51
|
Katsuyama Y, Matsuda K. Recent advance in the biosynthesis of nitrogen–nitrogen bond–containing natural products. Curr Opin Chem Biol 2020; 59:62-68. [DOI: 10.1016/j.cbpa.2020.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/22/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022]
|
52
|
Budhraja R, Karande S, Ding C, Ullrich MK, Wagner S, Reemtsma T, Adrian L. Characterization of membrane-bound metalloproteins in the anaerobic ammonium-oxidizing bacterium "Candidatus Kuenenia stuttgartiensis" strain CSTR1. Talanta 2020; 223:121711. [PMID: 33298257 DOI: 10.1016/j.talanta.2020.121711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 01/18/2023]
Abstract
Membrane-bound metalloproteins are the basis of biological energy conservation via respiratory processes, however, their biochemical characterization is difficult. Here, we followed a gel-based proteomics and metallomics approach to identify membrane-associated metalloproteins in the anaerobic ammonium-oxidizing "Candidatus Kuenenia stuttgartiensis" strain CSTR1. Membrane-associated protein complexes were separated by two dimensional Blue Native/SDS gel electrophoresis and subunits were identified by mass spectrometry; protein-bound metal ions were quantified from the gel by connecting either a desolvating nebulizer system or laser ablation to inductively coupled plasma triple quadrupole mass spectrometry (ICP-QqQ-MS). We identified most protein complexes predicted to be involved in anaerobic ammonium oxidation and carbon fixation. The ICP-QqQ-MS data showed the presence of Fe and Zn in a wide range of high molecular weight protein complexes (230-800 kDa). Mo was prominently found in gel slices with proteins of a size of 500-650 kDa, whereas Ni was only found using the desolvating nebulizer system in the protein range of 350-500 kDa. The detected protein complexes and their metal content were consistent with genome annotations. Gel-based metalloproteomics is a sensitive and reliable approach for the characterization of metalloproteins and could be used to characterize many multimeric metalloprotein complexes in biological systems.
Collapse
Affiliation(s)
- Rohit Budhraja
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Shubhangi Karande
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Leipzig, Germany
| | - Chang Ding
- Helmholtz Centre for Environmental Research - UFZ, Environmental Biotechnology, Leipzig, Germany
| | - Maria K Ullrich
- Helmholtz Centre for Environmental Research - UFZ, Analytical Chemistry, Leipzig, Germany
| | - Stephan Wagner
- Helmholtz Centre for Environmental Research - UFZ, Analytical Chemistry, Leipzig, Germany
| | - Thorsten Reemtsma
- Helmholtz Centre for Environmental Research - UFZ, Analytical Chemistry, Leipzig, Germany
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, Environmental Biotechnology, Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany.
| |
Collapse
|
53
|
Soler-Jofra A, Laureni M, Warmerdam M, Pérez J, van Loosdrecht MCM. Hydroxylamine metabolism of Ca. Kuenenia stuttgartiensis. WATER RESEARCH 2020; 184:116188. [PMID: 32739592 DOI: 10.1016/j.watres.2020.116188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Hydroxylamine is a key intermediate in several biological reactions of the global nitrogen cycle. However, the role of hydroxylamine in anammox is still not fully understood. In this work, the impact of hydroxylamine (also in combination with other substrates) on the metabolism of a planktonic enrichment culture of the anammox species Ca. Kuenenia stuttgartiensis was studied. Anammox bacteria were observed to produce ammonium both from hydroxylamine and hydrazine, and hydroxylamine was consumed simultaneously with nitrite. Hydrazine accumulation - signature for the presence of anammox bacteria - strongly depended on the available substrates, being higher with ammonium and lower with nitrite. Furthermore, the results presented here indicate that hydrazine accumulation is not the result of the inhibition of hydrazine dehydrogenase, as commonly assumed, but the product of hydroxylamine disproportionation. All kinetic parameters for the identified reactions were estimated by mathematical modelling. Moreover, the simultaneous consumption and growth on ammonium, nitrite and hydroxylamine of anammox bacteria was demonstrated, this was accompanied by a reduction in the nitrate production. Ultimately, this study advances the fundamental understanding of the metabolic versatility of anammox bacteria, and highlights the potential role played by metabolic intermediates (i.e. hydroxylamine, hydrazine) in shaping natural and engineered microbial communities.
Collapse
Affiliation(s)
- Aina Soler-Jofra
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, the Netherlands.
| | - Michele Laureni
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, the Netherlands
| | - Marieke Warmerdam
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, the Netherlands
| | - Julio Pérez
- Department of Chemical, Biological and Environmental Engineering, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Spain
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, the Netherlands
| |
Collapse
|
54
|
Smeulders MJ, Peeters SH, van Alen T, de Bruijckere D, Nuijten GHL, op den Camp HJM, Jetten MSM, van Niftrik L. Nutrient Limitation Causes Differential Expression of Transport- and Metabolism Genes in the Compartmentalized Anammox Bacterium Kuenenia stuttgartiensis. Front Microbiol 2020; 11:1959. [PMID: 32903544 PMCID: PMC7438415 DOI: 10.3389/fmicb.2020.01959] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria, members of the "Candidatus Brocadiaceae" family, play an important role in the nitrogen cycle and are estimated to be responsible for about half of the oceanic nitrogen loss to the atmosphere. Anammox bacteria combine ammonium with nitrite and produce dinitrogen gas via the intermediates nitric oxide and hydrazine (anammox reaction) while nitrate is formed as a by-product. These reactions take place in a specialized, membrane-enclosed compartment called the anammoxosome. Therefore, the substrates ammonium, nitrite and product nitrate have to cross the outer-, cytoplasmic-, and anammoxosome membranes to enter or exit the anammoxosome. The genomes of all anammox species harbor multiple copies of ammonium-, nitrite-, and nitrate transporter genes. Here we investigated how the distinct genes for ammonium-, nitrite-, and nitrate- transport were expressed during substrate limitation in membrane bioreactors. Transcriptome analysis of Kuenenia stuttgartiensis planktonic cells showed that four of the seven ammonium transporter homologs and two of the nine nitrite transporter homologs were significantly upregulated during ammonium-limited growth, while another ammonium transporter- and four nitrite transporter homologs were upregulated in nitrite limited growth conditions. The two nitrate transporters were expressed to similar levels in both conditions. In addition, genes encoding enzymes involved in the anammox reaction were differentially expressed, with those using nitrite as a substrate being upregulated under nitrite limited growth and those using ammonium as a substrate being upregulated during ammonium limitation. Taken together, these results give a first insight in the potential role of the multiple nutrient transporters in regulating transport of substrates and products in and out of the compartmentalized anammox cell.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, Netherlands
| |
Collapse
|
55
|
Ma J, Wang K, Gong H, Yuan Q, Yang M, He C, Shi C, San E. Integrating floc, aggregate and carrier to reap high-quality anammox biofilm. BIORESOURCE TECHNOLOGY 2020; 309:123325. [PMID: 32330801 DOI: 10.1016/j.biortech.2020.123325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
This work investigated the effects of integration of floc, aggregate and carrier (IFAC) on anammox biofilm quality and development mechanisms. The IFAC system harvested high-quality anammox biofilm with a reduction of 60% in the formation period, an increment of 282.14%~397.26% in mechanical stability, an enhancement of 10.18 ~ 21.56% in ecological stability and an improvement of 9.44%~46.18% in abundance of the phylum Planctomycetes. Aggregates enabled carriers to accumulate initial biomass efficiently and equipped biofilm with additional joint forces. Floc promoted accumulation of terminal biomass, enhanced ecological stability by improving community diversity and raised abundance of the phylum Planctomycetes by assisting anammox consortium settlement. A model of the development procedure of high-quality anammox biofilm was established and a strategy for pre-designing the IFAC system to reap high-quality biofilm was proposed. We expect our findings to provide theoretical guidance for designs and applications of anammox process with excellent stability.
Collapse
Affiliation(s)
- Jinyuan Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Kaijun Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
| | - Hui Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Quan Yuan
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Meijuan Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Conghui He
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Chuan Shi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Erfu San
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| |
Collapse
|
56
|
Ali M, Shaw DR, Albertsen M, Saikaly PE. Comparative Genome-Centric Analysis of Freshwater and Marine ANAMMOX Cultures Suggests Functional Redundancy in Nitrogen Removal Processes. Front Microbiol 2020; 11:1637. [PMID: 32733431 PMCID: PMC7358590 DOI: 10.3389/fmicb.2020.01637] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/23/2020] [Indexed: 11/24/2022] Open
Abstract
There is a lack of understanding of the interaction between anammox bacteria and the flanking microbial communities in both freshwater (non-saline) and marine (saline) ecosystems. Here, we present a comparative genome-based exploration of two different anammox bioreactors, through the analysis of 23 metagenome-assembled genomes (MAGs), 12 from freshwater anammox reactor (FWR), and 11 from marine anammox reactor (MWR). To understand the contribution of individual members to community functions, we applied the index of replication (iRep) to determine bacteria that are actively replicating. Using genomic content and iRep information, we provided a potential ecological role for the dominant members of the community based on the reactor operating conditions. In the non-saline system, anammox (Candidatus Brocadia sinica) and auxotrophic neighboring bacteria belonging to the phyla Ignavibacteriae and Chloroflexi might interact to reduce nitrate to nitrite for direct use by anammox bacteria. Whereas, in the saline reactor, anammox bacterium (Ca. Scalindua erythraensis) and flanking community belonging to phyla Planctomycetes (different than anammox bacteria)—which persistently growing in the system—may catabolize detritus and extracellular material and recycle nitrate to nitrite for direct use by anammox bacteria. Despite different microbial communities, there was functional redundancy in both ecosystems. These results signify the potential application of marine anammox bacteria for treating saline N-rich wastewaters.
Collapse
Affiliation(s)
- Muhammad Ali
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dario Rangel Shaw
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mads Albertsen
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Pascal E Saikaly
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| |
Collapse
|
57
|
Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
Collapse
Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
58
|
Bhuyar P, Rahim MHA, Sundararaju S, Ramaraj R, Maniam GP, Govindan N. Synthesis of silver nanoparticles using marine macroalgae Padina sp. and its antibacterial activity towards pathogenic bacteria. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2020. [DOI: 10.1186/s43088-019-0031-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Background
Marine algae used as a food source for ocean life and range in color from red to green to brown grow along rocky shorelines around the world. The synthesis of silver nanoparticles by marine alga Padina sp. and its characterization were fulfilled by using UV-visible spectrophotometer, Fourier transform infrared spectroscopy, scanning electron microscopy and field emission scanning electron microscopy, and energy-dispersive X-ray spectroscopy.
Results
UV-visible absorption spectrum revealed that the formation of Ag nanoparticles was increased by the addition of marine algae and the spectral peak observed between a wavelength of ~ 420 nm and 445 nm. In addition, SEM and FESEM images examined the surface morphology and the size of the synthesized NPs was relatively uniform in size ~ 25–60 nm. Energy-dispersive X-ray spectroscopy analysis confirmed the purity of Ag NPs with atomic percentage of 48.34% Ag. The synthesized Ag NPs showed highly potent antibacterial activity. The Staphylococcus aureus and Pseudomonas aeruginosa were found to be more susceptible to silver nanoparticles by forming 15.17 ± 0.58 mm and 13.33 ± 0.76 mm of diameter of the inhibition zone, respectively.
Conclusions
The study suggested that marine alga Padina sp. could be an alternative source for the production of Ag nanoparticles and are efficient antimicrobial compounds against both gram-negative and gram-positive bacteria which can be a promising material against infectious bacteria.
Collapse
|
59
|
Ferousi C, Lindhoud S, Baymann F, Hester ER, Reimann J, Kartal B. Discovery of a functional, contracted heme-binding motif within a multiheme cytochrome. J Biol Chem 2019; 294:16953-16965. [PMID: 31582564 DOI: 10.1074/jbc.ra119.010568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/02/2019] [Indexed: 11/06/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria convert nitrite and ammonium via nitric oxide (NO) and hydrazine into dinitrogen gas by using a diverse array of proteins, including numerous c-type cytochromes. Many new catalytic and spectroscopic properties of c-type cytochromes have been unraveled by studies on the biochemical pathways underlying the anammox process. The unique anammox intermediate hydrazine is produced by a multiheme cytochrome c protein, hydrazine synthase, through the comproportionation of ammonium and NO and the input of three electrons. It is unclear how these electrons are delivered to hydrazine synthase. Here, we report the discovery of a functional tetraheme c-type cytochrome from the anammox bacterium Kuenenia stuttgartiensis with a naturally-occurring contracted Cys-Lys-Cys-His (CKCH) heme-binding motif, which is encoded in the hydrazine synthase gene cluster. The purified tetraheme protein (named KsTH) exchanged electrons with hydrazine synthase. Complementary spectroscopic techniques revealed that this protein harbors four low-spin hexa-coordinated hemes with His/Lys (heme 1), His/Cys (heme 2), and two His/His ligations (hemes 3 and 4). A genomic database search revealed that c-type cytochromes with a contracted CXCH heme-binding motif are present throughout the bacterial and archaeal domains in the tree of life, suggesting that this heme recognition site may be employed by many different groups of microorganisms.
Collapse
Affiliation(s)
- Christina Ferousi
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Simon Lindhoud
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Frauke Baymann
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, Marseille Cedex 09, France
| | - Eric R Hester
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
| |
Collapse
|
60
|
Akram M, Reimann J, Dietl A, Menzel A, Versantvoort W, Kartal B, Jetten MSM, Barends TRM. A nitric oxide-binding heterodimeric cytochrome c complex from the anammox bacterium Kuenenia stuttgartiensis binds to hydrazine synthase. J Biol Chem 2019; 294:16712-16728. [PMID: 31548310 DOI: 10.1074/jbc.ra119.008788] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/17/2019] [Indexed: 01/17/2023] Open
Abstract
Anaerobic ammonium oxidation (anammox) is a microbial process responsible for significant nitrogen loss from the oceans and other ecosystems. The redox reactions at the heart of anammox are catalyzed by large multiheme enzyme complexes that rely on small cytochrome c proteins for electron shuttling. Among the most highly abundant of these cytochromes is a unique heterodimeric complex composed of class I and class II c-type cytochromes called NaxLS, which has distinctive biochemical and spectroscopic properties. Here, we present the 1.7 Å resolution crystal structure of this complex from the anammox organism Kuenenia stuttgartiensis (KsNaxLS). The structure reveals that the heme irons in each subunit exhibit a rare His/Cys ligation, which, as we show by substitution, causes the observed unusual spectral properties. Unlike its individual subunits, the KsNaxLS complex binds nitric oxide (NO) only at the distal heme side, forming 6cNO adducts. This is likely due to steric immobilization of the proximal heme-binding motifs upon complex formation, a finding that may be of functional relevance, because NO is an intermediate in the central anammox metabolism. Pulldown experiments with K. stuttgartiensis cell-free extract showed that the KsNaxLS complex binds specifically to one of the central anammox enzyme complexes, hydrazine synthase, which uses NO as one of its substrates. It is therefore possible that the KsNaxLS complex plays a role in binding the volatile NO to retain it in the cell for transfer to hydrazine synthase. Alternatively, we propose that KsNaxLS may shuttle electrons to this enzyme complex.
Collapse
Affiliation(s)
- Mohd Akram
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen 6525AJ, The Netherlands
| | - Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Andreas Menzel
- Coherent X-ray Scattering Group, Paul Scherrer Institute, WLGA/223, Villigen 5232, Switzerland
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen 6525AJ, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen 6525AJ, The Netherlands
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| |
Collapse
|
61
|
Russ L, van Alen TA, Jetten MSM, Op den Camp HJM, Kartal B. Interactions of anaerobic ammonium oxidizers and sulfide-oxidizing bacteria in a substrate-limited model system mimicking the marine environment. FEMS Microbiol Ecol 2019; 95:5555569. [DOI: 10.1093/femsec/fiz137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/26/2019] [Indexed: 11/14/2022] Open
Abstract
ABSTRACTIn nature anaerobic ammonium oxidation (anammox) and denitrification processes convert fixed nitrogen to gaseous nitrogen compounds, which are then released to the atmosphere. While anammox bacteria produce N2 from ammonium and nitrite, in the denitrification process nitrate and nitrite are converted to N2 and the greenhouse gas nitrous oxide (N2O). Furthermore, nitrite needed by the anammox bacteria can be supplied by nitrate reduction to nitrite. Consequently, the interplay between nitrogen-transforming microorganisms control the amount of harmless N2 or the greenhouse gas N2O released to the atmosphere. Therefore, it is important to understand the interactions of these microorganisms in the natural environment, where dynamic conditions result in fluctuating substrate concentrations. Here, we studied the interactions between the sulfide-oxidizing denitrifier Sedimenticola selenatireducens and the anammox bacterium Scalindua brodae in a bioreactor mimicking the marine environment by creating sulfide, ammonium and nitrate limitation in distinct operational phases. Through a microbial interaction, Se. selenatireducens reduced nitrate to nitrite, which together with the supplied ammonium was converted to N2 by Sc. Brodae. Using comparative transcriptomics, we determined that Sc. Brodae and Se. selenatireducens had significant responses to ammonium and nitrate limitation, respectively, indicating that the activities of these microorganisms are regulated by different nitrogen compounds.
Collapse
Affiliation(s)
- Lina Russ
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Theo A van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| |
Collapse
|
62
|
Tao Y, Huang X, Gao D, Wang X, Chen C, Liang H, van Loosdrecht MCM. NanoSIMS reveals unusual enrichment of acetate and propionate by an anammox consortium dominated by Jettenia asiatica. WATER RESEARCH 2019; 159:223-232. [PMID: 31100576 DOI: 10.1016/j.watres.2019.05.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria convert ammonium and nitrite into N2 in a chemolithoautotrophic way, meaning that they utilize CO2/HCO3 solely as their carbon sources. Such autotrophic behavior limits their competitiveness with heterotrophic microorganisms in both natural environments and engineered systems. Recently, environmental metagenomic results have indicated the capability of anammox bacteria to metabolize short-chain fatty acids, further confirmed by limited experimental evidence based on highly enriched cultures. However, clear evidence is difficult to get because of the limits of traditional methodologies which rely on the availability of a pure anammox culture. In this study, we identified and quantified the uptake of acetate and propionate, on a single-cell level, by an anammox consortium that was dominated by Candidatus Jettenia asiatica (relative abundance of 96%). The consortium, growing in granular form with an average relative abundance of anammox bacteria of 96.0%, was firstly incubated in a13C-labelled acetate or propionate medium; then microtome sections were scanned by a nanometer-scale secondary ion mass spectrometer (NanoSIMS). The NanoSIMS scannings revealed that the consortium enriched acetate and propionate at a >10 times higher efficiency than bicarbonate incorporation. Our results also suggest that acetate or propionate was likely not assimilated by J. asiatica directly, but firstly oxidized to CO2, which then served as carbon sources for the follow-up autotrophy in J. asiatica cells. Furthermore, more [15N]ammonium was enriched by the propionate-fed consortium than the acetate-fed consortium despite that exactly the same amount of 13C atoms were supplied. Our study strongly indicates an alternative lifestyle, namely organotrophy, in addition to chemolithoautotrophy of anammox bacteria, making it more versatile than often expected. It suggests that the niche of anammox bacteria in both natural and engineered ecosystems can be much broader than usual assumed. Recognising this is important for their role in wastewater treatment and the global nitrogen turn-over rates.
Collapse
Affiliation(s)
- Yu Tao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xiaoli Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Xiaolong Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Chunhong Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Hong Liang
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | | |
Collapse
|
63
|
Recreating ancient metabolic pathways before enzymes. Bioorg Med Chem 2019; 27:2292-2297. [DOI: 10.1016/j.bmc.2019.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/02/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022]
|
64
|
Liu C, Liu K, Tian M, Lin W. A ratiometric fluorescent probe for hydrazine detection with large fluorescence change ratio and its application for fluorescence imaging in living cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 212:42-47. [PMID: 30594852 DOI: 10.1016/j.saa.2018.12.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 11/26/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Hydrazine and its derivatives are one of the most important raw chemical materials that have extensive utilization in many areas. It is also widely applied as pharmaceutical derivatives, such as the antipsychotic drug, anti-infective drug, and antitumor drug. However, hydrazine is a highly toxic reagent which can bring severe damage to human and animals. Herein, we have reported a new benzothiazole substituted naphthalene based probe for hydrazine with huge fluorescence change ratio. The fluorescence change ratio at F390/F509 is up to 200-fold in the presence of hydrazine in 60 min. The probe exhibited negligible cytotoxicity toward HeLa cells and was applied for hydrazine detection successfully in HeLa cells.
Collapse
Affiliation(s)
- Chuang Liu
- Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, PR China
| | - Keyin Liu
- Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, PR China
| | - Minggang Tian
- Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, PR China
| | - Weiying Lin
- Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, PR China.
| |
Collapse
|
65
|
Akram M, Dietl A, Mersdorf U, Prinz S, Maalcke W, Keltjens J, Ferousi C, de Almeida NM, Reimann J, Kartal B, Jetten MSM, Parey K, Barends TRM. A 192-heme electron transfer network in the hydrazine dehydrogenase complex. SCIENCE ADVANCES 2019; 5:eaav4310. [PMID: 31001586 PMCID: PMC6469936 DOI: 10.1126/sciadv.aav4310] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/28/2019] [Indexed: 05/21/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (-750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.
Collapse
Affiliation(s)
- M. Akram
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - A. Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - U. Mersdorf
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - S. Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - W. Maalcke
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - J. Keltjens
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - C. Ferousi
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - N. M. de Almeida
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - J. Reimann
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - B. Kartal
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - M. S. M. Jetten
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - K. Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
- Corresponding author. (K.P.); (T.R.M.B.)
| | - T. R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Corresponding author. (K.P.); (T.R.M.B.)
| |
Collapse
|
66
|
Shimizu T, Lengalova A, Martínek V, Martínková M. Heme: emergent roles of heme in signal transduction, functional regulation and as catalytic centres. Chem Soc Rev 2019; 48:5624-5657. [DOI: 10.1039/c9cs00268e] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular mechanisms of unprecedented functions of exchangeable/labile heme and heme proteins including transcription, DNA binding, protein kinase activity, K+ channel functions, cis–trans isomerization, N–N bond formation, and other functions are described.
Collapse
Affiliation(s)
- Toru Shimizu
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Alzbeta Lengalova
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Václav Martínek
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Markéta Martínková
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| |
Collapse
|
67
|
Raghavan V, Johnson JL, Stec DF, Song B, Zajac G, Baranska M, Harris CM, Schley ND, Polavarapu PL, Harris TM. Absolute Configurations of Naturally Occurring [5]- and [3]-Ladderanoic Acids: Isolation, Chiroptical Spectroscopy, and Crystallography. JOURNAL OF NATURAL PRODUCTS 2018; 81:2654-2666. [PMID: 30562024 DOI: 10.1021/acs.jnatprod.8b00458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We have isolated mixtures of [5]- and [3]-ladderanoic acids 1a and 2a from the biomass of an anammox bioreactor and have separated the acids and their phenacyl esters for the first time by HPLC. The absolute configurations of the naturally occurring acids and their phenacyl esters are assigned as R at the site of side-chain attachment by comparison of experimental specific rotations with corresponding values predicted using quantum chemical (QC) methods. The absolute configurations for 1a and 2a were independently verified by comparison of experimental Raman optical activity spectra with corresponding spectra predicted using QC methods. The configurational assignments of 1a and 2a and of the phenacyl ester of 1a were also confirmed by X-ray crystallography.
Collapse
Affiliation(s)
- Vijay Raghavan
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Jordan L Johnson
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Donald F Stec
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Bongkeun Song
- Department of Biological Sciences , Virginia Institute of Marine Science , Gloucester Point , Virginia 23062 , United States
| | - Grzegorz Zajac
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
| | - Malgorzata Baranska
- Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET) , Jagiellonian University , Bobrzynskiego 14 , 30-348 Krakow , Poland
| | - Constance M Harris
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Nathan D Schley
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Prasad L Polavarapu
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Thomas M Harris
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
- Department of Biological Sciences , Virginia Institute of Marine Science , Gloucester Point , Virginia 23062 , United States
| |
Collapse
|
68
|
Ghosh A, Paul I, Saha S, Paululat T, Schmittel M. Machine Metathesis: Thermal and Catalyzed Exchange of Piston Rods in Multicomponent Nanorotor/Nanoslider Ensemble. Org Lett 2018; 20:7973-7976. [PMID: 30525699 DOI: 10.1021/acs.orglett.8b03541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Three-component nanorotor R1 ( k298 = 80 kHz) and two-component slider-on-deck DS2 ( k298 = 440 kHz) were prepared from rotator S1 and stator [Cu3(1)]3+ and from S2 and deck D, respectively. Mixing of R1 with DS2 leads to clean metathesis, furnishing the slower nanodevices R2 ( k298 = 29.6 kHz) and DS1 ( k298 = 32.2 kHz). Exchange of the piston rods S1 and S2 is completed within 22 min (uncatalyzed) or 3 min (catalyzed) at 298 K.
Collapse
Affiliation(s)
- Amit Ghosh
- Center of Micro- and Nanochemistry and Engineering , University of Siegen, Organische Chemie I , Adolf-Reichwein-Str. 2 , D-57068 Siegen , Germany
| | - Indrajit Paul
- Center of Micro- and Nanochemistry and Engineering , University of Siegen, Organische Chemie I , Adolf-Reichwein-Str. 2 , D-57068 Siegen , Germany
| | - Suchismita Saha
- Center of Micro- and Nanochemistry and Engineering , University of Siegen, Organische Chemie I , Adolf-Reichwein-Str. 2 , D-57068 Siegen , Germany
| | - Thomas Paululat
- University of Siegen, Organische Chemie II , Adolf-Reichwein-Str. 2 , D-57068 Siegen , Germany
| | - Michael Schmittel
- Center of Micro- and Nanochemistry and Engineering , University of Siegen, Organische Chemie I , Adolf-Reichwein-Str. 2 , D-57068 Siegen , Germany
| |
Collapse
|
69
|
Kang D, Lin Q, Xu D, Hu Q, Li Y, Ding A, Zhang M, Zheng P. Color characterization of anammox granular sludge: Chromogenic substance, microbial succession and state indication. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:1320-1327. [PMID: 30045512 DOI: 10.1016/j.scitotenv.2018.06.172] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/13/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Vision is a direct and convenient way to get information, and color characteristics are important visual information to identify objects. In this study, the L*a*b* color space was introduced for the first time to digitize the surface color of anammox granular sludge (AnGS). Three AnGSs under typical biological loading rates were chosen and the color value a*/b* was found to have a positive correlation with the specific anammox activity and the biological loading rate of AnGS. Cytochrome c was detected to be the key chromogenic substance determining the red hue of AnGS. The concentration of cytochrome c was highly consistent with the abundance of anammox bacteria. Nitrospira was observed to compete with Candidatus Kuenenia for nitrite under survival state, resulting in the obvious decrease of a* value; while the growth of sulfur-related Limnobacter and Thiobacillus was enhanced under starvation state, leading to the production of Fe-S compounds covering over the surface and decrease of a* and b* value simultaneously. The unique color characteristics of AnGS were evaluated as a visual indicator to serve the on-line control and better judgement of anammox process.
Collapse
Affiliation(s)
- Da Kang
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiujian Lin
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dongdong Xu
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qianyi Hu
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yiyu Li
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Aqiang Ding
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Meng Zhang
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
70
|
Peeters SH, van Niftrik L. Trending topics and open questions in anaerobic ammonium oxidation. Curr Opin Chem Biol 2018; 49:45-52. [PMID: 30308437 DOI: 10.1016/j.cbpa.2018.09.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/04/2018] [Accepted: 09/21/2018] [Indexed: 02/07/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are major players in the biological nitrogen cycle and can be applied in wastewater treatment for the removal of nitrogen compounds. Anammox bacteria anaerobically convert the substrates ammonium and nitrite into dinitrogen gas in a specialized intracellular compartment called the anammoxosome. The anammox cell biology, physiology and biochemistry is of exceptional interest but also difficult to study because of the lack of a pure culture, standard cultivation techniques and genetic tools. Here we review the most important recent developments regarding the cell structure - anammoxosome and cell envelope - and anammox energy metabolism - nitrite reductase, hydrazine synthase and energy conversion - including the trending topics electro-anammox, extracellular polymeric substances and ladderane lipids.
Collapse
Affiliation(s)
- Stijn H Peeters
- Department of Microbiology, Institute for Water & Wetland Research, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water & Wetland Research, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| |
Collapse
|
71
|
|
72
|
Moss FR, Shuken SR, Mercer JAM, Cohen CM, Weiss TM, Boxer SG, Burns NZ. Ladderane phospholipids form a densely packed membrane with normal hydrazine and anomalously low proton/hydroxide permeability. Proc Natl Acad Sci U S A 2018; 115:9098-9103. [PMID: 30150407 PMCID: PMC6140541 DOI: 10.1073/pnas.1810706115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ladderane lipids are unique to anaerobic ammonium-oxidizing (anammox) bacteria and are enriched in the membrane of the anammoxosome, an organelle thought to compartmentalize the anammox process, which involves the toxic intermediate hydrazine (N2H4). Due to the slow growth rate of anammox bacteria and difficulty of isolating pure ladderane lipids, experimental evidence of the biological function of ladderanes is lacking. We have synthesized two natural and one unnatural ladderane phosphatidylcholine lipids and compared their thermotropic properties in self-assembled bilayers to distinguish between [3]- and [5]-ladderane function. We developed a hydrazine transmembrane diffusion assay using a water-soluble derivative of a hydrazine sensor and determined that ladderane membranes are as permeable to hydrazine as straight-chain lipid bilayers. However, pH equilibration across ladderane membranes occurs 5-10 times more slowly than across straight-chain lipid membranes. Langmuir monolayer analysis and the rates of fluorescence recovery after photobleaching suggest that dense ladderane packing may preclude formation of proton/hydroxide-conducting water wires. These data support the hypothesis that ladderanes prevent the breakdown of the proton motive force rather than blocking hydrazine transmembrane diffusion in anammox bacteria.
Collapse
Affiliation(s)
- Frank R Moss
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Steven R Shuken
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jaron A M Mercer
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Carolyn M Cohen
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, Stanford University, Menlo Park, CA 94025
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305;
| | - Noah Z Burns
- Department of Chemistry, Stanford University, Stanford, CA 94305;
| |
Collapse
|
73
|
in ‘t Zandt MH, de Jong AEE, Slomp CP, Jetten MSM. The hunt for the most-wanted chemolithoautotrophic spookmicrobes. FEMS Microbiol Ecol 2018; 94:4966976. [PMID: 29873717 PMCID: PMC5989612 DOI: 10.1093/femsec/fiy064] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic 'Candidatus Methanothrix paradoxum', which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, 'Candidatus Methanoperedens nitroreducens' ANME-2d archaea and 'Candidatus Methylomirabilis oxyfera' bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although 'Candidatus Methanoperedens nitroreducens' and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.
Collapse
Affiliation(s)
- Michiel H in ‘t Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Anniek EE de Jong
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Caroline P Slomp
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
- Department of Earth Sciences, Geochemistry, Utrecht University, Princetonlaan 8a, 3584 CB Utrecht, The Netherlands
| | - Mike SM Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
74
|
Zhang K, Yang B, Ma Y, Lyu L, Pan Y, Wang Y, Li H, Zhu T. A novel anammox process combined with vibration technology. BIORESOURCE TECHNOLOGY 2018; 256:277-284. [PMID: 29459317 DOI: 10.1016/j.biortech.2018.01.128] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/23/2018] [Accepted: 01/27/2018] [Indexed: 06/08/2023]
Abstract
This study investigated a fixed bed anammox bioreactor that uses vibration techniques to treat synthetic inorganic wastewater. Continuous experiments indicated that the activity elevation period could be shorten to one third, when the nitrogen removal rate (NRR) reached 1 kg·N/m3·d with vibration. R2 achieved the maximum NRR of 3.3 kg·N/m3·d under the resonance state, which was 1.8 times higher than the control reactor. Analysis of vibration intensity suggested that anammox activity would be great improved with the increasing vibration. These results indicated that vibration played a key role in system performance. Furthermore, high-throughput sequencing showed that the reactor with the vibration had a higher proportion of anammox bacteria, which increased 7 times than the biofilm formation phase. Meanwhile, the proportion of Proteobacteria and Chloroflexi decreased by 37.1% and 7.78%, respectively. These results suggest that vibration could increase the anammox treatment performance and provide a better condition for the anammox bacteria.
Collapse
Affiliation(s)
- Kuo Zhang
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, PR China
| | - Bo Yang
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, PR China
| | - Yongguang Ma
- Liaoning Provincial Machinery Research Institute Co., Ltd., Shenyang 110004, PR China
| | - Liting Lyu
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, PR China
| | - Yuan Pan
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, PR China
| | - Youzhao Wang
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, PR China
| | - He Li
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, PR China
| | - Tong Zhu
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, Shenyang 110004, PR China.
| |
Collapse
|
75
|
Huson DH, Albrecht B, Bağcı C, Bessarab I, Górska A, Jolic D, Williams RBH. MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Biol Direct 2018; 13:6. [PMID: 29678199 PMCID: PMC5910613 DOI: 10.1186/s13062-018-0208-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/29/2018] [Indexed: 11/15/2022] Open
Abstract
Background There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets. Methods We describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods. Results All presented methods are implemented in the open source edition of MEGAN, and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community. Reviewers This article was reviewed by Nicola Segata together with Moreno Zolfo, Pete James Lockhart and Serghei Mangul. Conclusion This work extends the applicability of the widely-used metagenomic analysis software MEGAN to long reads. Our study suggests that the presented LAST+MEGAN-LR pipeline is sufficiently fast and accurate.
Collapse
Affiliation(s)
- Daniel H Huson
- Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany. .,Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
| | - Benjamin Albrecht
- Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany
| | - Caner Bağcı
- Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany.,IMPRS 'From Molecules to Organisms', Tübingen, Germany
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Anna Górska
- Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany.,IMPRS 'From Molecules to Organisms', Tübingen, Germany
| | - Dino Jolic
- Max-Planck Institute for Developmental Biology, Tübingen, 72076, Germany.,IMPRS 'From Molecules to Organisms', Tübingen, Germany
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| |
Collapse
|
76
|
Hira D, Kitamura R, Nakamura T, Yamagata Y, Furukawa K, Fujii T. Anammox Organism KSU-1 Expresses a Novel His/DOPA Ligated Cytochrome c. J Mol Biol 2018; 430:1189-1200. [DOI: 10.1016/j.jmb.2018.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 10/18/2022]
|
77
|
Blum JM, Su Q, Ma Y, Valverde-Pérez B, Domingo-Félez C, Jensen MM, Smets BF. The pH dependency of N-converting enzymatic processes, pathways and microbes: effect on net N2O production. Environ Microbiol 2018; 20:1623-1640. [DOI: 10.1111/1462-2920.14063] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/31/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Jan-Michael Blum
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Qingxian Su
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Yunjie Ma
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Borja Valverde-Pérez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Carlos Domingo-Félez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Barth F. Smets
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| |
Collapse
|
78
|
Lin YW. Structure and function of heme proteins regulated by diverse post-translational modifications. Arch Biochem Biophys 2018; 641:1-30. [DOI: 10.1016/j.abb.2018.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 01/08/2023]
|
79
|
Tonin F, Arends IWCE. Latest development in the synthesis of ursodeoxycholic acid (UDCA): a critical review. Beilstein J Org Chem 2018; 14:470-483. [PMID: 29520309 PMCID: PMC5827811 DOI: 10.3762/bjoc.14.33] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/05/2018] [Indexed: 12/13/2022] Open
Abstract
Ursodeoxycholic acid (UDCA) is a pharmaceutical ingredient widely used in clinics. As bile acid it solubilizes cholesterol gallstones and improves the liver function in case of cholestatic diseases. UDCA can be obtained from cholic acid (CA), which is the most abundant and least expensive bile acid available. The now available chemical routes for the obtainment of UDCA yield about 30% of final product. For these syntheses several protection and deprotection steps requiring toxic and dangerous reagents have to be performed, leading to the production of a series of waste products. In many cases the cholic acid itself first needs to be prepared from its taurinated and glycilated derivatives in the bile, thus adding to the complexity and multitude of steps involved of the synthetic process. For these reasons, several studies have been performed towards the development of microbial transformations or chemoenzymatic procedures for the synthesis of UDCA starting from CA or chenodeoxycholic acid (CDCA). This promising approach led several research groups to focus their attention on the development of biotransformations with non-pathogenic, easy-to-manage microorganisms, and their enzymes. In particular, the enzymatic reactions involved are selective hydrolysis, epimerization of the hydroxy functions (by oxidation and subsequent reduction) and the specific hydroxylation and dehydroxylation of suitable positions in the steroid rings. In this minireview, we critically analyze the state of the art of the production of UDCA by several chemical, chemoenzymatic and enzymatic routes reported, highlighting the bottlenecks of each production step. Particular attention is placed on the precursors availability as well as the substrate loading in the process. Potential new routes and recent developments are discussed, in particular on the employment of flow-reactors. The latter technology allows to develop processes with shorter reaction times and lower costs for the chemical and enzymatic reactions involved.
Collapse
Affiliation(s)
- Fabio Tonin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Isabel W C E Arends
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
80
|
|
81
|
Muchowska KB, Varma SJ, Chevallot-Beroux E, Lethuillier-Karl L, Li G, Moran J. Metals promote sequences of the reverse Krebs cycle. Nat Ecol Evol 2017; 1:1716-1721. [PMID: 28970480 PMCID: PMC5659384 DOI: 10.1038/s41559-017-0311-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/10/2017] [Indexed: 12/25/2022]
Abstract
The rTCA cycle (also known as the reverse Krebs cycle) is a central anabolic biochemical pathway whose origins are proposed to trace back to geochemistry, long before the advent of enzymes, RNA or cells, and whose imprint still remains intimately embedded in the structure of core metabolism. If it existed, a primordial version of the rTCA cycle would necessarily have been catalyzed by naturally occurring minerals at the earliest stage of the transition from geochemistry to biochemistry. Here we report non-enzymatic promotion of multiple reactions of the rTCA cycle in consecutive sequence, whereby 6 of its 11 reactions are promoted by Zn2+, Cr3+ and Fe0 in an acidic aqueous solution. Two distinct three-reaction sequences can be achieved under a common set of conditions. Selectivity is observed for reduction reactions producing rTCA cycle intermediates compared to those leading off-cycle. Reductive amination of ketoacids to furnish amino acids is observed under similar conditions. The emerging reaction network supports the feasibility of primitive anabolism in an acidic, metal-rich reducing environment.
Collapse
Affiliation(s)
- Kamila B Muchowska
- Institute of Supramolecular Science and Engineering (ISIS UMR 7006), University of Strasbourg, National Center for Scientific Research (CNRS), F-67000, Strasbourg, France
| | - Sreejith J Varma
- Institute of Supramolecular Science and Engineering (ISIS UMR 7006), University of Strasbourg, National Center for Scientific Research (CNRS), F-67000, Strasbourg, France
| | - Elodie Chevallot-Beroux
- Institute of Supramolecular Science and Engineering (ISIS UMR 7006), University of Strasbourg, National Center for Scientific Research (CNRS), F-67000, Strasbourg, France
| | - Lucas Lethuillier-Karl
- Institute of Supramolecular Science and Engineering (ISIS UMR 7006), University of Strasbourg, National Center for Scientific Research (CNRS), F-67000, Strasbourg, France
| | - Guang Li
- Institute of Supramolecular Science and Engineering (ISIS UMR 7006), University of Strasbourg, National Center for Scientific Research (CNRS), F-67000, Strasbourg, France
| | - Joseph Moran
- Institute of Supramolecular Science and Engineering (ISIS UMR 7006), University of Strasbourg, National Center for Scientific Research (CNRS), F-67000, Strasbourg, France.
| |
Collapse
|
82
|
Dietl A, Kieser C, Barends TRM. A Peltier-cooled microscope stage for protein crystal post-crystallization treatment. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717008755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Crystals of the multi-enzyme complex hydrazine synthase showed severe diffuse scattering and high mosaicity. Improved diffraction quality was achieved by soaking the crystals in highly concentrated betaine solutions at reduced temperatures. To enable this, a Peltier-cooled microscope stage was developed for the slow cooling of protein crystals immersed in cryoprotectants or other soaking solutions. Both the construction of the stage and its successful application to hydrazine synthase crystals are described.
Collapse
|
83
|
Speth DR, Lagkouvardos I, Wang Y, Qian PY, Dutilh BE, Jetten MSM. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria. MICROBIAL ECOLOGY 2017; 74:1-5. [PMID: 28074246 PMCID: PMC5486813 DOI: 10.1007/s00248-017-0929-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/01/2017] [Indexed: 05/21/2023]
Abstract
Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.
Collapse
Affiliation(s)
- Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.
- Division for Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| | - Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Technische Universität München, Freising, Germany
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
84
|
|
85
|
Ferousi C, Lindhoud S, Baymann F, Kartal B, Jetten MSM, Reimann J. Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria. Curr Opin Chem Biol 2017; 37:129-136. [DOI: 10.1016/j.cbpa.2017.03.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 02/07/2023]
|
86
|
Oshiki M, Takagi R, Hatamoto M, Yamaguchi T, Araki N. High-cell-density cultivation of Nitrosomonas europaea in a membrane bioreactor for performing protein purification and characterization studies. J GEN APPL MICROBIOL 2017; 62:330-333. [PMID: 27773917 DOI: 10.2323/jgam.2016.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | | | | | | | | |
Collapse
|
87
|
Kartal B, Keltjens JT. Anammox Biochemistry: a Tale of Heme c Proteins. Trends Biochem Sci 2016; 41:998-1011. [DOI: 10.1016/j.tibs.2016.08.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 11/30/2022]
|
88
|
Membrane-bound electron transport systems of an anammox bacterium: A complexome analysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1694-704. [DOI: 10.1016/j.bbabio.2016.07.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 11/24/2022]
|
89
|
Maalcke WJ, Reimann J, de Vries S, Butt JN, Dietl A, Kip N, Mersdorf U, Barends TRM, Jetten MSM, Keltjens JT, Kartal B. Characterization of Anammox Hydrazine Dehydrogenase, a Key N2-producing Enzyme in the Global Nitrogen Cycle. J Biol Chem 2016; 291:17077-92. [PMID: 27317665 PMCID: PMC5016112 DOI: 10.1074/jbc.m116.735530] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/07/2016] [Indexed: 11/06/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria derive their energy for growth from the oxidation of ammonium with nitrite as the electron acceptor. N2, the end product of this metabolism, is produced from the oxidation of the intermediate, hydrazine (N2H4). Previously, we identified N2-producing hydrazine dehydrogenase (KsHDH) from the anammox organism Kuenenia stuttgartiensis as the gene product of kustc0694 and determined some of its catalytic properties. In the genome of K. stuttgartiensis, kustc0694 is one of 10 paralogs related to octaheme hydroxylamine (NH2OH) oxidoreductase (HAO). Here, we characterized KsHDH as a covalently cross-linked homotrimeric octaheme protein as found for HAO and HAO-related hydroxylamine-oxidizing enzyme kustc1061 from K. stuttgartiensis Interestingly, the HDH trimers formed octamers in solution, each octamer harboring an amazing 192 c-type heme moieties. Whereas HAO and kustc1061 are capable of hydrazine oxidation as well, KsHDH was highly specific for this activity. To understand this specificity, we performed detailed amino acid sequence analyses and investigated the catalytic and spectroscopic (electronic absorbance, EPR) properties of KsHDH in comparison with the well defined HAO and kustc1061. We conclude that HDH specificity is most likely derived from structural changes around the catalytic heme 4 (P460) and of the electron-wiring circuit comprising seven His/His-ligated c-type hemes in each subunit. These nuances make HDH a globally prominent N2-producing enzyme, next to nitrous oxide (N2O) reductase from denitrifying microorganisms.
Collapse
Affiliation(s)
- Wouter J Maalcke
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Reimann
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Simon de Vries
- the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
| | - Julea N Butt
- the Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom, and
| | - Andreas Dietl
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Nardy Kip
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Ulrike Mersdorf
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas R M Barends
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Mike S M Jetten
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands, the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
| | - Jan T Keltjens
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands,
| |
Collapse
|
90
|
Oshiki M, Ali M, Shinyako-Hata K, Satoh H, Okabe S. Hydroxylamine-dependent anaerobic ammonium oxidation (anammox) by “Candidatus
Brocadia sinica”. Environ Microbiol 2016; 18:3133-43. [DOI: 10.1111/1462-2920.13355] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering; National Institute of Technology, Nagaoka College; Nagaoka Niigata 940-8532 Japan
| | - Muhammad Ali
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal; 23955-6900 Saudi Arabia
| | - Kaori Shinyako-Hata
- Tokyo Engineering Consultants Co., Ltd., Kasumigaseki, Chioyadaku, Tokyo 100-0013, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
| |
Collapse
|