obtain abundant biomass. Both CAT and LA cultures were inoculated in electrochemical cells (using yeast-extract-free seawater medium as an electrolyte) equipped with carbon-felt electrodes. In both cases, when potentials of +630 or +130 mV (vs. SHE) were applied, currents were consistently higher at +630 then at +130 mV, indicating more sulfide being oxidized at the higher potential. In addition, higher organic-acid and sulfate conversion rates were found at +630 mV with CAT, while no significant differences were found with LA at different potentials. The results of microbial-community analyses revealed a decrease in diversity for both CAT and LA after electrochemical incubation. In addition, some bacteria (e.g., Clostridium and Arcobacter) not well-known to be capable of extracellular electron transfer, were found to be dominant in the electrochemical cells. Thus, even though the different mixed cultures have different tolerances for sulfide, electrochemical-sulfide removal can lead to major population changes.
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Affiliation(s)
- Shiue-Lin Li
- Department of Earth Science, University of Southern California Los Angeles, CA, USA
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California Los Angeles, CA, USA
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9
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Research of Iron Reduction and the Iron Reductase Localization of Anammox Bacteria. Curr Microbiol 2014; 69:880-7. [DOI: 10.1007/s00284-014-0668-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/15/2014] [Indexed: 10/24/2022]
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Rachkevych N, Sybirna K, Boyko S, Boretsky Y, Sibirny A. Improving the efficiency of plasmid transformation in Shewanella oneidensis MR-1 by removing ClaI restriction site. J Microbiol Methods 2014; 99:35-7. [PMID: 24462975 DOI: 10.1016/j.mimet.2014.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/10/2014] [Accepted: 01/14/2014] [Indexed: 10/25/2022]
Abstract
Here we demonstrate that elimination of ClaI restriction site from the sequence of a plasmid DNA increases the efficiency of transformation of Shewanella oneidensis MR-1 significantly. To achieve reliable transformation of S. oneidensis MR-1 plasmids either lacking ClaI site or isolated from primary transformants of S. oneidensis should be used.
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Affiliation(s)
- Nazarii Rachkevych
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Kateryna Sybirna
- IBiTec-S, SB2SM, LMB (UMR CNRS 8221), DSV, CEA, 91191 Gif-sur-Yvette, France
| | - Solomiya Boyko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Yuriy Boretsky
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Andriy Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine; Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, 35-601 Rzeszow, Poland.
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11
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Li DB, Cheng YY, Wu C, Li WW, Li N, Yang ZC, Tong ZH, Yu HQ. Selenite reduction by Shewanella oneidensis MR-1 is mediated by fumarate reductase in periplasm. Sci Rep 2014; 4:3735. [PMID: 24435070 PMCID: PMC3894562 DOI: 10.1038/srep03735] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 12/05/2013] [Indexed: 11/09/2022] Open
Abstract
In situ reduction of selenite to elemental selenium (Se(0)), by microorganisms in sediments and soils is an important process and greatly affects the environmental distribution and the biological effects of selenium. However, the mechanism behind such a biological process remains unrevealed yet. Here we use Shewanella oneidensis MR-1, a widely-distributed dissimilatory metal-reducing bacterium with a powerful and diverse respiration capability, to evaluate the involvement of anaerobic respiration system in the microbial selenite reduction. With mutants analysis, we identify fumarate reductase FccA as the terminal reductase of selenite in periplasm. Moreover, we find that such a reduction is dependent on central respiration c-type cytochrome CymA. In contrast, nitrate reductase, nitrite reductase, and the Mtr electron transfer pathway do not work as selenite reductases. These findings reveal a previously unrecognized role of anaerobic respiration reductases of S. oneidensis MR-1 in selenite reduction and geochemical cycles of selenium in sediments and soils.
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Affiliation(s)
- Dao-Bo Li
- 1] School of Earth and Space Sciences [2] Department of Chemistry [3]
| | | | | | | | | | - Zong-Chuang Yang
- School of Life Sciences, University of Science & Technology of China, Hefei, 230026, China
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12
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Dong X, Zhang Y, Zhou J, Li N, Chen M. Reduction of Fe(III)EDTA in a NOx scrubber liquor by a denitrifying bacterium and the effects of inorganic sulfur compounds on this process. BIORESOURCE TECHNOLOGY 2012; 120:127-132. [PMID: 22784963 DOI: 10.1016/j.biortech.2012.06.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 06/03/2012] [Accepted: 06/05/2012] [Indexed: 06/01/2023]
Abstract
Biological reduction of Fe(III)EDTA is one of the key steps in nitrogen oxides removal in the integrated approach of metal chelate absorption combined with microbial reduction. Paracoccus denitrificans ZGL1 was used as a model bacterium to evaluate the process of Fe(III)EDTA reduction by such microorganisms that could carry out the simultaneous reduction of NO chelated by Fe(II)EDTA (Fe(II)EDTA-NO) and Fe(III)EDTA. Enzymes analysis indicated Fe(III)EDTA reductase of ZGL1 was located both in the membrane and cytoplasmic fractions. Glucose was identified as the most efficient electron donor for Fe(III)EDTA reduction. Better reduction performance was obtained with higher initial cell concentration corresponding to a specific reduction rate of 8.7 μmol h(-1) mg protein(-1). The presence of sulfate and thiosulfate had no influences on both cell growth and Fe(III)EDTA reduction. Fe(III)EDTA reduction rate and cell growth could be inhibited by addition of sulfite mainly due to its direct and indirect toxic effects.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
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13
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McMillan DGG, Marritt SJ, Butt JN, Jeuken LJC. Menaquinone-7 is specific cofactor in tetraheme quinol dehydrogenase CymA. J Biol Chem 2012; 287:14215-25. [PMID: 22393052 PMCID: PMC3340143 DOI: 10.1074/jbc.m112.348813] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Little is known about enzymatic quinone-quinol interconversions in the lipid membrane when compared with our knowledge of substrate transformations by globular enzymes. Here, the smallest example of a quinol dehydrogenase in nature, CymA, has been studied. CymA is a monotopic membrane tetraheme c-type cytochrome belonging to the NapC/NirT family and central to anaerobic respiration in Shewanella sp. Using protein-film electrochemistry, it is shown that vesicle-bound menaquinone-7 is not only a substrate for this enzyme but is also required as a cofactor when converting other quinones. Here, we propose that the high concentration of quinones in the membrane negates the evolutionary pressure to create a high affinity active site. However, the instability and reactivity of reaction intermediate, semiquinone, might require a cofactor that functions to minimize damaging side reactions.
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Affiliation(s)
- Duncan G G McMillan
- Institute of Membrane and Systems Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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14
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Parnell JJ, Callister SJ, Rompato G, Nicora CD, Paša-Tolić L, Williamson A, Pfrender ME. Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock. Sci Rep 2011; 1:25. [PMID: 22355544 PMCID: PMC3216512 DOI: 10.1038/srep00025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 06/16/2011] [Indexed: 12/04/2022] Open
Abstract
Shewanellae are microbial models for environmental stress response; however, the sequential expression of mechanisms in response to stress is poorly understood. Here we experimentally determine the response mechanisms of Shewanella amazonensis SB2B during sodium chloride stress using a novel liquid chromatography and accurate mass-time tag mass spectrometry time-course proteomics approach. The response of SB2B involves an orchestrated sequence of events comprising increased signal transduction associated with motility and restricted growth. Following a metabolic shift to branched chain amino acid degradation, motility and cellular replication proteins return to pre-perturbed levels. Although sodium chloride stress is associated with a change in the membrane fatty acid composition in other organisms, this is not the case for SB2B as fatty acid degradation pathways are not expressed and no change in the fatty acid profile is observed. These findings suggest that shifts in membrane composition may be an indirect physiological response to high NaCl stress.
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Affiliation(s)
- J Jacob Parnell
- Center for Integrated BioSystems and Department of Biology, Utah State University, Logan, UT, USA.
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15
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Partial functional replacement of CymA by SirCD in Shewanella oneidensis MR-1. J Bacteriol 2011; 193:2312-21. [PMID: 21378180 DOI: 10.1128/jb.01355-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gammaproteobacterium Shewanella oneidensis MR-1 utilizes a complex electron transfer network composed primarily of c-type cytochromes to respire under anoxic conditions a variety of compounds, including fumarate, nitrate, and dimethyl sulfoxide (DMSO), in addition to the minerals Fe(III) and Mn(IV). Central to several respiratory pathways is CymA, a cytoplasmic membrane-bound tetraheme c-type cytochrome that functions as the major hydroquinone dehydrogenase. To investigate functional redundancy and plasticity in S. oneidensis MR-1 electron transport, we isolated ΔcymA suppressor mutants and characterized one biochemically and genetically. Interestingly, in the characterized ΔcymA suppressor mutant, respiration of fumarate, ferric citrate, and DMSO was restored but that of nitrate was not. The suppression was found to be due to transcriptional activation of sirC and sirD, encoding a periplasmic iron sulfur protein and an integral membrane hydroquinone dehydrogenase, respectively. Biochemical in vitro reconstitution experiments confirmed electron transport between formate and fumarate via fumarate reductase by suppressor membrane fractions. The suppression was found to be caused by insertion of an ISSod1 element upstream of the sirCD transcriptional start site, generating a novel, constitutively active hybrid promoter. This work revealed that adaptation of an alternative electron transfer pathway from quinol to terminal oxidoreductases independent of CymA occurs rapidly in S. oneidensis MR-1.
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Phenotypic characterization of Shewanella oneidensis MR-1 under aerobic and anaerobic growth conditions by using fourier transform infrared spectroscopy and high-performance liquid chromatography analyses. Appl Environ Microbiol 2010; 76:6266-76. [PMID: 20675447 DOI: 10.1128/aem.00912-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis is able to conserve energy for growth by reducing a wide variety of terminal electron acceptors during anaerobic respiration, including several environmentally hazardous pollutants. This bacterium employs various electron transfer mechanisms for anaerobic respiration, including cell-bound reductases and secreted redox mediators. The aim of this study was to develop rapid tools for profiling the key metabolic changes associated with these different growth regimes and physiological responses. Initial experiments focused on comparing cells grown under aerobic and anaerobic conditions. Fourier transform infrared (FT-IR) spectroscopy with cluster analysis showed that there were significant changes in the metabolic fingerprints of the cells grown under these two culture conditions. FT-IR spectroscopy clearly differentiated cells of S. oneidensis MR-1 cultured at various growth points and cells grown using different electron acceptors, resulting in different phenotypic trajectories in the cluster analysis. This growth-related trajectory analysis is applied successfully for the first time, here with FT-IR spectroscopy, to investigate the phenotypic changes in contrasting S. oneidensis cells. High-performance liquid chromatography (HPLC) was also used to quantify the concentrations of flavin compounds, which have been identified recently as extracellular redox mediators released by a range of Shewanella species. The partial least-squares regression (PLSR) multivariate statistical technique was combined with FT-IR spectroscopy to predict the concentrations of the flavins secreted by cells of S. oneidensis MR-1, suggesting that this combination could be used as a rapid alternative to conventional chromatographic methods for analysis of flavins in cell cultures. Furthermore, coupling of the FT-IR spectroscopy and HPLC techniques appears to offer a potentially useful tool for rapid characterization of the Shewanella cell metabolome in various process environments.
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Farajollahi S, Marshall C, Guthrie JT. Bioinduced changes in the colored nitrocellulose-coated cellophane films, induced by the Shewanella J18 143 strain. J Appl Polym Sci 2010. [DOI: 10.1002/app.32212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Abstract
Anaerobic cultures of Shewanella oneidensis MR-1 reduced toxic Ag(I), forming nanoparticles of elemental Ag(0), as confirmed by X-ray diffraction analyses. The addition of 1 to 50 microM Ag(I) had a limited impact on growth, while 100 microM Ag(I) reduced both the doubling time and cell yields. At this higher Ag(I) concentration transmission electron microscopy showed the accumulation of elemental silver particles within the cell, while at lower concentrations the metal was exclusively reduced and precipitated outside the cell wall. Whole organism metabolite fingerprinting, using the method of Fourier transform infrared spectroscopy analysis of cells grown in a range of silver concentrations, confirmed that there were significant physiological changes at 100 microM silver. Principal component-discriminant function analysis scores and loading plots highlighted changes in certain functional groups, notably, lipids, amides I and II, and nucleic acids, as being discriminatory. Molecular analyses confirmed a dramatic drop in cellular yields of both the phospholipid fatty acids and their precursor molecules at high concentrations of silver, suggesting that the structural integrity of the cellular membrane was compromised at high silver concentrations, which was a result of intracellular accumulation of the toxic metal.
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Electrochemical interrogations of the Mtr cytochromes from Shewanella: opening a potential window. J Biol Inorg Chem 2008; 13:849-54. [DOI: 10.1007/s00775-008-0398-z] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 06/12/2008] [Indexed: 10/21/2022]
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20
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Ehrlich HL. Are gram-positive bacteria capable of electron transfer across their cell wall without an externally available electron shuttle? GEOBIOLOGY 2008; 6:220-224. [PMID: 18498525 DOI: 10.1111/j.1472-4669.2007.00135.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The extensive contributions by Terry Beveridge to our understanding of the differences in cell wall organization with respect to structure, chemistry and compartmentalization between gram-positive and gram-negative bacteria are summarized. These contributions greatly aided in conceptualization of recent discoveries concerning electron export and import across cell walls of some gram-negative bacteria. Although electron export and import across the cell wall by any gram-positive has not been documented so far, Beveridge's observations and concepts concerning cell walls of gram-positive bacteria suggest potential mechanisms by which such electron transfer may occur.
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Affiliation(s)
- H L Ehrlich
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, USA.
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21
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Hartshorne RS, Jepson BN, Clarke TA, Field SJ, Fredrickson J, Zachara J, Shi L, Butt JN, Richardson DJ. Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors. J Biol Inorg Chem 2007; 12:1083-94. [PMID: 17701062 DOI: 10.1007/s00775-007-0278-y] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Accepted: 07/09/2007] [Indexed: 10/23/2022]
Abstract
MtrC is a decaheme c-type cytochrome associated with the outer cell membrane of Fe(III)-respiring species of the Shewanella genus. It is proposed to play a role in anaerobic respiration by mediating electron transfer to extracellular mineral oxides that can serve as terminal electron acceptors. The present work presents the first spectropotentiometric and voltammetric characterization of MtrC, using protein purified from Shewanella oneidensis MR-1. Potentiometric titrations, monitored by UV-vis absorption and electron paramagnetic resonance (EPR) spectroscopy, reveal that the hemes within MtrC titrate over a broad potential range spanning between approximately +100 and approximately -500 mV (vs. the standard hydrogen electrode). Across this potential window the UV-vis absorption spectra are characteristic of low-spin c-type hemes and the EPR spectra reveal broad, complex features that suggest the presence of magnetically spin-coupled low-spin c-hemes. Non-catalytic protein film voltammetry of MtrC demonstrates reversible electrochemistry over a potential window similar to that disclosed spectroscopically. The voltammetry also allows definition of kinetic properties of MtrC in direct electron exchange with a solid electrode surface and during reduction of a model Fe(III) substrate. Taken together, the data provide quantitative information on the potential domain in which MtrC can operate.
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Affiliation(s)
- Robert S Hartshorne
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Taillefert M, Beckler JS, Carey E, Burns JL, Fennessey CM, DiChristina TJ. Shewanella putrefaciens produces an Fe(III)-solubilizing organic ligand during anaerobic respiration on insoluble Fe(III) oxides. J Inorg Biochem 2007; 101:1760-7. [PMID: 17765315 DOI: 10.1016/j.jinorgbio.2007.07.020] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 06/29/2007] [Accepted: 07/13/2007] [Indexed: 11/16/2022]
Abstract
The mechanism of Fe(III) reduction was investigated using voltammetric techniques in anaerobic incubations of Shewanella putrefaciens strain 200 supplemented with Fe(III) citrate or a suite of Fe(III) oxides as terminal electron acceptor. Results indicate that organic complexes of Fe(III) are produced during the reduction of Fe(III) at rates that correlate with the reactivity of the Fe(III) phase and bacterial cell density. Anaerobic Fe(III) solubilization activity is detected with either Fe(III) oxides or Fe(III) citrate, suggesting that the organic ligand produced is strong enough to destabilize Fe(III) from soluble or solid Fe(III) substrates. Results also demonstrate that Fe(III) oxide dissolution is not controlled by the intrinsic chemical reactivity of the Fe(III) oxides. Instead, the chemical reaction between the endogenous organic ligand is only affected by the number of reactive surface sites available to S. putrefaciens. This report describes the first application of voltammetric techniques to demonstrate production of soluble organic-Fe(III) complexes by any Fe(III)-reducing microorganism and is the first report of a Fe(III)-solubilizing ligand generated by a metal-reducing member of the genus Shewanella.
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Affiliation(s)
- Martial Taillefert
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0340, USA.
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Jiao Y, Newman DK. The pio operon is essential for phototrophic Fe(II) oxidation in Rhodopseudomonas palustris TIE-1. J Bacteriol 2007; 189:1765-73. [PMID: 17189359 PMCID: PMC1855732 DOI: 10.1128/jb.00776-06] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Accepted: 12/12/2006] [Indexed: 11/20/2022] Open
Abstract
Phototrophic Fe(II)-oxidizing bacteria couple the oxidation of ferrous iron [Fe(II)] to reductive CO(2) fixation by using light energy, but until recently, little has been understood about the molecular basis for this process. Here we report the discovery, with Rhodopseudomonas palustris TIE-1 as a model organism, of a three-gene operon, designated the pio operon (for phototrophic iron oxidation), that is necessary for phototrophic Fe(II) oxidation. The first gene in the operon, pioA, encodes a c-type cytochrome that is upregulated under Fe(II)-grown conditions. PioA contains a signal sequence and shares homology with MtrA, a decaheme c-type cytochrome from Shewanella oneidensis MR-1. The second gene, pioB, encodes a putative outer membrane beta-barrel protein. PioB is a homologue of MtrB from S. oneidensis MR-1. The third gene, pioC, encodes a putative high potential iron sulfur protein (HiPIP) with a twin-arginine translocation (Tat) signal sequence and is similar to the putative Fe(II) oxidoreductase (Iro) from Acidithiobacillus ferrooxidans. Like PioA, PioB and PioC appear to be secreted proteins. Deletion of the pio operon results in loss of Fe(II) oxidation activity and growth on Fe(II). Complementation studies confirm that the phenotype of this mutant is due to loss of the pio genes. Deletion of pioA alone results in loss of almost all Fe(II) oxidation activity; however, deletion of either pioB or pioC alone results in only partial loss of Fe(II) oxidation activity. Together, these results suggest that proteins encoded by the pio operon are essential and specific for phototrophic Fe(II) oxidation in R. palustris TIE-1.
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Affiliation(s)
- Yongqin Jiao
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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24
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Biju V, Pan D, Gorby YA, Fredrickson J, McLean J, Saffarini D, Lu HP. Combined spectroscopic and topographic characterization of nanoscale domains and their distributions of a redox protein on bacterial cell surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:1333-8. [PMID: 17241055 DOI: 10.1021/la061343z] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Redox protein nanoscale domains on the cell surface of a bacterium, Shewanella oneidensis MR1, grown in the absence and presence of electron acceptors, is topographically characterized using combined atomic force microscopy (AFM) and confocal surface enhanced Raman scattering (SERS) spectroscopy. The protruding nanoscale domains on the outer membrane of S. oneidensis were observed, as was their disappearance upon exposure to electron acceptors such as oxygen, nitrate, fumarate, and iron nitrilotriacetate (FeNTA). Using SERS spectroscopy, a redox heme protein was identified as a major component of the cell surface domains. This conclusion was further confirmed by the disappearance of Raman vibrational frequencies, characteristic of heme proteins, upon exposure of the cells to electron acceptors. Our experimental results from our AFM imaging and SERS spectroscopy, consistent with the literature, suggest the protruding nanoscale surface domains as heme-containing secretions. Our results on the distributions of redox proteins on microbial cell surfaces will be helpful for a mechanistic understanding of the behaviors of surface proteins and their interactions with redox environments.
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Affiliation(s)
- Vasudevanpillai Biju
- Fundamental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Xu M, Guo J, Kong X, Chen X, Sun G. Fe(III)-enhanced Azo Reduction by Shewanella decolorationis S12. Appl Microbiol Biotechnol 2007; 74:1342-9. [PMID: 17216448 DOI: 10.1007/s00253-006-0773-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 11/16/2006] [Accepted: 11/17/2006] [Indexed: 10/23/2022]
Abstract
Shewanella decolorationis S12 is capable of high rates of azo dye decolorization and dissimilatory Fe(III) reduction. Under anaerobic conditions, when Fe(III) and azo dye were copresent in S12 cultures, dissimilatory Fe(III) reduction and azo dye biodecolorization occurred simultaneously. Furthermore, the dye decolorization was enhanced by the presence of Fe(III). When 1 mM Fe(III) was added, the methyl red decolorizing efficiency was 72.1% after cultivation for 3 h, whereas the decolorizing efficiency was only 60.5% in Fe(III)-free medium. The decolorizing efficiencies increased as the concentration of Fe(III) was increased from 0 to 6 mM. Enzyme activities, which mediate the dye decolorization and Fe(III) reduction, were not affected by preadaption of cells to Fe(III) and azo dye nor by the addition of chloramphenicol. Both the Fe(III) reductase and the azo reductase were membrane associated. The respiratory electron transport chain inhibitors metyrapone, dicumarol, and stigmatellin showed significantly different effects on Fe(III) reduction than on azo dye decolorization.
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Affiliation(s)
- Meiying Xu
- Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou 510070, People's Republic of China
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Meshulam-Simon G, Behrens S, Choo AD, Spormann AM. Hydrogen metabolism in Shewanella oneidensis MR-1. Appl Environ Microbiol 2006; 73:1153-65. [PMID: 17189435 PMCID: PMC1828657 DOI: 10.1128/aem.01588-06] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis MR-1 is a facultative sediment microorganism which uses diverse compounds, such as oxygen and fumarate, as well as insoluble Fe(III) and Mn(IV) as electron acceptors. The electron donor spectrum is more limited and includes metabolic end products of primary fermenting bacteria, such as lactate, formate, and hydrogen. While the utilization of hydrogen as an electron donor has been described previously, we report here the formation of hydrogen from pyruvate under anaerobic, stationary-phase conditions in the absence of an external electron acceptor. Genes for the two S. oneidensis MR-1 hydrogenases, hydA, encoding a periplasmic [Fe-Fe] hydrogenase, and hyaB, encoding a periplasmic [Ni-Fe] hydrogenase, were found to be expressed only under anaerobic conditions during early exponential growth and into stationary-phase growth. Analyses of DeltahydA, DeltahyaB, and DeltahydA DeltahyaB in-frame-deletion mutants indicated that HydA functions primarily as a hydrogen-forming hydrogenase while HyaB has a bifunctional role and represents the dominant hydrogenase activity under the experimental conditions tested. Based on results from physiological and genetic experiments, we propose that hydrogen is formed from pyruvate by multiple parallel pathways, one pathway involving formate as an intermediate, pyruvate-formate lyase, and formate-hydrogen lyase, comprised of HydA hydrogenase and formate dehydrogenase, and a formate-independent pathway involving pyruvate dehydrogenase. A reverse electron transport chain is potentially involved in a formate-hydrogen lyase-independent pathway. While pyruvate does not support a fermentative mode of growth in this microorganism, pyruvate, in the absence of an electron acceptor, increased cell viability in anaerobic, stationary-phase cultures, suggesting a role in the survival of S. oneidensis MR-1 under stationary-phase conditions.
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Affiliation(s)
- Galit Meshulam-Simon
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305-5429, USA
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27
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Ruebush SS, Brantley SL, Tien M. Reduction of soluble and insoluble iron forms by membrane fractions of Shewanella oneidensis grown under aerobic and anaerobic conditions. Appl Environ Microbiol 2006; 72:2925-35. [PMID: 16597999 PMCID: PMC1449039 DOI: 10.1128/aem.72.4.2925-2935.2006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of iron substrates and growth conditions on in vitro dissimilatory iron reduction by membrane fractions of Shewanella oneidensis MR-1 was characterized. Membrane fractions were separated by sucrose density gradients from cultures grown with O(2), fumarate, and aqueous ferric citrate as the terminal electron acceptor. Marker enzyme assays and two-dimensional gel electrophoresis demonstrated the high degree of separation between the outer and cytosolic membrane. Protein expression pattern was similar between chelated iron- and fumarate-grown cultures, but dissimilar for oxygen-grown cultures. Formate-dependent ferric reductase activity was assayed with citrate-Fe(3+), ferrozine-Fe(3+), and insoluble goethite as electron acceptors. No activity was detected in aerobic cultures. For fumarate and chelated iron-grown cells, the specific activity for the reduction of soluble iron was highest in the cytosolic membrane. The reduction of ferrozine-Fe(3+) was greater than the reduction of citrate-Fe(3+). With goethite, the specific activity was highest in the total membrane fraction (containing both cytosolic and outer membrane), indicating participation of the outer membrane components in electron flow. Heme protein content and specific activity for iron reduction was highest with chelated iron-grown cultures with no heme proteins in aerobically grown membrane fractions. Western blots showed that CymA, a heme protein involved in iron reduction, expression was also higher in iron-grown cultures compared to fumarate- or aerobic-grown cultures. To study these processes, it is important to use cultures grown with chelated Fe(3+) as the electron acceptor and to assay ferric reductase activity using goethite as the substrate.
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Affiliation(s)
- Shane S Ruebush
- Department of Biochemistry and Molecular Biology, 408 Althouse Laboratory, Pennsylvania State University, University Park, PA 16802, USA
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28
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Gao W, Liu Y, Giometti CS, Tollaksen SL, Khare T, Wu L, Klingeman DM, Fields MW, Zhou J. Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1. BMC Genomics 2006; 7:76. [PMID: 16600046 PMCID: PMC1468410 DOI: 10.1186/1471-2164-7-76] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Accepted: 04/06/2006] [Indexed: 01/28/2023] Open
Abstract
Background Shewanella oneidensis MR-1 is a facultative, gram-negative bacterium capable of coupling the oxidation of organic carbon to a wide range of electron acceptors such as oxygen, nitrate and metals, and has potential for bioremediation of heavy metal contaminated sites. The complete 5-Mb genome of S. oneidensis MR-1 was sequenced and standard sequence-comparison methods revealed approximately 42% of the MR-1 genome encodes proteins of unknown function. Defining the functions of hypothetical proteins is a great challenge and may need a systems approach. In this study, by using integrated approaches including whole genomic microarray and proteomics, we examined knockout effects of the gene encoding SO1377 (gi24372955), a member of the conserved, hypothetical, bacterial protein family COG2268 (Clusters of Orthologous Group) in bacterium Shewanella oneidensis MR-1, under various physiological conditions. Results Compared with the wild-type strain, growth assays showed that the deletion mutant had a decreased growth rate when cultured aerobically, but not affected under anaerobic conditions. Whole-genome expression (RNA and protein) profiles revealed numerous gene and protein expression changes relative to the wild-type control, including some involved in iron metabolism, oxidative damage protection and respiratory electron transfer, e. g. complex IV of the respiration chain. Although total intracellular iron levels remained unchanged, whole-cell electron paramagnetic resonance (EPR) demonstrated that the level of free iron in mutant cells was 3 times less than that of the wild-type strain. Siderophore excretion in the mutant also decreased in iron-depleted medium. The mutant was more sensitive to hydrogen peroxide and gave rise to 100 times more colonies resistant to gentamicin or kanamycin. Conclusion Our results showed that the knock-out of SO1377 gene had pleiotropic effects and suggested that SO1377 may play a role in iron homeostasis and oxidative damage protection in S. oneidensis MR-1.
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Affiliation(s)
- Weimin Gao
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yongqing Liu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Carol S Giometti
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Sandra L Tollaksen
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Tripti Khare
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Liyou Wu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dawn M Klingeman
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew W Fields
- Department of Microbiology, Miami University, Oxford, OH 45056, USA
| | - Jizhong Zhou
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
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29
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Klonowska A, Heulin T, Vermeglio A. Selenite and tellurite reduction by Shewanella oneidensis. Appl Environ Microbiol 2005; 71:5607-9. [PMID: 16151159 PMCID: PMC1214622 DOI: 10.1128/aem.71.9.5607-5609.2005] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis MR-1 reduces selenite and tellurite preferentially under anaerobic conditions. The Se(0) and Te(0) deposits are located extracellularly and intracellularly, respectively. This difference in localization and the distinct effect of some inhibitors and electron acceptors on these reduction processes are taken as evidence of two independent pathways.
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Affiliation(s)
- Agnieszka Klonowska
- Laboratoire de Bioénergétique Cellulaire CEA/Cadarache, DSV-DEVM-UMR 6191 CNRS-CEA-Aix-Marseille II, 13108 Saint Paul lez Durance Cedex, France
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30
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Kim BC, Leang C, Ding YHR, Glaven RH, Coppi MV, Lovley DR. OmcF, a putative c-Type monoheme outer membrane cytochrome required for the expression of other outer membrane cytochromes in Geobacter sulfurreducens. J Bacteriol 2005; 187:4505-13. [PMID: 15968061 PMCID: PMC1151787 DOI: 10.1128/jb.187.13.4505-4513.2005] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Accepted: 03/21/2005] [Indexed: 11/20/2022] Open
Abstract
Outer membrane cytochromes are often proposed as likely agents for electron transfer to extracellular electron acceptors, such as Fe(III). The omcF gene in the dissimilatory Fe(III)-reducing microorganism Geobacter sulfurreducens is predicted to code for a small outer membrane monoheme c-type cytochrome. An OmcF-deficient strain was constructed, and its ability to reduce and grow on Fe(III) citrate was found to be impaired. Following a prolonged lag phase (150 h), the OmcF-deficient strain developed the ability to grow in Fe(III) citrate medium with doubling times and yields that were ca. 145% and 70% of those of the wild type, respectively. Comparison of the c-type cytochrome contents of outer membrane-enriched fractions prepared from wild-type and OmcF-deficient cultures confirmed the outer membrane association of OmcF and revealed multiple changes in the cytochrome content of the OmcF-deficient strain. These changes included loss of expression of two previously characterized outer membrane cytochromes, OmcB and OmcC, and overexpression of a third previously characterized outer membrane cytochrome, OmcS, during growth on Fe(III) citrate. The omcB and omcC transcripts could not be detected in the OmcF-deficient mutant by either reverse transcriptase PCR or Northern blot analyses. Expression of the omcF gene in trans restored both the capacity of the OmcF-deficient mutant to reduce Fe(III) and wild-type levels of omcB and omcC mRNA and protein. Thus, elimination of OmcF may impair Fe(III) reduction by influencing expression of OmcB, which has previously been demonstrated to play a critical role in Fe(III) reduction.
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Affiliation(s)
- Byoung-Chan Kim
- Department of Microbiology, 203 Morrill Science IVN, University of Massachusetts at Amherst, 639 North Pleasant St., Amherst, MA 01003, USA.
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31
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Liu Y, Gao W, Wang Y, Wu L, Liu X, Yan T, Alm E, Arkin A, Thompson DK, Fields MW, Zhou J. Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions. J Bacteriol 2005; 187:2501-7. [PMID: 15774893 PMCID: PMC1065217 DOI: 10.1128/jb.187.7.2501-2507.2005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Whole-genomic expression patterns were examined in Shewanella oneidensis cells exposed to elevated sodium chloride. Genes involved in Na(+) extrusion and glutamate biosynthesis were significantly up-regulated, and the majority of chemotaxis/motility-related genes were significantly down-regulated. The data also suggested an important role for metabolic adjustment in salt stress adaptation in S. oneidensis.
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Affiliation(s)
- Yongqing Liu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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32
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Gao W, Liu Y, Zhou J, Pan H. Effects of a strong static magnetic field on bacteriumShewanella oneidensis: An assessment by using whole genome microarray. Bioelectromagnetics 2005; 26:558-63. [PMID: 16037957 DOI: 10.1002/bem.20133] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The effect of a strong static 14.1 T magnetic field on log phase cells of bacterial strain Shewanella oneidensis MR-1 was evaluated by using whole genome microarray of this bacterium. Although differences were not observed between the treatment and control by measuring the optical density (OD), colony forming unit (CFU), as well as post-exposure growth of cells, transcriptional expression levels of 65 genes were altered according to our microarray data. Among these genes, 21 were upregulated while other 44 were downregulated, compared with control.
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Affiliation(s)
- Weimin Gao
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Abstract
Dissimilatory Fe(III) and Mn(IV) reduction has an important influence on the geochemistry of modern environments, and Fe(III)-reducing microorganisms, most notably those in the Geobacteraceae family, can play an important role in the bioremediation of subsurface environments contaminated with organic or metal contaminants. Microorganisms with the capacity to conserve energy from Fe(III) and Mn(IV) reduction are phylogenetically dispersed throughout the Bacteria and Archaea. The ability to oxidize hydrogen with the reduction of Fe(III) is a highly conserved characteristic of hyperthermophilic microorganisms and one Fe(III)-reducing Archaea grows at the highest temperature yet recorded for any organism. Fe(III)- and Mn(IV)-reducing microorganisms have the ability to oxidize a wide variety of organic compounds, often completely to carbon dioxide. Typical alternative electron acceptors for Fe(III) reducers include oxygen, nitrate, U(VI) and electrodes. Unlike other commonly considered electron acceptors, Fe(III) and Mn(IV) oxides, the most prevalent form of Fe(III) and Mn(IV) in most environments, are insoluble. Thus, Fe(III)- and Mn(IV)-reducing microorganisms face the dilemma of how to transfer electrons derived from central metabolism onto an insoluble, extracellular electron acceptor. Although microbiological and geochemical evidence suggests that Fe(III) reduction may have been the first form of microbial respiration, the capacity for Fe(III) reduction appears to have evolved several times as phylogenetically distinct Fe(III) reducers have different mechanisms for Fe(III) reduction. Geobacter species, which are representative of the family of Fe(III) reducers that predominate in a wide diversity of sedimentary environments, require direct contact with Fe(III) oxides in order to reduce them. In contrast, Shewanella and Geothrix species produce chelators that solubilize Fe(III) and release electron-shuttling compounds that transfer electrons from the cell surface to the surface of Fe(III) oxides not in direct contact with the cells. Electron transfer from the inner membrane to the outer membrane in Geobacter and Shewanella species appears to involve an electron transport chain of inner-membrane, periplasmic, and outer-membrane c-type cytochromes, but the cytochromes involved in these processes in the two organisms are different. In addition, Geobacter species specifically express flagella and pili during growth on Fe(III) and Mn(IV) oxides and are chemotactic to Fe(II) and Mn(II), which may lead Geobacter species to the oxides under anoxic conditions. The physiological characteristics of Geobacter species appear to explain why they have consistently been found to be the predominant Fe(III)- and Mn(IV)-reducing microorganisms in a variety of sedimentary environments. In comparison with other respiratory processes, the study of Fe(III) and Mn(IV) reduction is in its infancy, but genome-enabled approaches are rapidly advancing our understanding of this environmentally significant physiology.
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Affiliation(s)
- Derek R Lovley
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA 01003, USA.
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Back JH, Kim MS, Cho H, Chang IS, Lee J, Kim KS, Kim BH, Park YI, Han YS. Construction of bacterial artificial chromosome library from electrochemical microorganisms. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09738.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Myers JM, Antholine WE, Myers CR. Vanadium(V) reduction by Shewanella oneidensis MR-1 requires menaquinone and cytochromes from the cytoplasmic and outer membranes. Appl Environ Microbiol 2004; 70:1405-12. [PMID: 15006760 PMCID: PMC368379 DOI: 10.1128/aem.70.3.1405-1412.2004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The metal-reducing bacterium Shewanella oneidensis MR-1 displays remarkable anaerobic respiratory plasticity, which is reflected in the extensive number of electron transport components encoded in its genome. In these studies, several cell components required for the reduction of vanadium(V) were determined. V(V) reduction is mediated by an electron transport chain which includes cytoplasmic membrane components (menaquinone and the tetraheme cytochrome CymA) and the outer membrane (OM) cytochrome OmcB. A partial role for the OM cytochrome OmcA was evident. Electron spin resonance spectroscopy demonstrated that V(V) was reduced to V(IV). V(V) reduction did not support anaerobic growth. This is the first report delineating specific electron transport components that are required for V(V) reduction and of a role for OM cytochromes in the reduction of a soluble metal species.
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Affiliation(s)
- Judith M Myers
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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36
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Lloyd JR, Lovley DR, Macaskie LE. Biotechnological application of metal-reducing microorganisms. ADVANCES IN APPLIED MICROBIOLOGY 2004; 53:85-128. [PMID: 14696317 DOI: 10.1016/s0065-2164(03)53003-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Jonathan R Lloyd
- Williamson Research Centre for Molecular Environmental Studies, Department of Earth Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
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37
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Reyes-Ramirez F, Dobbin P, Sawers G, Richardson DJ. Characterization of transcriptional regulation of Shewanella frigidimarina Fe(III)-induced flavocytochrome c reveals a novel iron-responsive gene regulation system. J Bacteriol 2003; 185:4564-71. [PMID: 12867466 PMCID: PMC165765 DOI: 10.1128/jb.185.15.4564-4571.2003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterium Shewanella frigidimarina can grow anaerobically by utilizing Fe(III) as a respiratory electron acceptor. This results in the synthesis of a number of periplasmic c-type cytochromes, which are absent when the organism is grown in the absence of added Fe(III). One cytochrome, IfcA, is synthesized when Fe(III) is present as the sole respiratory electron acceptor or when it is present in combination with oxygen, fumarate, or nitrate. The ifcA gene was thus selected for a study of iron-responsive gene regulation of respiratory proteins in S. frigidimarina. The monocistronic ifcA gene clusters with two other monocistronic genes, ifcO, encoding a putative outer membrane porin, and ifcR, encoding a putative transcriptional regulator of the LysR superfamily. Analysis of transcription of all three genes under a range of growth conditions in the wild type and an ifcR insertion mutant and analysis of a strain that constitutively expresses ifcR revealed that iron regulation is exerted at the level of ifcR transcription. In the presence of Fe(III) IfcR is synthesized and acts positively to regulate expression of ifcO and ifcA. Control of Fe(III) respiration by this novel regulatory system differs markedly from Fur-mediated regulation of iron assimilation, in which Fur serves as an Fe(II)-activated repressor.
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Affiliation(s)
- Francisca Reyes-Ramirez
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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Pitts KE, Dobbin PS, Reyes-Ramirez F, Thomson AJ, Richardson DJ, Seward HE. Characterization of the Shewanella oneidensis MR-1 decaheme cytochrome MtrA: expression in Escherichia coli confers the ability to reduce soluble Fe(III) chelates. J Biol Chem 2003; 278:27758-65. [PMID: 12732647 DOI: 10.1074/jbc.m302582200] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Shewanella oneidensis MR-1 has the metabolic capacity to grow anaerobically using Fe(III) as a terminal electron acceptor. Growth under these conditions results in the de novo synthesis of a number of periplasmic c-type cytochromes, many of which are multiheme in nature and are thought to be involved in the Fe(III) respiratory process. To begin a biochemical study of these complex cytochromes, the mtrA gene that encodes an approximate 32-kDa periplasmic decaheme cytochrome has been heterologously expressed in Escherichia coli. Co-expression of mtrA with a plasmid that contains cytochrome c maturation genes leads to the assembly of a correctly targeted holoprotein, which covalently binds ten hemes. The recombinant MtrA protein has been characterized by magnetic circular dichroism, which shows that all ten hemes have bis-histidine axial ligation. EPR spectroscopy detected only eight of these hemes, all of which are low spin and provides evidence for a spin-coupled pair of hemes in the oxidized state. Redox titrations of MtrA have been carried out with optical- and EPR-monitored methods, and the hemes are shown to reduce over the potential range -100 to -400 mV. In intact cells of E. coli, MtrA is shown to obtain electrons from the host electron transport chain and pass these onto host oxidoreductases or a range of soluble Fe(III) species. This demonstrates the promiscuous nature of this decaheme cytochrome and its potential to serve as a soluble Fe(III) reductase in intact cells.
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Affiliation(s)
- Katy E Pitts
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences and School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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Ghosh D, Bal B, Kashyap VK, Pal S. Molecular phylogenetic exploration of bacterial diversity in a Bakreshwar (India) hot spring and culture of Shewanella-related thermophiles. Appl Environ Microbiol 2003; 69:4332-6. [PMID: 12839826 PMCID: PMC165147 DOI: 10.1128/aem.69.7.4332-4336.2003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial diversity of a hot spring in Bakreshwar, India, was investigated by a culture-independent approach. 16S ribosomal DNA clones derived from the sediment samples were found to be associated with gamma-Proteobacteria, cyanobacteria, and green nonsulfur and low-GC gram-positive bacteria. The first of the above phylotypes cobranches with Shewanella, a well-known iron reducer. This phylogenetic correlation has been exploited to develop culture conditions for thermophilic iron-reducing microorganisms.
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Affiliation(s)
- Dhritiman Ghosh
- Department of Life Science and Biotechnology, Jadavpur University, Calcutta 700 032, India
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Abstract
Almost all organisms require iron for enzymes involved in essential cellular reactions. Aerobic microbes living at neutral or alkaline pH encounter poor iron availability due to the insolubility of ferric iron. Assimilatory ferric reductases are essential components of the iron assimilatory pathway that generate the more soluble ferrous iron, which is then incorporated into cellular proteins. Dissimilatory ferric reductases are essential terminal reductases of the iron respiratory pathway in iron-reducing bacteria. While our understanding of dissimilatory ferric reductases is still limited, it is clear that these enzymes are distinct from the assimilatory-type ferric reductases. Research over the last 10 years has revealed that most bacterial assimilatory ferric reductases are flavin reductases, which can serve several physiological roles. This article reviews the physiological function and structure of assimilatory and dissimilatory ferric reductases present in the Bacteria, Archaea and Yeast. Ferric reductases do not form a single family, but appear to be distinct enzymes suggesting that several independent strategies for iron reduction may have evolved.
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Affiliation(s)
- Imke Schröder
- Department of Microbiology, Immunology and Molecular Genetics, University of California-Los Angeles, 1602 Molecular Sciences Bldg., Los Angeles, CA 90095-1489, USA.
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Abstract
The microbial reduction of metals has attracted recent interest as these transformations can play crucial roles in the cycling of both inorganic and organic species in a range of environments and, if harnessed, may offer the basis for a wide range of innovative biotechnological processes. Under certain conditions, however, microbial metal reduction can also mobilise toxic metals with potentially calamitous effects on human health. This review focuses on recent research on the reduction of a wide range of metals including Fe(III), Mn(IV) and other more toxic metals such as Cr(VI), Hg(II), Co(III), Pd(II), Au(III), Ag(I), Mo(VI) and V(V). The reduction of metalloids including As(V) and Se(VI) and radionuclides including U(VI), Np(V) and Tc(VII) is also reviewed. Rapid advances over the last decade have resulted in a detailed understanding of some of these transformations at a molecular level. Where known, the mechanisms of metal reduction are discussed, alongside the environmental impact of such transformations and possible biotechnological applications that could utilise these activities.
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Affiliation(s)
- Jonathan R Lloyd
- The Williamson Research Centre for Molecular Environmental Studies, Department of Earth Sciences, The University of Manchester, Manchester M13 9PL, UK.
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Roh Y, Liu SV, Li G, Huang H, Phelps TJ, Zhou J. Isolation and characterization of metal-reducing thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado. Appl Environ Microbiol 2002; 68:6013-20. [PMID: 12450823 PMCID: PMC134454 DOI: 10.1128/aem.68.12.6013-6020.2002] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2001] [Accepted: 08/29/2002] [Indexed: 11/20/2022] Open
Abstract
Five bacterial strains were isolated from anaerobic enrichment cultures that had originated from inoculations with samples collected from the deep subsurface environments of the millions-of-years-old, geologically and hydrologically isolated Piceance Basin in Colorado. Small-subunit rRNA gene-based analyses indicated that all of these bacteria were closely related to Thermoanaerobacter ethanolicus, with similarities of 99.4 to 99.5%. Three isolates (X513, X514, and X561) from the five bacterial strains were used to examine physiological characteristics. These thermophilic bacteria were able to use acetate, glucose, hydrogen, lactate, pyruvate, succinate, and xylose as electron donors while reducing Fe(III), cobalt(III), chromium(VI), manganese(IV), and uranium(VI) at 60 degrees C. One of the isolates (X514) was also able to utilize hydrogen as an electron donor for Fe(III) reduction. These bacteria exhibited diverse mineral precipitation capabilities, including the formation of magnetite (Fe(3)O(4)), siderite (FeCO(3)), rhodochrosite (MnCO(3)), and uraninite (UO(2)). The gas composition of the incubation headspace and the ionic composition of the incubation medium exerted profound influences on the types of minerals formed. The susceptibility of the thermophilic Fe(III)-reducing cultures to metabolic inhibitors specific for ferric reductase, hydrogenase, and electron transport indicated that iron reduction by these bacteria is an enzymatic process.
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Affiliation(s)
- Yul Roh
- Environmental Sciences Division, Oak Ridge National Laboratory, Tennessee 37831-6038, USA
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Myers CR, Myers JM. MtrB is required for proper incorporation of the cytochromes OmcA and OmcB into the outer membrane of Shewanella putrefaciens MR-1. Appl Environ Microbiol 2002; 68:5585-94. [PMID: 12406753 PMCID: PMC129928 DOI: 10.1128/aem.68.11.5585-5594.2002] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When grown under anaerobic conditions, Shewanella putrefaciens MR-1 synthesizes multiple outer membrane (OM) cytochromes, some of which have a role in the use of insoluble electron acceptors (e.g., MnO2) for anaerobic respiration. The cytochromes OmcA and OmcB are localized to the OM and the OM-like intermediate-density membrane (IM) in MR-1. The components necessary for proper localization of these cytochromes to the OM have not been identified. A gene replacement mutant (strain MTRB1) lacking the putative OM protein MtrB was isolated and characterized. The specific cytochrome content of the OM of MTRB1 was only 36% that of MR-1. This was not the result of a general decline in cytochrome content, however, because the cytoplasmic membrane (CM) and soluble fractions were not cytochrome deficient. While OmcA and OmcB were detected in the OM and IM fractions of MTRB1, significant amounts were mislocalized to the CM. OmcA was also detected in the soluble fraction of MTRB1. While OmcA and OmcB in MR-1 fractions were resistant to solubilization with Triton X-100 in the presence of Mg2+, Triton X-100 readily solubilized these proteins from all subcellular fractions of MTRB1. Together, these data suggest that MtrB is required for the proper localization and insertion of OmcA and OmcB into the OM of MR-1. The inability of MTRB1 to properly insert these, and possibly other, proteins into its OM likely contributes to its marked deficiency in manganese(IV) and iron(III) reduction. While the localization of another putative OM cytochrome (MtrF) could not be directly determined, an mtrF gene replacement mutant exhibited wild-types rates of Mn(IV) and Fe(III) reduction. Therefore, even if MtrF were mislocalized in MTRB1, it would not contribute to the loss of metal reduction activity in this strain.
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Affiliation(s)
- Charles R Myers
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
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Beliaev AS, Thompson DK, Fields MW, Wu L, Lies DP, Nealson KH, Zhou J. Microarray transcription profiling of a Shewanella oneidensis etrA mutant. J Bacteriol 2002; 184:4612-6. [PMID: 12142431 PMCID: PMC135233 DOI: 10.1128/jb.184.16.4612-4616.2002] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA microarrays were used to examine the effect of an insertional mutation in the Shewanella oneidensis etrA (electron transport regulator) locus on gene expression under anaerobic conditions. The mRNA levels of 69 genes with documented functions in energy and carbon metabolism, regulation, transport, and other cellular processes displayed significant alterations in transcript abundance in an etrA-mutant genetic background. This is the first microarray study indicating a possible involvement of EtrA in the regulation of gene expression in S. oneidensis MR-1.
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Affiliation(s)
- Alex S Beliaev
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6038, USA
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Myers JM, Myers CR. Genetic complementation of an outer membrane cytochrome omcB mutant of Shewanella putrefaciens MR-1 requires omcB plus downstream DNA. Appl Environ Microbiol 2002; 68:2781-93. [PMID: 12039733 PMCID: PMC123961 DOI: 10.1128/aem.68.6.2781-2793.2002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobically grown cells of the metal-reducing bacterium Shewanella putrefaciens MR-1 contain multiple outer membrane (OM) cytochromes. A gene replacement mutant (strain OMCB1) lacking the OM cytochrome OmcB is markedly deficient in the reduction of MnO2 and exhibits reduced rates of Fe(III) reduction. The levels of other OM cytochromes are also decreased in OMCB1. Complementation of OMCB1 with wild-type omcB did not restore any of these defects. However, a 21-kb genomic fragment from MR-1, which included omcB and 19 kb of downstream DNA, fully restored MnO2 and Fe(III) reduction and the full complement of OM cytochromes to OMCB1. A 14.7-kb DNA fragment, including omcB and 12 kb of downstream DNA, provided only a modest increase in MnO2 reduction and OM cytochrome content, but it fully restored Fe(III) citrate reduction and partially restored FeOOH reduction. While omcB mRNA was readily detected in this complement, the OmcB protein was not detected in any cellular compartment. The restoration of Fe(III) reduction despite the absence of OmcB suggests that OmcB itself is not required for Fe(III) reduction. Another OM cytochrome, OmcA, was mislocalized to the cytoplasmic membrane of OMCB1. Only the 21-kb genomic fragment was able to restore proper localization of OmcA to the OM. This 21-kb fragment does not contain omcA, but it does contain several open reading frames (ORFs) downstream from omcB. The most downstream of these ORFs (altA) encodes a putative AraC-like transcriptional regulator. However, a gene replacement mutant of altA resembled the wild type with respect to MnO2 reduction, OM cytochrome content, and the localization of OmcA and OmcB to the OM. Since OMCB1 continues to express genes immediately downstream from omcB, the lack of expression of this downstream DNA does not explain its phenotype or the need for the large complementing fragment. The results suggest that the DNA downstream of omcB must be present in cis in order to restore Fe(III) reduction, MnO2 reduction, OM cytochrome content, and the localization of OmcA and OmcB to the OM.
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Affiliation(s)
- Judith M Myers
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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Thompson DK, Beliaev AS, Giometti CS, Tollaksen SL, Khare T, Lies DP, Nealson KH, Lim H, Yates J, Brandt CC, Tiedje JM, Zhou J. Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl Environ Microbiol 2002; 68:881-92. [PMID: 11823232 PMCID: PMC126683 DOI: 10.1128/aem.68.2.881-892.2002] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The iron-directed, coordinate regulation of genes depends on the fur (ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. To investigate the biological function of a fur homolog in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1, a fur knockout strain (FUR1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, DNA microarrays containing 691 arrayed genes, and two-dimensional polyacrylamide gel electrophoresis. Physiological studies indicated that FUR1 was similar to the wild-type strain when they were compared for anaerobic growth and reduction of various electron acceptors. Transcription profiling, however, revealed that genes with predicted functions in electron transport, energy metabolism, transcriptional regulation, and oxidative stress protection were either repressed (ccoNQ, etrA, cytochrome b and c maturation-encoding genes, qor, yiaY, sodB, rpoH, phoB, and chvI) or induced (yggW, pdhC, prpC, aceE, fdhD, and ppc) in the fur mutant. Disruption of fur also resulted in derepression of genes (hxuC, alcC, fhuA, hemR, irgA, and ompW) putatively involved in iron uptake. This agreed with the finding that the fur mutant produced threefold-higher levels of siderophore than the wild-type strain under conditions of sufficient iron. Analysis of a subset of the FUR1 proteome (i.e., primarily soluble cytoplasmic and periplasmic proteins) indicated that 11 major protein species reproducibly showed significant (P < 0.05) differences in abundance relative to the wild type. Protein identification using mass spectrometry indicated that the expression of two of these proteins (SodB and AlcC) correlated with the microarray data. These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems.
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Affiliation(s)
- Dorothea K Thompson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Saffarini DA, Blumerman SL, Mansoorabadi KJ. Role of menaquinones in Fe(III) reduction by membrane fractions of Shewanella putrefaciens. J Bacteriol 2002; 184:846-8. [PMID: 11790756 PMCID: PMC139511 DOI: 10.1128/jb.184.3.846-848.2002] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two Tn5-generated mutants of Shewanella putrefaciens with insertions in menD and menB were isolated and analyzed. Both mutants were deficient in the use of several terminal electron acceptors, including Fe(III). This deficiency was overcome by the addition of menaquinone (vitamin K(2)). Isolated membrane fractions from both mutants were unable to reduce Fe(III) in the absence of added menaquinone when formate was used as the electron donor. These results indicate that menaquinones are essential components for the reduction of Fe(III) by both whole cells and purified membrane fractions when formate or lactate is used as the electron donor.
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Affiliation(s)
- Daad A Saffarini
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave., Milwaukee, WI 53211, USA.
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Glasauer S, Langley S, Beveridge TJ. Intracellular iron minerals in a dissimilatory iron-reducing bacterium. Science 2002; 295:117-9. [PMID: 11778045 DOI: 10.1126/science.1066577] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Among prokaryotes, there are few examples of controlled mineral formation; the formation of crystalline iron oxides and sulfides [magnetite (Fe3O4) or greigite (Fe3S4)] by magnetotactic bacteria is an exception. Shewanella putrefaciens CN32, a Gram-negative, facultative anaerobic bacterium that is capable of dissimilatory iron reduction, produced microscopic intracellular grains of iron oxide minerals during growth on two-line ferrihydrite in a hydrogen-argon atmosphere. The minerals, formed at iron concentrations found in the soil and sedimentary environments where these bacteria are active, could represent an unexplored pathway for the cycling of iron by bacteria.
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Affiliation(s)
- Susan Glasauer
- Department of Microbiology, College of Biological Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Lloyd JR, Macaskie LE. Chapter 11 Biochemical basis of microbe-radionuclide interactions. RADIOACTIVITY IN THE ENVIRONMENT 2002. [DOI: 10.1016/s1569-4860(02)80040-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Maier TM, Myers CR. Isolation and characterization of a Shewanella putrefaciens MR-1 electron transport regulator etrA mutant: reassessment of the role of EtrA. J Bacteriol 2001; 183:4918-26. [PMID: 11466298 PMCID: PMC99549 DOI: 10.1128/jb.183.16.4918-4926.2001] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2000] [Accepted: 05/23/2001] [Indexed: 11/20/2022] Open
Abstract
Shewanella putrefaciens MR-1 has emerged as a good model to study anaerobic respiration and electron transport-linked metal reduction. Its remarkable respiratory plasticity suggests the potential for a complex regulatory system to coordinate electron acceptor use in the absence of O(2). It had previously been suggested that EtrA (electron transport regulator A), an analog of Fnr (fumarate nitrate regulator) from Escherichia coli, may regulate gene expression for anaerobic electron transport. An etrA knockout strain (ETRA-153) was isolated from MR-1 using a gene replacement strategy. Reverse transcription-PCR analysis of total RNA demonstrated the loss of the etrA mRNA in ETRA-153. ETRA-153 cells retained the ability to grow on all electron acceptors tested, including fumarate, trimethylamine N-oxide (TMAO), thiosulfate, dimethyl sulfoxide, ferric citrate, nitrate, and O(2), as well as the ability to reduce ferric citrate, manganese(IV), nitrate, and nitrite. EtrA is therefore not necessary for growth on, or the reduction of, these electron acceptors. However, ETRA-153 had reduced initial growth rates on fumarate and nitrate but not on TMAO. The activities for fumarate and nitrate reductase were lower in ETRA-153, as were the levels of fumarate reductase protein and transcript. ETRA-153 was also deficient in one type of ubiquinone. These results are in contrast to those previously reported for the putative etrA mutant METR-1. Molecular analysis of METR-1 indicated that its etrA gene is not interrupted; its reported phenotype was likely due to the use of inappropriate anaerobic growth conditions.
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Affiliation(s)
- T M Maier
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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