1
|
Wang J, Wang Z, Liu C, Song M, Xu Q, Liu Y, Yan H. Genome analysis of a newly isolated Bacillus velezensis-YW01 for biodegrading acetaldehyde. Biodegradation 2024; 35:539-549. [PMID: 38573500 DOI: 10.1007/s10532-024-10075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/16/2024] [Indexed: 04/05/2024]
Abstract
Acetaldehyde (AL), a primary carcinogen, not only pollutes the environment, but also endangers human health after drinking alcohol. Here a promising bacterial strain was successfully isolated from a white wine cellar pool in the province of Shandong, China, and identified as Bacillus velezensis-YW01 with 16 S rDNA sequence. Using AL as sole carbon source, initial AL of 1 g/L could be completely biodegraded by YW01 within 84 h and the cell-free extracts of YW01 has also been detected to biodegrade the AL, which indicate that YW01 is a high-potential strain for the biodegradation of AL. The optimal culture conditions and the biodegradation of AL of YW01 are at pH 7.0 and 38 °C, respectively. To further analyze the biodegradation mechanism of AL, the whole genome of YW01 was sequenced. Genes ORF1040, ORF1814 and ORF0127 were revealed in KEGG, which encode for acetaldehyde dehydrogenase. Furthermore, ORF0881 and ORF052 encode for ethanol dehydrogenase. This work provides valuable information for exploring metabolic pathway of converting ethanol to AL and subsequently converting AL to carboxylic acid compounds, which opened up potential pathways for the development of microbial catalyst against AL.
Collapse
Affiliation(s)
- Jingjing Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Zhihao Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Chao Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Meijie Song
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Qianqian Xu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| |
Collapse
|
2
|
Interspecies Formate Exchange Drives Syntrophic Growth of Syntrophotalea carbinolica and Methanococcus maripaludis. Appl Environ Microbiol 2022; 88:e0115922. [PMID: 36374033 PMCID: PMC9746305 DOI: 10.1128/aem.01159-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The complete remineralization of organic matter in anoxic environments relies on communities of microorganisms that ferment organic acids and alcohols to CH4. This is accomplished through syntrophic association of H2 or formate producing bacteria and methanogenic archaea, where exchange of these intermediates enables growth of both organisms. While these communities are essential to Earth's carbon cycle, our understanding of the dynamics of H2 or formate exchanged is limited. Here, we establish a model partnership between Syntrophotalea carbinolica and Methanococcus maripaludis. Through sequencing a transposon mutant library of M. maripaludis grown with ethanol oxidizing S. carbinolica, we found that genes encoding the F420-dependent formate dehydrogenase (Fdh) and F420-dependent methylene-tetrahydromethanopterin dehydrogenase (Mtd) are important for growth. Competitive growth of M. maripaludis mutants defective in either H2 or formate metabolism verified that, across multiple substrates, interspecies formate exchange was dominant in these communities. Agitation of these cultures to facilitate diffusive loss of H2 to the culture headspace resulted in an even greater competitive advantage for M. maripaludis strains capable of oxidizing formate. Finally, we verified that an M. maripaludis Δmtd mutant had a defect during syntrophic growth. Together, these results highlight the importance of formate exchange for the growth of methanogens under syntrophic conditions. IMPORTANCE In the environment, methane is typically generated by fermentative bacteria and methanogenic archaea working together in a process called syntrophy. Efficient exchange of small molecules like H2 or formate is essential for growth of both organisms. However, difficulties in determining the relative contribution of these intermediates to methanogenesis often hamper efforts to understand syntrophic interactions. Here, we establish a model syntrophic coculture composed of S. carbinolica and the genetically tractable methanogen M. maripaludis. Using mutant strains of M. maripaludis that are defective for either H2 or formate metabolism, we determined that interspecies formate exchange drives syntrophic growth of these organisms. Together, these results advance our understanding of the degradation of organic matter in anoxic environments.
Collapse
|
3
|
Genetically encoded probiotic EcN 1917 alleviates alcohol-induced acute liver injury and restore gut microbiota homeostasis. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
|
4
|
Detman A, Bucha M, Treu L, Chojnacka A, Pleśniak Ł, Salamon A, Łupikasza E, Gromadka R, Gawor J, Gromadka A, Drzewicki W, Jakubiak M, Janiga M, Matyasik I, Błaszczyk MK, Jędrysek MO, Campanaro S, Sikora A. Evaluation of acidogenesis products' effect on biogas production performed with metagenomics and isotopic approaches. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:125. [PMID: 34051845 PMCID: PMC8164749 DOI: 10.1186/s13068-021-01968-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/06/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. RESULTS Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%-67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. CONCLUSIONS In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.
Collapse
Affiliation(s)
- Anna Detman
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Michał Bucha
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Laura Treu
- Department of Biology, University of Padova, Padova, Italy
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw, University of Life Sciences, Warsaw, Poland
| | - Łukasz Pleśniak
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | | | - Ewa Łupikasza
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Robert Gromadka
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | | | - Wojciech Drzewicki
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | - Marta Jakubiak
- Institute of Geological Sciences, University of Wroclaw, Wrocław, Poland
| | - Marek Janiga
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Irena Matyasik
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Mieczysław K Błaszczyk
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw, University of Life Sciences, Warsaw, Poland
| | | | | | - Anna Sikora
- Institute of Biochemistry and Biophysics PAS, Warsaw, Poland.
| |
Collapse
|
5
|
Lee MH, Lee J, Jung SK, Kang D, Park MS, Cha GD, Cho KW, Song JH, Moon S, Yun YS, Kim SJ, Lim YW, Kim DH, Kang K. A Biodegradable Secondary Battery and its Biodegradation Mechanism for Eco-Friendly Energy-Storage Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2004902. [PMID: 33533125 DOI: 10.1002/adma.202004902] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 12/10/2020] [Indexed: 06/12/2023]
Abstract
The production of rechargeable batteries is rapidly expanding, and there are going to be new challenges in the near future about how the potential environmental impact caused by the disposal of the large volume of the used batteries can be minimized. Herein, a novel strategy is proposed to address these concerns by applying biodegradable device technology. An eco-friendly and biodegradable sodium-ion secondary battery (SIB) is developed through extensive material screening followed by the synthesis of biodegradable electrodes and their seamless assembly with an unconventional biodegradable separator, electrolyte, and package. Each battery component decomposes in nature into non-toxic compounds or elements via hydrolysis and/or fungal degradation, with all of the biodegradation products naturally abundant and eco-friendly. Detailed biodegradation mechanisms and toxicity influence of each component on living organisms are determined. In addition, this new SIB delivers performance comparable to that of conventional non-degradable SIBs. The strategy and findings suggest a novel eco-friendly biodegradable paradigm for large-scale rechargeable battery systems.
Collapse
Affiliation(s)
- Myeong Hwan Lee
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- Department of Materials Science and Engineering, Research Institute of Advanced Materials (RIAM), Seoul National University, Seoul, 08826, Republic of Korea
| | - Jongha Lee
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung-Kyun Jung
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- Department of Materials Science and Engineering, Research Institute of Advanced Materials (RIAM), Seoul National University, Seoul, 08826, Republic of Korea
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dayoung Kang
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Myung Soo Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Gi Doo Cha
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyoung Won Cho
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jun-Hyuk Song
- Department of Materials Science and Engineering, Research Institute of Advanced Materials (RIAM), Seoul National University, Seoul, 08826, Republic of Korea
| | - Sehwan Moon
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- Department of Materials Science and Engineering, Research Institute of Advanced Materials (RIAM), Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Soo Yun
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Seok Joo Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dae-Hyeong Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- Department of Materials Science and Engineering, Research Institute of Advanced Materials (RIAM), Seoul National University, Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kisuk Kang
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- Department of Materials Science and Engineering, Research Institute of Advanced Materials (RIAM), Seoul National University, Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Engineering Research, College of Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| |
Collapse
|
6
|
Baesman SM, Sutton JM, Fierst JL, Akob DM, Oremland RS. Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments. Int J Syst Evol Microbiol 2021; 71. [PMID: 33570486 DOI: 10.1099/ijsem.0.004698] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93T, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93T was capable of acetylenotrophic and diazotrophic growth, grew at 22-37 °C, pH 6.3-8.5 and in the presence of 10-45 g l-1 NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93T represented a member of the genus Syntrophotalea with highest 16S rRNA gene sequence similarities to Syntrophotalea acetylenica DSM 3246T (96.6 %), Syntrophotalea carbinolica DSM 2380T (96.5 %), and Syntrophotalea venetiana DSM 2394T (96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93T had low genome-wide average nucleotide identity (81-87.5 %) and <70 % digital DNA-DNA hybridization value with other members of the genus Syntrophotalea. The phylogenetic position of SFB93T within the family Syntrophotaleaceae and as a novel member of the genus Syntrophotalea was confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species, Syntrophotalea acetylenivorans sp. nov., is proposed, with SFB93T (=DSM 106009T=JCM 33327T=ATCC TSD-118T) as the type strain.
Collapse
Affiliation(s)
- Shaun M Baesman
- U.S. Geological Survey, 345 Middlefield Road, Menlo Park, California, USA
| | - John M Sutton
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Janna L Fierst
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Denise M Akob
- U.S. Geological Survey, 12201 Sunrise Valley Dr., MS 954 Reston, Virginia, USA
| | - Ronald S Oremland
- U.S. Geological Survey, 345 Middlefield Road, Menlo Park, California, USA
| |
Collapse
|
7
|
Trifunović D, Berghaus N, Müller V. Growth of the acetogenic bacterium Acetobacterium woodii by dismutation of acetaldehyde to acetate and ethanol. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:58-62. [PMID: 31715654 DOI: 10.1111/1758-2229.12811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 06/10/2023]
Abstract
Acetogenic bacteria are a group of strictly anaerobic bacteria that may have been first life forms on Earth since they employ an ancient pathway for CO2 fixation into acetyl-CoA that is coupled to the synthesis of ATP, the Wood-Ljungdahl pathway. Electrons for CO2 reduction are derived from oxidation of H2 or CO and thus, these bacteria can grow lithotrophically on gases present on early Earth. Among the organic molecules present on early Earth is acetaldehyde, a highly volatile C2 compound. Here, we demonstrate that the acetogenic model bacterium Acetobacterium woodii grows on acetaldehyde. Acetaldehyde is dismutated to ethanol and acetyl-CoA, most likely by the bifunctional alcohol dehydrogenase AdhE. Acetyl-CoA is converted to acetate by two subsequent enzymes, phosphotransacetylase and acetate kinase, accompanied by the synthesis of ATP by substrate-level phosphorylation. Apparently, growth on acetaldehyde does not employ the Wood-Ljungdahl pathway. Our finding opens the possibility of a simple and ancient metabolic pathway with only three enzymes that allows for biomass (acetyl-CoA) and ATP formation on early Earth.
Collapse
Affiliation(s)
- Dragan Trifunović
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Natalie Berghaus
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| |
Collapse
|
8
|
Keller A, Schink B, Müller N. Energy-Conserving Enzyme Systems Active During Syntrophic Acetate Oxidation in the Thermophilic Bacterium Thermacetogenium phaeum. Front Microbiol 2019; 10:2785. [PMID: 31849917 PMCID: PMC6895022 DOI: 10.3389/fmicb.2019.02785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/15/2019] [Indexed: 11/13/2022] Open
Abstract
The thermophilic acetogen Thermacetogenium phaeum uses the Wood-Ljungdahl pathway (WLP) in both directions, either for the production of acetate from various compounds or for the oxidation of acetate in syntrophic cooperation with methanogens. In this study, energy-conserving enzyme systems in T. phaeum were investigated in both metabolic directions. A gene cluster containing a membrane-bound periplasmically oriented formate dehydrogenase directly adjacent to putative menaquinone synthesis genes was identified in the genome. The protein products of these genes were identified by total proteome analysis, and menaquinone MK-7 had been found earlier as the dominant quinone in the membrane. Enzyme assays with membrane preparations and anthraquinone-2,6-disulfonate as electron acceptor verified the presence of a quinone-dependent formate dehydrogenase. A quinone-dependent methylene-THF reductase is active in the soluble fraction and in the membrane fraction. From these results we conclude a reversed electron transport system from methyl-THF oxidation to CO2 reduction yielding formate as reduced product which is transferred to the methanogenic partner. The redox potential difference between methyl-THF (Eo' = -200 mV) and formate (Eo' = -432 mV) does not allow electron transfer through syntrophic formate removal alone. We postulate that part of the ATP conserved by substrate-level phosphorylation has to be invested into the generation of a transmembrane proton gradient by ATPase. This proton gradient could drive the endergonic oxidation of methyl-THF in an enzyme reaction similar to the membrane-bound reversed electron transport system previously observed in the syntrophically butyrate-oxidizing bacterium Syntrophomonas wolfei. To balance the overall ATP budget in acetate oxidation, we postulate that acetate is activated through an ATP-independent path via aldehyde:ferredoxin oxidoreductase (AOR) and subsequent oxidation of acetaldehyde to acetyl-CoA.
Collapse
Affiliation(s)
- Anja Keller
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, Universität Konstanz, Konstanz, Germany
| |
Collapse
|
9
|
Xie X, Müller N. Enhanced aniline degradation by Desulfatiglans anilini in a synthetic microbial community with the phototrophic purple sulfur bacterium Thiocapsa roseopersicina. Syst Appl Microbiol 2019; 42:125998. [PMID: 31345671 DOI: 10.1016/j.syapm.2019.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 11/30/2022]
Abstract
Desulfatiglans anilini is a sulfate-reducing bacterium (SRB) capable of oxidizing aniline, although growth and aniline turnover rates are slow, making it difficult to analyze the metabolism of the strain. Therefore, this study was designed to investigate the effect of sulfide on growth of D. anilini cultures, in order to improve its growth and aniline turnover rates, and study the biochemical mechanisms of sulfide inhibition. Hydrogen sulfide was found to inhibit growth of D. anilini, regardless of whether the strain was grown with aniline or phenol, and complete inhibition was observed at 20mM hydrogen sulfide. For improving the growth of D. anilini with aniline, the sulfide-consuming phototrophic bacterium Thiocapsa roseopersicina was co-cultured in a synthetic microbial community with D. anilini using a co-cultivation device that continuously removed hydrogen sulfide from the culture. The doubling time of D. anilini with aniline was 15 days in the co-cultivation device, compared to 26 days in the absence of a sulfide-oxidizing partner. Moreover, the aniline degradation rate was significantly increased by a factor of 2.66 during co-cultivation of D. anilini with T. roseopersicina. The initial carboxylation reaction during aniline degradation was measured in cell-free extracts of D. anilini with carbon dioxide (CO2) as a co-substrate in the presence of aniline and ATP. The effects of hydrogen sulfide on this aniline carboxylating system and on phenylphosphate synthase activity for phenol activation were studied, and it was concluded that hydrogen sulfide severely inhibited these enzyme activities.
Collapse
Affiliation(s)
- Xiaoman Xie
- Department of Biology, University of Konstanz, Constance, Germany; Konstanz Research School Chemical Biology, Constance, Germany
| | - Nicolai Müller
- Department of Biology, University of Konstanz, Constance, Germany.
| |
Collapse
|
10
|
Nguyen LN, Johir MAH, Commault A, Bustamante H, Aurisch R, Lowrie R, Nghiem LD. Impacts of mixing on foaming, methane production, stratification and microbial community in full-scale anaerobic co-digestion process. BIORESOURCE TECHNOLOGY 2019; 281:226-233. [PMID: 30825825 DOI: 10.1016/j.biortech.2019.02.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
This study investigated the impact of mixing on key factors including foaming, substrate stratification, methane production and microbial community in three full scale anaerobic digesters. Digester foaming was observed at one plant that co-digested sewage sludge and food waste, and was operated without mixing. The lack of mixing led to uneven distribution of total chemical oxygen demand (tCOD) and volatile solid (VS) as well as methane production within the digester. 16S rRNA gene-based community analysis clearly differentiated the microbial community from the top and bottom. By contrast, foaming and substrate stratification were not observed at the other two plants with internal circulation mixing. The abundance of methanogens (Methanomicrobia) at the top was about four times higher than at the bottom, correlating to much higher methane production from the top verified by ex-situ biomethane assay, causing foaming. This result is consistent with foaming potential assessment of digestate samples from the digester.
Collapse
Affiliation(s)
- Luong N Nguyen
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia.
| | - Md Abu Hasan Johir
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia
| | - Audrey Commault
- Climate Change Cluster (C3), University of Technology Sydney, NSW 2007, Australia
| | | | | | | | - Long D Nghiem
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia; NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| |
Collapse
|
11
|
Keller A, Schink B, Müller N. Alternative Pathways of Acetogenic Ethanol and Methanol Degradation in the Thermophilic Anaerobe Thermacetogenium phaeum. Front Microbiol 2019; 10:423. [PMID: 30949135 PMCID: PMC6436200 DOI: 10.3389/fmicb.2019.00423] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/18/2019] [Indexed: 11/26/2022] Open
Abstract
Growth of the anaerobic thermophile Thermacetogenium phaeum with methanol, ethanol, ethanolamine, and acetate was investigated in axenic cultures and in syntrophic cultures with Methanothermobacter thermautotrophicus. Microcompartment genes were identified in the T. phaeum genome, and presence of microcompartments was confirmed by transmission electron microscopy and proteome analysis. These genes were expressed only during growth with ethanolamine. Proteome data were compared after growth with all four substrates, and activities of key enzymes of the Wood–Ljungdahl pathway and of enzyme systems leading to production or degradation of acetaldehyde such as alcohol dehydrogenase, aldehyde:ferredoxin oxidoreductase, acetate kinase, and phosphate acetyltransferase were measured in cytoplasmic fractions. Accounting of fermentation stoichiometries and growth yields with all four substrates showed that ethanol and methanol oxidation follow the same stoichiometries as in Acetobacterium woodii. On the other hand, the pathways of ethanol and methanol degradations vary between both organisms. Growth yields of T. phaeum were substantially lower than reported for A. woodii. Since T. phaeum has no Rnf complex encoded in its genome, the mechanisms of ATP synthesis have to be different from those of A. woodii. In addition to the central degradation pathways also found in A. woodii, T. phaeum maintains enzyme systems that compensate for the absence of an Rnf-complex but which on the other hand cause a loss of energy. On the basis of our data, pathways of methanol and ethanol degradation in T. phaeum are discussed.
Collapse
Affiliation(s)
- Anja Keller
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, Universität Konstanz, Konstanz, Germany
| |
Collapse
|
12
|
Im S, Yun YM, Song YC, Kim DH. Enhanced anaerobic digestion of glycerol by promoting DIET reaction. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.11.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
13
|
Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment. ISME JOURNAL 2018; 13:277-289. [PMID: 30206424 PMCID: PMC6331629 DOI: 10.1038/s41396-018-0269-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/11/2018] [Accepted: 07/26/2018] [Indexed: 11/08/2022]
Abstract
Coastal saltmarsh sediments represent an important source of natural methane emissions, much of which originates from quaternary and methylated amines, such as choline and trimethylamine. In this study, we combine DNA stable isotope probing with high throughput sequencing of 16S rRNA genes and 13C2-choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline. Microcosm incubation with 13C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers. Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides. Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway. Together, our data provide a new insight on the diversity of choline utilizing organisms in coastal sediments and support a syntrophic relationship between Bacteria and Archaea as the dominant route for methanogenesis from choline in this environment.
Collapse
|
14
|
Enzymes involved in the anaerobic degradation of phenol by the sulfate-reducing bacterium Desulfatiglans anilini. BMC Microbiol 2018; 18:93. [PMID: 30157755 PMCID: PMC6114531 DOI: 10.1186/s12866-018-1238-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 08/17/2018] [Indexed: 11/11/2022] Open
Abstract
Background The sulfate-reducing bacterium Desulfatiglans anilini can grow with phenol as sole source of carbon and energy under strictly anaerobic, sulfate-reducing conditions. In the nitrate-reducing bacterium Thauera aromatica, the enzymes involved in phenol degradation have been well elucidated, whereas the anaerobic phenol degradation pathway by D. anilini was not studied in detail yet. Results The pathway of anaerobic phenol degradation by the sulfate-reducing bacterium Desulfatiglans anilini was studied by identification of genes coding for phenylphosphate synthase (encoded by pps genes) and phenylphosphate carboxylase (encoded by ppc genes) in the genome of D. anilini, by analysis of the transcription and translation of pps-ppc genes, and by measurement of phenylphosphate synthase activity in cell-free extracts of phenol-grown cells. The majority of genes involved in phenol degradation were found to be organized in one gene cluster. The gene cluster contained genes ppsα (phenylphosphate synthase alpha subunit), ppsβ (phenylphosphate synthase beta subunit), ppcβ (phenylphosphate carboxylase beta subunit), as well as 4-hydroxybenzoyl-CoA ligase and 4-hydroxylbenzoyl-CoA reductase-encoding genes. The genes ppsγ (phenylphosphate synthase gamma subunit), ppcα (phenylphosphate carboxylase alpha subunit) and ppcδ (phenylphosphate carboxylase delta subunit) were located elsewhere in the genome of D. anilini, and no obvious homologue of ppcγ (phenylphosphate carboxylase gamma subunit) was found in the genome. Induction of genes pps and ppc during growth on phenol was confirmed by reverse transcription polymerase chain reaction. Total proteome analysis revealed that the abundance of enzymes encoded by the gene cluster under study was much higher in phenol-grown cells than that in benzoate-grown cells. In in-vitro enzyme assays with cell-free extracts of phenol-grown cells, phenylphosphate was formed from phenol in the presence of ATP, Mg2+, Mn2+, K+ as co-factors. Conclusions The genes coding for enzymes involved in the anaerobic phenol degradation pathway were identified in the sulfate-reducing bacterium D. anilini. The results indicate that the first steps of anaerobic phenol degradation in D. anilini are phosphorylation of phenol to phenylphosphate by phenylphosphate synthase and carboxylation of phenylphosphate by phenylphosphate carboxylase. Electronic supplementary material The online version of this article (10.1186/s12866-018-1238-0) contains supplementary material, which is available to authorized users.
Collapse
|
15
|
Detman A, Mielecki D, Pleśniak Ł, Bucha M, Janiga M, Matyasik I, Chojnacka A, Jędrysek MO, Błaszczyk MK, Sikora A. Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:116. [PMID: 29721040 PMCID: PMC5910564 DOI: 10.1186/s13068-018-1106-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 04/04/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Anaerobic digestion, whose final products are methane and carbon dioxide, ensures energy flow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Effective utilization of lactate has been observed in many experimental approaches used to study anaerobic digestion. Interestingly, anaerobic lactate oxidation and lactate oxidizers as a physiological group in methane-yielding microbial communities have not received enough attention in the context of the acetogenic step of anaerobic digestion. This study focuses on metabolic transformation of lactate during the acetogenic and methanogenic steps of anaerobic digestion in methane-yielding bioreactors. RESULTS Methane-yielding microbial communities instead of pure cultures of acetate producers were used to process artificial lactate-rich media to methane and carbon dioxide in up-flow anaerobic sludge blanket reactors. The media imitated the mixture of acidic products found in anaerobic environments/digesters where lactate fermentation dominates in acidogenesis. Effective utilization of lactate and biogas production was observed. 16S rRNA profiling was used to examine the selected methane-yielding communities. Among Archaea present in the bioreactors, the order Methanosarcinales predominated. The acetoclastic pathway of methane formation was further confirmed by analysis of the stable carbon isotope composition of methane and carbon dioxide. The domain Bacteria was represented by Bacteroidetes, Firmicutes, Proteobacteria, Synergistetes, Actinobacteria, Spirochaetes, Tenericutes, Caldithrix, Verrucomicrobia, Thermotogae, Chloroflexi, Nitrospirae, and Cyanobacteria. Available genome sequences of species and/or genera identified in the microbial communities were searched for genes encoding the lactate-oxidizing metabolic machinery homologous to those of Acetobacterium woodii and Desulfovibrio vulgaris. Furthermore, genes for enzymes of the reductive acetyl-CoA pathway were present in the microbial communities. CONCLUSIONS The results indicate that lactate is oxidized mainly to acetate during the acetogenic step of AD and this comprises the acetotrophic pathway of methanogenesis. The genes for lactate utilization under anaerobic conditions are widespread in the domain Bacteria. Lactate oxidation to the substrates for methanogens is the most energetically attractive process in comparison to butyrate, propionate, or ethanol oxidation.
Collapse
Affiliation(s)
- Anna Detman
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Damian Mielecki
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Łukasz Pleśniak
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Bucha
- Faculty of Earth Sciences, University of Silesia in Katowice, Sosnowiec, Poland
| | - Marek Janiga
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Irena Matyasik
- Oil and Gas Institute, National Research Institute, Cracow, Poland
| | - Aleksandra Chojnacka
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Anna Sikora
- Department of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
16
|
Müller N, Timmers P, Plugge CM, Stams AJM, Schink B. Syntrophy in Methanogenic Degradation. (ENDO)SYMBIOTIC METHANOGENIC ARCHAEA 2018. [DOI: 10.1007/978-3-319-98836-8_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
17
|
Losey NA, Mus F, Peters JW, Le HM, McInerney MJ. Syntrophomonas wolfei Uses an NADH-Dependent, Ferredoxin-Independent [FeFe]-Hydrogenase To Reoxidize NADH. Appl Environ Microbiol 2017; 83:e01335-17. [PMID: 28802265 PMCID: PMC5626996 DOI: 10.1128/aem.01335-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/29/2017] [Indexed: 12/19/2022] Open
Abstract
Syntrophomonas wolfei syntrophically oxidizes short-chain fatty acids (four to eight carbons in length) when grown in coculture with a hydrogen- and/or formate-using methanogen. The oxidation of 3-hydroxybutyryl-coenzyme A (CoA), formed during butyrate metabolism, results in the production of NADH. The enzyme systems involved in NADH reoxidation in S. wolfei are not well understood. The genome of S. wolfei contains a multimeric [FeFe]-hydrogenase that may be a mechanism for NADH reoxidation. The S. wolfei genes for the multimeric [FeFe]-hydrogenase (hyd1ABC; SWOL_RS05165, SWOL_RS05170, SWOL_RS05175) and [FeFe]-hydrogenase maturation proteins (SWOL_RS05180, SWOL_RS05190, SWOL_RS01625) were coexpressed in Escherichia coli, and the recombinant Hyd1ABC was purified and characterized. The purified recombinant Hyd1ABC was a heterotrimer with an αβγ configuration and a molecular mass of 115 kDa. Hyd1ABC contained 29.2 ± 1.49 mol of Fe and 0.7 mol of flavin mononucleotide (FMN) per mole enzyme. The purified, recombinant Hyd1ABC reduced NAD+ and oxidized NADH without the presence of ferredoxin. The HydB subunit of the S. wolfei multimeric [FeFe]-hydrogenase lacks two iron-sulfur centers that are present in known confurcating NADH- and ferredoxin-dependent [FeFe]-hydrogenases. Hyd1ABC is a NADH-dependent hydrogenase that produces hydrogen from NADH without the need of reduced ferredoxin, which differs from confurcating [FeFe]-hydrogenases. Hyd1ABC provides a mechanism by which S. wolfei can reoxidize NADH produced during syntrophic butyrate oxidation when low hydrogen partial pressures are maintained by a hydrogen-consuming microorganism.IMPORTANCE Our work provides mechanistic understanding of the obligate metabolic coupling that occurs between hydrogen-producing fatty and aromatic acid-degrading microorganisms and their hydrogen-consuming partners in the process called syntrophy (feeding together). The multimeric [FeFe]-hydrogenase used NADH without the involvement of reduced ferredoxin. The multimeric [FeFe]-hydrogenase would produce hydrogen from NADH only when hydrogen concentrations were low. Hydrogen production from NADH by Syntrophomonas wolfei would likely cease before any detectable amount of cell growth occurred. Thus, continual hydrogen production requires the presence of a hydrogen-consuming partner to keep hydrogen concentrations low and explains, in part, the obligate requirement that S. wolfei has for a hydrogen-consuming partner organism during growth on butyrate. We have successfully expressed genes encoding a multimeric [FeFe]-hydrogenase in E. coli, demonstrating that such an approach can be advantageous to characterize complex redox proteins from difficult-to-culture microorganisms.
Collapse
Affiliation(s)
- Nathaniel A Losey
- Department of Plant Biology and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
| | - Florence Mus
- Department of Chemistry and Biochemistry, Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Huynh M Le
- Department of Plant Biology and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael J McInerney
- Department of Plant Biology and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
| |
Collapse
|
18
|
Schink B, Montag D, Keller A, Müller N. Hydrogen or formate: Alternative key players in methanogenic degradation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:189-202. [PMID: 28205388 DOI: 10.1111/1758-2229.12524] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hydrogen and formate are important electron carriers in methanogenic degradation in anoxic environments such as sediments, sewage sludge digestors and biogas reactors. Especially in the terminal steps of methanogenesis, they determine the energy budgets of secondary (syntrophically) fermenting bacteria and their methanogenic partners. The literature provides considerable data on hydrogen pool sizes in such habitats, but little data exist for formate concentrations due to technical difficulties in formate determination at low concentration. Recent evidence from biochemical and molecular biological studies indicates that several secondary fermenters can use both hydrogen and formate for electron release, and may do so even simultaneously. Numerous strictly anaerobic bacteria contain enzymes which equilibrate hydrogen and formate pools to energetically equal values, and recent measurements in sewage digestors and biogas reactors indicate that - beyond occasional fluctuations - the pool sizes of hydrogen and formate are indeed energetically nearly equivalent. Nonetheless, a thermophilic archaeon from a submarine hydrothermal vent, Thermococcus onnurineus, can obtain ATP from the conversion of formate to hydrogen plus bicarbonate at 80°C, indicating that at least in this extreme environment the pools of formate and hydrogen are likely to be sufficiently different to support such an unusual type of energy conservation.
Collapse
Affiliation(s)
- Bernhard Schink
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Dominik Montag
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Anja Keller
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| | - Nicolai Müller
- Department of Biology, Microbial Ecology, University of Konstanz, Konstanz, D-78457, Germany
| |
Collapse
|
19
|
Boll M, Einsle O, Ermler U, Kroneck PMH, Ullmann GM. Structure and Function of the Unusual Tungsten Enzymes Acetylene Hydratase and Class II Benzoyl-Coenzyme A Reductase. J Mol Microbiol Biotechnol 2016; 26:119-37. [PMID: 26959374 DOI: 10.1159/000440805] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In biology, tungsten (W) is exclusively found in microbial enzymes bound to a bis-pyranopterin cofactor (bis-WPT). Previously known W enzymes catalyze redox oxo/hydroxyl transfer reactions by directly coordinating their substrates or products to the metal. They comprise the W-containing formate/formylmethanofuran dehydrogenases belonging to the dimethyl sulfoxide reductase (DMSOR) family and the aldehyde:ferredoxin oxidoreductase (AOR) families, which form a separate enzyme family within the Mo/W enzymes. In the last decade, initial insights into the structure and function of two unprecedented W enzymes were obtained: the acetaldehyde forming acetylene hydratase (ACH) belongs to the DMSOR and the class II benzoyl-coenzyme A (CoA) reductase (BCR) to the AOR family. The latter catalyzes the reductive dearomatization of benzoyl-CoA to a cyclic diene. Both are key enzymes in the degradation of acetylene (ACH) or aromatic compounds (BCR) in strictly anaerobic bacteria. They are unusual in either catalyzing a nonredox reaction (ACH) or a redox reaction without coordinating the substrate or product to the metal (BCR). In organic chemical synthesis, analogous reactions require totally nonphysiological conditions depending on Hg2+ (acetylene hydration) or alkali metals (benzene ring reduction). The structural insights obtained pave the way for biological or biomimetic approaches to basic reactions in organic chemistry.
Collapse
Affiliation(s)
- Matthias Boll
- Fakultx00E4;t fx00FC;r Biologie/Mikrobiologie, Institut fx00FC;r Biochemie, Albert-Ludwigs-Universitx00E4;t Freiburg, Freiburg, Germany
| | | | | | | | | |
Collapse
|
20
|
Acetylene hydratase: a non-redox enzyme with tungsten and iron-sulfur centers at the active site. J Biol Inorg Chem 2016; 21:29-38. [PMID: 26790879 DOI: 10.1007/s00775-015-1330-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/30/2015] [Indexed: 01/05/2023]
Abstract
In living systems, tungsten is exclusively found in microbial enzymes coordinated by the pyranopterin cofactor, with additional metal coordination provided by oxygen and/or sulfur, and/or selenium atoms in diverse arrangements. Prominent examples are formate dehydrogenase, formylmethanofuran dehydrogenase, and aldehyde oxidoreductase all of which catalyze redox reactions. The bacterial enzyme acetylene hydratase (AH) stands out of its class as it catalyzes the conversion of acetylene to acetaldehyde, clearly a non-redox reaction and a reaction distinct from the reduction of acetylene to ethylene by nitrogenase. AH harbors two pyranopterins bound to W, and a [4Fe-4S] cluster. W is coordinated by four dithiolene sulfur atoms, one cysteine sulfur, and one oxygen ligand. AH activity requires a strong reductant suggesting W(IV) as the active oxidation state. Two different types of reaction pathways have been proposed. The 1.26 Å structure reveals a water molecule coordinated to W which could gain a partially positive net charge by the adjacent protonated Asp-13, enabling a direct attack of C2H2. To access the W-Asp site, a substrate channel was evolved distant from where it is found in other members of the DMSOR family. Computational studies of this second shell mechanism led to unrealistically high energy barriers, and alternative pathways were proposed where C2H2 binds directly to W. The architecture of the catalytic cavity, the specificity for C2H2 and the results from site-directed mutagenesis do not support this first shell mechanism. More investigations including structural information on the binding of C2H2 are needed to present a conclusive answer.
Collapse
|
21
|
A New Class of Tungsten-Containing Oxidoreductase in Caldicellulosiruptor, a Genus of Plant Biomass-Degrading Thermophilic Bacteria. Appl Environ Microbiol 2015; 81:7339-47. [PMID: 26276113 DOI: 10.1128/aem.01634-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/30/2015] [Indexed: 12/18/2022] Open
Abstract
Caldicellulosiruptor bescii grows optimally at 78°C and is able to decompose high concentrations of lignocellulosic plant biomass without the need for thermochemical pretreatment. C. bescii ferments both C5 and C6 sugars primarily to hydrogen gas, lactate, acetate, and CO2 and is of particular interest for metabolic engineering applications given the recent availability of a genetic system. Developing optimal strains for technological use requires a detailed understanding of primary metabolism, particularly when the goal is to divert all available reductant (electrons) toward highly reduced products such as biofuels. During an analysis of the C. bescii genome sequence for oxidoreductase-type enzymes, evidence was uncovered to suggest that the primary redox metabolism of C. bescii has a completely uncharacterized aspect involving tungsten, a rarely used element in biology. An active tungsten utilization pathway in C. bescii was demonstrated by the heterologous production of a tungsten-requiring, aldehyde-oxidizing enzyme (AOR) from the hyperthermophilic archaeon Pyrococcus furiosus. Furthermore, C. bescii also contains a tungsten-based AOR-type enzyme, here termed XOR, which is phylogenetically unique, representing a completely new member of the AOR tungstoenzyme family. Moreover, in C. bescii, XOR represents ca. 2% of the cytoplasmic protein. XOR is proposed to play a key, but as yet undetermined, role in the primary redox metabolism of this cellulolytic microorganism.
Collapse
|