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Winiarska A, Hege D, Gemmecker Y, Kryściak-Czerwenka J, Seubert A, Heider J, Szaleniec M. Tungsten Enzyme Using Hydrogen as an Electron Donor to Reduce Carboxylic Acids and NAD . ACS Catal 2022; 12:8707-8717. [PMID: 35874620 PMCID: PMC9295118 DOI: 10.1021/acscatal.2c02147] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Tungsten-dependent
aldehyde oxidoreductases (AORs) catalyze the
oxidation of aldehydes to acids and are the only known enzymes reducing
non-activated acids using electron donors with low redox potentials.
We report here that AOR from Aromatoleum aromaticum (AORAa) catalyzes the reduction of organic
acids not only with low-potential Eu(II) or Ti(III) complexes but
also with H2 as an electron donor. Additionally, AORAa catalyzes the H2-dependent reduction
of NAD+ or benzyl viologen. The rate of H2-dependent
NAD+ reduction equals to 10% of that of aldehyde oxidation,
representing the highest H2 turnover rate observed among
the Mo/W enzymes. As AORAa simultaneously
catalyzes the reduction of acids and NAD+, we designed
a cascade reaction utilizing a NAD(P)H-dependent alcohol dehydrogenase
to reduce organic acids to the corresponding alcohols with H2 as the only reductant. The newly discovered W-hydrogenase side activity
of AORAa may find applications in either
NADH recycling or conversion of carboxylic acids to more useful biochemicals.
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Affiliation(s)
- Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
| | - Dominik Hege
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Yvonne Gemmecker
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Joanna Kryściak-Czerwenka
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
| | - Andreas Seubert
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Johann Heider
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany.,Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
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2
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Buessecker S, Palmer M, Lai D, Dimapilis J, Mayali X, Mosier D, Jiao JY, Colman DR, Keller LM, St John E, Miranda M, Gonzalez C, Gonzalez L, Sam C, Villa C, Zhuo M, Bodman N, Robles F, Boyd ES, Cox AD, St Clair B, Hua ZS, Li WJ, Reysenbach AL, Stott MB, Weber PK, Pett-Ridge J, Dekas AE, Hedlund BP, Dodsworth JA. An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea. Nat Commun 2022; 13:3773. [PMID: 35773279 PMCID: PMC9246946 DOI: 10.1038/s41467-022-31452-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/17/2022] [Indexed: 11/19/2022] Open
Abstract
Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.
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Affiliation(s)
- Steffen Buessecker
- Department of Earth System Science, Stanford University, Stanford, CA, USA.
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA.
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Joshua Dimapilis
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Damon Mosier
- Department of Biology, California State University, San Bernardino, CA, USA
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Lisa M Keller
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Emily St John
- Department of Biology, Portland State University, Portland, OR, USA
| | - Michelle Miranda
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Cristina Gonzalez
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Lizett Gonzalez
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Christian Sam
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Christopher Villa
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Madeline Zhuo
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Nicholas Bodman
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Fernando Robles
- Department of Biology, California State University, San Bernardino, CA, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Alysia D Cox
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Brian St Clair
- Department of Chemistry and Geochemistry, Montana Technological University, Butte, MT, USA
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
- College of Fisheries, Henan Normal University, Xinxiang, PR China
| | | | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of Merced, Merced, CA, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, USA.
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3
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Arthur R, Antonczyk S, Off S, Scherer PA. Mesophilic and Thermophilic Anaerobic Digestion of Wheat Straw in a CSTR System with 'Synthetic Manure': Impact of Nickel and Tungsten on Methane Yields, Cell Count, and Microbiome. Bioengineering (Basel) 2022; 9:bioengineering9010013. [PMID: 35049722 PMCID: PMC8772805 DOI: 10.3390/bioengineering9010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
Lignocellulosic residues, such as straw, are currently considered as candidates for biogas production. Therefore, straw fermentations were performed to quantitatively estimate methane yields and cell counts, as well as to qualitatively determine the microbiome. Six fully automated, continuously stirred biogas reactors were used: three mesophilic (41 °C) and three thermophilic (58 °C). They were fed every 8 h with milled wheat straw suspension in a defined, buffered salt solution, called 'synthetic manure'. Total reflection X-ray fluorescence spectrometry analyses showed nickel and tungsten deficiency in the straw suspension. Supplementation of nickel and subsequently tungsten, or with an increasing combined dosage of both elements, resulted in a final concentration of approximately 0.1 mg/L active, dissolved tungsten ions, which caused an increase of the specific methane production, up to 63% under mesophilic and 31% under thermophilic conditions. That is the same optimal range for pure cultures of methanogens or bacteria found in literature. A simultaneous decrease of volatile fatty acids occurred. The Ni/W effect occurred with all three organic loading rates, being 4.5, 7.5, and 9.0 g volatile solids per litre and day, with a concomitant hydraulic retention time of 18, 10, or 8 days, respectively. A maximum specific methane production of 0.254 m3 CH4, under standard temperature and pressure per kg volatile solids (almost 90% degradation), was obtained. After the final supplementation of tungsten, the cell counts of methanogens increased by 300%, while the total microbial cell counts increased by only 3-62%. The mesophilic methanogenic microflora was shifted from the acetotrophic Methanosaeta to the hydrogenotrophic Methanoculleus (85%) by tungsten, whereas the H2-CO2-converter, Methanothermobacter, always dominated in the thermophilic fermenters.
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Affiliation(s)
- Richard Arthur
- Energy Systems Engineering Department, Koforidua Technical University, Koforidua P.O. Box KF 981, Ghana;
| | - Sebastian Antonczyk
- Research Center for Biomass Utilization, Faculty Life Sciences, Hamburg University of Applied Sciences (HAW), 20099 Hamburg, Germany; (S.A.); (S.O.)
| | - Sandra Off
- Research Center for Biomass Utilization, Faculty Life Sciences, Hamburg University of Applied Sciences (HAW), 20099 Hamburg, Germany; (S.A.); (S.O.)
| | - Paul A. Scherer
- Research Center for Biomass Utilization, Faculty Life Sciences, Hamburg University of Applied Sciences (HAW), 20099 Hamburg, Germany; (S.A.); (S.O.)
- Correspondence:
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4
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Harnessing Escherichia coli for Bio-Based Production of Formate under Pressurized H 2 and CO 2 Gases. Appl Environ Microbiol 2021; 87:e0029921. [PMID: 34647819 DOI: 10.1128/aem.00299-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli is a Gram-negative bacterium that is a workhorse for biotechnology. The organism naturally performs a mixed-acid fermentation under anaerobic conditions where it synthesizes formate hydrogenlyase (FHL-1). The physiological role of the enzyme is the disproportionation of formate into H2 and CO2. However, the enzyme has been observed to catalyze hydrogenation of CO2 given the correct conditions, and so it has possibilities in bio-based carbon capture and storage if it can be harnessed as a hydrogen-dependent CO2 reductase (HDCR). In this study, an E. coli host strain was engineered for the continuous production of formic acid from H2 and CO2 during bacterial growth in a pressurized batch bioreactor. Incorporation of tungsten, in place of molybdenum, in FHL-1 helped to impose a degree of catalytic bias on the enzyme. This work demonstrates that it is possible to couple cell growth to simultaneous, unidirectional formate production from carbon dioxide and develops a process for growth under pressurized gases. IMPORTANCE Greenhouse gas emissions, including waste carbon dioxide, are contributing to global climate change. A basket of solutions is needed to steadily reduce emissions, and one approach is bio-based carbon capture and storage. Here, we present our latest work on harnessing a novel biological solution for carbon capture. The Escherichia coli formate hydrogenlyase (FHL-1) was engineered to be constitutively expressed. Anaerobic growth under pressurized H2 and CO2 gases was established, and aqueous formic acid was produced as a result. Incorporation of tungsten into the enzyme in place of molybdenum proved useful in poising FHL-1 as a hydrogen-dependent CO2 reductase (HDCR).
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5
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Abstract
The accumulation of carbon dioxide in the atmosphere as a result of human activities has caused a number of adverse circumstances in the world. For this reason, the proposed solutions lie within the aim of reducing carbon dioxide emissions have been quite valuable. However, as the human activity continues to increase on this planet, the possibility of reducing carbon dioxide emissions decreases with the use of conventional methods. The emergence of compounds than can be used in different fields by converting the released carbon dioxide into different chemicals will construct a fundamental solution to the problem. Although electro-catalysis or photolithography methods have emerged for this purpose, they have not been able to achieve successful results. Alternatively, another proposed solution are enzyme based systems. Among the enzyme-based systems, pyruvate decarboxylase, carbonic anhydrase and dehydrogenases have been the most studied enzymes. Pyruvate dehydrogenase and carbonic anhydrase have either been an expensive method or were incapable of producing the desired result due to the reaction cascade they catalyze. However, the studies reporting the production of industrial chemicals from carbon dioxide using dehydrogenases and in particular, the formate dehydrogenase enzyme, have been remarkable. Moreover, reported studies have shown the existence of more active and stable enzymes, especially the dehydrogenase family that can be identified from the biome. In addition to this, their redesign through protein engineering can have an immense contribution to the increased use of enzyme-based methods in CO2 reduction, resulting in an enormous expansion of the industrial capacity.
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6
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Functional prediction of environmental variables using metabolic networks. Sci Rep 2021; 11:12192. [PMID: 34108539 PMCID: PMC8190111 DOI: 10.1038/s41598-021-91486-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/05/2021] [Indexed: 11/23/2022] Open
Abstract
In this manuscript, we propose a novel approach to assess relationships between environment and metabolic networks. We used a comprehensive dataset of more than 5000 prokaryotic species from which we derived the metabolic networks. We compute the scope from the reconstructed graphs, which is the set of all metabolites and reactions that can potentially be synthesized when provided with external metabolites. We show using machine learning techniques that the scope is an excellent predictor of taxonomic and environmental variables, namely growth temperature, oxygen tolerance, and habitat. In the literature, metabolites and pathways are rarely used to discriminate species. We make use of the scope underlying structure—metabolites and pathways—to construct the predictive models, giving additional information on the important metabolic pathways needed to discriminate the species, which is often absent in other metabolic network properties. For example, in the particular case of growth temperature, glutathione biosynthesis pathways are specific to species growing in cold environments, whereas tungsten metabolism is specific to species in warm environments, as was hinted in current literature. From a machine learning perspective, the scope is able to reduce the dimension of our data, and can thus be considered as an interpretable graph embedding.
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7
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Kelley BR, Lu J, Haley KP, Gaddy JA, Johnson JG. Metal homeostasis in pathogenic Epsilonproteobacteria: mechanisms of acquisition, efflux, and regulation. Metallomics 2021; 13:mfaa002. [PMID: 33570133 PMCID: PMC8043183 DOI: 10.1093/mtomcs/mfaa002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/25/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022]
Abstract
Epsilonproteobacteria are a diverse class of eubacteria within the Proteobacteria phylum that includes environmental sulfur-reducing bacteria and the human pathogens, Campylobacter jejuni and Helicobacter pylori. These pathogens infect and proliferate within the gastrointestinal tracts of multiple animal hosts, including humans, and cause a variety of disease outcomes. While infection of these hosts provides nutrients for the pathogenic Epsilonproteobacteria, many hosts have evolved a variety of strategies to either sequester metals from the invading pathogen or exploit the toxicity of metals and drive their accumulation as an antimicrobial strategy. As a result, C. jejuni and H. pylori have developed mechanisms to sense changes in metal availability and regulate their physiology in order to respond to either metal limitation or accumulation. In this review, we will discuss the challenges of metal availability at the host-pathogen interface during infection with C. jejuni and H. pylori and describe what is currently known about how these organisms alter their gene expression and/or deploy bacterial virulence factors in response to these environments.
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Affiliation(s)
- Brittni R Kelley
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Jacky Lu
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, USA
| | - Kathryn P Haley
- Department of Biology, Grand Valley State University, Grand Rapids, MI, USA
| | - Jennifer A Gaddy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, USA
- Tennessee Valley Healthcare Systems, Department of Veterans Affairs, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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8
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Matharu RK, Ciric L, Ren G, Edirisinghe M. Comparative Study of the Antimicrobial Effects of Tungsten Nanoparticles and Tungsten Nanocomposite Fibres on Hospital Acquired Bacterial and Viral Pathogens. NANOMATERIALS 2020; 10:nano10061017. [PMID: 32466574 PMCID: PMC7352352 DOI: 10.3390/nano10061017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/17/2020] [Accepted: 05/19/2020] [Indexed: 02/08/2023]
Abstract
A significant proportion of patients acquire hospital associated infections as a result of care within the NHS each year. Numerous antimicrobial strategies, such as antibiotics and surface modifications to medical facilities and instruments, have been devised in an attempt to reduce the incidence of nosocomial infections, but most have been proven unsuccessful and unsustainable due to antibiotic resistance. Therefore, the need to discover novel materials that can combat pathogenic microorganisms is ongoing. Novel technologies, such as the potential use of nanomaterials and nanocomposites, hold promise for reducing these infections in the fight against antimicrobial resistance. In this study, the antimicrobial activity of tungsten, tungsten carbide and tungsten oxide nanoparticles were tested against Escherichia coli, Staphylococcus aureus and bacteriophage T4 (DNA virus). The most potent nanoparticles, tungsten oxide, were incorporated into polymeric fibres using pressurised gyration and characterised using scanning electron microscopy and energy dispersive X-ray spectroscopy. The antimicrobial activity of tungsten oxide/polymer nanocomposite fibres was also studied. The results suggest the materials in this study promote mediation of the inhibition of microbial growth in suspension.
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Affiliation(s)
- Rupy Kaur Matharu
- Department of Mechanical Engineering, University College London, Torrington Place, London WC1E 7JE, UK;
- Department of Civil, Environmental & Geomatic Engineering, University College London, Chadwick Building, Gower Street, London WC1E 6BT, UK;
| | - Lena Ciric
- Department of Civil, Environmental & Geomatic Engineering, University College London, Chadwick Building, Gower Street, London WC1E 6BT, UK;
| | - Guogang Ren
- School of Engineering and Technology, University of Hertfordshire, Hatfield AL10 9AB, UK;
| | - Mohan Edirisinghe
- Department of Mechanical Engineering, University College London, Torrington Place, London WC1E 7JE, UK;
- Correspondence:
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9
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Lacasse MJ, Sebastiampillai S, Côté JP, Hodkinson N, Brown ED, Zamble DB. A whole-cell, high-throughput hydrogenase assay to identify factors that modulate [NiFe]-hydrogenase activity. J Biol Chem 2019; 294:15373-15385. [PMID: 31455635 DOI: 10.1074/jbc.ra119.008101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
[NiFe]-hydrogenases have attracted attention as potential therapeutic targets or components of a hydrogen-based economy. [NiFe]-hydrogenase production is a complicated process that requires many associated accessory proteins that supply the requisite cofactors and substrates. Current methods for measuring hydrogenase activity have low throughput and often require specialized conditions and reagents. In this work, we developed a whole-cell high-throughput hydrogenase assay based on the colorimetric reduction of benzyl viologen to explore the biological networks of these enzymes in Escherichia coli We utilized this assay to screen the Keio collection, a set of nonlethal single-gene knockouts in E. coli BW25113. The results of this screen highlighted the assay's specificity and revealed known components of the intricate network of systems that underwrite [NiFe]-hydrogenase activity, including nickel homeostasis and formate dehydrogenase activities as well as molybdopterin and selenocysteine biosynthetic pathways. The screen also helped identify several new genetic components that modulate hydrogenase activity. We examined one E. coli strain with undetectable hydrogenase activity in more detail (ΔeutK), finding that nickel delivery to the enzyme active site was completely abrogated, and tracked this effect to an ancillary and unannotated lack of the fumarate and nitrate reduction (FNR) anaerobic regulatory protein. Collectively, these results demonstrate that the whole-cell assay developed here can be used to uncover new information about bacterial [NiFe]-hydrogenase production and to probe the cellular components of microbial nickel homeostasis.
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Affiliation(s)
- Michael J Lacasse
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | | | - Jean-Philippe Côté
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Nicholas Hodkinson
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada .,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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10
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Zhu W, Miyata N, Winter MG, Arenales A, Hughes ER, Spiga L, Kim J, Sifuentes-Dominguez L, Starokadomskyy P, Gopal P, Byndloss MX, Santos RL, Burstein E, Winter SE. Editing of the gut microbiota reduces carcinogenesis in mouse models of colitis-associated colorectal cancer. J Exp Med 2019; 216:2378-2393. [PMID: 31358565 PMCID: PMC6781011 DOI: 10.1084/jem.20181939] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/28/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022] Open
Abstract
Enterobacteriaceae family members such as E. coli exacerbate development of intestinal malignancy. Zhu et al. report that targeting the metabolism of protumoral Enterobacteriaceae by tungstate prevents tumor development in murine models of colitis-associated colorectal cancer. Chronic inflammation and gut microbiota dysbiosis, in particular the bloom of genotoxin-producing E. coli strains, are risk factors for the development of colorectal cancer. Here, we sought to determine whether precision editing of gut microbiota metabolism and composition could decrease the risk for tumor development in mouse models of colitis-associated colorectal cancer (CAC). Expansion of experimentally introduced E. coli strains in the azoxymethane/dextran sulfate sodium colitis model was driven by molybdoenzyme-dependent metabolic pathways. Oral administration of sodium tungstate inhibited E. coli molybdoenzymes and selectively decreased gut colonization with genotoxin-producing E. coli and other Enterobacteriaceae. Restricting the bloom of Enterobacteriaceae decreased intestinal inflammation and reduced the incidence of colonic tumors in two models of CAC, the azoxymethane/dextran sulfate sodium colitis model and azoxymethane-treated, Il10-deficient mice. We conclude that metabolic targeting of protumoral Enterobacteriaceae during chronic inflammation is a suitable strategy to prevent the development of malignancies arising from gut microbiota dysbiosis.
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Affiliation(s)
- Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Naoteru Miyata
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX.,Digestive Disease Center, International University of Health and Welfare, Mita Hospital, Japan
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Alexandre Arenales
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elizabeth R Hughes
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiwoong Kim
- Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Petro Starokadomskyy
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Purva Gopal
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Mariana X Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Renato L Santos
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX .,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
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11
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Characterization of thiosulfate reductase from Pyrobaculum aerophilum heterologously produced in Pyrococcus furiosus. Extremophiles 2019; 24:53-62. [PMID: 31278423 DOI: 10.1007/s00792-019-01112-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
The genome of the archaeon Pyrobaculum aerophilum (Topt ~ 100 °C) contains an operon (PAE2859-2861) encoding a putative pyranopterin-containing oxidoreductase of unknown function and metal content. These genes (with one gene modified to encode a His-affinity tag) were inserted into the fermentative anaerobic archaeon, Pyrococcus furiosus (Topt ~ 100 °C). Dye-linked assays of cytoplasmic extracts from recombinant P. furiosus show that the P. aerophilum enzyme is a thiosulfate reductase (Tsr) and reduces thiosulfate but not polysulfide. The enzyme (Tsr-Mo) from molybdenum-grown cells contains Mo (Mo:W = 9:1) while the enzyme (Tsr-W) from tungsten-grown cells contains mainly W (Mo:W = 1:6). Purified Tsr-Mo has over ten times the activity (Vmax = 1580 vs. 141 µmol min-1 mg-1) and twice the affinity for thiosulfate (Km = ~ 100 vs. ~ 200 μM) than Tsr-W and is reduced at a lower potential (Epeak = - 255 vs - 402 mV). Tsr-Mo and Tsr-W proteins are heterodimers lacking the membrane anchor subunit (PAE2861). Recombinant P. furiosus expressing P. aerophilum Tsr could not use thiosulfate as a terminal electron acceptor. P. furiosus contains five pyranopterin-containing enzymes, all of which utilize W. P. aerophilum Tsr-Mo is the first example of an active Mo-containing enzyme produced in P. furiosus.
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12
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Blazevic A, Albu M, Mitsche S, Rittmann SKMR, Habler G, Milojevic T. Biotransformation of Scheelite CaWO 4 by the Extreme Thermoacidophile Metallosphaera sedula: Tungsten-Microbial Interface. Front Microbiol 2019; 10:1492. [PMID: 31312192 PMCID: PMC6614383 DOI: 10.3389/fmicb.2019.01492] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/14/2019] [Indexed: 01/04/2023] Open
Abstract
The tungsten-microbial interactions and microbial bioprocessing of tungsten ores, which are still underexplored, are the focus of the current study. Here we show that the biotransformation of tungsten mineral scheelite performed by the extreme thermoacidophile Metallosphaera sedula leads to the breakage of scheelite structure and subsequent tungsten solubilization. Total soluble tungsten is significantly higher in cultures containing M. sedula grown on scheelite than the abiotic control, indicating active bioleaching. Advanced analytical electron microscopy was used in order to achieve nanoscale resolution ultrastructural studies of M. sedula grown on tungsten bearing scheelite. In particular, we describe that M. sedula mediated the biotransformation of scheelite, which was accompanied by the release of tungsten into solution and tungsten biomineralization of the cell surface. Furthermore, we observed intracellular incorporation of redox heterogenous Mn- and Fe-containing nano-clusters. Our results highlight unique metallophilic life in hostile environments extending the knowledge of tungsten biogeochemistry. Based on these findings biohydrometallurgical processing of tungsten ores can be further explored. Importantly, biogenic tungsten carbide-like nanolayers described herein are potential targets for developing nanomaterial biotechnology.
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Affiliation(s)
- Amir Blazevic
- Extremophiles/Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Mihaela Albu
- Graz Centre for Electron Microscopy, Graz, Austria
| | | | - Simon K-M R Rittmann
- Archaea Physiology and Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Gerlinde Habler
- Department of Lithospheric Research, University of Vienna, Vienna, Austria
| | - Tetyana Milojevic
- Extremophiles/Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
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Milojevic T, Albu M, Blazevic A, Gumerova N, Konrad L, Cyran N. Nanoscale Tungsten-Microbial Interface of the Metal Immobilizing Thermoacidophilic Archaeon Metallosphaera sedula Cultivated With Tungsten Polyoxometalate. Front Microbiol 2019; 10:1267. [PMID: 31275255 PMCID: PMC6593293 DOI: 10.3389/fmicb.2019.01267] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 05/22/2019] [Indexed: 12/15/2022] Open
Abstract
Inorganic systems based upon polyoxometalate (POM) clusters provide an experimental approach to develop artificial life. These artificial symmetric anionic macromolecules with oxidometalate polyhedra as building blocks were shown to be well suited as inorganic frameworks for complex self-assembling and organizing systems with emergent properties. Analogously to mineral cells based on iron sulfides, POMs are considered as inorganic cells in facilitating prelife chemical processes and displaying “life-like” characteristics. However, the relevance of POMs to life-sustaining processes (e.g., microbial respiration) has not yet been addressed, while iron sulfides are very well known as ubiquitous mineral precursors and energy sources for chemolithotrophic metabolism. Metallosphaera sedula is an extreme metallophilic and thermoacidophilic archaeon, which flourishes in hot acid and respires by metal oxidation. In the present study we provide our observations on M. sedula cultivated on tungsten polyoxometalate (W-POM). The decomposition of W-POM macromolecular clusters and the appearance of low molecular weight W species (e.g., WO) in the presence of M. sedula have been detected by electrospray ionization mass spectrometry (ESI-MS) analysis. Here, we document the presence of metalloorganic assemblages at the interface between M. sedula and W-POM resolved down to the nanometer scale using scanning and transmission electron microscopy (SEM and TEM) coupled to electron energy loss spectroscopy (EELS). High-resolution TEM (HR-TEM) and selected-area electron diffraction (SAED) patterns indicated the deposition of redox heterogeneous tungsten species on the S-layer of M. sedula along with the accumulation of intracellular tungsten-bearing nanoparticles, i.e., clusters of tungsten atoms. These results reveal the effectiveness of the analytical spectroscopy coupled to the wet chemistry approach as a tool in the analysis of metal–microbial interactions and microbial cultivation on supramolecular self-assemblages based on inorganic metal clusters. We discuss the possible mechanism of W-POM decomposition by M. sedula in light of unique electrochemical properties of POMs. The findings presented herein highlight unique metallophilicity in hostile environments, extending our knowledge of the relevance of POMs to life-sustaining processes, understanding of the transition of POMs as inorganic prebiotic model to life-sustainable material precursors and revealing biogenic signatures obtained after the decomposition of an artificial inorganic compound, which previously was not associated with any living matter.
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Affiliation(s)
- Tetyana Milojevic
- Extremophiles/Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Mihaela Albu
- Graz Centre for Electron Microscopy, Graz, Austria
| | - Amir Blazevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Nadiia Gumerova
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Lukas Konrad
- Graz Centre for Electron Microscopy, Graz, Austria
| | - Norbert Cyran
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
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Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments. mSphere 2019; 4:4/3/e00631-18. [PMID: 31167950 PMCID: PMC6553558 DOI: 10.1128/msphere.00631-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions. Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named “Methylotetracoccus oryzae” C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems. IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.
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Scott IM, Rubinstein GM, Poole FL, Lipscomb GL, Schut GJ, Williams-Rhaesa AM, Stevenson DM, Amador-Noguez D, Kelly RM, Adams MWW. The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde 3-phosphate during glycolysis. J Biol Chem 2019; 294:9995-10005. [PMID: 31097544 DOI: 10.1074/jbc.ra118.007120] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/13/2019] [Indexed: 01/22/2023] Open
Abstract
Caldicellulosiruptor bescii is an extremely thermophilic, cellulolytic bacterium with a growth optimum at 78 °C and is the most thermophilic cellulose degrader known. It is an attractive target for biotechnological applications, but metabolic engineering will require an in-depth understanding of its primary pathways. A previous analysis of its genome uncovered evidence that C. bescii may have a completely uncharacterized aspect to its redox metabolism, involving a tungsten-containing oxidoreductase of unknown function. Herein, we purified and characterized this new member of the aldehyde ferredoxin oxidoreductase family of tungstoenzymes. We show that it is a heterodimeric glyceraldehyde-3-phosphate (GAP) ferredoxin oxidoreductase (GOR) present not only in all known Caldicellulosiruptor species, but also in 44 mostly anaerobic bacterial genera. GOR is phylogenetically distinct from the monomeric GAP-oxidizing enzyme found previously in several Archaea. We found that its large subunit (GOR-L) contains a single tungstopterin site and one iron-sulfur [4Fe-4S] cluster, that the small subunit (GOR-S) contains four [4Fe-4S] clusters, and that GOR uses ferredoxin as an electron acceptor. Deletion of either subunit resulted in a distinct growth phenotype on both C5 and C6 sugars, with an increased lag phase, but higher cell densities. Using metabolomics and kinetic analyses, we show that GOR functions in parallel with the conventional GAP dehydrogenase, providing an alternative ferredoxin-dependent glycolytic pathway. These two pathways likely facilitate the recycling of reduced redox carriers (NADH and ferredoxin) in response to environmental H2 concentrations. This metabolic flexibility has important implications for the future engineering of this and related species.
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Affiliation(s)
- Israel M Scott
- From the Department of Biochemistry and Molecular Biology and
| | | | - Farris L Poole
- From the Department of Biochemistry and Molecular Biology and
| | - Gina L Lipscomb
- From the Department of Biochemistry and Molecular Biology and
| | - Gerrit J Schut
- From the Department of Biochemistry and Molecular Biology and
| | | | - David M Stevenson
- the Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Daniel Amador-Noguez
- the Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Robert M Kelly
- the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
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Arndt F, Schmitt G, Winiarska A, Saft M, Seubert A, Kahnt J, Heider J. Characterization of an Aldehyde Oxidoreductase From the Mesophilic Bacterium Aromatoleum aromaticum EbN1, a Member of a New Subfamily of Tungsten-Containing Enzymes. Front Microbiol 2019; 10:71. [PMID: 30766522 PMCID: PMC6365974 DOI: 10.3389/fmicb.2019.00071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
The biochemical properties of a new tungsten-containing aldehyde oxidoreductase from the mesophilic betaproteobacterium Aromatoleum aromaticum EbN1 (AORAa) are presented in this study. The enzyme was purified from phenylalanine-grown cells of an overexpressing mutant lacking the gene for an aldehyde dehydrogenase normally involved in anaerobic phenylalanine degradation. AORAa catalyzes the oxidation of a broad variety of aldehydes to the respective acids with either viologen dyes or NAD+ as electron acceptors. In contrast to previously known AORs, AORAa is a heterohexameric protein consisting of three different subunits, a large subunit containing the W-cofactor and an Fe-S cluster, a small subunit containing four Fe-S clusters, and a medium subunit containing an FAD cofactor. The presence of the expected cofactors have been confirmed by elemental analysis and spectrophotometric methods. AORAa has a pH optimum of 8.0, a temperature optimum of 40°C and is completely inactive at 50°C. Compared to archaeal AORs, AORAa is remarkably resistant against exposure to air, exhibiting a half-life time of 1 h as purified enzyme and being completely unaffected in cell extracts. Kinetic parameters of AORAa have been obtained for the oxidation of one aliphatic and two aromatic aldehydes, resulting in about twofold higher kcat values with benzyl viologen than with NAD+ as electron acceptor. Finally, we obtained evidence that AORAa is also catalyzing the reverse reaction, reduction of benzoate to benzaldehyde, albeit at very low rates and under conditions strongly favoring acid reduction, e.g., low pH and using Ti(III) citrate as electron donor of very low redox potential. AORAa appears to be a prototype of a new subfamily of bacterial AOR-like tungsten-enzymes, which differ from the previously known archaeal AORs mostly by their multi-subunit composition, their low sensitivity against oxygen, and the ability to use NAD+ as electron acceptor.
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Affiliation(s)
- Fabian Arndt
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Georg Schmitt
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland
| | - Martin Saft
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Andreas Seubert
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Jörg Kahnt
- Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Germany
| | - Johann Heider
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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17
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Schmitt G, Arndt F, Kahnt J, Heider J. Adaptations to a Loss-of-Function Mutation in the Betaproteobacterium Aromatoleum aromaticum: Recruitment of Alternative Enzymes for Anaerobic Phenylalanine Degradation. J Bacteriol 2017; 199:e00383-17. [PMID: 28784814 PMCID: PMC5637171 DOI: 10.1128/jb.00383-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/30/2017] [Indexed: 12/22/2022] Open
Abstract
Anaerobic phenylalanine (Phe) degradation in the betaproteobacterium Aromatoleum aromaticum involves transamination and decarboxylation to phenylacetaldehyde, followed by oxidation to phenylacetate. The latter reaction is catalyzed simultaneously by two enzymes, a highly specific phenylacetaldehyde dehydrogenase (PDH) and a rather unspecific tungsten-dependent aldehyde oxidoreductase (AOR). Attempting to establish increased synthesis of AOR, we constructed a mutant lacking the gene for PDH. This mutant still grew on phenylalanine, exhibiting increased AOR activities on medium containing tungstate. In the absence of tungstate, the mutant showed initially severe growth deficiency, but it resumed growth on Phe after longer incubation times. Moreover, the growth rates of the mutant increased during several reinoculation cycles on either tungstate-proficient or -deficient media, reaching the same values as recorded in wild-type strains. We confirmed AOR as the major alternative enzyme serving Phe degradation under tungstate-supplied conditions and identified and characterized the alternative NAD-dependent aldehyde dehydrogenase AldB taking over the function under tungstate-deficient conditions. Sequence analysis of the respective genes from adapted cultures under either growth condition revealed a mutation in the upstream region of the aor operon and a mutation within the coding region of aldB, which are likely involved in the observed adaptation of the deletion mutant to regain fast growth on Phe.IMPORTANCE The betaproteobacterium Aromatoleum aromaticum degrades many aromatic compounds under denitrifying conditions. One of the steps of phenylalanine degradation is catalyzed by two simultaneously induced enzymes, a NAD(P)-dependent phenylacetaldehyde dehydrogenase and a W-containing aldehyde oxidoreductase. We report here that the latter fully complements a constructed deletion mutant lacking the gene for phenylacetaldehyde dehydrogenase and is overproduced after several reinoculations. Moreover, an alternative NAD-dependent dehydrogenase is recruited to resume growth in tungstate-free medium, which does not allow the production of aldehyde oxidoreductase. This alternative enzyme is overproduced and seems to have acquired a point mutation in the active center. Our research illustrates the flexibility of environmentally important bacteria in adapting their metabolic pathways to new challenges within only a few generations.
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Affiliation(s)
- G Schmitt
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, Marburg, Germany
| | - F Arndt
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, Marburg, Germany
| | - J Kahnt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - J Heider
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
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18
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Habib U, Hoffman M. Effect of molybdenum and tungsten on the reduction of nitrate in nitrate reductase, a DFT study. Chem Cent J 2017; 11:35. [PMID: 29086812 PMCID: PMC5405038 DOI: 10.1186/s13065-017-0263-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 04/11/2017] [Indexed: 12/03/2022] Open
Abstract
The molybdenum and tungsten active site model complexes, derived from the protein X-ray crystal structure of the first W-containing nitrate reductase isolated from Pyrobaculum aerophilum, were computed for nitrate reduction at the COSMO-B3LYP/SDDp//B3LYP/Lanl2DZ(p) energy level of density functional theory. The molybdenum containing active site model complex (Mo–Nar) has the largest activation energy (34.4 kcal/mol) for the oxygen atom transfer from the nitrate to the metal center as compared to the tungsten containing active site model complex (W–Nar) (12.0 kcal/mol). Oxidation of the educt complex is close to thermoneutral (−1.9 kcal/mol) for the Mo active site model complex but strongly exothermic (−34.7 kcal/mol) for the W containing active site model complex, however, the MVI to MIV reduction requires equal amount of reductive power for both metal complexes, Mo–Nar or W–Nar.
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Affiliation(s)
- Uzma Habib
- Research Center for Modeling and Simulation (RCMS), National University of Science and Technology (NUST), H-12, Islamabad, Pakistan.
| | - Matthias Hoffman
- Institute of Inorganic Chemistry, Heidelberg University, Heidelberg, Germany
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19
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Beam JP, Bernstein HC, Jay ZJ, Kozubal MA, Jennings RD, Tringe SG, Inskeep WP. Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs. Front Microbiol 2016; 7:25. [PMID: 26913020 PMCID: PMC4753309 DOI: 10.3389/fmicb.2016.00025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/11/2016] [Indexed: 11/25/2022] Open
Abstract
Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3–3.5; temperature = 68–75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4–40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14–30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1–2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day−1, and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems.
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Affiliation(s)
- Jacob P Beam
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Hans C Bernstein
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State UniversityBozeman, MT, USA; Biodetection Science and Biological Science Division, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Zackary J Jay
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State UniversityBozeman, MT, USA; Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State UniversityBozeman, MT, USA
| | - Mark A Kozubal
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Ryan deM Jennings
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
| | - Susannah G Tringe
- United States Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Thermal Biology Institute, Montana State University Bozeman, MT, USA
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20
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Acetylene hydratase: a non-redox enzyme with tungsten and iron-sulfur centers at the active site. J Biol Inorg Chem 2016; 21:29-38. [PMID: 26790879 DOI: 10.1007/s00775-015-1330-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/30/2015] [Indexed: 01/05/2023]
Abstract
In living systems, tungsten is exclusively found in microbial enzymes coordinated by the pyranopterin cofactor, with additional metal coordination provided by oxygen and/or sulfur, and/or selenium atoms in diverse arrangements. Prominent examples are formate dehydrogenase, formylmethanofuran dehydrogenase, and aldehyde oxidoreductase all of which catalyze redox reactions. The bacterial enzyme acetylene hydratase (AH) stands out of its class as it catalyzes the conversion of acetylene to acetaldehyde, clearly a non-redox reaction and a reaction distinct from the reduction of acetylene to ethylene by nitrogenase. AH harbors two pyranopterins bound to W, and a [4Fe-4S] cluster. W is coordinated by four dithiolene sulfur atoms, one cysteine sulfur, and one oxygen ligand. AH activity requires a strong reductant suggesting W(IV) as the active oxidation state. Two different types of reaction pathways have been proposed. The 1.26 Å structure reveals a water molecule coordinated to W which could gain a partially positive net charge by the adjacent protonated Asp-13, enabling a direct attack of C2H2. To access the W-Asp site, a substrate channel was evolved distant from where it is found in other members of the DMSOR family. Computational studies of this second shell mechanism led to unrealistically high energy barriers, and alternative pathways were proposed where C2H2 binds directly to W. The architecture of the catalytic cavity, the specificity for C2H2 and the results from site-directed mutagenesis do not support this first shell mechanism. More investigations including structural information on the binding of C2H2 are needed to present a conclusive answer.
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21
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Hagedoorn PL. Microbial Metalloproteomics. Proteomes 2015; 3:424-439. [PMID: 28248278 PMCID: PMC5217388 DOI: 10.3390/proteomes3040424] [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: 09/01/2015] [Revised: 11/04/2015] [Accepted: 11/23/2015] [Indexed: 12/12/2022] Open
Abstract
Metalloproteomics is a rapidly developing field of science that involves the comprehensive analysis of all metal-containing or metal-binding proteins in a biological sample. The purpose of this review is to offer a comprehensive overview of the research involving approaches that can be categorized as inductively coupled plasma (ICP)-MS based methods, X-ray absorption/fluorescence, radionuclide based methods and bioinformatics. Important discoveries in microbial proteomics will be reviewed, as well as the outlook to new emerging approaches and research areas.
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Affiliation(s)
- Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands.
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22
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A New Class of Tungsten-Containing Oxidoreductase in Caldicellulosiruptor, a Genus of Plant Biomass-Degrading Thermophilic Bacteria. Appl Environ Microbiol 2015; 81:7339-47. [PMID: 26276113 DOI: 10.1128/aem.01634-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/30/2015] [Indexed: 12/18/2022] Open
Abstract
Caldicellulosiruptor bescii grows optimally at 78°C and is able to decompose high concentrations of lignocellulosic plant biomass without the need for thermochemical pretreatment. C. bescii ferments both C5 and C6 sugars primarily to hydrogen gas, lactate, acetate, and CO2 and is of particular interest for metabolic engineering applications given the recent availability of a genetic system. Developing optimal strains for technological use requires a detailed understanding of primary metabolism, particularly when the goal is to divert all available reductant (electrons) toward highly reduced products such as biofuels. During an analysis of the C. bescii genome sequence for oxidoreductase-type enzymes, evidence was uncovered to suggest that the primary redox metabolism of C. bescii has a completely uncharacterized aspect involving tungsten, a rarely used element in biology. An active tungsten utilization pathway in C. bescii was demonstrated by the heterologous production of a tungsten-requiring, aldehyde-oxidizing enzyme (AOR) from the hyperthermophilic archaeon Pyrococcus furiosus. Furthermore, C. bescii also contains a tungsten-based AOR-type enzyme, here termed XOR, which is phylogenetically unique, representing a completely new member of the AOR tungstoenzyme family. Moreover, in C. bescii, XOR represents ca. 2% of the cytoplasmic protein. XOR is proposed to play a key, but as yet undetermined, role in the primary redox metabolism of this cellulolytic microorganism.
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Abstract
In microaerophilic or anaerobic environments, Pseudomonas aeruginosa utilizes nitrate reduction for energy production, a process dependent on the availability of the oxyanionic form of molybdenum, molybdate (MoO4 (2-)). Here, we show that molybdate acquisition in P. aeruginosa occurs via a high-affinity ATP-binding cassette permease (ModABC). ModA is a cluster D-III solute binding protein capable of interacting with molybdate or tungstate oxyanions. Deletion of the modA gene reduces cellular molybdate concentrations and results in inhibition of anaerobic growth and nitrate reduction. Further, we show that conditions that permit nitrate reduction also cause inhibition of biofilm formation and an alteration in fatty acid composition of P. aeruginosa. Collectively, these data highlight the importance of molybdate for anaerobic growth of P. aeruginosa and reveal novel consequences of nitrate reduction on biofilm formation and cell membrane composition.
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Sparacino-Watkins C, Stolz JF, Basu P. Nitrate and periplasmic nitrate reductases. Chem Soc Rev 2014; 43:676-706. [PMID: 24141308 DOI: 10.1039/c3cs60249d] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types--periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed.
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New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. J Bacteriol 2013; 195:4466-75. [PMID: 23913324 DOI: 10.1128/jb.00679-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The trace elements molybdenum and tungsten are essential components of cofactors of many metalloenzymes. However, in sulfate-reducing bacteria, high concentrations of molybdate and tungstate oxyanions inhibit growth, thus requiring the tight regulation of their homeostasis. By a combination of bioinformatic and experimental techniques, we identified a novel regulator family, tungstate-responsive regulator (TunR), controlling the homeostasis of tungstate and molybdate in sulfate-reducing deltaproteobacteria. The effector-sensing domains of these regulators are similar to those of the known molybdate-responsive regulator ModE, while their DNA-binding domains are homologous to XerC/XerD site-specific recombinases. Using a comparative genomics approach, we identified DNA motifs and reconstructed regulons for 40 TunR family members. Positional analysis of TunR sites and putative promoters allowed us to classify most TunR proteins into two groups: (i) activators of modABC genes encoding a high-affinity molybdenum and tungsten transporting system and (ii) repressors of genes for toluene sulfonate uptake (TSUP) family transporters. The activation of modA and modBC genes by TunR in Desulfovibrio vulgaris Hildenborough was confirmed in vivo, and we discovered that the activation was diminished in the presence of tungstate. A predicted 30-bp TunR-binding motif was confirmed by in vitro binding assays. A novel TunR family of bacterial transcriptional factors controls tungstate and molybdate homeostasis in sulfate-reducing deltaproteobacteria. We proposed that TunR proteins participate in protection of the cells from the inhibition by these oxyanions. To our knowledge, this is a unique case of a family of bacterial transcriptional factors evolved from site-specific recombinases.
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Sousa FL, Thiergart T, Landan G, Nelson-Sathi S, Pereira IAC, Allen JF, Lane N, Martin WF. Early bioenergetic evolution. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130088. [PMID: 23754820 PMCID: PMC3685469 DOI: 10.1098/rstb.2013.0088] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood-Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent-ocean interface via the ATP synthase, (iii) harnessing of Na(+) gradients generated by H(+)/Na(+) antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type 'reduced iron → reduced carbon' at the beginning of bioenergetic evolution.
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Affiliation(s)
- Filipa L. Sousa
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Thorsten Thiergart
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Giddy Landan
- Institute of Genomic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - John F. Allen
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, UK
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - Nick Lane
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
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Patterson-Fortin LM, Vakulskas CA, Yakhnin H, Babitzke P, Romeo T. Dual posttranscriptional regulation via a cofactor-responsive mRNA leader. J Mol Biol 2012; 425:3662-77. [PMID: 23274138 DOI: 10.1016/j.jmb.2012.12.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 01/08/2023]
Abstract
Riboswitches are cis-acting mRNA elements that regulate gene expression in response to ligand binding. Recently, a class of riboswitches was proposed to respond to the molybdenum cofactor (Moco), which serves as a redox center for metabolic enzymes. The 5' leader of the Escherichia coli moaABCDE transcript exemplifies this candidate riboswitch class. This mRNA encodes enzymes for Moco biosynthesis, and moaA expression is feedback inhibited by Moco. Previous RNA-seq analyses showed that moaA mRNA copurified with the RNA binding protein CsrA (carbon storage regulator), suggesting that CsrA binds to this RNA in vivo. Among its global regulatory roles, CsrA represses stationary phase metabolism and activates central carbon metabolism. Here, we used gel mobility shift analysis to determine that CsrA binds specifically and with high affinity to the moaA 5' mRNA leader. Northern blotting and studies with a series of chromosomal lacZ reporter fusions showed that CsrA posttranscriptionally activates moaA expression without altering moaA mRNA levels, indicative of translation control. Deletion analyses, nucleotide replacement studies and footprinting with CsrA-FeBABE identified two sites for CsrA binding. Toeprinting assays suggested that CsrA binding causes changes in moaA RNA structure. We propose that the moaA mRNA leader forms an aptamer, which serves as a target of posttranscriptional regulation by at least two different factors, Moco and the protein CsrA. While we are not aware of similar dual posttranscriptional regulatory mechanisms, additional examples are likely to emerge.
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Affiliation(s)
- Laura M Patterson-Fortin
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA
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Chellapandi P. In silico description of cobalt and nickel assimilation systems in the genomes of methanogens. SYSTEMS AND SYNTHETIC BIOLOGY 2012. [PMID: 23205154 DOI: 10.1007/s11693-011-9087-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Methanogens are a diverse group of organisms that can live in a wide range of environments. Herein, cobalt and tungsten assimilation pathways have proposed to be established in the genomes of Methanococcus maripaludies C5 and Methanosarcina mazei Go1, respectively. All of the proteins involved in the proposed pathways were identified from public domain databases and then complied manually to reconstruct the pathways. The function of proteins with unknown function was assigned by a combined prediction approach. Totally, 17 proteins were identified to cobalt transport and assimilation processes whereas 7 proteins reported to tungsten assimilation system. Phylogenetic analysis of this study revealed that heavy metal transporter of methanogens could be evolved from closely related members in the different genera of methanogens. Nevertheless, genes encoding for metal resistance proteins could be originated from thermophilic and sulfur reducing bacteria. Many metalloenzymes in methanogens were very unique to the species of methanogens. It implied that these metal ions were utilized to produce the precursors for energy driven processes of methanogens. This study suggested that in combination of systems models and evolutionary inference can only correlate metabolic fluxes and physiological changes in methanogens. In silico models of this study will provide insights to design experiments for heavy metal assimilation processes of methanogens growing under heavy metal-rich environments and or in a laboratory condition.
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Affiliation(s)
- P Chellapandi
- Department of Bioinformatics, Centre for Excellence in Life Sciences, Bharathidasan University, Tiruchirappalli, 620024 Tamil Nadu India
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A first analysis of metallome biosignatures of hyperthermophilic Archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:789278. [PMID: 23243390 PMCID: PMC3518089 DOI: 10.1155/2012/789278] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/27/2012] [Accepted: 09/29/2012] [Indexed: 11/18/2022]
Abstract
To date, no experimental data has been reported for the metallome of hyperthermophilic microorganisms although their metal requirements for growth are known to be unique. Here, experiments were conducted to determine (i) cellular trace metal concentrations of the hyperthermophilic Archaea Methanococcus jannaschii and Pyrococcus furiosus, and (ii) a first estimate of the metallome for these hyperthermophilic species via ICP-MS. The metal contents of these cells were compared to parallel experiments using the mesophilic bacterium Escherichia coli grown under aerobic and anaerobic conditions. Fe and Zn were typically the most abundant metals in cells. Metal concentrations for E. coli grown aerobically decreased in the order Fe > Zn > Cu > Mo > Ni > W > Co. In contrast, M. jannaschii and P. furiosus show almost the reverse pattern with elevated Ni, Co, and W concentrations. Of the three organisms, a biosignature is potentially demonstrated for the methanogen M. jannaschii that may, in part, be related to the metallome requirements of methanogenesis. The bioavailability of trace metals more than likely has varied through time. If hyperthermophiles are very ancient, then the trace metal patterns observed here may begin to provide some insights regarding Earth's earliest cells and in turn, early Earth chemistry.
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Adamakis IDS, Panteris E, Eleftheriou EP. Tungsten Toxicity in Plants. PLANTS (BASEL, SWITZERLAND) 2012; 1:82-99. [PMID: 27137642 PMCID: PMC4844263 DOI: 10.3390/plants1020082] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/09/2012] [Accepted: 11/13/2012] [Indexed: 11/17/2022]
Abstract
Tungsten (W) is a rare heavy metal, widely used in a range of industrial, military and household applications due to its unique physical properties. These activities inevitably have accounted for local W accumulation at high concentrations, raising concerns about its effects for living organisms. In plants, W has primarily been used as an inhibitor of the molybdoenzymes, since it antagonizes molybdenum (Mo) for the Mo-cofactor (MoCo) of these enzymes. However, recent advances indicate that, beyond Mo-enzyme inhibition, W has toxic attributes similar with those of other heavy metals. These include hindering of seedling growth, reduction of root and shoot biomass, ultrastructural malformations of cell components, aberration of cell cycle, disruption of the cytoskeleton and deregulation of gene expression related with programmed cell death (PCD). In this article, the recent available information on W toxicity in plants and plant cells is reviewed, and the knowledge gaps and the most pertinent research directions are outlined.
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Affiliation(s)
| | - Emmanuel Panteris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece.
| | - Eleftherios P Eleftheriou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece.
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Amigó-Correig M, Barceló-Batllori S, Soria G, Krezymon A, Benani A, Pénicaud L, Tudela R, Planas AM, Fernández E, Carmona MDC, Gomis R. Anti-obesity sodium tungstate treatment triggers axonal and glial plasticity in hypothalamic feeding centers. PLoS One 2012; 7:e39087. [PMID: 22802935 PMCID: PMC3389016 DOI: 10.1371/journal.pone.0039087] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/18/2012] [Indexed: 12/24/2022] Open
Abstract
Objective This study aims at exploring the effects of sodium tungstate treatment on hypothalamic plasticity, which is known to have an important role in the control of energy metabolism. Methods Adult lean and high-fat diet-induced obese mice were orally treated with sodium tungstate. Arcuate and paraventricular nuclei and lateral hypothalamus were separated and subjected to proteomic analysis by DIGE and mass spectrometry. Immunohistochemistry and in vivo magnetic resonance imaging were also performed. Results Sodium tungstate treatment reduced body weight gain, food intake, and blood glucose and triglyceride levels. These effects were associated with transcriptional and functional changes in the hypothalamus. Proteomic analysis revealed that sodium tungstate modified the expression levels of proteins involved in cell morphology, axonal growth, and tissue remodeling, such as actin, CRMP2 and neurofilaments, and of proteins related to energy metabolism. Moreover, immunohistochemistry studies confirmed results for some targets and further revealed tungstate-dependent regulation of SNAP25 and HPC-1 proteins, suggesting an effect on synaptogenesis as well. Functional test for cell activity based on c-fos-positive cell counting also suggested that sodium tungstate modified hypothalamic basal activity. Finally, in vivo magnetic resonance imaging showed that tungstate treatment can affect neuronal organization in the hypothalamus. Conclusions Altogether, these results suggest that sodium tungstate regulates proteins involved in axonal and glial plasticity. The fact that sodium tungstate could modulate hypothalamic plasticity and networks in adulthood makes it a possible and interesting therapeutic strategy not only for obesity management, but also for other neurodegenerative illnesses like Alzheimer’s disease.
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Affiliation(s)
- Marta Amigó-Correig
- Diabetes and Obesity Laboratory, Institut d’investigacions Biomèdiques August Pi i Sunyer, Endocrinology and Nutrition Unit-Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Sílvia Barceló-Batllori
- Diabetes and Obesity Laboratory, Institut d’investigacions Biomèdiques August Pi i Sunyer, Endocrinology and Nutrition Unit-Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain
| | - Guadalupe Soria
- Department of Brain Ischemia and Neurodegeneration, Institut d’Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas, Institut d’investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Experimental 7T MRI Unit, Institut d’investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Alice Krezymon
- Taste and Food Science Center, UMR 6265-CNRS, 1324-INRA, University of Bourgogne, Dijon, France
| | - Alexandre Benani
- Taste and Food Science Center, UMR 6265-CNRS, 1324-INRA, University of Bourgogne, Dijon, France
| | - Luc Pénicaud
- Taste and Food Science Center, UMR 6265-CNRS, 1324-INRA, University of Bourgogne, Dijon, France
| | - Raúl Tudela
- Experimental 7T MRI Unit, Institut d’investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Group of Biomedical Imaging of the University of Barcelona, Barcelona, Spain
| | - Anna Maria Planas
- Department of Brain Ischemia and Neurodegeneration, Institut d’Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas, Institut d’investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Experimental 7T MRI Unit, Institut d’investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Eduardo Fernández
- Bioengineering Institute and Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Miguel Hernández University, Elche, Spain
| | - Maria del Carmen Carmona
- Diabetes and Obesity Laboratory, Institut d’investigacions Biomèdiques August Pi i Sunyer, Endocrinology and Nutrition Unit-Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain
- * E-mail: (MCC); (RG)
| | - Ramon Gomis
- Diabetes and Obesity Laboratory, Institut d’investigacions Biomèdiques August Pi i Sunyer, Endocrinology and Nutrition Unit-Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- * E-mail: (MCC); (RG)
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Stahl M, Butcher J, Stintzi A. Nutrient acquisition and metabolism by Campylobacter jejuni. Front Cell Infect Microbiol 2012; 2:5. [PMID: 22919597 PMCID: PMC3417520 DOI: 10.3389/fcimb.2012.00005] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 01/21/2012] [Indexed: 12/03/2022] Open
Abstract
The gastrointestinal pathogen Campylobacter jejuni is able to colonize numerous different hosts and compete against the gut microbiota. To do this, it must be able to efficiently acquire sufficient nutrients from its environment to support its survival and rapid growth in the intestine. However, despite almost 50 years of research, many aspects as to how C. jejuni accomplishes this feat remain poorly understood. C. jejuni lacks many of the common metabolic pathways necessary for the use of glucose, galactose, or other carbohydrates upon which most other microbes thrive. It does however make efficient use of citric acid cycle intermediates and various amino acids. C. jejuni readily uses the amino acids aspartate, glutamate, serine, and proline, with certain strains also possessing additional pathways allowing for the use of glutamine and asparagine. More recent work has revealed that some C. jejuni strains can metabolize the sugar l-fucose. This finding has upset years of dogma that C. jejuni is an asaccharolytic organism. C. jejuni also possesses diverse mechanisms for the acquisition of various transition metals that are required for metabolic activities. In particular, iron acquisition is critical for the formation of iron–sulfur complexes. C. jejuni is also unique in possessing both molybdate and tungsten cofactored proteins and thus has an unusual regulatory scheme for these metals. Together these various metabolic and acquisition pathways help C. jejuni to compete and thrive in wide variety of hosts and environments.
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Affiliation(s)
- Martin Stahl
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa Ottawa, ON, Canada
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Academic aspects of lunar water resources and their relevance to lunar protolife. Int J Mol Sci 2011; 12:6051-76. [PMID: 22016644 PMCID: PMC3189768 DOI: 10.3390/ijms12096051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 08/31/2011] [Indexed: 11/16/2022] Open
Abstract
Water ice has been discovered on the moon by radar backscatter at the North Pole and by spectrometry at the South Pole in the Cabeus crater with an extrapolated volume for both poles of conservatively 10(9) metric tons. Various exogenic and endogenic sources of this water have been proposed. This paper focuses on endogenic water sources by fumaroles and hot springs in shadowed polar craters. A survey of theoretical and morphological details supports a volcanic model. Release of water and other constituents by defluidization over geological time was intensified in the Hadean Eon (c.a. 4600 to 4000 My). Intensification factors include higher heat flow by now-extinct radionuclides, tidal flexing and higher core temperatures. Lesser gravity would promote deeper bubble nucleation in lunar magmas, slower rise rates of gases and enhanced subsidence of lunar caldera floors. Hadean volcanism would likely have been more intense and regional in nature as opposed to suture-controlled location of calderas in Phanerozoic Benioff-style subduction environments. Seventy-seven morphological, remote sensing and return sample features were categorized into five categories ranging from a volcano-tectonic origin only to impact origin only. Scores for the most logical scenario were 69 to eight in favor of lunar volcanism. Ingredients in the Cabeus plume analysis showed many volcanic fluids and their derivatives plus a large amount of mercury. Mercury-rich fumaroles are well documented on Earth and are virtually absent in cometary gases and solids. There are no mercury anomalies in terrestrial impact craters. Volcanic fluids and their derivatives in lunar shadow can theoretically evolve into protolife. Energy for this evolution can be provided by vent flow charging intensified in the lunar Hadean and by charge separation on freezing fumarolic fluids in shadow. Fischer-Tropsch reactions on hydrothermal clays can yield lipids, polycyclic aromatic hydrocarbons and amino acids. Soluble polyphosphates are available in volcanic fluids as well as vital catalysts such as tungsten. We conclude that the high volume of polar water resources supports the likelihood of lunar volcanism and that lunar volcanism supports the likelihood of protolife.
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Tungsten and molybdenum regulation of formate dehydrogenase expression in Desulfovibrio vulgaris Hildenborough. J Bacteriol 2011; 193:2909-16. [PMID: 21498650 DOI: 10.1128/jb.00042-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Formate is an important energy substrate for sulfate-reducing bacteria in natural environments, and both molybdenum- and tungsten-containing formate dehydrogenases have been reported in these organisms. In this work, we studied the effect of both metals on the levels of the three formate dehydrogenases encoded in the genome of Desulfovibrio vulgaris Hildenborough, with lactate, formate, or hydrogen as electron donors. Using Western blot analysis, quantitative real-time PCR, activity-stained gels, and protein purification, we show that a metal-dependent regulatory mechanism is present, resulting in the dimeric FdhAB protein being the main enzyme present in cells grown in the presence of tungsten and the trimeric FdhABC₃ protein being the main enzyme in cells grown in the presence of molybdenum. The putatively membrane-associated formate dehydrogenase is detected only at low levels after growth with tungsten. Purification of the three enzymes and metal analysis shows that FdhABC₃ specifically incorporates Mo, whereas FdhAB can incorporate both metals. The FdhAB enzyme has a much higher catalytic efficiency than the other two. Since sulfate reducers are likely to experience high sulfide concentrations that may result in low Mo bioavailability, the ability to use W is likely to constitute a selective advantage.
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Wu SY, Lai MC. Methanogenic archaea isolated from Taiwan's Chelungpu fault. Appl Environ Microbiol 2011; 77:830-8. [PMID: 21148697 PMCID: PMC3028716 DOI: 10.1128/aem.01539-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 11/30/2010] [Indexed: 11/20/2022] Open
Abstract
Terrestrial rocks, petroleum reservoirs, faults, coal seams, and subseafloor gas hydrates contain an abundance of diverse methanoarchaea. However, reports on the isolation, purification, and characterization of methanoarchaea in the subsurface environment are rare. Currently, no studies investigating methanoarchaea within fault environments exist. In this report, we succeeded in obtaining two new methanogen isolates, St545Mb(T) of newly proposed species Methanolobus chelungpuianus and Methanobacterium palustre FG694aF, from the Chelungpu fault, which is the fault that caused a devastating earthquake in central Taiwan in 1999. Strain FG694aF was isolated from a fault gouge sample obtained at 694 m below land surface (mbls) and is an autotrophic, mesophilic, nonmotile, thin, filamentous-rod-shaped organism capable of using H(2)-CO(2) and formate as substrates for methanogenesis. The morphological, biochemical, and physiological characteristics and 16S rRNA gene sequence analysis revealed that this isolate belongs to Methanobacterium palustre. The mesophilic strain St545Mb(T), isolated from a sandstone sample at 545 mbls, is a nonmotile, irregular, coccoid organism that uses methanol and trimethylamine as substrates for methanogenesis. The 16S rRNA gene sequence of strain St545Mb(T) was 99.0% similar to that of Methanolobus psychrophilus strain R15 and was 96 to 97.5% similar to the those of other Methanolobus species. However, the optimal growth temperature and total cell protein profile of strain St545Mb(T) were different from those of M. psychrophilus strain R15, and whole-genome DNA-DNA hybridization revealed less than 20% relatedness between these two strains. On the basis of these observations, we propose that strain St545Mb(T) (DSM 19953(T); BCRC AR10030; JCM 15159) be named Methanolobus chelungpuianus sp. nov. Moreover, the environmental DNA database survey indicates that both Methanolobus chelungpuianus and Methanobacterium palustre are widespread in the subsurface environment.
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Affiliation(s)
- Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
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A selenium-dependent xanthine dehydrogenase triggers biofilm proliferation in Enterococcus faecalis through oxidant production. J Bacteriol 2011; 193:1643-52. [PMID: 21257770 DOI: 10.1128/jb.01063-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Selenium has been shown to be present as a labile cofactor in a small class of molybdenum hydroxylase enzymes in several species of clostridia that specialize in the fermentation of purines and pyrimidines. This labile cofactor is poorly understood, yet recent bioinformatic studies have suggested that Enterococcus faecalis could serve as a model system to better understand the way in which this enzyme cofactor is built and the role of these metalloenzymes in the physiology of the organism. An mRNA that encodes a predicted selenium-dependent molybdenum hydroxylase (SDMH) has also been shown to be specifically increased during the transition from planktonic growth to biofilm growth. Based on these studies, we examined whether this organism produces an SDMH and probed whether selenoproteins may play a role in biofilm physiology. We observed a substantial increase in biofilm density upon the addition of uric acid to cells grown in a defined culture medium, but only when molybdate (Mo) and selenite (Se) were also added. We also observed a significant increase in biofilm density in cells cultured in tryptic soy broth with 1% glucose (TSBG) when selenite was added. In-frame deletion of selD, which encodes selenophosphate synthetase, also blocked biofilm formation that occurred upon addition of selenium. Moreover, mutation in the gene encoding the molybdoenzyme (xdh) prevented the induction of biofilm proliferation upon supplementation with selenium. Tungstate or auranofin addition also blocked this enhanced biofilm density, likely through inhibition of molybdenum or selenium cofactor synthesis. A large protein complex labeled with (75)Se is present in higher concentrations in biofilms than in planktonic cells, and the same complex is formed in TSBG. Xanthine dehydrogenase activity correlates with the presence of this labile selenoprotein complex and is absent in a selD or an xdh mutant. Enhanced biofilm density correlates strongly with higher levels of extracellular peroxide, which is produced upon the addition of selenite to TSBG. Peroxide levels are not increased in either the selD or the xdh mutant upon addition of selenite. Extracellular superoxide production, a phenomenon well established to be linked to clinical isolates, is abolished in both mutant strains. Taken together, these data provide evidence that an SDMH is involved in biofilm formation in Enterococcus faecalis, contributing to oxidant production either directly or alternatively through its involvement in redox-dependent processes linked to oxidant production.
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Ma Z, Jacobsen FE, Giedroc DP. Coordination chemistry of bacterial metal transport and sensing. Chem Rev 2009; 109:4644-81. [PMID: 19788177 PMCID: PMC2783614 DOI: 10.1021/cr900077w] [Citation(s) in RCA: 426] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zhen Ma
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128 USA
| | - Faith E. Jacobsen
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47401-7005 USA
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Abstract
The cellular concentrations of certain metabolites are assiduously monitored to achieve appropriate levels of gene expression. Although proteins have long been known to act as sensors in this capacity, metabolite-binding RNAs, or riboswitches, also play an important role. More than 20 distinct classes of riboswitches have been identified to date, and insights to the molecular recognition strategies of a significant subset of these have been provided by detailed structural studies. This diverse set of metabolite-sensing RNAs is found to exploit a variety of distinct mechanisms to regulate genes that are fundamental to metabolism.
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Affiliation(s)
- Adam Roth
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA.
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Zivanovic Y, Armengaud J, Lagorce A, Leplat C, Guérin P, Dutertre M, Anthouard V, Forterre P, Wincker P, Confalonieri F. Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol 2009; 10:R70. [PMID: 19558674 PMCID: PMC2718504 DOI: 10.1186/gb-2009-10-6-r70] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 05/29/2009] [Accepted: 06/26/2009] [Indexed: 11/15/2022] Open
Abstract
The genome sequence of Thermococcus gammatolerans, a radioresistant archaeon, is described; a proteomic analysis reveals that radioresistance may be due to unknown DNA repair enzymes. Background Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. It is one of the most radioresistant organisms known amongst the Archaea. We report the determination and annotation of its complete genome sequence, its comparison with other Thermococcales genomes, and a proteomic analysis. Results T. gammatolerans has a circular chromosome of 2.045 Mbp without any extra-chromosomal elements, coding for 2,157 proteins. A thorough comparative genomics analysis revealed important but unsuspected genome plasticity differences between sequenced Thermococcus and Pyrococcus species that could not be attributed to the presence of specific mobile elements. Two virus-related regions, tgv1 and tgv2, are the only mobile elements identified in this genome. A proteogenome analysis was performed by a shotgun liquid chromatography-tandem mass spectrometry approach, allowing the identification of 10,931 unique peptides corresponding to 951 proteins. This information concurrently validates the accuracy of the genome annotation. Semi-quantification of proteins by spectral count was done on exponential- and stationary-phase cells. Insights into general catabolism, hydrogenase complexes, detoxification systems, and the DNA repair toolbox of this archaeon are revealed through this genome and proteome analysis. Conclusions This work is the first archaeal proteome investigation done at the stage of primary genome annotation. This archaeon is shown to use a large variety of metabolic pathways even under a rich medium growth condition. This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized rather than a larger arsenal of known DNA repair enzymes.
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Affiliation(s)
- Yvan Zivanovic
- Laboratoire de Génomique des Archae, Université Paris-Sud 11, CNRS, UMR8621, Bât400 F-91405 Orsay, France.
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Precambrian lunar volcanic protolife. Int J Mol Sci 2009; 10:2681-2721. [PMID: 19582224 PMCID: PMC2705511 DOI: 10.3390/ijms10062681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 05/28/2009] [Accepted: 06/03/2009] [Indexed: 11/20/2022] Open
Abstract
Five representative terrestrial analogs of lunar craters are detailed relevant to Precambrian fumarolic activity. Fumarolic fluids contain the ingredients for protolife. Energy sources to derive formaldehyde, amino acids and related compounds could be by flow charging, charge separation and volcanic shock. With no photodecomposition in shadow, most fumarolic fluids at 40 K would persist over geologically long time periods. Relatively abundant tungsten would permit creation of critical enzymes, Fischer-Tropsch reactions could form polycyclic aromatic hydrocarbons and soluble volcanic polyphosphates would enable assembly of nucleic acids. Fumarolic stimuli factors are described. Orbital and lander sensors specific to protolife exploration including combined Raman/laser-induced breakdown spectrocsopy are evaluated.
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Ronconi L, Sadler PJ. Applications of heteronuclear NMR spectroscopy in biological and medicinal inorganic chemistry. Coord Chem Rev 2008; 252:2239-2277. [PMID: 32226090 PMCID: PMC7094630 DOI: 10.1016/j.ccr.2008.01.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 01/15/2008] [Indexed: 11/30/2022]
Abstract
There is a wide range of potential applications of inorganic compounds, and metal coordination complexes in particular, in medicine but progress is hampered by a lack of methods to study their speciation. The biological activity of metal complexes is determined by the metal itself, its oxidation state, the types and number of coordinated ligands and their strength of binding, the geometry of the complex, redox potential and ligand exchange rates. For organic drugs a variety of readily observed spin I = 1/2 nuclei can be used (1H, 13C, 15N, 19F, 31P), but only a few metals fall into this category. Most are quadrupolar nuclei giving rise to broad lines with low detection sensitivity (for biological systems). However we show that, in some cases, heteronuclear NMR studies can provide new insights into the biological and medicinal chemistry of a range of elements and these data will stimulate further advances in this area.
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Key Words
- ADP, adenosine diphosphate
- AES, atomic emission spectroscopy
- AMP, adenosine monophosphate
- ATP, adenosine triphosphate
- BNCT, boron neutron capture therapy
- BPG, 2,3-bisphosphoglycerate
- BSA, bovine serum albumin
- BSH, sodium borocaptate
- Bioinorganic chemistry
- Biological systems
- DNA, deoxyribonucleic acid
- EDTA-N4, ethylenediaminetetraacetamide
- EFG, electric field gradient
- GMP, guanosine monophosphate
- HMQC, heteronuclear multiple quantum correlation
- Heteronuclear NMR spectroscopy
- Im, imidazole
- In, indazole
- MQF, multiple quantum filtered
- MRI, magnetic resonance imaging
- Medicinal inorganic chemistry
- Metallopharmaceuticals
- NOE, nuclear Overhauser effect
- PET, positron emission tomography
- Quadrupolar nuclei
- RBC, red blood cell
- RNA, ribonucleic acid
- SDS, sodium dodecyl sulfate
- rRNA, ribosomal ribonucleic acid
- tRNA, transfer ribonucleic acid
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Affiliation(s)
- Luca Ronconi
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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Reversible interconversion of carbon dioxide and formate by an electroactive enzyme. Proc Natl Acad Sci U S A 2008; 105:10654-8. [PMID: 18667702 DOI: 10.1073/pnas.0801290105] [Citation(s) in RCA: 299] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbon dioxide (CO(2)) is a kinetically and thermodynamically stable molecule. It is easily formed by the oxidation of organic molecules, during combustion or respiration, but is difficult to reduce. The production of reduced carbon compounds from CO(2) is an attractive proposition, because carbon-neutral energy sources could be used to generate fuel resources and sequester CO(2) from the atmosphere. However, available methods for the electrochemical reduction of CO(2) require excessive overpotentials (are energetically wasteful) and produce mixtures of products. Here, we show that a tungsten-containing formate dehydrogenase enzyme (FDH1) adsorbed to an electrode surface catalyzes the efficient electrochemical reduction of CO(2) to formate. Electrocatalysis by FDH1 is thermodynamically reversible--only small overpotentials are required, and the point of zero net catalytic current defines the reduction potential. It occurs under thoroughly mild conditions, and formate is the only product. Both as a homogeneous catalyst and on the electrode, FDH1 catalyzes CO(2) reduction with a rate more than two orders of magnitude faster than that of any known catalyst for the same reaction. Formate oxidation is more than five times faster than CO(2) reduction. Thermodynamically, formate and hydrogen are oxidized at similar potentials, so formate is a viable energy source in its own right as well as an industrially important feedstock and a stable intermediate in the conversion of CO(2) to methanol and methane. FDH1 demonstrates the feasibility of interconverting CO(2) and formate electrochemically, and it is a template for the development of robust synthetic catalysts suitable for practical applications.
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Takács M, Tóth A, Bogos B, Varga A, Rákhely G, Kovács KL. Formate hydrogenlyase in the hyperthermophilic archaeon, Thermococcus litoralis. BMC Microbiol 2008; 8:88. [PMID: 18522724 PMCID: PMC2432063 DOI: 10.1186/1471-2180-8-88] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2007] [Accepted: 06/03/2008] [Indexed: 12/02/2022] Open
Abstract
Background Thermococcus litoralis is a heterotrophic facultative sulfur dependent hyperthermophilic Archaeon, which was isolated from a shallow submarine thermal spring. It has been successfully used in a two-stage fermentation system, where various keratinaceous wastes of animal origin were converted to biohydrogen. In this system T. litoralis performed better than its close relative, P. furiosus. Therefore, new alternative enzymes involved in peptide and hydrogen metabolism were assumed in T. litoralis. Results An about 10.5 kb long genomic region was isolated and sequenced from Thermococcus litoralis. In silico analysis revealed that the region contained a putative operon consisting of eight genes: the fdhAB genes coding for a formate dehydrogenase and the mhyCDEFGH genes encoding a [NiFe] hydrogenase belonging to the group of the H2-evolving, energy-conserving, membrane-bound hydrogenases. Reverse transcription linked quantitative Real-Time PCR and Western blotting experiments showed that the expression of the fdh-mhy operon was up-regulated during fermentative growth on peptides and down-regulated in cells cultivated in the presence of sulfur. Immunoblotting and protein separation experiments performed on cell fractions indicated that the formate dehydrogenase part of the complex is associated to the membrane-bound [NiFe] hydrogenase. Conclusion The formate dehydrogenase together with the membrane-bound [NiFe] hydrogenase formed a formate hydrogenlyase (formate dehydrogenase coupled hydrogenase, FDH-MHY) complex. The expression data suggested that its physiological role is linked to the removal of formate likely generated during anaerobic peptide fermentation.
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Affiliation(s)
- Mária Takács
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
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Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol Microbiol 2008; 68:918-32. [PMID: 18363797 PMCID: PMC2408646 DOI: 10.1111/j.1365-2958.2008.06208.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have identified a highly conserved RNA motif located upstream of genes encoding molybdate transporters, molybdenum cofactor (Moco) biosynthesis enzymes, and proteins that utilize Moco as a coenzyme. Bioinformatics searches have identified 176 representatives in γ-Proteobacteria, δ-Proteobacteria, Clostridia, Actinobacteria, Deinococcus-Thermus species and DNAs from environmental samples. Using genetic assays, we demonstrate that a Moco RNA in Escherichia coli associated with the Moco biosynthetic operon controls gene expression in response to Moco production. In addition, we provide evidence indicating that this conserved RNA discriminates against closely related analogues of Moco. These results, together with extensive phylogenetic conservation and typical gene control structures near some examples, indicate that representatives of this structured RNA represent a novel class of riboswitches that sense Moco. Furthermore, we identify variants of this RNA that are likely to be triggered by the related tungsten cofactor (Tuco), which carries tungsten in place of molybdenum as the metal constituent.
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Affiliation(s)
- Elizabeth E Regulski
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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Park MO, Mizutani T, Jones PR. Glyceraldehyde-3-phosphate ferredoxin oxidoreductase from Methanococcus maripaludis. J Bacteriol 2007; 189:7281-9. [PMID: 17704226 PMCID: PMC2168465 DOI: 10.1128/jb.00828-07] [Citation(s) in RCA: 12] [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 genome sequence of the non-sugar-assimilating mesophile Methanococcus maripaludis contains three genes encoding enzymes: a nonphosphorylating NADP(+)-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR); all these enzymes are potentially capable of catalyzing glyceraldehyde-3-phosphate (G3P) metabolism. GAPOR, whose homologs have been found mainly in archaea, catalyzes the reduction of ferredoxin coupled with oxidation of G3P. GAPOR has previously been isolated and characterized only from a sugar-assimilating hyperthermophile, Pyrococcus furiosus (GAPOR(Pf)), and contains the rare metal tungsten as an irreplaceable cofactor. Active recombinant M. maripaludis GAPOR (GAPOR(Mm)) was purified from Escherichia coli grown in minimal medium containing 100 muM sodium molybdate. In contrast, GAPOR(Mm) obtained from cells grown in medium containing tungsten (W) and W and molybdenum (Mo) or in medium without added W and Mo did not display any activity. Activity and transcript analysis of putative G3P-metabolizing enzymes and corresponding genes were performed with M. maripaludis cultured under autotrophic conditions in chemically defined medium. The activity of GAPOR(Mm) was constitutive throughout the culture period and exceeded that of GAPDH at all time points. As GAPDH activity was detected in only the gluconeogenic direction and GAPN activity was completely absent, only GAPOR(Mm) catalyzes oxidation of G3P in M. maripaludis. Recombinant GAPOR(Mm) is posttranscriptionally regulated as it exhibits pronounced and irreversible substrate inhibition and is completely inhibited by 1 muM ATP. With support from flux balance analysis, it is concluded that the major physiological role of GAPOR(Mm) in M. maripaludis most likely involves only nonoptimal growth conditions.
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Affiliation(s)
- Myong-Ok Park
- Research and Development Division, Fujirebio Inc, Hachioji-shi, Tokyo, Japan
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Seiffert GB, Ullmann GM, Messerschmidt A, Schink B, Kroneck PMH, Einsle O. Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase. Proc Natl Acad Sci U S A 2007; 104:3073-7. [PMID: 17360611 PMCID: PMC1805521 DOI: 10.1073/pnas.0610407104] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The tungsten-iron-sulfur enzyme acetylene hydratase stands out from its class because it catalyzes a nonredox reaction, the hydration of acetylene to acetaldehyde. Sequence comparisons group the protein into the dimethyl sulfoxide reductase family, and it contains a bis-molybdopterin guanine dinucleotide-ligated tungsten atom and a cubane-type [4Fe:4S] cluster. The crystal structure of acetylene hydratase at 1.26 A now shows that the tungsten center binds a water molecule that is activated by an adjacent aspartate residue, enabling it to attack acetylene bound in a distinct, hydrophobic pocket. This mechanism requires a strong shift of pK(a) of the aspartate, caused by a nearby low-potential [4Fe:4S] cluster. To access this previously unrecognized W-Asp active site, the protein evolved a new substrate channel distant from where it is found in other molybdenum and tungsten enzymes.
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Affiliation(s)
| | - G. Matthias Ullmann
- Strukturbiologie/Bioinformatik, Universität Bayreuth, 95477 Bayreuth, Germany
| | - Albrecht Messerschmidt
- Abteilung Proteomik und Signaltransduktion, Max-Planck-Institut für Biochemie, 82152 Martinsried, Germany; and
| | - Bernhard Schink
- *Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Peter M. H. Kroneck
- *Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Oliver Einsle
- Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- To whom correspondence may be addressed. E-mail: or
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Bellenger JP, Arnaud-Neu F, Asfari Z, Myneni SCB, Stiefel EI, Kraepiel AML. Complexation of oxoanions and cationic metals by the biscatecholate siderophore azotochelin. J Biol Inorg Chem 2006; 12:367-76. [PMID: 17171370 DOI: 10.1007/s00775-006-0194-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 11/13/2006] [Indexed: 10/23/2022]
Abstract
Azotochelin is a biscatecholate siderophore produced by the nitrogen-fixing soil bacterium Azotobacter vinelandii. The complexation properties of azotochelin with a series of oxoanions [Mo(VI), W(VI) and V(V)] and divalent cations [Cu(II), Zn(II), Co(II) and Mn(II)] were investigated by potentiometry, UV-vis and X-ray spectroscopy. Azotochelin forms a strong 1:1 complex with molybdate (log K=7.6+/-0.4) and with tungstate and vanadate; the stability of the complexes increases in the order Mo<V<W (log KappMo=7.3+/-0.4; log KappV=8.8+/-0.4 and log KappW=9.0+/-0.4 at pH 6.6). The Mo atom in the 1:1 Mo-azotochelin complex is bound to two oxo groups in a cis position and to the two catecholate groups of azotochelin, resulting in a slightly distorted octahedral configuration. Below pH 5, azotochelin appears to form polynuclear complexes with Mo in addition to the 1:1 complex. Azotochelin also forms strong complexes with divalent metals. Of the metals studied, Cu(II) binds most strongly to azotochelin (log betaCuLH2-=-12.9+/-0.1), followed by Zn(II) log betaZnL3-=-24.1+/-0.14, log betaZnLH2-=-17.83+/-0.09), Mn(II) (log betaMnL3-=-29, log betaMnLH2-=-18.6+/-0.8, log betaMnLH2-=-11.5+/-0.7) and Co(II) (log betaCoLH2-=-23.0+/-0.3, log betaCoLH2-=-13.5+/-0.2). Since very few organic ligands are known to bind strongly to oxoanions (and particularly molybdate) at circumneutral pH, the unusual properties of azotochelin may be used for the separation and concentration of oxoanions in the laboratory and in the field. In addition, azotochelin may prove useful for the investigation of the biogeochemistry of Mo, W and V in aquatic and terrestrial systems.
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Bevers LE, Hagedoorn PL, Krijger GC, Hagen WR. Tungsten transport protein A (WtpA) in Pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters. J Bacteriol 2006; 188:6498-505. [PMID: 16952940 PMCID: PMC1595483 DOI: 10.1128/jb.00548-06] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel tungstate and molybdate binding protein has been discovered from the hyperthermophilic archaeon Pyrococcus furiosus. This tungstate transport protein A (WtpA) is part of a new ABC transporter system selective for tungstate and molybdate. WtpA has very low sequence similarity with the earlier-characterized transport proteins ModA for molybdate and TupA for tungstate. Its structural gene is present in the genome of numerous archaea and some bacteria. The identification of this new tungstate and molybdate binding protein clarifies the mechanism of tungstate and molybdate transport in organisms that lack the known uptake systems associated with the ModA and TupA proteins, like many archaea. The periplasmic protein of this ABC transporter, WtpA (PF0080), was cloned and expressed in Escherichia coli. Using isothermal titration calorimetry, WtpA was observed to bind tungstate (dissociation constant [K(D)] of 17 +/- 7 pM) and molybdate (K(D) of 11 +/- 5 nM) with a stoichiometry of 1.0 mol oxoanion per mole of protein. These low K(D) values indicate that WtpA has a higher affinity for tungstate than do ModA and TupA and an affinity for molybdate similar to that of ModA. A displacement titration of molybdate-saturated WtpA with tungstate showed that the tungstate effectively replaced the molybdate in the binding site of the protein.
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Affiliation(s)
- Loes E Bevers
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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Pratte BS, Thiel T. High-affinity vanadate transport system in the cyanobacterium Anabaena variabilis ATCC 29413. J Bacteriol 2006; 188:464-8. [PMID: 16385036 PMCID: PMC1347300 DOI: 10.1128/jb.188.2.464-468.2006] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-affinity vanadate transport systems have not heretofore been identified in any organism. Anabaena variabilis, which can fix nitrogen by using an alternative V-dependent nitrogenase, transported vanadate well. The concentration of vanadate giving half-maximum V-nitrogenase activity when added to V-starved cells was about 3 x 10(-9) M. The genes for an ABC-type vanadate transport system, vupABC, were found in A. variabilis about 5 kb from the major cluster of genes encoding the V-nitrogenase, and like those genes, the vupABC genes were repressed by molybdate; however, unlike the V-nitrogenase genes the vanadate transport genes were expressed in vegetative cells. A vupB mutant failed to grow by using V-nitrogenase unless high levels of vanadate were provided, suggesting that there was also a low-affinity vanadate transport system that functioned in the vupB mutant. The vupABC genes belong to a family of putative metal transport genes that include only one other characterized transport system, the tungstate transport genes of Eubacterium acidaminophilum. Similar genes are not present in the complete genomes of other bacterial strains that have a V-nitrogenase, including Azotobacter vinelandii, Rhodopseudomonas palustris, and Methanosarcina barkeri.
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Affiliation(s)
- Brenda S Pratte
- Department of Biology, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121-4499, USA
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Hagedoorn PL, Chen T, Schröder I, Piersma SR, de Vries S, Hagen WR. Purification and characterization of the tungsten enzyme aldehyde:ferredoxin oxidoreductase from the hyperthermophilic denitrifier Pyrobaculum aerophilum. J Biol Inorg Chem 2005; 10:259-69. [PMID: 15772818 DOI: 10.1007/s00775-005-0637-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Accepted: 02/21/2005] [Indexed: 11/27/2022]
Abstract
A tungsten-containing aldehyde:ferredoxin oxidoreductase (AOR) has been purified to homogeneity from Pyrobaculum aerophilum. The N-terminal sequence of the isolated enzyme matches a single open reading frame in the genome. Metal analysis and electron paramagnetic resonance (EPR) spectroscopy indicate that the P. aerophilum AOR contains one tungsten center and one [4Fe-4S](2+/1+) cluster per 68-kDa monomer. Native AOR is a homodimer. EPR spectroscopy of the purified enzyme that has been reduced with the substrate crotonaldehyde revealed a W(V) species with g(zyx) values of 1.952, 1.918, 1.872. The substrate-reduced AOR also contains a [4Fe-4S](1+) cluster with S=3/2 and zero field splitting parameters D=7.5 cm(-1) and E/D=0.22. Molybdenum was absent from the enzyme preparation. The P. aerophilum AOR lacks the amino acid sequence motif indicative for binding of mononuclear iron that is typically found in other AORs. Furthermore, the P. aerophilum AOR utilizes a 7Fe ferredoxin as the putative physiological redox partner, instead of a 4Fe ferredoxin as in Pyrococcus furiosus. This 7Fe ferredoxin has been purified from P. aerophilum, and the amino acid sequence has been identified using mass spectrometry. Direct electrochemistry of the ferredoxin showed two one-electron transitions, at -306 and -445 mV. In the presence of 55 microM ferredoxin the AOR activity is 17% of the activity obtained with 1 mM benzyl viologen as an electron acceptor.
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Affiliation(s)
- Peter L Hagedoorn
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands.
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