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Wang M, Ryan KS. Reductases Produce Nitric Oxide in an Alternative Pathway to Form the Diazeniumdiolate Group of l-Alanosine. J Am Chem Soc 2023. [PMID: 37478476 DOI: 10.1021/jacs.3c04447] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
l-Alanosine is a diazeniumdiolate (N-nitrosohydroxylamine) antibiotic that inhibits MTAP-deficient tumor cells by blocking de novo adenine biosynthesis. Previous work revealed the early steps in the biosynthesis of l-alanosine. In the present study, we used genome mining to discover two new l-alanosine-producing strains that lack the aspartate-nitrosuccinate pathway genes found in the original l-alanosine producer. Instead, nitrate is reduced with a unique set of nitrate-nitrite reductases. These enzymes are typically used as part of the nitrogen cycle for denitrification or assimilation, and our report here shows how enzymes from the nitrogen cycle can be repurposed for the biosynthesis of specialized metabolites. The widespread distribution of nitric-oxide-producing reductases also indicates a potential for the discovery of new nitric-oxide-derived natural products.
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Affiliation(s)
- Menghua Wang
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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2
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Singh AK, Nakhate SP, Gupta RK, Chavan AR, Poddar BJ, Prakash O, Shouche YS, Purohit HJ, Khardenavis AA. Mining the landfill soil metagenome for denitrifying methanotrophic taxa and validation of methane oxidation in microcosm. ENVIRONMENTAL RESEARCH 2022; 215:114199. [PMID: 36058281 DOI: 10.1016/j.envres.2022.114199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/21/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50-60 cm) and, active process of aerobic denitrification in the top soil (0-10 cm). This was also reflected from the higher abundance of bacterial domain in the top soil metagenome represented by dominant phyla Proteobacteria and Actinobacteria which are prime decomposers of organic matter in landfill soils. The multiple fold higher relative abundances of the two most abundant genera; Streptomyces and Intrasporangium in the top soil depicted greater denitrifying taxa in top soil than the bottom soil. Amongst the aerobic methanotrophs, the genera Methylomonas, Methylococcus, Methylocella, and Methylacidiphilum were abundantly found in the top soil metagenome that were essential for oxidizing methane generated in the landfill. On the other hand, the dominance of archaeal domain represented by Methanosarcina and Methanoculleus in the bottom soil highlighted the complete anaerobic digestion of organic components via acetoclasty, carboxydotrophy, hydrogenotrophy, methylotrophy. Functional characterization revealed a higher abundance of methane monooxygenase gene in the top soil and methyl coenzyme M reductase gene in the bottom soil that correlated with the higher relative abundance of aerobic methanotrophs in the top soil while methane generation being the active process in the highly anaerobic bottom soil in the landfill. The activity dependent abundance of endogenous microbial communities in the different zones of the landfill was further validated by microcosm studies in serum bottles which established the ability of the methanotrophic community for methane metabolism in the top soil and their potential to serve as sink for methane. The study provides a better understanding about the methanotrophs in correlation with their endogenous environment, so that these bacteria can be used in resolving the environmental issues related to methane and nitrogen management at landfill site.
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Affiliation(s)
- Ashish Kumar Singh
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Suraj Prabhakarrao Nakhate
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakesh Kumar Gupta
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Atul Rajkumar Chavan
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bhagyashri Jagdishprasad Poddar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Sciences, Pune, Maharashtra, 411007, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Sciences, Pune, Maharashtra, 411007, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anshuman Arun Khardenavis
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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3
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Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. G-Quadruplex Structures in Bacteria: Functional Properties and Prospects for Use as Biotargets. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2022. [DOI: 10.1134/s1990750822040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4
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The NtrYX Two-Component System of Paracoccus denitrificans Is Required for the Maintenance of Cellular Iron Homeostasis and for a Complete Denitrification under Iron-Limited Conditions. Int J Mol Sci 2022; 23:ijms23169172. [PMID: 36012437 PMCID: PMC9409073 DOI: 10.3390/ijms23169172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 02/08/2023] Open
Abstract
Denitrification consists of the sequential reduction of nitrate to nitrite, nitric oxide, nitrous oxide, and dinitrogen. Nitrous oxide escapes to the atmosphere, depending on copper availability and other environmental factors. Iron is also a key element because many proteins involved in denitrification contain iron-sulfur or heme centers. The NtrYX two-component regulatory system mediates the responses in a variety of metabolic processes, including denitrification. A quantitative proteomic analysis of a Paracoccus denitrificans NtrY mutant grown under denitrifying conditions revealed the induction of different TonB-dependent siderophore transporters and proteins related to iron homeostasis. This mutant showed lower intracellular iron content than the wild-type strain, and a reduced growth under denitrifying conditions in iron-limited media. Under iron-rich conditions, it releases higher concentrations of siderophores and displayes lower nitrous oxide reductase (NosZ) activity than the wild-type, thus leading to nitrous oxide emission. Bioinformatic and qRT-PCR analyses revealed that NtrYX is a global transcriptional regulatory system that responds to iron starvation and, in turn, controls expression of the iron-responsive regulators fur, rirA, and iscR, the denitrification regulators fnrP and narR, the nitric oxide-responsive regulator nnrS, and a wide set of genes, including the cd1-nitrite reductase NirS, nitrate/nitrite transporters and energy electron transport proteins.
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5
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6
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Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. [G-quadruplex structures in bacteria: functional properties and prospects for use as biotargets]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:93-103. [PMID: 35485483 DOI: 10.18097/pbmc20226802093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
G-quadruplexes (G4), non-canonical secondary DNA structures, are intensively investigated for a long time. In eukaryotic organisms they play an important role in the regulation of gene expression and DNA repair. G4 have also been found in the genomes of numerous bacteria and archaea, but their functional role has not yet been fully explored. Nevertheless, their participation in the formation of antigenic variability, pathogenicity, antibiotic resistance and survival in extreme conditions has been established. Currently, many tools have been developed to detect potential G4 sequences and confirm their formation ability. Since the controlled formation and resolution of the quadruplex are significant means for the regulation of genes critical for survival, a promising direction is the search for ligands - compounds that can have a stabilizing effect on the quadruplex structure and thereby alter gene expression. Currently, a number of ligands are already known, their use stops the growth of pathogenic microorganisms. G4 ligands are of interest as potential antibiotics, which are extremely relevant due to the wide spread of drug resistant pathogens.
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Affiliation(s)
- E A Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - D A Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - I N Bodoev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - M V Zaychikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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7
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Olaya-Abril A, Hidalgo-Carrillo J, Luque-Almagro VM, Fuentes-Almagro C, Urbano FJ, Moreno-Vivián C, Richardson DJ, Roldán MD. Effect of pH on the denitrification proteome of the soil bacterium Paracoccus denitrificans PD1222. Sci Rep 2021; 11:17276. [PMID: 34446760 PMCID: PMC8390676 DOI: 10.1038/s41598-021-96559-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/23/2021] [Indexed: 11/25/2022] Open
Abstract
Denitrification is a respiratory process by which nitrate is reduced to dinitrogen. Incomplete denitrification results in the emission of the greenhouse gas nitrous oxide and this is potentiated in acidic soils, which display reduced denitrification rates and high N2O/N2 ratios compared to alkaline soils. In this work, impact of pH on the proteome of the soil denitrifying bacterium Paracoccus denitrificans PD1222 was analysed with nitrate as sole energy and nitrogen source under anaerobic conditions at pH ranging from 6.5 to 7.5. Quantitative proteomic analysis revealed that the highest difference in protein representation was observed when the proteome at pH 6.5 was compared to the reference proteome at pH 7.2. However, this difference in the extracellular pH was not enough to produce modification of intracellular pH, which was maintained at 6.5 ± 0.1. The biosynthetic pathways of several cofactors relevant for denitrification and nitrogen assimilation like cobalamin, riboflavin, molybdopterin and nicotinamide were negatively affected at pH 6.5. In addition, peptide representation of reductases involved in nitrate assimilation and denitrification were reduced at pH 6.5. Data highlight the strong negative impact of pH on NosZ synthesis and intracellular copper content, thus impairing active NosZ assembly and, in turn, leading to elevated nitrous oxide emissions.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Jesús Hidalgo-Carrillo
- Departamento de Química Orgánica, Universidad de Córdoba, Edificio Marie Curie, Campus de Rabanales, 14071, Córdoba, Spain
| | - Víctor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Carlos Fuentes-Almagro
- Servicio Central de Apoyo a la Investigación (SCAI), Unidad de Proteómica, Universidad de Córdoba, Campus de Rabanales, 14071, Córdoba, Spain
| | - Francisco J Urbano
- Departamento de Química Orgánica, Universidad de Córdoba, Edificio Marie Curie, Campus de Rabanales, 14071, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain.
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8
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Salas A, Cabrera JJ, Jiménez-Leiva A, Mesa S, Bedmar EJ, Richardson DJ, Gates AJ, Delgado MJ. Bacterial nitric oxide metabolism: Recent insights in rhizobia. Adv Microb Physiol 2021; 78:259-315. [PMID: 34147187 DOI: 10.1016/bs.ampbs.2021.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N2-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.
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Affiliation(s)
- Ana Salas
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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9
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Li L, Zhang B, He C, Zhang H. Hydrodynamics- and hydrochemistry-affected microbial selenate reduction in aquifer: Performance and mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:145331. [PMID: 33736316 DOI: 10.1016/j.scitotenv.2021.145331] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Selenate [Se(VI)] with higher content in groundwater will be harmful for human beings. Hence, effective treatment for Se(VI) in aquifer should be conducted reasonably. Microbial reduction of Se(VI) to elemental selenium with weak movability and toxicity has attracted significant attention due to its high efficiency and no secondary contamination. However, hydrodynamic and hydrochemical influences with corresponding mechanisms during Se(VI) bioreduction are still not clear. In this study, influences of flow rate, initial Se(VI) and organic concentrations, coexisting nitrate were evaluated. Se(VI) removal efficiency and capacity reached 96.42 ± 6.82% and 41.28 ± 3.41 (g/m3·d) with flow rate of 0.56 mL/min, initial Se(VI) and chemical organic demand concentrations of 10 mg/L and 400 mg/L. Dechloromonas and Pseudomonas were presumably contributed to Se(VI) reduction, with upregulated serA and tatC genes. Solid Se0 was identified as the final product from Se(VI) reduction. These results will be beneficial for the further comprehending of Se(VI) remediation in aquifer.
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Affiliation(s)
- Liuliu Li
- School of Water Resources and Environment, Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China
| | - Baogang Zhang
- School of Water Resources and Environment, Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China.
| | - Chao He
- School of Water Resources and Environment, Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China
| | - Han Zhang
- School of Water Resources and Environment, Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China
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10
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Amanullah S, Saha P, Nayek A, Ahmed ME, Dey A. Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis. Chem Soc Rev 2021; 50:3755-3823. [DOI: 10.1039/d0cs01405b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Paramita Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhijit Nayek
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Md Estak Ahmed
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhishek Dey
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
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11
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Ruan Y, Ma B, Cai C, Cai L, Gu J, Lu HF, Xu XY, Zhang M. Kinetic affinity index informs the divisions of nitrate flux in aerobic denitrification. BIORESOURCE TECHNOLOGY 2020; 309:123345. [PMID: 32305844 DOI: 10.1016/j.biortech.2020.123345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Aerobic denitrification is attracting increasing attention since its advantage of complete nitrogen removal in a single aerobic reactor with simplified configurations. This study investigated the nitrate kinetic affinity (half-saturation index, Km) by an isolated aerobic denitrifier named P. balearica strain RAD-17. It turned out that strain RAD-17 had a high Km of 162.5 mg-N/L and maximum nitrate reduction rate of 21.7 mg-N/(L•h), enabling it to treat high-strength nitrogen wastewater with high efficiency. Further analysis illustrated that Km was the critical value for the change of growth yield rate along initial nitrate concentrations. Nitrogen balance results elucidated an opposite nitrogen flux to cell synthesis and nitrogen loss during aerobic denitrification. Moreover, the expression of functional genes provided proofs for these phenotypic results at transcriptional level. Consequently, Km could be an indicator for nitrate flux division directing to respiration and assimilation in aerobic denitrifiers, shedding light on its regulation for wastewater treatment.
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Affiliation(s)
- Yunjie Ruan
- Institute of Agricultural Bio-Environmental Engineering, College of Bio-Systems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China; The Rural Development Academy, Zhejiang University, Hangzhou 310058, PR China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chen Cai
- Advanced Water Management Centre, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lei Cai
- Laboratory of Microbial Resources, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, China
| | - Jun Gu
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Hui-Feng Lu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Xiang-Yang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Meng Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China; Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore.
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12
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Tan W, Liao TH, Wang J, Ye Y, Wei YC, Zhou HK, Xiao Y, Zhi XY, Shao ZH, Lyu LD, Zhao GP. A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation. J Biol Chem 2020; 295:5051-5066. [PMID: 32111737 DOI: 10.1074/jbc.ra120.012859] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrate is one of the major inorganic nitrogen sources for microbes. Many bacterial and archaeal lineages have the capacity to express assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite. Although a nitrate assimilatory pathway in mycobacteria has been proposed and validated physiologically and genetically, the putative NAS enzyme has yet to be identified. Here, we report the characterization of a novel NAS encoded by Mycolicibacterium smegmatis Msmeg_4206, designated NasN, which differs from the canonical NASs in its structure, electron transfer mechanism, enzymatic properties, and phylogenetic distribution. Using sequence analysis and biochemical characterization, we found that NasN is an NADPH-dependent, diflavin-containing monomeric enzyme composed of a canonical molybdopterin cofactor-binding catalytic domain and an FMN-FAD/NAD-binding, electron-receiving/transferring domain, making it unique among all previously reported hetero-oligomeric NASs. Genetic studies revealed that NasN is essential for aerobic M. smegmatis growth on nitrate as the sole nitrogen source and that the global transcriptional regulator GlnR regulates nasN expression. Moreover, unlike the NADH-dependent heterodimeric NAS enzyme, NasN efficiently supports bacterial growth under nitrate-limiting conditions, likely due to its significantly greater catalytic activity and oxygen tolerance. Results from a phylogenetic analysis suggested that the nasN gene is more recently evolved than those encoding other NASs and that its distribution is limited mainly to Actinobacteria and Proteobacteria. We observed that among mycobacterial species, most fast-growing environmental mycobacteria carry nasN, but that it is largely lacking in slow-growing pathogenic mycobacteria because of multiple independent genomic deletion events along their evolution.
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Affiliation(s)
- Wei Tan
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Tian-Hua Liao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jin Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yu Ye
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China
| | - Yu-Chen Wei
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China
| | - Hao-Kui Zhou
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhi-Hui Shao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Guo-Ping Zhao
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China .,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai-MOST Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai 201203, China
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13
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Pinchbeck BJ, Soriano-Laguna MJ, Sullivan MJ, Luque-Almagro VM, Rowley G, Ferguson SJ, Roldán MD, Richardson DJ, Gates AJ. A dual functional redox enzyme maturation protein for respiratory and assimilatory nitrate reductases in bacteria. Mol Microbiol 2019; 111:1592-1603. [PMID: 30875449 PMCID: PMC6618116 DOI: 10.1111/mmi.14239] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2019] [Indexed: 12/16/2022]
Abstract
Nitrate is available to microbes in many environments due to sustained use of inorganic fertilizers on agricultural soils and many bacterial and archaeal lineages have the capacity to express respiratory (Nar) and assimilatory (Nas) nitrate reductases to utilize this abundant respiratory substrate and nutrient for growth. Here, we show that in the denitrifying bacterium Paracoccus denitrificans, NarJ serves as a chaperone for both the anaerobic respiratory nitrate reductase (NarG) and the assimilatory nitrate reductase (NasC), the latter of which is active during both aerobic and anaerobic nitrate assimilation. Bioinformatic analysis suggests that the potential for this previously unrecognized role for NarJ in functional maturation of other cytoplasmic molybdenum‐dependent nitrate reductases may be phylogenetically widespread as many bacteria contain both Nar and Nas systems.
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Affiliation(s)
- Benjamin J Pinchbeck
- Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Manuel J Soriano-Laguna
- Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Matthew J Sullivan
- School of Medical Science, Gold Coast campus, Griffith University, Southport, QLD 4222, Australia
| | - Victor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, 1 planta, Campus de Rabanales, Universidad de Córdoba, Córdoba 14071, Spain
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Stuart J Ferguson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - M Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, 1 planta, Campus de Rabanales, Universidad de Córdoba, Córdoba 14071, Spain
| | - David J Richardson
- Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrew J Gates
- Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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14
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Jiang Y, Yang K, Shang Y, Zhang H, Wei L, Wang H. Response and recovery of aerobic granular sludge to pH shock for simultaneous removal of aniline and nitrogen. CHEMOSPHERE 2019; 221:366-374. [PMID: 30641378 DOI: 10.1016/j.chemosphere.2018.12.207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/22/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
Considering the pH fluctuation in industrial wastewater, the response and resilience to pH shock should be investigated during aerobic granular sludge (AGS) system operation. In this work, three AGS reactors, namely R1, R2, and R3 for simultaneous removal of aniline and nitrogen were exposed to neutral, acidic, and alkaline conditions, respectively. The removal efficiency of aniline and chemical oxygen demand with pH variation was over 99.9% and 91.0%, respectively after stable in the three reactors. The aniline removal rate modestly decreased in R2 and R3 after pH varied and denitrification was slightly improved in acidic environment with average removal efficiency of 61.2%. The mature AGS could maintain settleability in R1 and R2 with 30 min sludge volume index below 35 mL g-1 but was unstable under alkaline condition. Correspondingly, the secretion of extracellular polymeric substances especially protein decreased notably in R3. The bacterial groups varied with pH shock, but some could recover after adjustment to original pH value. Proteobacteria was the predominant phylum in the three reactors and Bacteroidetes was enriched in alkaline conditions. In addition, the main functional genera such as Achromobacter, Defluviimonas, Enterobacter, Pseudomonas, and Pseudoxanthomonas, were detected in the system and were found to be responsible for reduction of aniline and nitrogen.
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Affiliation(s)
- Yu Jiang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Kai Yang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Yu Shang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Huining Zhang
- School of Civil Engineering, Lanzhou University of Technology, Lanzhou 730000, China
| | - Li Wei
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hongyu Wang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China.
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15
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Refojo PN, Sena FV, Calisto F, Sousa FM, Pereira MM. The plethora of membrane respiratory chains in the phyla of life. Adv Microb Physiol 2019; 74:331-414. [PMID: 31126533 DOI: 10.1016/bs.ampbs.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.
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Affiliation(s)
- Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal; University of Lisboa, Faculty of Sciences, BIOISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
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16
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Lai CY, Dong QY, Zhao HP. Oxygen exposure deprives antimonate-reducing capability of a methane fed biofilm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:1152-1159. [PMID: 30743828 DOI: 10.1016/j.scitotenv.2018.07.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 06/09/2023]
Abstract
This work is aiming at achieving antimonate (Sb(V)) bio-reduction in a methane (CH4) based membrane biofilm reactor (MBfR), and elucidating the effect of oxygen (O2) on the performance of the biofilm. Scanning electron microscope (SEM), energy dispersive X-ray (EDS) and X-ray photoelectron spectroscopy (XPS) confirm Sb2O3 precipitates were the main product formed from Sb(V) reduction in the CH4-fed biofilm. Illumina sequencing shows Thermomonas may be responsible for Sb(V) reduction. Moreover, we found 8 mg/L of O2 in the influent irreversibly inhibited Sb(V) reduction. Metagenomic prediction by Reconstruction of Unobserved State (PICRUSt) shows that the biofilm lacked efficient defense system to the oxidative stress, leading to the great suppress of key biological metabolisms such as TCA cycle, glycolysis and DNA replication, as well as potential Sb(V) reductases, by O2. However, methanotrophs Methylomonas and Methylosinus were enriched in the biofilm with O2 intrusion, in accordance with the enhanced abundance of genes encoding aerobic CH4 oxidation. These insights evoke the theoretical guidance of microbial remediation using CH4 as the electron donor towards Sb(V) contamination, and will give us a strong reference with regard to wastewater disposal.
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Affiliation(s)
- Chun-Yu Lai
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China; Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Qiu-Yi Dong
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - He-Ping Zhao
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China; Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China.
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17
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Olaya-Abril A, Hidalgo-Carrillo J, Luque-Almagro VM, Fuentes-Almagro C, Urbano FJ, Moreno-Vivián C, Richardson DJ, Roldán MD. Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222. Front Microbiol 2018; 9:1137. [PMID: 29896187 PMCID: PMC5987163 DOI: 10.3389/fmicb.2018.01137] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 05/14/2018] [Indexed: 11/24/2022] Open
Abstract
Denitrification is a respiratory process that produces nitrous oxide as an intermediate, which may escape to the atmosphere before its reduction to dinitrogen through the nitrous oxide reductase NosZ. In this work, the denitrification process carried out by Paracoccus denitrificans PD1222 has been explored through a quantitative proteomic analysis. Under anaerobic conditions, with nitrate as sole nitrogen source, the synthesis of all the enzymes involved in denitrification, the respiratory nitrate, nitrite, nitric oxide, and nitrous oxide reductases, was increased. However, the periplasmic and assimilatory nitrate reductases decreased. Synthesis of transporters for alcohols, D-methionine, sulfate and copper, most of the enzymes involved in the tricarboxylic acid cycle, and proteins involved in other metabolic processes like lysine catabolism, fatty acids degradation and acetyl-CoA synthesis, was increased during denitrification in P. denitrificans PD1222. As consequence, an enhanced production of the central metabolite acetyl-CoA was observed. After establishing the key features of the denitrification proteome, its changes by the influence of a competitive electron acceptor, oxygen, or competitive nitrogen source, ammonium, were evaluated.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | | | | | | | | | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - David J. Richardson
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - María D. Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
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18
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Mozejko-Ciesielska J, Pokoj T, Ciesielski S. Transcriptome remodeling of Pseudomonas putida KT2440 during mcl-PHAs synthesis: effect of different carbon sources and response to nitrogen stress. J Ind Microbiol Biotechnol 2018; 45:433-446. [PMID: 29736608 PMCID: PMC6028892 DOI: 10.1007/s10295-018-2042-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/27/2018] [Indexed: 01/15/2023]
Abstract
Bacterial response to environmental stimuli is essential for survival. In response to fluctuating environmental conditions, the physiological status of bacteria can change due to the actions of transcriptional regulatory machinery. The synthesis and accumulation of polyhydroxyalkanoates (PHAs) are one of the survival strategies in harsh environments. In this study, we used transcriptome analysis of Pseudomonas putida KT2440 to gain a genome-wide view of the mechanisms of environmental-friendly biopolymers accumulation under nitrogen-limiting conditions during conversion of metabolically different carbon sources (sodium gluconate and oleic acid). Transcriptomic data revealed that phaG expression is associated with medium-chain-length-PHAs' synthesis not only on sodium gluconate but also on oleic acid, suggesting that PhaG may play a role in this process, as well. Moreover, genes involved in the β-oxidation pathway were induced in the PHAs production phase when sodium gluconate was supplied as the only carbon and energy source. The transition from exponential growth to stationary phase caused a significant expression of genes involved in nitrogen metabolism, energy supply, and transport system. In this study, several molecular mechanisms, which drive mcl-PHAs synthesis, have been investigated. The identified genes may provide valuable information to improve the efficiency of this bioprocess and make it more economically feasible.
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Affiliation(s)
- Justyna Mozejko-Ciesielska
- Department of Microbiology and Mycology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Tomasz Pokoj
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Slawomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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19
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Olaya-Abril A, Luque-Almagro VM, Manso I, Gates AJ, Moreno-Vivián C, Richardson DJ, Roldán MD. Poly(3-hydroxybutyrate) hyperproduction by a global nitrogen regulator NtrB mutant strain of Paracoccus denitrificans PD1222. FEMS Microbiol Lett 2018; 365:4705890. [PMID: 29228177 PMCID: PMC5812496 DOI: 10.1093/femsle/fnx251] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 11/29/2017] [Indexed: 12/27/2022] Open
Abstract
Paracoccus denitrificans PD1222 accumulates short-length polyhydroxyalkanoates, poly(3-hydroxybutyrate), under nitrogen-deficient conditions. Polyhydroxybutyrate metabolism requires the 3-ketoacyl-CoA thiolase PhaA, the acetoacetyl-CoA dehydrogenase/reductase PhaB and the synthase PhaC for polymerization. Additionally, P. denitrificans PD1222 grows aerobically with nitrate as sole nitrogen source. Nitrate assimilation is controlled negatively by ammonium through the two-component NtrBC system. NtrB is a sensor kinase that autophosphorylates a histidine residue under low-nitrogen concentrations and, in turn, transfers a phosphoryl group to an aspartate residue of the response regulator NtrC protein, which acts as a transcriptional activator of the P. denitrificans PD1222 nasABGHC genes. The P. denitrificans PD1222 NtrB mutant was unable to use nitrate efficiently as nitrogen source when compared to the wild-type strain, and it also overproduced poly(3-hydroxybutyrate). Acetyl-CoA concentration in the P. denitrificans PD1222 NtrB mutant strain was higher than in the wild-type strain. The expression of the phaC gene was also increased in the NtrB mutant when compared to the wild-type strain. These results suggest that accumulation of poly(3-hydroxybutyrate) in the NtrB mutant strain of PD1222 responds to the high levels of acetyl-CoA that accumulate in the cytoplasm as consequence of its inability to efficiently use nitrate as nitrogen source.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1a planta, Campus de Rabanales, Córdoba, 14071, Spain
| | - Víctor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1a planta, Campus de Rabanales, Córdoba, 14071, Spain
| | - Isabel Manso
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1a planta, Campus de Rabanales, Córdoba, 14071, Spain
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1a planta, Campus de Rabanales, Córdoba, 14071, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1a planta, Campus de Rabanales, Córdoba, 14071, Spain
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20
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Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans. Biochem J 2017; 474:1769-1787. [PMID: 28385879 PMCID: PMC5424462 DOI: 10.1042/bcj20170115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/04/2017] [Accepted: 04/06/2017] [Indexed: 01/05/2023]
Abstract
Transcriptional adaptation to nitrate-dependent anabolism by Paracoccus denitrificans PD1222 was studied. A total of 74 genes were induced in cells grown with nitrate as N-source compared with ammonium, including nasTSABGHC and ntrBC genes. The nasT and nasS genes were cotranscribed, although nasT was more strongly induced by nitrate than nasS. The nasABGHC genes constituted a transcriptional unit, which is preceded by a non-coding region containing hairpin structures involved in transcription termination. The nasTS and nasABGHC transcripts were detected at similar levels with nitrate or glutamate as N-source, but nasABGHC transcript was undetectable in ammonium-grown cells. The nitrite reductase NasG subunit was detected by two-dimensional polyacrylamide gel electrophoresis in cytoplasmic fractions from nitrate-grown cells, but it was not observed when either ammonium or glutamate was used as the N-source. The nasT mutant lacked both nasABGHC transcript and nicotinamide adenine dinucleotide (NADH)-dependent nitrate reductase activity. On the contrary, the nasS mutant showed similar levels of the nasABGHC transcript to the wild-type strain and displayed NasG protein and NADH–nitrate reductase activity with all N-sources tested, except with ammonium. Ammonium repression of nasABGHC was dependent on the Ntr system. The ntrBC and ntrYX genes were expressed at low levels regardless of the nitrogen source supporting growth. Mutational analysis of the ntrBCYX genes indicated that while ntrBC genes are required for nitrate assimilation, ntrYX genes can only partially restore growth on nitrate in the absence of ntrBC genes. The existence of a regulation mechanism for nitrate assimilation in P. denitrificans, by which nitrate induction operates at both transcriptional and translational levels, is proposed.
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21
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Ghosh S, Ayayee PA, Valverde-Barrantes OJ, Blackwood CB, Royer TV, Leff LG. Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates. BMC Microbiol 2017; 17:87. [PMID: 28376715 PMCID: PMC5381026 DOI: 10.1186/s12866-017-0993-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/29/2017] [Indexed: 01/10/2023] Open
Abstract
Background The nitrogen (N) cycle consists of complex microbe-mediated transformations driven by a variety of factors, including diversity and concentrations of N compounds. In this study, we examined taxonomic diversity and N substrate utilization by heterotrophic bacteria isolated from streams under complex and simple N-enrichment conditions. Results Diversity estimates differed among isolates from the enrichments, but no significant composition were detected. Substrate utilization and substrate range of bacterial assemblages differed within and among enrichments types, and not simply between simple and complex N-enrichments. Conclusions N substrate use patterns differed between isolates from some complex and simple N-enrichments while others were unexpectedly similar. Taxonomic composition of isolates did not differ among enrichments and was unrelated to N use suggesting strong functional redundancy. Ultimately, our results imply that the available N pool influences physiology and selects for bacteria with various abilities that are unrelated to their taxonomic affiliation. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0993-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suchismita Ghosh
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA
| | - Paul A Ayayee
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA.
| | - Oscar J Valverde-Barrantes
- International Center for Tropical Botany (ICTB), Florida International University, Miami, FL, 33199, USA
| | | | - Todd V Royer
- School of Public and Environmental Affairs, Indiana University, Bloomington, Bloomington, IN, 47405, USA
| | - Laura G Leff
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA
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22
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López MF, Cabrera JJ, Salas A, Delgado MJ, López-García SL. Dissecting the role of NtrC and RpoN in the expression of assimilatory nitrate and nitrite reductases in Bradyrhizobium diazoefficiens. Antonie Van Leeuwenhoek 2017; 110:531-542. [PMID: 28040856 DOI: 10.1007/s10482-016-0821-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/19/2016] [Indexed: 11/28/2022]
Abstract
Bradyrhizobium diazoefficiens, a nitrogen-fixing endosymbiont of soybeans, is a model strain for studying rhizobial denitrification. This bacterium can also use nitrate as the sole nitrogen (N) source during aerobic growth by inducing an assimilatory nitrate reductase encoded by nasC located within the narK-bjgb-flp-nasC operon along with a nitrite reductase encoded by nirA at a different chromosomal locus. The global nitrogen two-component regulatory system NtrBC has been reported to coordinate the expression of key enzymes in nitrogen metabolism in several bacteria. In this study, we demonstrate that disruption of ntrC caused a growth defect in B. diazoefficiens cells in the presence of nitrate or nitrite as the sole N source and a decreased activity of the nitrate and nitrite reductase enzymes. Furthermore, the expression of narK-lacZ or nirA-lacZ transcriptional fusions was significantly reduced in the ntrC mutant after incubation under nitrate assimilation conditions. A B. diazoefficiens rpoN 1/2 mutant, lacking both copies of the gene encoding the alternative sigma factor σ54, was also defective in aerobic growth with nitrate as the N source as well as in nitrate and nitrite reductase expression. These results demonstrate that the NtrC regulator is required for expression of the B. diazoefficiens nasC and nirA genes and that the sigma factor RpoN is also involved in this regulation.
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Affiliation(s)
- María F López
- Instituto de Biotecnología y Biología Molecular (IBBM), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT La Plata-CONICET, Calles 47 y 115, B1900AJL, La Plata, Argentina
| | - Juan J Cabrera
- Estación Experimental del Zaidín, CSIC, PO Box 419, 18080, Granada, Spain
| | - Ana Salas
- Estación Experimental del Zaidín, CSIC, PO Box 419, 18080, Granada, Spain
| | - María J Delgado
- Estación Experimental del Zaidín, CSIC, PO Box 419, 18080, Granada, Spain.
| | - Silvina L López-García
- Instituto de Biotecnología y Biología Molecular (IBBM), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT La Plata-CONICET, Calles 47 y 115, B1900AJL, La Plata, Argentina.
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23
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Waller ZAE, Pinchbeck BJ, Buguth BS, Meadows TG, Richardson DJ, Gates AJ. Control of bacterial nitrate assimilation by stabilization of G-quadruplex DNA. Chem Commun (Camb) 2016; 52:13511-13514. [PMID: 27805200 PMCID: PMC5123632 DOI: 10.1039/c6cc06057a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Here we present a chemical-biology study in the model soil bacterium Paracoccus denitrificans, where we show ligand-specific control of nitrate assimilation. Stabilization of a G-quadruplex in the promoter region of the nas genes, encoding the assimilatory nitrate/nitrite reductase system, is achieved using known quadruplex ligands and results in attenuation of gene transcription.
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Affiliation(s)
- Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ, UK.
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24
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Goddard AD, Bali S, Mavridou DAI, Luque-Almagro VM, Gates AJ, Dolores Roldán M, Newstead S, Richardson DJ, Ferguson SJ. The Paracoccus denitrificans NarK-like nitrate and nitrite transporters-probing nitrate uptake and nitrate/nitrite exchange mechanisms. Mol Microbiol 2016; 103:117-133. [PMID: 27696579 PMCID: PMC5217062 DOI: 10.1111/mmi.13546] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2016] [Indexed: 12/17/2022]
Abstract
Nitrate and nitrite transport across biological membranes is often facilitated by protein transporters that are members of the major facilitator superfamily. Paracoccus denitrificans contains an unusual arrangement whereby two of these transporters, NarK1 and NarK2, are fused into a single protein, NarK, which delivers nitrate to the respiratory nitrate reductase and transfers the product, nitrite, to the periplasm. Our complementation studies, using a mutant lacking the nitrate/proton symporter NasA from the assimilatory nitrate reductase pathway, support that NarK1 functions as a nitrate/proton symporter while NarK2 is a nitrate/nitrite antiporter. Through the same experimental system, we find that Escherichia coli NarK and NarU can complement deletions in both narK and nasA in P. denitrificans, suggesting that, while these proteins are most likely nitrate/nitrite antiporters, they can also act in the net uptake of nitrate. Finally, we argue that primary sequence analysis and structural modelling do not readily explain why NasA, NarK1 and NarK2, as well as other transporters from this protein family, have such different functions, ranging from net nitrate uptake to nitrate/nitrite exchange.
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Affiliation(s)
- Alan D Goddard
- School of Life Sciences, University of Lincoln, Lincoln, LN6 7TS, UK.,School of Life and Health Sciences, Aston University, Birmingham, B4 7ET, UK.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Shilpa Bali
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Despoina A I Mavridou
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, Kensington, London, SW7 2DD, UK
| | - Victor M Luque-Almagro
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1a planta, Campus de Rabanales, Córdoba, 14071, Spain
| | - Andrew J Gates
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - M Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1a planta, Campus de Rabanales, Córdoba, 14071, Spain
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - David J Richardson
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Stuart J Ferguson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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Wen LL, Lai CY, Yang Q, Chen JX, Zhang Y, Ontiveros-Valencia A, Zhao HP. Quantitative detection of selenate-reducing bacteria by real-time PCR targeting the selenate reductase gene. Enzyme Microb Technol 2016; 85:19-24. [DOI: 10.1016/j.enzmictec.2016.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/04/2016] [Accepted: 01/04/2016] [Indexed: 12/26/2022]
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Hassan J, Bergaust LL, Molstad L, de Vries S, Bakken LR. Homeostatic control of nitric oxide (NO) at nanomolar
concentrations in denitrifying bacteria - modelling and experimental determination of NO reductase kinetics in vivo
in P
aracoccus denitrificans. Environ Microbiol 2016; 18:2964-78. [DOI: 10.1111/1462-2920.13129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/01/2015] [Accepted: 11/08/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Junaid Hassan
- Department of Environmental Sciences; Norwegian University of Life Sciences; Ås Norway
| | - Linda L. Bergaust
- Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Ås Norway
| | - Lars Molstad
- Department of Environmental Sciences; Norwegian University of Life Sciences; Ås Norway
| | - Simon de Vries
- Department of Biotechnology; Delft University of Technology; the Netherlands
| | - Lars R. Bakken
- Department of Environmental Sciences; Norwegian University of Life Sciences; Ås Norway
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Hassan J, Qu Z, Bergaust LL, Bakken LR. Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes. PLoS Comput Biol 2016; 12:e1004621. [PMID: 26731685 PMCID: PMC4701171 DOI: 10.1371/journal.pcbi.1004621] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/22/2015] [Indexed: 11/20/2022] Open
Abstract
Denitrifying bacteria accumulate NO2−, NO, and N2O, the amounts depending on transcriptional regulation of core denitrification genes in response to O2-limiting conditions. The genes include nar, nir, nor and nosZ, encoding NO3−-, NO2−-, NO- and N2O reductase, respectively. We previously constructed a dynamic model to simulate growth and respiration in batch cultures of Paracoccus denitrificans. The observed denitrification kinetics were adequately simulated by assuming a stochastic initiation of nir-transcription in each cell with an extremely low probability (0.5% h-1), leading to product- and substrate-induced transcription of nir and nor, respectively, via NO. Thus, the model predicted cell diversification: after O2 depletion, only a small fraction was able to grow by reducing NO2−. Here we have extended the model to simulate batch cultivation with NO3−, i.e., NO2−, NO, N2O, and N2 kinetics, measured in a novel experiment including frequent measurements of NO2−. Pa. denitrificans reduced practically all NO3− to NO2− before initiating gas production. The NO2− production is adequately simulated by assuming stochastic nar-transcription, as that for nirS, but with a higher probability (0.035 h-1) and initiating at a higher O2 concentration. Our model assumes that all cells express nosZ, thus predicting that a majority of cells have only N2O-reductase (A), while a minority (B) has NO2−-, NO- and N2O-reductase. Population B has a higher cell-specific respiration rate than A because the latter can only use N2O produced by B. Thus, the ratio BA is low immediately after O2 depletion, but increases throughout the anoxic phase because B grows faster than A. As a result, the model predicts initially low but gradually increasing N2O concentration throughout the anoxic phase, as observed. The modelled cell diversification neatly explains the observed denitrification kinetics and transient intermediate accumulations. The result has major implications for understanding the relationship between genotype and phenotype in denitrification research. Denitrifiers generally respire O2, but if O2 becomes limiting, they may switch to anaerobic respiration (denitrification) by producing NO3−-, NO2−-, NO- and/or N2O reductase, encoded by nar, nir, nor, and nosZ genes, respectively. Denitrification causes transient accumulation of NO2− and NO/N2O emissions, depending on the activity of the four reductases. Denitrifiers lacking nosZ produce ~100% N2O, whereas organisms with only nosZ are net consumers of N2O. Full-fledged denitrifiers are equipped with all four reductases, genetic regulation of which determines NO2− accumulation and NO/N2O emissions. Paracoccus denitrificans is a full-fledged denitrifying bacterium, and here we present a modelling approach to understand its gene regulation. We found that the observed transient accumulation of NO2− and N2O can be neatly explained by assuming cell diversification: all cells expressing nosZ, while a minority expressing nar and nir+nor. Thus, the model predicts that in a batch culture of this organism, only a minor sub-population is full-fledged denitrifier. The cell diversification is a plausible outcome of stochastic initiation of nar- and nir transcription, which then becomes autocatalytic by NO2−and NO, respectively. The findings are important for understanding the regulation of denitrification in bacteria: product-induced transcription of denitrification genes is common, and we surmise that diversification in response to anoxia is widespread.
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Affiliation(s)
- Junaid Hassan
- Department of Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
- * E-mail:
| | - Zhi Qu
- Department of Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Linda L. Bergaust
- Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R. Bakken
- Department of Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
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An integrated biochemical system for nitrate assimilation and nitric oxide detoxification in Bradyrhizobium japonicum. Biochem J 2015; 473:297-309. [PMID: 26564204 PMCID: PMC4724949 DOI: 10.1042/bj20150880] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022]
Abstract
Rhizobia are recognized to establish N2-fixing symbiotic interactions with legume plants. Bradyrhizobium japonicum, the symbiont of soybeans, can denitrify and grow under free-living conditions with nitrate (NO3 (-)) or nitrite (NO2 (-)) as sole nitrogen source. Unlike related bacteria that assimilate NO3 (-), genes encoding the assimilatory NO3 (-) reductase (nasC) and NO2 (-) reductase (nirA) in B. japonicum are located at distinct chromosomal loci. The nasC gene is located with genes encoding an ABC-type NO3 (-) transporter, a major facilitator family NO3 (-)/NO2 (-) transporter (NarK), flavoprotein (Flp) and single-domain haemoglobin (termed Bjgb). However, nirA clusters with genes for a NO3 (-)/NO2 (-)-responsive regulator (NasS-NasT). In the present study, we demonstrate NasC and NirA are both key for NO3 (-) assimilation and that growth with NO3 (-), but not NO2 (-) requires flp, implying Flp may function as electron donor to NasC. In addition, bjgb and flp encode a nitric oxide (NO) detoxification system that functions to mitigate cytotoxic NO formed as a by-product of NO3 (-) assimilation. Additional experiments reveal NasT is required for NO3 (-)-responsive expression of the narK-bjgb-flp-nasC transcriptional unit and the nirA gene and that NasS is also involved in the regulatory control of this novel bipartite assimilatory NO3 (-)/NO2 (-) reductase pathway.
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Hassan J, Bergaust LL, Wheat ID, Bakken LR. Low probability of initiating nirS transcription explains observed gas kinetics and growth of bacteria switching from aerobic respiration to denitrification. PLoS Comput Biol 2014; 10:e1003933. [PMID: 25375393 PMCID: PMC4222654 DOI: 10.1371/journal.pcbi.1003933] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 09/17/2014] [Indexed: 01/22/2023] Open
Abstract
In response to impending anoxic conditions, denitrifying bacteria sustain respiratory metabolism by producing enzymes for reducing nitrogen oxyanions/-oxides (NOx) to N2 (denitrification). Since denitrifying bacteria are non-fermentative, the initial production of denitrification proteome depends on energy from aerobic respiration. Thus, if a cell fails to synthesise a minimum of denitrification proteome before O2 is completely exhausted, it will be unable to produce it later due to energy-limitation. Such entrapment in anoxia is recently claimed to be a major phenomenon in batch cultures of the model organism Paracoccus denitrificans on the basis of measured e−-flow rates to O2 and NOx. Here we constructed a dynamic model and explicitly simulated actual kinetics of recruitment of the cells to denitrification to directly and more accurately estimate the recruited fraction (). Transcription of nirS is pivotal for denitrification, for it triggers a cascade of events leading to the synthesis of a full-fledged denitrification proteome. The model is based on the hypothesis that nirS has a low probability (, h−1) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification. We assume that the recruitment is initiated as [O2] falls below a critical threshold and terminates (assuming energy-limitation) as [O2] exhausts. With = 0.005 h−1, the model robustly simulates observed denitrification kinetics for a range of culture conditions. The resulting (fraction of the cells recruited to denitrification) falls within 0.038–0.161. In contrast, if the recruitment of the entire population is assumed, the simulated denitrification kinetics deviate grossly from those observed. The phenomenon can be understood as a ‘bet-hedging strategy’: switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia turns out to be a ‘false alarm’. In response to oxygen-limiting conditions, denitrifying bacteria produce a set of enzymes to convert / to N2 via NO and N2O. The process (denitrification) helps generate energy for survival and growth during anoxia. Denitrification is imperative for the nitrogen cycle and has far-reaching consequences including contribution to global warming and destruction of stratospheric ozone. Recent experiments provide circumstantial evidence for a previously unknown phenomenon in the model denitrifying bacterium Paracoccus denitrificans: as O2 depletes, only a marginal fraction of its population appears to switch to denitrification. We hypothesise that the low success rate is due to a) low probability for the cells to initiate the transcription of genes (nirS) encoding a key denitrification enzyme (NirS), and b) a limited time-window in which NirS must be produced. Based on this hypothesis, we constructed a dynamic model of denitrification in Pa. denitrificans. The simulation results show that, within the limited time available, a probability of 0.005 h−1 for each cell to initiate nirS transcription (resulting in the recruitment of 3.8–16.1% cells to denitrification) is sufficient to adequately simulate experimental data. The result challenges conventional outlook on the regulation of denitrification in general and that of Pa. denitrificans in particular.
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Affiliation(s)
- Junaid Hassan
- Department of Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Linda L. Bergaust
- Department of Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - I. David Wheat
- Department of Geography, University of Bergen, Bergen, Norway
| | - Lars R. Bakken
- Department of Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
- * E-mail:
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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32
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Lai CY, Yang X, Tang Y, Rittmann BE, Zhao HP. Nitrate shaped the selenate-reducing microbial community in a hydrogen-based biofilm reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:3395-3402. [PMID: 24579788 DOI: 10.1021/es4053939] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
To study the effect of nitrate (NO3(-)) on selenate (SeO4(2-)) reduction, we tested a H2-based biofilm with a range of influent NO3(-) loadings. When SeO4(2-) was the only electron acceptor (stage 1), 40% of the influent SeO4(2-) was reduced to insoluble elemental selenium (Se(0)). SeO4(2-) reduction was dramatically inhibited when NO3(-) was added at a surface loading larger than 1.14 g of N m(-2) day(-1), when H2 delivery became limiting and only 80% of the input NO3(-) was reduced (stage 2). In stage 3, when NO3(-) was again removed from the influent, SeO4(2-) reduction was re-established and increased to 60% conversion to Se(0). SeO4(2-) reduction remained stable at 60% in stages 4 and 5, when the NO3(-) surface loading was re-introduced at ≤ 0.53 g of N m(-2) day(-1), allowing for complete NO3(-) reduction. The selenate-reducing microbial community was significantly reshaped by the high NO3(-) surface loading in stage 2, and it remained stable through stages 3-5. In particular, the abundance of α-Proteobacteria decreased from 30% in stage 1 to less than 10% of total bacteria in stage 2. β-Proteobacteria, which represented about 55% of total bacteria in the biofilm in stage 1, increased to more than 90% of phylotypes in stage 2. Hydrogenophaga, an autotrophic denitrifier, was positively correlated with NO3(-) flux. Thus, introducing a NO3(-) loading high enough to cause H2 limitation and suppress SeO4(2-) reduction had a long-lasting effect on the microbial community structure, which was confirmed by principal coordinate analysis, although SeO4(2-) reduction remained intact.
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Affiliation(s)
- Chun-Yu Lai
- Ministry of Education, Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University , Hangzhou 310029, People's Republic of China
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Luque-Almagro VM, Lyall VJ, Ferguson SJ, Roldán MD, Richardson DJ, Gates AJ. Nitrogen oxyanion-dependent dissociation of a two-component complex that regulates bacterial nitrate assimilation. J Biol Chem 2013; 288:29692-702. [PMID: 24005668 PMCID: PMC3795266 DOI: 10.1074/jbc.m113.459032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitrogen is an essential nutrient for growth and is readily available to microbes in many environments in the form of ammonium and nitrate. Both ions are of environmental significance due to sustained use of inorganic fertilizers on agricultural soils. Diverse species of bacteria that have an assimilatory nitrate/nitrite reductase system (NAS) can use nitrate or nitrite as the sole nitrogen source for growth when ammonium is limited. In Paracoccus denitrificans, the pathway-specific two-component regulator for NAS expression is encoded by the nasT and nasS genes. Here, we show that the putative RNA-binding protein NasT is a positive regulator essential for expression of the nas gene cluster (i.e. nasABGHC). By contrast, a nitrogen oxyanion-binding sensor (NasS) is required for nitrate/nitrite-responsive control of nas gene expression. The NasS and NasT proteins co-purify as a stable heterotetrameric regulatory complex, NasS-NasT. This protein-protein interaction is sensitive to nitrate and nitrite, which cause dissociation of the NasS-NasT complex into monomeric NasS and an oligomeric form of NasT. NasT has been shown to bind the leader RNA for nasA. Thus, upon liberation from the complex, the positive regulator NasT is free to up-regulate nas gene expression.
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Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions. J Bacteriol 2013; 195:4769-77. [PMID: 23974024 DOI: 10.1128/jb.00860-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Anaerobic growth and survival are integral parts of the life cycle of many marine bacteria. To identify genes essential for the anoxic life of Dinoroseobacter shibae, a transposon library was screened for strains impaired in anaerobic denitrifying growth. Transposon insertions in 35 chromosomal and 18 plasmid genes were detected. The essential contribution of plasmid genes to anaerobic growth was confirmed with plasmid-cured D. shibae strains. A combined transcriptome and proteome approach identified oxygen tension-regulated genes. Transposon insertion sites of a total of 1,527 mutants without an anaerobic growth phenotype were determined to identify anaerobically induced but not essential genes. A surprisingly small overlap of only three genes (napA, phaA, and the Na(+)/Pi antiporter gene Dshi_0543) between anaerobically essential and induced genes was found. Interestingly, transposon mutations in genes involved in dissimilatory and assimilatory nitrate reduction (napA, nasA) and corresponding cofactor biosynthesis (genomic moaB, moeB, and dsbC and plasmid-carried dsbD and ccmH) were found to cause anaerobic growth defects. In contrast, mutation of anaerobically induced genes encoding proteins required for the later denitrification steps (nirS, nirJ, nosD), dimethyl sulfoxide reduction (dmsA1), and fermentation (pdhB1, arcA, aceE, pta, acs) did not result in decreased anaerobic growth under the conditions tested. Additional essential components (ferredoxin, cccA) of the anaerobic electron transfer chain and central metabolism (pdhB) were identified. Another surprise was the importance of sodium gradient-dependent membrane processes and genomic rearrangements via viruses, transposons, and insertion sequence elements for anaerobic growth. These processes and the observed contributions of cell envelope restructuring (lysM, mipA, fadK), C4-dicarboxylate transport (dctM1, dctM3), and protease functions to anaerobic growth require further investigation to unravel the novel underlying adaptation strategies.
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Bao P, Huang H, Hu ZY, Häggblom M, Zhu YG. Impact of temperature, CO2
fixation and nitrate reduction on selenium reduction, by a paddy soil Clostridium
strain. J Appl Microbiol 2013. [DOI: 10.1111/jam.12084] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- P. Bao
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - H. Huang
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Z.-Y. Hu
- College of Resources and Environment; Graduate University of Chinese Academy of Sciences; Beijing China
| | - M.M. Häggblom
- Rutgers University; Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; New Brunswick NJ USA
| | - Y.-G. Zhu
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment, Chinese Academy of Sciences; Xiamen China
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Heylen K, Keltjens J. Redundancy and modularity in membrane-associated dissimilatory nitrate reduction in Bacillus. Front Microbiol 2012; 3:371. [PMID: 23087684 PMCID: PMC3475470 DOI: 10.3389/fmicb.2012.00371] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/28/2012] [Indexed: 11/13/2022] Open
Abstract
The genomes of two phenotypically denitrifying type strains of the genus Bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed. Results suggest that denitrification proceeds in the periplasmic space and in an analogous fashion as in Gram-negative organisms, yet with the participation of proteins that tend to be membrane-bound or membrane-associated. A considerable degree of functional redundancy was observed with marked differences between B. azotoformans LMG 9581(T) and B. bataviensis LMG 21833(T). In addition to the already characterized menaquinol/cyt c-dependent nitric oxide reductase (Suharti et al., 2001, 2004) of which the encoding genes could be identified now, evidence for another novel nitric oxide reductase (NOR) was found. Also, our analyses confirm earlier findings on branched electron transfer with both menaquinol and cytochrome c as reductants. Quite unexpectedly, both bacilli have the disposal of two parallel pathways for nitrite reduction enabling a life style as a denitrifier and as an ammonifying bacterium.
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Affiliation(s)
- Kim Heylen
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, University of Ghent Gent, Belgium
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38
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Izumi A, Schnell R, Schneider G. Crystal structure of NirD, the small subunit of the nitrite reductase NirbD from Mycobacterium tuberculosis
at 2.0 Å resolution. Proteins 2012; 80:2799-803. [DOI: 10.1002/prot.24177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/01/2012] [Accepted: 08/26/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Atsushi Izumi
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden
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Feng Z, Hou T, Li Y. Concerted movement in pH-dependent gating of FocA from molecular dynamics simulations. J Chem Inf Model 2012; 52:2119-31. [PMID: 22747061 DOI: 10.1021/ci300250q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
FocA, a member of the formate-nitrite transporter (FNT) family, transports formate and nitrite across biological membranes in cellular organisms. The export and uptake of formate in bacteria are both mediated by FocA, which undergoes a pH-dependent functional switch. Recently, the crystal structures of Escherichia coli FocA (EcFocA), Vibrio cholerae FocA (VcFocA), and Salmonella typhimurium FocA (StFocA) were reported. We performed molecular dynamics (MD) on StFocA and EcFocA with different states of His209 (protonated and unprotonated), representing different pH conditions of FocA. The N-terminal helix in each protomer of StFocA covers and blocks the formate channel. At neutral or high pH (MD simulations with unprotonated His209), the concerted movement of the N-terminal helices of pairs of protomers of StFocA opens its formate channel. At low pH (MD simulations with protonated His209), protonated His209 interacts tightly with its neighboring residue Asn262, and the channel becomes narrower, so that the formate can hardly pass through the channel. We obtained similar results for EcFocA. Our study shows that pairs of protomers of FocA move in a concerted way to achieve its pH-dependent gating function, which provides information on the dynamics of the gating mechanism of FNT proteins and aquaporins.
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Affiliation(s)
- Zhiwei Feng
- Institute of Functional Nano & Soft Materials and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
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Abstract
In the context of the global nitrogen cycle, the importance of inorganic nitrate for the nutrition and growth of marine and freshwater autotrophic phytoplankton has long been recognized. In contrast, the utilization of nitrate by heterotrophic bacteria has historically received less attention because the primary role of these organisms has classically been considered to be the decomposition and mineralization of dissolved and particulate organic nitrogen. In the pre-genome sequence era, it was known that some, but not all, heterotrophic bacteria were capable of growth on nitrate as a sole nitrogen source. However, examination of currently available prokaryotic genome sequences suggests that assimilatory nitrate reductase (Nas) systems are widespread phylogenetically in bacterial and archaeal heterotrophs. Until now, regulation of nitrate assimilation has been mainly studied in cyanobacteria. In contrast, in heterotrophic bacterial strains, the study of nitrate assimilation regulation has been limited to Rhodobacter capsulatus, Klebsiella oxytoca, Azotobacter vinelandii and Bacillus subtilis. In Gram-negative bacteria, the nas genes are subjected to dual control: ammonia repression by the general nitrogen regulatory (Ntr) system and specific nitrate or nitrite induction. The Ntr system is widely distributed in bacteria, whereas the nitrate/nitrite-specific control is variable depending on the organism.
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41
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A haloarchaeal ferredoxin electron donor that plays an essential role in nitrate assimilation. Biochem Soc Trans 2011; 39:1844-8. [DOI: 10.1042/bst20110709] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the absence of ammonium, many organisms, including the halophilic archaeon Haloferax volcanii DS2 (DM3757), may assimilate inorganic nitrogen from nitrate or nitrite, using a ferredoxin-dependent assimilatory NO3−/NO2− reductase pathway. The small acidic ferredoxin Hv-Fd plays an essential role in the electron transfer cascade required for assimilatory nitrate and nitrite reduction by the cytoplasmic NarB- and NirA-type reductases respectively. UV–visible absorbance and EPR spectroscopic characterization of purified Hv-Fd demonstrate that this protein binds a single [2Fe–2S] cluster, and potentiometric titration reveals that the cluster shares similar redox properties with those present in plant-type ferredoxins.
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