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Yao T, Huang Y, Huai Z, Liu X, Liu X, Liu Y, Sun H, Pang Y. Response mechanisms to acid stress promote LF82 replication in macrophages. Front Cell Infect Microbiol 2023; 13:1255083. [PMID: 37881369 PMCID: PMC10595154 DOI: 10.3389/fcimb.2023.1255083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
Background Adherent-invasive E. coli (AIEC) LF82 is capable of adhering to and invading intestinal epithelial cells, as well as replicating within macrophages without inducing host cell death. Methods We compared the transcriptomics of LF82 at pH=7.5 and pH=5.8 by RNA-sequencing, and qRT-PCR verified differentially expressed genes (DEGs). The deletion mutants of DEGs in the treatment group (pH=5.8) compared to the control group (pH=7.5) were constructed by λ recombinant. The replication differences between the mutants and WT infected Raw 264.7 at 24 h.p.i were analyzed by combining LB solid plate count and confocal observation. NH4Cl and chloroquine diphosphate (CQ) were used for acid neutralization to study the effect of pH on the replication of LF82 in macrophages. Na2NO3 was added to RPMI 1640 to study the effect of nitrate on the replication of LF82 in macrophages. 0.3% solid LB was used for flagellar motility assay and Hela was used to study flagellar gene deletion mutants and WT adhesion and invasion ability. Results In this study, we found that infection with LF82 results in acidification of macrophages. Subsequent experiments demonstrated that an intracellular acidic environment is necessary for LF82 replication. Transcriptome and phenotypic analysis showed that high expression of acid shock genes and acid fitness genes promotes LF82 replication in macrophages. Further, we found that the replication of LF82 in macrophages was increased under nitrate treatment, and nitrogen metabolism genes of LF82 were upregulated in acid treatment. The replication in macrophages of ΔnarK, ΔnarXL, ΔnarP, and Δhmp were decreased. In addition, we found that the expression of flagellar genes was downregulated in acidic pH and after LF82 invading macrophages. Motility assay shows that the movement of LF82 on an acidic semisolid agar plate was limited. Further results showed that ΔfliC and ΔfliD decreased in motility, adhesion ability, and invasion of host cells, but no significant effect on replication in macrophages was observed. Conclusion In this study, we simulated the acidic environment in macrophages, combined with transcriptome technology, and explained from the genetic level that LF82 promotes replication by activating its acid shock and fitness system, enhancing nitrate utilization, and inhibiting flagellar function.
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Affiliation(s)
- Ting Yao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Yu Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Zimeng Huai
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Xingmei Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Xiaowen Liu
- Academy of Psychology and Behavior, Faculty of Psychology, Tianjin Normal University, Tianjin, China
| | - Yutao Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Hao Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Yu Pang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
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2
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Chon NL, Schultz NJ, Zheng H, Lin H. Anion Pathways in the NarK Nitrate/Nitrite Exchanger. J Chem Inf Model 2023; 63:5142-5152. [PMID: 37585651 PMCID: PMC10482320 DOI: 10.1021/acs.jcim.3c00295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Indexed: 08/18/2023]
Abstract
NarK nitrate/nitrite antiporter imports nitrate (a mineral form of the essential element nitrogen) into the cell and exports nitrite (a metabolite that can be toxic in high concentrations) out of the cell. However, many details about its operational mechanism remain poorly understood. In this work, we performed steered molecular dynamics simulations of anion translocations and quantum-chemistry model calculations of the binding sites to study the wild-type NarK protein and its R89K mutant. Our results shed light on the importance of the two strictly conserved binding-site arginine residues (R89 and R305) and two glycine-rich signature motifs (G164-M176 and G408-F419) in anion movement through the pore. We also observe conformational changes of the protein during anion migration. For the R89K mutant, our quantum calculations reveal a competition for a proton between the anion (especially nitrite) and lysine, which can potentially slow down or even trap the anion in the pore. Our findings provide a possible explanation for the striking experimental finding that the arginine-to-lysine mutation, despite preserving the charge, impedes or abolishes anion transport in such mutants of NarK and other similar nitrate/nitrite exchangers.
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Affiliation(s)
- Nara Lee Chon
- Department
of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Natalie Jean Schultz
- Department
of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Hongjin Zheng
- Department
of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Hai Lin
- Department
of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
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3
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Yılmaz H, Erdoğan EM, Ergenekon P, Özkan M. Comparison of ion selectivities of nitrite channel NirC and water channel aquaporin. World J Microbiol Biotechnol 2023; 39:120. [PMID: 36918441 DOI: 10.1007/s11274-023-03553-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023]
Abstract
nirC gene coding for the nitrite channel of E. coli K12 was cloned into the pET28a vector and expressed in E. coli BL21 cells. 28.5 kDa NirC monomer was purified from membrane components of E. coli. Selectivity of NirC for different ions including nitrite, nitrate, sulfate, formate, and acetate anions, and a divalent cation, magnesium, was compared with that of bacterial aquaporin from Halomonas elongata. Water and ion permeability values were determined by measuring the light scattering rates of proteoliposomes containing NirC and aquaporins during their water loss and gain. NirC shows a selective permeability to nitrite and is more resistant to the entry of other anions as compared to aquaporin. The single channel permeability of NirC for nitrite is about 10-fold that of a single aquaporin channel. Both aquaporin and NirC channel proteins were impermeable to MgCl2 and (NH4)2SO4 and their permeability to other tested ions was remarkably lower as compared to nitrite ions. The study also presents the 3D model and channel characteristics of NirC. The translocation channel of E. coli NirC is determined to be larger, and its length is shorter than aquaporin channels. Although the NirC channel throat is more hydrophobic than aquaporin, its water permeability is almost equal to that of aquaporin. The hydrophobic nature of the NirC channel might play an important role in the selective permeability of the channel for nitrite ions.
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Affiliation(s)
- Hilal Yılmaz
- Environmental Engineering Department, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Esra Meşe Erdoğan
- Environmental Engineering Department, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Pınar Ergenekon
- Environmental Engineering Department, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Melek Özkan
- Environmental Engineering Department, Gebze Technical University, 41400, Kocaeli, Turkey.
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4
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Kammel M, Pinske C, Sawers RG. FocA and its central role in fine-tuning pH homeostasis of enterobacterial formate metabolism. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36197793 DOI: 10.1099/mic.0.001253] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
During enterobacterial mixed-acid fermentation, formate is generated from pyruvate by the glycyl-radical enzyme pyruvate formate-lyase (PflB). In Escherichia coli, especially at low pH, formate is then disproportionated to CO2 and H2 by the cytoplasmically oriented, membrane-associated formate hydrogenlyase (FHL) complex. If electron acceptors are available, however, formate is oxidized by periplasmically oriented, respiratory formate dehydrogenases. Formate translocation across the cytoplasmic membrane is controlled by the formate channel, FocA, a member of the formate-nitrite transporter (FNT) family of homopentameric anion channels. This review highlights recent advances in our understanding of how FocA helps to maintain intracellular formate and pH homeostasis during fermentation. Efflux and influx of formate/formic acid are distinct processes performed by FocA and both are controlled through protein interaction between FocA's N-terminal domain with PflB. Formic acid efflux by FocA helps to maintain cytoplasmic pH balance during exponential-phase growth. Uptake of formate against the electrochemical gradient (inside negative) is energetically and mechanistically challenging for a fermenting bacterium unless coupled with proton/cation symport. Translocation of formate/formic acid into the cytoplasm necessitates an active FHL complex, whose synthesis also depends on formate. Thus, FocA, FHL and PflB function together to govern formate homeostasis. We explain how FocA achieves efflux of formic acid and propose mechanisms for pH-dependent uptake of formate both with and without proton symport. We propose that FocA displays both channel- and transporter-like behaviour. Whether this translocation behaviour is shared by other members of the FNT family is also discussed.
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Affiliation(s)
- Michelle Kammel
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Constanze Pinske
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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5
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Kammel M, Sawers RG. Distinguishing functional from structural roles of conserved pore residues during formate translocation by the FocA anion channel. Microbiologyopen 2022; 11:e1312. [PMID: 36031960 PMCID: PMC9380403 DOI: 10.1002/mbo3.1312] [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: 05/23/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/10/2022] Open
Abstract
The formate‐specific anion channel FocA of Escherichia coli belongs to the superfamily of homopentameric formate‐nitrite transporters (FNT). Minimally nine amino acid residues are conserved in the formate translocation pore of each protomer of the pentamer, including a histidine (H209) and a threonine (T91), both of which are crucial for bidirectional formate translocation through the pore. Information regarding in vivo functional or structural roles for the other seven conserved residues is limited, or nonexistent. Here, we conducted an amino acid‐exchange analysis of these seven conserved residues. Using an established formate‐responsive lacZ‐based assay to monitor changes in intracellular formate levels and anaerobic growth rate due to the inhibitory formate analog hypophosphite, we identified five of the seven residues analyzed to be important for the structural integrity of the pentamer, in particular, two highly conserved asparagine residues, N213 and N262. The remaining two conserved residues, K156 and N172, were essential for formate/hypophosphite translocation. K156 is located on the periplasmic fringe of the pore and aids the attraction of formate to the channel. Here, we show that this residue is also important for formate efflux from the cytoplasm to the periplasm, suggesting a role in formate release from the pore. N172 could be replaced by alanine with retention of low‐level bidirectional anion translocation function; however, exchange for threonine abolished anion translocation. N172 is, therefore, crucial for bidirectional formate translocation, possibly through its interaction with the conserved pore residue, T91.
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Affiliation(s)
- Michelle Kammel
- Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany
| | - R Gary Sawers
- Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany
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6
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Ameliorating effect of nitrate on nitrite inhibition for denitrifying P-accumulating organisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149133. [PMID: 34311377 DOI: 10.1016/j.scitotenv.2021.149133] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/17/2021] [Accepted: 07/14/2021] [Indexed: 02/08/2023]
Abstract
Lowered air supply and organic carbon need are the key factors to reduce wastewater treatment costs and thereby, avoid eutrophication. Denitrifying PO43-- removal (DPR) process using nitrate instead of oxygen for PO43- uptake was started up in the sequencing batch reactor (SBR) at a nitrate dosing rate of 20-25 mg N L-1 d-1. Operation with a real municipal wastewater supplied with CH3COONa, K2HPO4 and KNO3 succeeded in the cultivation of biomass containing denitrifying polyphosphate accumulating organisms (DPAOs). The durations of SBR process anaerobic/anoxic/oxic cycles were 1.5 h, 3.5 h and 1 h, respectively. SBR operation resulted in a maximum PO43--P uptake of 17 mg PO43--P g-1 MLSS. The highest TN and PO43- removal efficiencies were observed during the first half of reactor operation at 77 (±10) % and 71 (±5) %, respectively. An average COD removal rate of 172 (±98) mg g-1 MLSS and a high average removal efficiency of 89 (±4) % were achieved. Nitrite effect with/without nitrate as DPR electron acceptor was investigated in batch-scale to show possibilities to use high nitrite and nitrate contents simultaneously as electron acceptors for the anoxic phosphate uptake. Nitrate attenuation against nitrite toxicity can be economically justified in full-scale treatment applications in which wastewater has a high nitrogen content. Nitrate attenuated nitrite toxicity (caused by nitrite content at 5-100 mg NO2--N L-1) when using supplemental additions of nitrate (at concentrations of 45-200 mg NO3--N L-1) in batch tests. Illumina sequencing emphasized that during biomass adaption microbial community changed by lowered aerobic cycle length and by lowered nitrate dosing towards representation of key DPAO/PAO- organisms, such as Candidatus Accumulibacter, Xanthomonadaceae, Comomonadaceae, Saprospiraceae and Rhodocyclaceae. This study showed that DPAO biomass adaption to nitrate maintained an efficient COD, nitrogen and phosphorus removal and the biomass can be applied for treatment of wastewater containing high nitrite and nitrate content.
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7
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Martín-Rodríguez AJ, Rhen M, Melican K, Richter-Dahlfors A. Nitrate Metabolism Modulates Biosynthesis of Biofilm Components in Uropathogenic Escherichia coli and Acts as a Fitness Factor During Experimental Urinary Tract Infection. Front Microbiol 2020; 11:26. [PMID: 32082279 PMCID: PMC7005491 DOI: 10.3389/fmicb.2020.00026] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/08/2020] [Indexed: 11/15/2022] Open
Abstract
To successfully colonize a variety of environments, bacteria can coordinate complex collective behaviors such as biofilm formation. To thrive in oxygen limited niches, bacteria’s versatile physiology enables the utilization of alternative electron acceptors. Nitrate, the second most favorable electron acceptor after oxygen, plays a prominent role in the physiology of uropathogenic Escherichia coli (UPEC) and is abundantly found in urine. Here we analyzed the role of extracellular nitrate in the pathogenesis of the UPEC strain CFT073 with an initial focus on biofilm formation. Colony morphotyping in combination with extensive mutational, transcriptional, and protein expression analyses of CFT073 wild-type and mutants deficient in one or several nitrate reductases revealed an association between nitrate reduction and the biosynthesis of biofilm extracellular matrix components. We identified a role for the nitrate response regulator NarL in modulating expression of the biofilm master regulator CsgD. To analyze the role of nitrate reduction during infection in vivo, we tested wild-type CFT073 and a nitrate reductase null mutant in an ascending urinary tract infection (UTI) model. Individually, each strain colonized extensively, suggesting that nitrate reduction is expendable during UTI. However, during competitive co-infection, the strain incapable of nitrate reduction was strongly outcompeted. This suggests that nitrate reduction can be considered a non-essential but advantageous fitness factor for UPEC pathogenesis. This implies that UPEC rapidly adapts their metabolic needs to the microenvironment of infected tissue. Collectively, this work demonstrates a unique association between nitrate respiration, biofilm formation, and UPEC pathogenicity, highlighting how the use of alternative electron acceptors enables bacterial pathogens to adapt to challenging infectious microenvironments.
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Affiliation(s)
| | - Mikael Rhen
- Department of Neuroscience, Swedish Medical Nanoscience Center, Karolinska Institutet, Solna, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Keira Melican
- Department of Neuroscience, Swedish Medical Nanoscience Center, Karolinska Institutet, Solna, Sweden
| | - Agneta Richter-Dahlfors
- Department of Neuroscience, Swedish Medical Nanoscience Center, Karolinska Institutet, Solna, Sweden
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8
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Guo H, Chen C, Lee DJ. Nitrogen and sulfur metabolisms of Pseudomonas sp. C27 under mixotrophic growth condition. BIORESOURCE TECHNOLOGY 2019; 293:122169. [PMID: 31561980 DOI: 10.1016/j.biortech.2019.122169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 05/16/2023]
Abstract
Pseudomonas sp. C27 is a facultative autotrophic bacterium that can grow mixotrophically to undergo denitrifying sulfide removal (DSR) reactions with both organic matters and sulfide as electron donors. A detailed understanding of how the C27 strain simultaneously removes nitrogen, sulfur and carbon from water is critical for optimal DSR process design and implementation. This study is the first to reveal the pathways of nitrogen and sulfur metabolisms, identifying a total of 47 proteins that are related to the nitrogen metabolism and seven proteins to the sulfur metabolism of strain C27 using iTRAQ and LC-MS/MS techniques. The proposed pathway of nitrogen metabolism for strain C27 from external nitrate to nitrogen gas and phosphate with a coupled ammonia cycle is based on the identified proteins, and suggests that nitrate was not essential for nitrogen metabolism and could be replaced by nitrite as the sole nitrogen source for C27.
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Affiliation(s)
- Hongliang Guo
- College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; College of Technology and Engineering, National Taiwan Normal University, Taipei 10610, Taiwan; College of Engineering, Tunghai University, Taichung 40070, Taiwan.
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9
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Gonzalez E, Pitre FE, Pagé AP, Marleau J, Guidi Nissim W, St-Arnaud M, Labrecque M, Joly S, Yergeau E, Brereton NJB. Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. MICROBIOME 2018; 6:53. [PMID: 29562928 PMCID: PMC5863371 DOI: 10.1186/s40168-018-0432-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/02/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life. METHODS Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed. RESULTS The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation. CONCLUSIONS Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.
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Affiliation(s)
- E Gonzalez
- Canadian Center for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montréal, H3A 1A4, Canada
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - F E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - A P Pagé
- Aquatic and Crop Resource Development (ACRD), National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - J Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
| | - W Guidi Nissim
- Department of Agri-food and Environmental Science, University of Florence, Viale delle Idee, Sesto Fiorentino, FI, Italy
| | - M St-Arnaud
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - M Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - S Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - E Yergeau
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - N J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.
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10
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Atkovska K, Hub JS. Energetics and mechanism of anion permeation across formate-nitrite transporters. Sci Rep 2017; 7:12027. [PMID: 28931899 PMCID: PMC5607303 DOI: 10.1038/s41598-017-11437-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/24/2017] [Indexed: 01/13/2023] Open
Abstract
Formate-nitrite transporters (FNTs) facilitate the translocation of monovalent polyatomic anions, such as formate and nitrite, across biological membranes. FNTs are widely distributed among pathogenic bacteria and eukaryotic parasites, but they lack human homologues, making them attractive drug targets. The mechanisms and energetics involved in anion permeation across the FNTs have remained largely unclear. Both, channel and transporter mode of function have been proposed, with strong indication of proton coupling to the permeation process. We combine molecular dynamics simulations, quantum mechanical calculations, and pK a calculations, to compute the energetics of the complete permeation cycle of an FNT. We find that anions as such, are not able to traverse the FNT pore. Instead, anion binding into the pore is energetically coupled to protonation of a centrally located histidine. In turn, the histidine can protonate the permeating anion, thereby enabling its release. Such mechanism can accommodate the functional diversity among the FNTs, as it may facilitate both, export and import of substrates, with or without proton co-transport. The mechanism excludes proton leakage via the Grotthuss mechanism, and it rationalises the selectivity for weak acids.
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Affiliation(s)
- Kalina Atkovska
- University of Goettingen, Institute for Microbiology and Genetics, Goettingen, 37077, Germany.,University of Goettingen, Göttingen Center for Molecular Biosciences, Goettingen, 37077, Germany
| | - Jochen S Hub
- University of Goettingen, Institute for Microbiology and Genetics, Goettingen, 37077, Germany. .,University of Goettingen, Göttingen Center for Molecular Biosciences, Goettingen, 37077, Germany.
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11
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Koch CD, Gladwin MT, Freeman BA, Lundberg JO, Weitzberg E, Morris A. Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health. Free Radic Biol Med 2017; 105:48-67. [PMID: 27989792 PMCID: PMC5401802 DOI: 10.1016/j.freeradbiomed.2016.12.015] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/18/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
Recent insights into the bioactivation and signaling actions of inorganic, dietary nitrate and nitrite now suggest a critical role for the microbiome in the development of cardiac and pulmonary vascular diseases. Once thought to be the inert, end-products of endothelial-derived nitric oxide (NO) heme-oxidation, nitrate and nitrite are now considered major sources of exogenous NO that exhibit enhanced vasoactive signaling activity under conditions of hypoxia and stress. The bioavailability of nitrate and nitrite depend on the enzymatic reduction of nitrate to nitrite by a unique set of bacterial nitrate reductase enzymes possessed by specific bacterial populations in the mammalian mouth and gut. The pathogenesis of pulmonary hypertension (PH), obesity, hypertension and CVD are linked to defects in NO signaling, suggesting a role for commensal oral bacteria to shape the development of PH through the formation of nitrite, NO and other bioactive nitrogen oxides. Oral supplementation with inorganic nitrate or nitrate-containing foods exert pleiotropic, beneficial vascular effects in the setting of inflammation, endothelial dysfunction, ischemia-reperfusion injury and in pre-clinical models of PH, while traditional high-nitrate dietary patterns are associated with beneficial outcomes in hypertension, obesity and CVD. These observations highlight the potential of the microbiome in the development of novel nitrate- and nitrite-based therapeutics for PH, CVD and their risk factors.
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Affiliation(s)
- Carl D Koch
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA.
| | - Mark T Gladwin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA; Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh PA 15261, USA
| | - Bruce A Freeman
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh PA 15261, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jon O Lundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, S-17177 Stockholm, Sweden
| | - Eddie Weitzberg
- Department of Physiology and Pharmacology, Karolinska Institutet, S-17177 Stockholm, Sweden
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA; Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh PA 15261, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Physiology and Pharmacology, Karolinska Institutet, S-17177 Stockholm, Sweden
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12
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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: 20] [Impact Index Per Article: 2.5] [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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13
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Li G, Sierra-Alvarez R, Vilcherrez D, Weiss S, Gill C, Krzmarzick MJ, Abrell L, Field JA. Nitrate Reverses Severe Nitrite Inhibition of Anaerobic Ammonium Oxidation (Anammox) Activity in Continuously-Fed Bioreactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:10518-10526. [PMID: 27597320 DOI: 10.1021/acs.est.6b01560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nitrite (NO2-) substrate under certain conditions can cause failure of N-removal processes relying on anaerobic ammonium oxidizing (anammox) bacteria. Detoxification of NO2- can potentially be achieved by using exogenous nitrate (NO3-). In this work, continuous experiments in bioreactors with anammox bacteria closely related to "Candidatus Brocadia caroliniensis" were conducted to evaluate the effectiveness of short NO3- additions to reverse NO2- toxicity. The results show that a timely NO3- addition immediately after a NO2- stress event completely reversed the NO2- inhibition. This reversal occurs without NO3- being metabolized as evidence by lack of any 30N2 formation from 15N-NO3-. The maximum recovery rate was observed with 5 mM NO3- added for 3 days; however, slower but significant recovery was also observed with 5 mM NO3- for 1 day or 2 mM NO3- for 3 days. Without NO3- addition, long-term NO2- inhibition of anammox biomass resulted in irreversible damage of the cells. These results suggest that a short duration dose of NO3- to an anammox bioreactor can rapidly restore the activity of NO2--stressed anammox cells. On the basis of the results, a hypothesis about the detoxification mechanism related to narK genes in anammox bacteria is proposed and discussed.
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Affiliation(s)
- Guangbin Li
- Department of Chemical and Environmental Engineering, University of Arizona , 1133 E. James E. Rogers Way, Tucson, Arizona 85721-001, United States
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, University of Arizona , 1133 E. James E. Rogers Way, Tucson, Arizona 85721-001, United States
| | - David Vilcherrez
- Department of Chemical and Environmental Engineering, University of Arizona , 1133 E. James E. Rogers Way, Tucson, Arizona 85721-001, United States
| | - Stefan Weiss
- Department of Chemical and Environmental Engineering, University of Arizona , 1133 E. James E. Rogers Way, Tucson, Arizona 85721-001, United States
| | - Callie Gill
- Department of Chemical and Environmental Engineering, University of Arizona , 1133 E. James E. Rogers Way, Tucson, Arizona 85721-001, United States
| | - Mark J Krzmarzick
- School of Civil and Environmental Engineering, Oklahoma State University , 207 Engineering, South Stillwater, Oklahoma 74078, United States
| | - Leif Abrell
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721-0041, United States
- Department of Soil, Water & Environmental Science, University of Arizona , Tucson, Arizona 85721-0041, United States
| | - Jim A Field
- Department of Chemical and Environmental Engineering, University of Arizona , 1133 E. James E. Rogers Way, Tucson, Arizona 85721-001, United States
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14
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Sawers RG, Falke D, Fischer M. Oxygen and Nitrate Respiration in Streptomyces coelicolor A3(2). Adv Microb Physiol 2016; 68:1-40. [PMID: 27134020 DOI: 10.1016/bs.ampbs.2016.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Streptomyces species belong to the phylum Actinobacteria and can only grow with oxygen as a terminal electron acceptor. Like other members of this phylum, such as corynebacteria and mycobacteria, the aerobic respiratory chain lacks a soluble cytochrome c. It is therefore implicit that direct electron transfer between the cytochrome bc1 and the cytochrome aa3 oxidase complexes occurs. The complex developmental cycle of streptomycetes manifests itself in the production of spores, which germinate in the presence of oxygen into a substrate mycelium that greatly facilitates acquisition of nutrients necessary to support their saprophytic lifestyle in soils. Due to the highly variable oxygen levels in soils, streptomycetes have developed means of surviving long periods of hypoxia or even anaerobiosis but they fail to grow under these conditions. Little to nothing is understood about how they maintain viability under conditions of oxygen limitation. It is assumed that they can utilise a number of different electron acceptors to help them maintain a membrane potential, one of which is nitrate. The model streptomycete remains Streptomyces coelicolor A3(2), and it synthesises three nonredundant respiratory nitrate reductases (Nar). These Nar enzymes are synthesised during different phases of the developmental cycle and they are functional only under oxygen-limiting (<5% oxygen in air) conditions. Nevertheless, the regulation of their synthesis does not appear to be responsive to nitrate and in the case of Nar1, it appears to be developmentally regulated. This review highlights some of the novel aspects of our current, but somewhat limited, knowledge of respiration in these fascinating bacteria.
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Affiliation(s)
- R G Sawers
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany.
| | - D Falke
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - M Fischer
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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15
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Abstract
Mycobacteria inhabit a wide range of intracellular and extracellular environments. Many of these environments are highly dynamic and therefore mycobacteria are faced with the constant challenge of redirecting their metabolic activity to be commensurate with either replicative growth or a non-replicative quiescence. A fundamental feature in this adaptation is the ability of mycobacteria to respire, regenerate reducing equivalents and generate ATP via oxidative phosphorylation. Mycobacteria harbor multiple primary dehydrogenases to fuel the electron transport chain and two terminal respiratory oxidases, an aa3 -type cytochrome c oxidase and cytochrome bd-type menaquinol oxidase, are present for dioxygen reduction coupled to the generation of a protonmotive force. Hypoxia leads to the downregulation of key respiratory complexes, but the molecular mechanisms regulating this expression are unknown. Despite being obligate aerobes, mycobacteria have the ability to metabolize in the absence of oxygen and a number of reductases are present to facilitate the turnover of reducing equivalents under these conditions (e.g. nitrate reductase, succinate dehydrogenase/fumarate reductase). Hydrogenases and ferredoxins are also present in the genomes of mycobacteria suggesting the ability of these bacteria to adapt to an anaerobic-type of metabolism in the absence of oxygen. ATP synthesis by the membrane-bound F1FO-ATP synthase is essential for growing and non-growing mycobacteria and the enzyme is able to function over a wide range of protonmotive force values (aerobic to hypoxic). The discovery of lead compounds that target respiration and oxidative phosphorylation in Mycobacterium tuberculosis highlights the importance of this area for the generation of new front line drugs to combat tuberculosis.
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16
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Nolan JV, Godwin IR, de Raphélis-Soissan V, Hegarty RS. Managing the rumen to limit the incidence and severity of nitrite poisoning in nitrate-supplemented ruminants. ANIMAL PRODUCTION SCIENCE 2016. [DOI: 10.1071/an15324] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Inclusion of nitrate (NO3−) in ruminant diets is a means of increasing non-protein nitrogen intake while at the same time reducing emissions of enteric methane (CH4) and, in Australia, gaining carbon credits. Rumen microorganisms contain intracellular enzymes that use hydrogen (H2) released during fermentation to reduce NO3− to nitrite (NO2−), and then reduce the resulting NO2− to ammonia or gaseous intermediates such as nitrous oxide (N2O) and nitric oxide (NO). This diversion of H2 reduces CH4 formation in the rumen. If NO2− accumulates in the rumen, it may inhibit growth of methanogens and other microorganisms and this may further reduce CH4 production, but also lower feed digestibility. If NO2− is absorbed and enters red blood cells, methaemoglobin is formed and this lowers the oxygen-carrying capacity of the blood. Nitric oxide produced from absorbed NO2− reduces blood pressure, which, together with the effects of methaemoglobin, can, at times, lead to extreme hypoxia and death. Nitric oxide, which can be formed in the gut as well as in tissues, has a variety of physiological effects, e.g. it reduces primary rumen contractions and slows passage of digesta, potentially limiting feed intake. It is important to find management strategies that minimise the accumulation of NO2−; these include slowing the rate of presentation of NO3– to rumen microbes or increasing the rate of removal of NO2−, or both. The rate of reduction of NO3− to NO2− depends on the level of NO3− in feed and its ingestion rate, which is related to the animal’s feeding behaviour. After NO3− is ingested, its peak concentration in the rumen depends on its rate of solubilisation. Once in solution, NO3− is imported by bacteria and protozoa and quickly reduced to NO2−. One management option is to encapsulate the NO3− supplement to lower its solubility. Acclimating animals to NO3− is an established management strategy that appears to limit NO2− accumulation in the rumen by increasing microbial nitrite reductase activity more than nitrate reductase activity; however, it does not guarantee complete protection from NO2− poisoning. Adding concentrates into nitrate-containing diets also helps reduce the risk of poisoning and inclusion of microbial cultures with enhanced NO2−-reducing properties is another potential management option. A further possibility is to inhibit NO2− absorption. Animals differ in their tolerance to NO3− supplementation, so there may be opportunities for breeding animals more tolerant of dietary NO3−. Our review aims to integrate current knowledge of microbial processes responsible for accumulation of NO2− in rumen fluid and to identify management options that could minimise the risks of NO2− poisoning while reducing methane emissions and maintaining or enhancing livestock production.
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17
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Nitrate reduction to nitrite, nitric oxide and ammonia by gut bacteria under physiological conditions. PLoS One 2015; 10:e0119712. [PMID: 25803049 PMCID: PMC4372352 DOI: 10.1371/journal.pone.0119712] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/16/2015] [Indexed: 12/18/2022] Open
Abstract
The biological nitrogen cycle involves step-wise reduction of nitrogen oxides to ammonium salts and oxidation of ammonia back to nitrites and nitrates by plants and bacteria. Neither process has been thought to have relevance to mammalian physiology; however in recent years the salivary bacterial reduction of nitrate to nitrite has been recognized as an important metabolic conversion in humans. Several enteric bacteria have also shown the ability of catalytic reduction of nitrate to ammonia via nitrite during dissimilatory respiration; however, the importance of this pathway in bacterial species colonizing the human intestine has been little studied. We measured nitrite, nitric oxide (NO) and ammonia formation in cultures of Escherichia coli, Lactobacillus and Bifidobacterium species grown at different sodium nitrate concentrations and oxygen levels. We found that the presence of 5 mM nitrate provided a growth benefit and induced both nitrite and ammonia generation in E.coli and L.plantarum bacteria grown at oxygen concentrations compatible with the content in the gastrointestinal tract. Nitrite and ammonia accumulated in the growth medium when at least 2.5 mM nitrate was present. Time-course curves suggest that nitrate is first converted to nitrite and subsequently to ammonia. Strains of L.rhamnosus, L.acidophilus and B.longum infantis grown with nitrate produced minor changes in nitrite or ammonia levels in the cultures. However, when supplied with exogenous nitrite, NO gas was readily produced independently of added nitrate. Bacterial production of lactic acid causes medium acidification that in turn generates NO by non-enzymatic nitrite reduction. In contrast, nitrite was converted to NO by E.coli cultures even at neutral pH. We suggest that the bacterial nitrate reduction to ammonia, as well as the related NO formation in the gut, could be an important aspect of the overall mammalian nitrate/nitrite/NO metabolism and is yet another way in which the microbiome links diet and health.
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18
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Hou X, McMillan M, Coumans JVF, Poljak A, Raftery MJ, Pereg L. Cellular responses during morphological transformation in Azospirillum brasilense and Its flcA knockout mutant. PLoS One 2014; 9:e114435. [PMID: 25502569 PMCID: PMC4264754 DOI: 10.1371/journal.pone.0114435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/10/2014] [Indexed: 01/25/2023] Open
Abstract
FlcA is a response regulator controlling flocculation and the morphological transformation of Azospirillum cells from vegetative to cyst-like forms. To understand the cellular responses of Azospirillum to conditions that cause morphological transformation, proteins differentially expressed under flocculation conditions in A. brasilense Sp7 and its flcA knockout mutant were investigated. Comparison of 2-DE protein profiles of wild-type (Sp7) and a flcA deletion mutant (Sp7-flcAΔ) revealed a total of 33 differentially expressed 2-DE gel spots, with 22 of these spots confidently separated to allow protein identification. Analysis of these spots by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and MASCOT database searching identified 48 proteins (≥10% emPAI in each spot). The functional characteristics of these proteins included carbon metabolism (beta-ketothiolase and citrate synthase), nitrogen metabolism (Glutamine synthetase and nitric oxide synthase), stress tolerance (superoxide dismutase, Alkyl hydroperoxidase and ATP-dependent Clp protease proteolytic subunit) and morphological transformation (transducer coupling protein). The observed differences between Sp7 wild-type and flcA− strains enhance our understanding of the morphological transformation process and help to explain previous phenotypical observations. This work is a step forward in connecting the Azospirillum phenome and genome.
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Affiliation(s)
- Xingsheng Hou
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- Department of Microbiology and Immunology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Mary McMillan
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
| | - Joëlle V. F. Coumans
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- School of Rural Medicine, University of New England, Armidale, New South Wales, Australia
| | - Anne Poljak
- Bioanalytical Mass Spectrometry Facility, Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
- The School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Lily Pereg
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
- * E-mail: mailto:
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19
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Abstract
Some eukaryotes, such as plant and fungi, are capable of utilizing nitrate as the sole nitrogen source. Once transported into the cell, nitrate is reduced to ammonium by the consecutive action of nitrate and nitrite reductase. How nitrate assimilation is balanced with nitrate and nitrite efflux is unknown, as are the proteins involved. The nitrate assimilatory yeast Hansenula polymorpha was used as a model to dissect these efflux systems. We identified the sulfite transporters Ssu1 and Ssu2 as effective nitrate exporters, Ssu2 being quantitatively more important, and we characterize the Nar1 protein as a nitrate/nitrite exporter. The use of strains lacking either SSU2 or NAR1 along with the nitrate reductase gene YNR1 showed that nitrate reductase activity is not required for net nitrate uptake. Growth test experiments indicated that Ssu2 and Nar1 exporters allow yeast to cope with nitrite toxicity. We also have shown that the well-known Saccharomyces cerevisiae sulfite efflux permease Ssu1 is also able to excrete nitrite and nitrate. These results characterize for the first time essential components of the nitrate/nitrite efflux system and their impact on net nitrate uptake and its regulation.
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20
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Kotur Z, Siddiqi YM, Glass ADM. Characterization of nitrite uptake in Arabidopsis thaliana: evidence for a nitrite-specific transporter. THE NEW PHYTOLOGIST 2013; 200:201-210. [PMID: 23763619 DOI: 10.1111/nph.12358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/08/2013] [Indexed: 05/16/2023]
Abstract
Nitrite-specific plasma membrane transporters have been described in bacteria, algae and fungi, but there is no evidence of a nitrite-specific plasma membrane transporter in higher plants. We have used 13NO2(-) to characterize nitrite influx into roots of Arabidopsis thaliana. Hydroponically grown Arabidopsis mutants, defective in high-affinity nitrate transport, were used to distinguish between nitrate and nitrite uptake by means of the short-lived tracers 13NO2(-) and 13NO3(-). This approach allowed us to characterize a nitrite-specific transporter. The Atnar2.1-2 mutant, lacking a functional high-affinity nitrate transport system, is capable of nitrite influx that is constitutive and thermodynamically active. The corresponding fluxes conform to a rectangular hyperbola, exhibiting saturation at concentrations above 200 μM (Km = 185 μM and Vmax = 1.89 μmol g(-1) FW h(-1)). Nitrite influx via the putative nitrite transporter is not subject to competitive inhibition by nitrate but is downregulated after 6 h exposure to ammonium. These results signify the existence of a nitrite-specific transporter in Arabidopsis. This transporter enables Atnar2.1-2 mutants, which are incapable of sustained growth on low nitrate, to maintain significant growth on low nitrite. In wild-type plants, this nitrite flux may increase nitrogen acquisition and also participate in the induction of genes specifically induced by nitrite.
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Affiliation(s)
- Zorica Kotur
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T1Z4, Canada
| | - Yaeesh M Siddiqi
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T1Z4, Canada
| | - Anthony D M Glass
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T1Z4, Canada
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21
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Abstract
Mineral nitrogen in nature is often found in the form of nitrate (NO3-). Numerous microorganisms evolved to assimilate nitrate and use it as a major source of mineral nitrogen uptake1. Nitrate, which is central in nitrogen metabolism, is first reduced to nitrite (NO2-) through a two-electron reduction reaction2,3. The accumulation of cellular nitrite can be harmful because nitrite can be reduced to the cytotoxic nitric oxide. Instead, nitrite is rapidly removed from the cell by channels and transporters, or reduced to ammonium or dinitrogen through the action of assimilatory enzymes3. Despite decades of effort no structure is currently available for any nitrate transport protein and the mechanism by which nitrate is transported remains largely obscure. Here we report the structure of a bacterial nitrate/nitrite transport protein, NarK, from Escherichia coli, with and without substrate. The structures reveal a positively charged substrate-translocation pathway lacking protonatable residues, suggesting that NarK functions as a nitrate/nitrite exchanger and that H+s are unlikely to be co-transported. Conserved arginine residues form the substrate-binding pocket, which is formed by association of helices from the two halves of NarK. Key residues that are important for substrate recognition and transport are identified and related to extensive mutagenesis and functional studies. We propose that NarK exchanges nitrate for nitrite by a rocker-switch mechanism facilitated by inter-domain H-bond networks.
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22
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Structure and mechanism of a nitrate transporter. Cell Rep 2013; 3:716-23. [PMID: 23523348 DOI: 10.1016/j.celrep.2013.03.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/20/2013] [Accepted: 03/06/2013] [Indexed: 11/23/2022] Open
Abstract
The nitrate/nitrite transporters NarK and NarU play an important role in nitrogen homeostasis in bacteria and belong to the nitrate/nitrite porter family (NNP) of the major facilitator superfamily (MFS) fold. The structure and functional mechanism of NarK and NarU remain unknown. Here, we report the crystal structure of NarU at a resolution of 3.1 Å and systematic biochemical characterization. The two molecules of NarU in an asymmetric unit exhibit two distinct conformational states: occluded and partially inward-open. The substrate molecule nitrate appears to be coordinated by four highly conserved, charged, or polar amino acids. Structural and biochemical analyses allowed the identification of key amino acids that are involved in substrate gating and transport. The observed conformational differences of NarU, together with unique sequence features of the NNP family transporters, suggest a transport mechanism that might deviate from the canonical rocker-switch model.
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23
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Bhat SA, Singh N, Trivedi A, Kansal P, Gupta P, Kumar A. The mechanism of redox sensing in Mycobacterium tuberculosis. Free Radic Biol Med 2012; 53:1625-41. [PMID: 22921590 DOI: 10.1016/j.freeradbiomed.2012.08.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 08/03/2012] [Accepted: 08/03/2012] [Indexed: 12/25/2022]
Abstract
Tuberculosis epidemics have defied constraint despite the availability of effective treatment for the past half-century. Mycobacterium tuberculosis, the causative agent of TB, is continually exposed to a number of redox stressors during its pathogenic cycle. The mechanisms used by Mtb to sense redox stress and to maintain redox homeostasis are central to the success of Mtb as a pathogen. Careful analysis of the Mtb genome has revealed that Mtb lacks classical redox sensors such as FNR, FixL, and OxyR. Recent studies, however, have established that Mtb is equipped with various sophisticated redox sensors that can detect diverse types of redox stress, including hypoxia, nitric oxide, carbon monoxide, and the intracellular redox environment. Some of these sensors, such as heme-based DosS and DosT, are unique to mycobacteria, whereas others, such as the WhiB proteins and anti-σ factor RsrA, are unique to actinobacteria. This article provides a comprehensive review of the literature on these redox-sensory modules in the context of TB pathogenesis.
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Affiliation(s)
- Shabir Ahmad Bhat
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India
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24
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Giffin MM, Raab RW, Morganstern M, Sohaskey CD. Mutational analysis of the respiratory nitrate transporter NarK2 of Mycobacterium tuberculosis. PLoS One 2012; 7:e45459. [PMID: 23029022 PMCID: PMC3445494 DOI: 10.1371/journal.pone.0045459] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/22/2012] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium tuberculosis induces nitrate reductase activity in response to decreasing oxygen levels. This is due to regulation of both the transcription and the activity of the nitrate transporter NarK2. A model of NarK2 structure is proposed containing 12 membrane spanning regions consistent with other members of the major facilitator superfamily. The role of the proton gradient was determined by exposing M. tuberculosis to uncouplers. Nitrite production decreased indicating that the importation of nitrate involved an H+/nitrate symporter. The addition of nitrite before nitrate had no effect, suggesting no role for a nitrate/nitrite antiporter. In addition the NarK2 knockout mutant showed no defect in nitrite export. NarK2 is proposed to be a Type I H+/nitrate symporter. Site directed mutagenesis was performed changing 23 amino acids of NarK2. This allowed the identification of important regions and amino acids of this transporter. Five of these mutants were inactive for nitrate transport, seven produced reduced activity and eleven mutants retained wild type activity. NarK2 is inactivated in the presence of oxygen by an unknown mechanism. However none of the mutants, including those with mutated cysteines, were altered in their response to oxygen levels. The assimilatory nitrate transporter NasA of Bacillus subtilis was expressed in the M. tuberculosis NarK2 mutant. It remained active during aerobic incubation showing that the point of oxygen control is NarK2.
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25
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Simon J, Klotz MG. Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:114-35. [PMID: 22842521 DOI: 10.1016/j.bbabio.2012.07.005] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/10/2012] [Accepted: 07/19/2012] [Indexed: 11/18/2022]
Abstract
Nitrogen is an essential element of life that needs to be assimilated in its most reduced form, ammonium. On the other hand, nitrogen exists in a multitude of oxidation states and, consequently, nitrogen compounds (NCs) serve as electron donor and/or acceptors in many catabolic pathways including various forms of microbial respiration that contribute to the global biogeochemical nitrogen cycle. Some of these NCs are also known as reactive nitrogen species able to cause nitrosative stress because of their high redox reactivity. The best understood processes of the nitrogen cycle are denitrification and ammonification (both beginning with nitrate reduction to nitrite), nitrification (aerobic oxidation of ammonium and nitrite) and anaerobic ammonium oxidation (anammox). This review presents examples of the diverse architecture, either elucidated or anticipated, and the high degree of modularity of the corresponding respiratory electron transport processes found in Bacteria and Archaea, and relates these to their respective bioenergetic mechanisms of proton motive force generation. In contrast to the multiplicity of enzymes that catalyze NC transformations, the number of proteins or protein modules involved in connecting electron transport to and from these enzymes with the quinone/quinol pool is comparatively small. These quinone/quinol-reactive protein modules consist of cytochromes b and c and iron-sulfur proteins. Conclusions are drawn towards the evolutionary relationships of bioenergetic systems involved in NC transformation and deduced aspects of the evolution of the biogeochemical nitrogen cycle are presented. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany.
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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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Trivedi A, Singh N, Bhat SA, Gupta P, Kumar A. Redox biology of tuberculosis pathogenesis. Adv Microb Physiol 2012; 60:263-324. [PMID: 22633061 DOI: 10.1016/b978-0-12-398264-3.00004-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most successful human pathogens. Mtb is persistently exposed to numerous oxidoreductive stresses during its pathogenic cycle of infection and transmission. The distinctive ability of Mtb, not only to survive the redox stress manifested by the host but also to use it for synchronizing the metabolic pathways and expression of virulence factors, is central to its success as a pathogen. This review describes the paradigmatic redox and hypoxia sensors employed by Mtb to continuously monitor variations in the intracellular redox state and the surrounding microenvironment. Two component proteins, namely, DosS and DosT, are employed by Mtb to sense changes in oxygen, nitric oxide, and carbon monoxide levels, while WhiB3 and anti-sigma factor RsrA are used to monitor changes in intracellular redox state. Using these and other unidentified redox sensors, Mtb orchestrates its metabolic pathways to survive in nutrient-deficient, acidic, oxidative, nitrosative, and hypoxic environments inside granulomas or infectious lesions. A number of these metabolic pathways are unique to mycobacteria and thus represent potential drug targets. In addition, Mtb employs versatile machinery of the mycothiol and thioredoxin systems to ensure a reductive intracellular environment for optimal functioning of its proteins even upon exposure to oxidative stress. Mtb also utilizes a battery of protective enzymes, such as superoxide dismutase (SOD), catalase (KatG), alkyl hydroperoxidase (AhpC), and peroxiredoxins, to neutralize the redox stress generated by the host immune system. This chapter reviews the current understanding of mechanisms employed by Mtb to sense and neutralize redox stress and their importance in TB pathogenesis and drug development.
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28
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Unkles SE, Symington VF, Kotur Z, Wang Y, Siddiqi MY, Kinghorn JR, Glass ADM. Physiological and biochemical characterization of AnNitA, the Aspergillus nidulans high-affinity nitrite transporter. EUKARYOTIC CELL 2011; 10:1724-32. [PMID: 22021238 PMCID: PMC3232726 DOI: 10.1128/ec.05199-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Accepted: 10/12/2011] [Indexed: 11/20/2022]
Abstract
High-affinity nitrite influx into mycelia of Aspergillus nidulans has been characterized by use of (13)NO(2)(-), giving average K(m) and V(max) values of 48 ± 8 μM and 228 ± 49 nmol mg(-1) dry weight (DW) h(-1), respectively. Kinetic analysis of a plot that included an additional large number of low-concentration fluxes gave an excellent monophasic fit (r(2) = 0.96), with no indication of sigmoidal kinetics. Two-dimensional (2D) and three-dimensional (3D) models of AnNitA are presented, and the possible roles of conserved asparagine residues N122 (transmembrane domain 3 ]Tm 3]), N173 (Tm 4), N214 (Tm 5), and N246 (Tm 6) are discussed.
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Affiliation(s)
- Shiela E. Unkles
- School of Biology, University of St. Andrews, St. Andrews, Fife KY16 9TH, United Kingdom
| | - Vicki F. Symington
- School of Biology, University of St. Andrews, St. Andrews, Fife KY16 9TH, United Kingdom
| | - Zorica Kotur
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ye Wang
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - M. Yaeesh Siddiqi
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - James R. Kinghorn
- School of Biology, University of St. Andrews, St. Andrews, Fife KY16 9TH, United Kingdom
| | - Anthony D. M. Glass
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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A composite biochemical system for bacterial nitrate and nitrite assimilation as exemplified by Paracoccus denitrificans. Biochem J 2011; 435:743-53. [PMID: 21348864 DOI: 10.1042/bj20101920] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The denitrifying bacterium Paracoccus denitrificans can grow aerobically or anaerobically using nitrate or nitrite as the sole nitrogen source. The biochemical pathway responsible is expressed from a gene cluster comprising a nitrate/nitrite transporter (NasA), nitrite transporter (NasH), nitrite reductase (NasB), ferredoxin (NasG) and nitrate reductase (NasC). NasB and NasG are essential for growth with nitrate or nitrite as the nitrogen source. NADH serves as the electron donor for nitrate and nitrite reduction, but only NasB has a NADH-oxidizing domain. Nitrate and nitrite reductase activities show the same Km for NADH and can be separated by anion-exchange chromatography, but only fractions containing NasB retain the ability to oxidize NADH. This implies that NasG mediates electron flux from the NADH-oxidizing site in NasB to the sites of nitrate and nitrite reduction in NasC and NasB respectively. Delivery of extracellular nitrate to NasBGC is mediated by NasA, but both NasA and NasH contribute to nitrite uptake. The roles of NasA and NasC can be substituted during anaerobic growth by the biochemically distinct membrane-bound respiratory nitrate reductase (Nar), demonstrating functional overlap. nasG is highly conserved in nitrate/nitrite assimilation gene clusters, which is consistent with a key role for the NasG ferredoxin, as part of a phylogenetically widespread composite nitrate and nitrite reductase system.
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Wang Y, Huang Y, Wang J, Cheng C, Huang W, Lu P, Xu YN, Wang P, Yan N, Shi Y. Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel. Nature 2010; 462:467-72. [PMID: 19940917 DOI: 10.1038/nature08610] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2009] [Accepted: 10/26/2009] [Indexed: 11/09/2022]
Abstract
FocA is a representative member of the formate-nitrite transporter family, which transports short-chain acids in bacteria, archaea, fungi, algae and parasites. The structure and transport mechanism of the formate-nitrite transporter family remain unknown. Here we report the crystal structure of Escherichia coli FocA at 2.25 A resolution. FocA forms a symmetric pentamer, with each protomer consisting of six transmembrane segments. Despite a lack of sequence homology, the overall structure of the FocA protomer closely resembles that of aquaporin and strongly argues that FocA is a channel, rather than a transporter. Structural analysis identifies potentially important channel residues, defines the channel path and reveals two constriction sites. Unlike aquaporin, FocA is impermeable to water but allows the passage of formate. A structural and biochemical investigation provides mechanistic insights into the channel activity of FocA.
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Affiliation(s)
- Yi Wang
- Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
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31
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Cook GM, Berney M, Gebhard S, Heinemann M, Cox RA, Danilchanka O, Niederweis M. Physiology of mycobacteria. Adv Microb Physiol 2009; 55:81-182, 318-9. [PMID: 19573696 DOI: 10.1016/s0065-2911(09)05502-7] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis is a prototrophic, metabolically flexible bacterium that has achieved a spread in the human population that is unmatched by any other bacterial pathogen. The success of M. tuberculosis as a pathogen can be attributed to its extraordinary stealth and capacity to adapt to environmental changes throughout the course of infection. These changes include: nutrient deprivation, hypoxia, various exogenous stress conditions and, in the case of the pathogenic species, the intraphagosomal environment. Knowledge of the physiology of M. tuberculosis during this process has been limited by the slow growth of the bacterium in the laboratory and other technical problems such as cell aggregation. Advances in genomics and molecular methods to analyze the M. tuberculosis genome have revealed that adaptive changes are mediated by complex regulatory networks and signals, resulting in temporal gene expression coupled to metabolic and energetic changes. An important goal for bacterial physiologists will be to elucidate the physiology of M. tuberculosis during the transition between the diverse conditions encountered by M. tuberculosis. This review covers the growth of the mycobacterial cell and how environmental stimuli are sensed by this bacterium. Adaptation to different environments is described from the viewpoint of nutrient acquisition, energy generation, and regulation. To gain quantitative understanding of mycobacterial physiology will require a systems biology approach and recent efforts in this area are discussed.
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Affiliation(s)
- Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
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32
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Kern M, Simon J. Electron transport chains and bioenergetics of respiratory nitrogen metabolism in Wolinella succinogenes and other Epsilonproteobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:646-56. [PMID: 19171117 DOI: 10.1016/j.bbabio.2008.12.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 12/23/2008] [Indexed: 12/16/2022]
Abstract
Recent phylogenetic analyses have established that the Epsilonproteobacteria form a globally ubiquitous group of ecologically significant organisms that comprises a diverse range of free-living bacteria as well as host-associated organisms like Wolinella succinogenes and pathogenic Campylobacter and Helicobacter species. Many Epsilonproteobacteria reduce nitrate and nitrite and perform either respiratory nitrate ammonification or denitrification. The inventory of epsilonproteobacterial genomes from 21 different species was analysed with respect to key enzymes involved in respiratory nitrogen metabolism. Most ammonifying Epsilonproteobacteria employ two enzymic electron transport systems named Nap (periplasmic nitrate reductase) and Nrf (periplasmic cytochrome c nitrite reductase). The current knowledge on the architecture and function of the corresponding proton motive force-generating respiratory chains using low-potential electron donors are reviewed in this article and the role of membrane-bound quinone/quinol-reactive proteins (NapH and NrfH) that are representative of widespread bacterial electron transport modules is highlighted. Notably, all Epsilonproteobacteria lack a napC gene in their nap gene clusters. Possible roles of the Nap and Nrf systems in anabolism and nitrosative stress defence are also discussed. Free-living denitrifying Epsilonproteobacteria lack the Nrf system but encode cytochrome cd(1) nitrite reductase, at least one nitric oxide reductase and a characteristic cytochrome c nitrous oxide reductase system (cNosZ). Interestingly, cNosZ is also found in some ammonifying Epsilonproteobacteria and enables nitrous oxide respiration in W. succinogenes.
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Affiliation(s)
- Melanie Kern
- Institute of Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
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A single channel for nitrate uptake, nitrite export and nitrite uptake by Escherichia coli NarU and a role for NirC in nitrite export and uptake. Biochem J 2008; 417:297-304. [DOI: 10.1042/bj20080746] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Two related polytopic membrane proteins of the major facilitator family, NarK and NarU, catalyse nitrate uptake, nitrite export and nitrite uptake across the Escherichia coli cytoplasmic membrane by an unknown mechanism. A 12-helix model of NarU was constructed based upon six alkaline phosphatase and β-galactosidase fusions to NarK and the predicted hydropathy for the NarK family. Fifteen residues conserved in the NarK-NarU protein family were substituted by site-directed mutagenesis, including four residues that are essential for nitrate uptake by Aspergillus nidulans: arginines Arg87 and Arg303 in helices 2 and 8, and two glycines in a nitrate signature motif. Despite the wide range of substitutions studied, in no case did mutation result in loss of one biochemical function without simultaneous loss of all other functions. A NarU+ NirC+ strain grew more rapidly and accumulated nitrite more rapidly than the isogenic NarU+ NirC− strain. Only the NirC+ strain consumed nitrite rapidly during the later stages of growth. Under conditions in which the rate of nitrite reduction was limited by the rate of nitrite uptake, NirC+ strains reduced nitrite up to 10 times more rapidly than isogenic NarU+ strains, indicating that both nitrite efflux and nitrite uptake are largely dependent on NirC. Isotope tracer experiments with [15N]nitrate and [14N]nitrite revealed that [15N]nitrite accumulated in the extracellular medium even when there was a net rate of nitrite uptake and reduction. We propose that NarU functions as a single channel for nitrate uptake and nitrite expulsion, either as a nitrate–nitrite antiporter, or more likely as a nitrate/H+ or nitrite/H+ channel.
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Goddard AD, Moir JWB, Richardson DJ, Ferguson SJ. Interdependence of two NarK domains in a fused nitrate/nitrite transporter. Mol Microbiol 2008; 70:667-81. [PMID: 18823285 DOI: 10.1111/j.1365-2958.2008.06436.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrate uptake is essential for various bacterial processes and combines with nitrite export to form the usual initial steps of denitrification, a process that reduces nitrate to dinitrogen gas. Although many bacterial species contain NarK-like transporters that are proposed to function as either nitrate/proton symporters or nitrate/nitrite antiporters based on sequence homology, these transporters remain, in general, poorly characterized. Several bacteria appear to contain a transporter that is a fusion of two NarK-like proteins, although the significance of this arrangement remains elusive. We demonstrate that NarK from Paracoccus denitrificans is expressed as a fusion of two NarK-like transporters. NarK1 and NarK2 are separately capable of supporting anaerobic denitrifying growth but with growth defects that are partially mitigated by coexpression of the two domains. NarK1 appears to be a nitrate/proton symporter with high affinity for nitrate and NarK2 a nitrate/nitrite antiporter with lower affinity for nitrate. Each transporter requires two conserved arginine residues for activity. A transporter consisting of inactivated NarK1 fused to active NarK2 has a dramatically increased affinity for nitrate compared with NarK2 alone, implying a functional interaction between the two domains. A potential model for nitrate and nitrite transport in P. denitrificans is proposed.
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Affiliation(s)
- Alan D Goddard
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
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35
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Abstract
The growth and nutritional requirements of mycobacteria have been intensively studied since the discovery of Mycobacterium tuberculosis more than a century ago. However, the identity of many transporters for essential nutrients of M. tuberculosis and other mycobacteria is still unknown despite a wealth of genomic data and the availability of sophisticated genetic tools. Recently, considerable progress has been made in recognizing that two lipid permeability barriers have to be overcome in order for a nutrient molecule to reach the cytoplasm of mycobacteria. Uptake processes are discussed by comparing M. tuberculosis with Mycobacterium smegmatis. For example, M. tuberculosis has only five recognizable carbohydrate transporters in the inner membrane, while M. smegmatis has 28 such transporters at its disposal. The specificities of inner-membrane transporters for sulfate, phosphate and some amino acids have been determined. Outer-membrane channel proteins in both organisms are thought to contribute to nutrient uptake. In particular, the Msp porins have been shown to be required for uptake of carbohydrates, amino acids and phosphate by M. smegmatis. The set of porins also appears to be different for M. tuberculosis and M. smegmatis. These differences likely reflect the lifestyles of these mycobacteria and the availability of nutrients in their natural habitats: the soil and the human body. The comprehensive identification and the biochemical and structural characterization of the nutrient transporters of M. tuberculosis will not only promote our understanding of the physiology of this important human pathogen, but might also be exploited to improve tuberculosis chemotherapy.
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Affiliation(s)
- Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, AL 35294, USA
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36
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Law CJ, Almqvist J, Bernstein A, Goetz RM, Huang Y, Soudant C, Laaksonen A, Hovmöller S, Wang DN. Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT. J Mol Biol 2008; 378:828-39. [PMID: 18395745 DOI: 10.1016/j.jmb.2008.03.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 03/05/2008] [Accepted: 03/13/2008] [Indexed: 10/22/2022]
Abstract
Active transport of substrates across cytoplasmic membranes is of great physiological, medical and pharmaceutical importance. The glycerol-3-phosphate (G3P) transporter (GlpT) of the E. coli inner membrane is a secondary active antiporter from the ubiquitous major facilitator superfamily that couples the import of G3P to the efflux of inorganic phosphate (P(i)) down its concentration gradient. Integrating information from a novel combination of structural, molecular dynamics simulations and biochemical studies, we identify the residues involved directly in binding of substrate to the inward-facing conformation of GlpT, thus defining the structural basis for the substrate-specificity of this transporter. The substrate binding mechanism involves protonation of a histidine residue at the binding site. Furthermore, our data suggest that the formation and breaking of inter- and intradomain salt bridges control the conformational change of the transporter that accompanies substrate translocation across the membrane. The mechanism we propose may be a paradigm for organophosphate:phosphate antiporters.
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Affiliation(s)
- Christopher J Law
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
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37
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Abstract
The major facilitator superfamily (MFS) represents the largest group of secondary active membrane transporters, and its members transport a diverse range of substrates. Recent work shows that MFS antiporters, and perhaps all members of the MFS, share the same three-dimensional structure, consisting of two domains that surround a substrate translocation pore. The advent of crystal structures of three MFS antiporters sheds light on their fundamental mechanism; they operate via a single binding site, alternating-access mechanism that involves a rocker-switch type movement of the two halves of the protein. In the sn-glycerol-3-phosphate transporter (GlpT) from Escherichia coli, the substrate-binding site is formed by several charged residues and a histidine that can be protonated. Salt-bridge formation and breakage are involved in the conformational changes of the protein during transport. In this review, we attempt to give an account of a set of mechanistic principles that characterize all MFS antiporters.
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Affiliation(s)
- Christopher J. Law
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, U.S.A;
| | - Peter C. Maloney
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, U.S.A;
| | - Da-Neng Wang
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, U.S.A;
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38
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Wang Y, Li W, Siddiqi Y, Symington VF, Kinghorn JR, Unkles SE, Glass ADM. Nitrite transport is mediated by the nitrite-specific high-affinity NitA transporter and by nitrate transporters NrtA, NrtB in Aspergillus nidulans. Fungal Genet Biol 2007; 45:94-102. [PMID: 18024100 DOI: 10.1016/j.fgb.2007.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 09/27/2007] [Accepted: 10/01/2007] [Indexed: 11/17/2022]
Abstract
Disruption of the Aspergillus nidulans high-affinity nitrate transporter genes (nrtA and nrtB) prevents growth on nitrate but not nitrite. We identified a distinct nitrite transporter (K(m)=4.2+/-1 microM, V(max)=168+/-21 nmolmg(-1)DW(-1)h(-1)), designated NitA. Disruption of nrtA, nrtB and nitA blocked growth on nitrite, despite low rates of nitrite depletion we ascribe to passive nitrous acid permeation. Growth of the single mutant nitA16 on nitrite was wild-type, suggesting that NrtA and/or NrtB transports nitrite as well as nitrate. Indeed, NrtA and NrtB transport nitrite at higher rates than NitA; K(m) and V(max) values were 16+/-4 microM and 808+/-67 nmolmg(-1)DW(-1)h(-1) (NrtA) and 11+/-1 microM and 979+/-17 nmolmg(-1)DW(-1)h(-1) (NrtB). We suggest that NrtA is a nitrate/nitrite transporter, NrtB absorbs nitrite in preference to nitrate and NitA is exclusively a nitrite transporter.
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Affiliation(s)
- Ye Wang
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada
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Clegg SJ, Jia W, Cole JA. Role of the Escherichia coli nitrate transport protein, NarU, in survival during severe nutrient starvation and slow growth. MICROBIOLOGY-SGM 2006; 152:2091-2100. [PMID: 16804183 DOI: 10.1099/mic.0.28688-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Escherichia coli K-12 strains expressing either NarU or NarK as the only nitrate transport protein are both able to support nitrate-dependent anaerobic growth. The narK gene is highly expressed during anaerobic growth in the presence of nitrate, consistent with a role for NarK in nitrate transport coupled to nitrate reduction by the most active nitrate reductase encoded by the adjacent narGHJI operon. The physiological role of NarU is unknown. Reverse transcriptase PCR experiments established that, unlike the monocistronic narK gene, narU is co-transcribed with narZ as the first gene of a five-gene narUZYWV operon. The narK and narU genes were fused in-frame to a myc tag: the encoded fusion proteins complemented the nitrate-dependent growth defect of chromosomal narK and narU mutations. A commercial anti-Myc antibody was used to detect NarK and NarU in membrane fractions. During anaerobic growth in the presence of nitrate, the quantity of NarU-Myc accumulated during exponential growth was far less than that of NarK-Myc, but NarU was more abundant than NarK in stationary-phase cultures in the absence of nitrate. Although the concentration of NarU-Myc increased considerably during the post-exponential phase of growth, NarK-Myc was still more abundant than NarU-Myc in stationary-phase bacteria in the presence of nitrate. In chemostat competition experiments, a strain expressing only narU had a selective advantage relative to a strain expressing only narK during nutrient starvation or very slow growth, but NarK(+) bacteria had a much greater selective advantage during rapid growth. The data suggest that NarU confers a selective advantage during severe nutrient starvation or slow growth, conditions similar to those encountered in vivo.
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Affiliation(s)
- Stephanie J Clegg
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Wenjing Jia
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jeffrey A Cole
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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40
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Sharma V, Noriega CE, Rowe JJ. Involvement of NarK1 and NarK2 proteins in transport of nitrate and nitrite in the denitrifying bacterium Pseudomonas aeruginosa PAO1. Appl Environ Microbiol 2006; 72:695-701. [PMID: 16391109 PMCID: PMC1352271 DOI: 10.1128/aem.72.1.695-701.2006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two transmembrane proteins were tentatively classified as NarK1 and NarK2 in the Pseudomonas genome project and hypothesized to play an important physiological role in nitrate/nitrite transport in Pseudomonas aeruginosa. The narK1 and narK2 genes are located in a cluster along with the structural genes for the nitrate reductase complex. Our studies indicate that the transcription of all these genes is initiated from a single promoter and that the gene complex narK1K2GHJI constitutes an operon. Utilizing an isogenic narK1 mutant, a narK2 mutant, and a narK1K2 double mutant, we explored their effect on growth under denitrifying conditions. While the DeltanarK1::Gm mutant was only slightly affected in its ability to grow under denitrification conditions, both the DeltanarK2::Gm and DeltanarK1K2::Gm mutants were found to be severely restricted in nitrate-dependent, anaerobic growth. All three strains demonstrated wild-type levels of nitrate reductase activity. Nitrate uptake by whole-cell suspensions demonstrated both the DeltanarK2::Gm and DeltanarK1K2::Gm mutants to have very low yet different nitrate uptake rates, while the DeltanarK1::Gm mutant exhibited wild-type levels of nitrate uptake. Finally, Escherichia coli narK rescued both the DeltanarK2::Gm and DeltanarK1K2::Gm mutants with respect to anaerobic respiratory growth. Our results indicate that only the NarK2 protein is required as a nitrate/nitrite transporter by Pseudomonas aeruginosa under denitrifying conditions.
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Affiliation(s)
- Vandana Sharma
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469-2320, USA
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41
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Serrani F, Berardi E. The NII2 gene of Hansenula polymorpha is involved in nitrite assimilation. FEMS Yeast Res 2005; 5:999-1007. [PMID: 16144777 DOI: 10.1016/j.femsyr.2005.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Revised: 05/12/2005] [Accepted: 06/01/2005] [Indexed: 10/25/2022] Open
Abstract
To establish a basis for genetic and molecular studies of nitrite assimilation in the methylotrophic yeast Hansenula polymorpha, we isolated and characterised six nitrite-negative mutants still capable of growing on nitrate. Gene isolation work yielded the NII2 gene, encoding a membrane protein homologous to the Saccharomyces cerevisiae Pho86p. Sequence analysis revealed an ORF of 860 bp encoding a 286-amino-acid protein with a predicted molecular mass of 32.8 kDa. This protein is shorter than its S. cerevisiae homologue, and is predicted to lack an ER-retention signal. Cell suspension work revealed that the null mutant is unable to take up nitrite from the medium.
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Affiliation(s)
- Federica Serrani
- Laboratorio di Genetica Microbica, DiSA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
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