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Zhang R, Ye Z, Guo X, Yang Y, Li G. Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater. ENVIRONMENT INTERNATIONAL 2024; 188:108755. [PMID: 38772206 DOI: 10.1016/j.envint.2024.108755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.
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Affiliation(s)
- Ruihuan Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhencheng Ye
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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Zhang Z, Guo H, Sun J, Gong X, Wang C, Wang H. Anaerobic phenanthrene biodegradation by a newly isolated sulfate-reducer, strain PheS1, and exploration of the biotransformation pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149148. [PMID: 34311378 DOI: 10.1016/j.scitotenv.2021.149148] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Phenanthrene is a widespread and harmful polycyclic aromatic hydrocarbon that is difficult to anaerobically biodegrade. Current challenges in anaerobic phenanthrene bioremediation are a lack of degrading cultures and limited knowledge of biotransformation pathways. Under sulfate-reducing conditions, pure-cultures and biotransformation processes for anaerobic phenanthrene biodegradation are poorly understood. In this study, strain PheS1, which is phylogenetically closely related to Desulfotomaculum, was found to be a sulfate-reducing phenanthrene-degrading bacterium. Anaerobic phenanthrene biodegradation using PheS1 was proposed based on metabolite and genome analyses, and the initial step was identified as carboxylation based on the detection of 2-phenanthroic acid, [13C]-2-phenanthroic acid, and [D9]-2- phenanthroic acid when phenanthrene+HCO3-, phenanthrene+H13CO3-, and [D10]-phenanthrene+HCO3- were used as the substrate, respectively. PheS1 genome ubiD gene encoding of carboxylase putatively involved in the biodegradation was performed. Next, benzene ring reduction and cleavage that produced benzene compounds and cyclohexane derivative were reported to occur in the downstream biotransformation processes. Additionally, benzene, naphthalene, benz[a]anthracene, and anthracene can be utilised by PheS1, whereas pyrene and benz[a]pyrene cannot. We discovered a new phenanthrene-degrading sulfate-reducer and provided the anaerobic phenanthrene biotransformation pathway under sulfate-reducing conditions, which can act as a reference for practical applications in bioremediation and for studying the molecular mechanisms of phenanthrene in anaerobic zones.
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Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoqiang Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Kung JW, Meier AK, Willistein M, Weidenweber S, Demmer U, Ermler U, Boll M. Structural Basis of Cyclic 1,3-Diene Forming Acyl-Coenzyme A Dehydrogenases. Chembiochem 2021; 22:3173-3177. [PMID: 34555236 PMCID: PMC9293079 DOI: 10.1002/cbic.202100421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/15/2021] [Indexed: 11/20/2022]
Abstract
The biologically important, FAD‐containing acyl‐coenzyme A (CoA) dehydrogenases (ACAD) usually catalyze the anti‐1,2‐elimination of a proton and a hydride of aliphatic CoA thioesters. Here, we report on the structure and function of an ACAD from anaerobic bacteria catalyzing the unprecedented 1,4‐elimination at C3 and C6 of cyclohex‐1‐ene‐1‐carboxyl‐CoA (Ch1CoA) to cyclohex‐1,5‐diene‐1‐carboxyl‐CoA (Ch1,5CoA) and at C3 and C4 of the latter to benzoyl‐CoA. Based on high‐resolution Ch1CoA dehydrogenase crystal structures, the unorthodox reactivity is explained by the presence of a catalytic aspartate base (D91) at C3, and by eliminating the catalytic glutamate base at C1. Moreover, C6 of Ch1CoA and C4 of Ch1,5CoA are positioned towards FAD‐N5 to favor the biologically relevant C3,C6‐ over the C3,C4‐dehydrogenation activity. The C1,C2‐dehydrogenation activity was regained by structure‐inspired amino acid exchanges. The results provide the structural rationale for the extended catalytic repertoire of ACADs and offer previously unknown biocatalytic options for the synthesis of cyclic 1,3‐diene building blocks.
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Affiliation(s)
- Johannes W Kung
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Anne-Katrin Meier
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Max Willistein
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Sina Weidenweber
- Max-Planck-Institute for Biophysics, Max-von-Laue-Strasse 3, 60438, Frankfurt, Germany
| | - Ulrike Demmer
- Max-Planck-Institute for Biophysics, Max-von-Laue-Strasse 3, 60438, Frankfurt, Germany
| | - Ulrich Ermler
- Max-Planck-Institute for Biophysics, Max-von-Laue-Strasse 3, 60438, Frankfurt, Germany
| | - Matthias Boll
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
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Hattenrath-Lehmann TK, Nanjappa D, Zhang H, Yu L, Goleski JA, Lin S, Gobler CJ. Transcriptomic and isotopic data reveal central role of ammonium in facilitating the growth of the mixotrophic dinoflagellate, Dinophysis acuminata. HARMFUL ALGAE 2021; 104:102031. [PMID: 34023078 DOI: 10.1016/j.hal.2021.102031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Dinophysis spp. are mixotrophs that are dependent on specific prey, but are also potentially reliant on dissolved nutrients. The extent to which Dinophysis relies on exogenous N and the specific biochemical pathways important for supporting its autotrophic and heterotrophic growth are unknown. Here, the nutritional ecology of Dinophysis was explored using two approaches: 1) 15N tracer experiments were conducted to quantify the concentration-dependent uptake rates and associated kinetics of various N compounds (nitrate, ammonium, urea) of Dinophysis cultures and 2) the transcriptomic responses of Dinophysis cultures grown with multiple combinations of prey and nutrients were assessed via dinoflagellate spliced leader-based transcriptome profiling. Of the N compounds examined, ammonium had the highest Vmax and affinity coefficient, and lowest Ks for both pre-starved and pre-fed cultures, collectively demonstrating the preference of Dinophysis for this N source while little-to-no nitrate uptake was observed. During the transcriptome experiments, Dinophysis grown with nitrate and without prey had the largest number of genes with lower transcript abundances, did not increase abundance of transcripts associated with nitrate/nitrite uptake or reduction, and displayed no cellular growth, suggesting D. acuminata is not capable of growing on nitrate. When offered prey, the transcriptomic response of Dinophysis included the production of phagolysosomes, enzymes involved in protein and lipid catabolism, and N acquisition through amino acid degradation pathways. Compared with cultures only offered ammonium or prey, cultures offered both ammonium and prey had the largest number of genes with increased transcript abundances, the highest growth rate, and the unique activation of multiple pathways involved in cellular catabolism, further evidencing the ability of Dinophysis to grow optimally as a mixotroph. Collectively, this study evidences the key role ammonium plays in the mixotrophic growth of Dinophysis and reveals the precise biochemical pathways that facilitate its mixotrophic growth.
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Affiliation(s)
- Theresa K Hattenrath-Lehmann
- Stony Brook University, School of Marine and Atmospheric Sciences, 239 Montauk Hwy, Southampton, NY 11968, United States
| | - Deepak Nanjappa
- Stony Brook University, School of Marine and Atmospheric Sciences, 239 Montauk Hwy, Southampton, NY 11968, United States
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, United States
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China
| | - Jennifer A Goleski
- Stony Brook University, School of Marine and Atmospheric Sciences, 239 Montauk Hwy, Southampton, NY 11968, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, United States; State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China
| | - Christopher J Gobler
- Stony Brook University, School of Marine and Atmospheric Sciences, 239 Montauk Hwy, Southampton, NY 11968, United States.
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Dhar K, Subashchandrabose SR, Venkateswarlu K, Krishnan K, Megharaj M. Anaerobic Microbial Degradation of Polycyclic Aromatic Hydrocarbons: A Comprehensive Review. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 251:25-108. [PMID: 31011832 DOI: 10.1007/398_2019_29] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to humans and other living organisms. Biodegradation is the major route of detoxification and removal of PAHs from the environment. Aerobic biodegradation of PAHs has been the subject of extensive research; however, reports on anaerobic biodegradation of PAHs are so far limited. Microbial degradation of PAHs under anaerobic conditions is difficult because of the slow growth rate of anaerobes and low energy yield in the metabolic processes. Despite the limitations, some anaerobic bacteria degrade PAHs under nitrate-reducing, sulfate-reducing, iron-reducing, and methanogenic conditions. Anaerobic biodegradation, though relatively slow, is a significant process of natural attenuation of PAHs from the impacted anoxic environments such as sediments, subsurface soils, and aquifers. This review is intended to provide comprehensive details on microbial degradation of PAHs under various reducing conditions, to describe the degradation mechanisms, and to identify the areas that should receive due attention in further investigations.
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Affiliation(s)
- Kartik Dhar
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Department of Microbiology, University of Chittagong, Chittagong, Bangladesh
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, India
| | - Kannan Krishnan
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia.
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Zhang M, Kang Z, Guo X, Guo S, Xiao D, Liu Y, Ma C, Gao C, Xu P. Regulation of Glutarate Catabolism by GntR Family Regulator CsiR and LysR Family Regulator GcdR in Pseudomonas putida KT2440. mBio 2019; 10:e01570-19. [PMID: 31363033 PMCID: PMC6667623 DOI: 10.1128/mbio.01570-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/02/2019] [Indexed: 01/16/2023] Open
Abstract
Glutarate, a metabolic intermediate in the catabolism of several amino acids and aromatic compounds, can be catabolized through both the glutarate hydroxylation pathway and the glutaryl-coenzyme A (glutaryl-CoA) dehydrogenation pathway in Pseudomonas putida KT2440. The elucidation of the regulatory mechanism could greatly aid in the design of biotechnological alternatives for glutarate production. In this study, it was found that a GntR family protein, CsiR, and a LysR family protein, GcdR, regulate the catabolism of glutarate by repressing the transcription of csiD and lhgO, two key genes in the glutarate hydroxylation pathway, and by activating the transcription of gcdH and gcoT, two key genes in the glutaryl-CoA dehydrogenation pathway, respectively. Our data suggest that CsiR and GcdR are independent and that there is no cross-regulation between the two pathways. l-2-Hydroxyglutarate (l-2-HG), a metabolic intermediate in the glutarate catabolism with various physiological functions, has never been elucidated in terms of its metabolic regulation. Here, we reveal that two molecules, glutarate and l-2-HG, act as effectors of CsiR and that P. putida KT2440 uses CsiR to sense glutarate and l-2-HG and to utilize them effectively. This report broadens our understanding of the bacterial regulatory mechanisms of glutarate and l-2-HG catabolism and may help to identify regulators of l-2-HG catabolism in other species.IMPORTANCE Glutarate is an attractive dicarboxylate with various applications. Clarification of the regulatory mechanism of glutarate catabolism could help to block the glutarate catabolic pathways, thereby improving glutarate production through biotechnological routes. Glutarate is a toxic metabolite in humans, and its accumulation leads to a hereditary metabolic disorder, glutaric aciduria type I. The elucidation of the functions of CsiR and GcdR as regulators that respond to glutarate could help in the design of glutarate biosensors for the rapid detection of glutarate in patients with glutaric aciduria type I. In addition, CsiR was identified as a regulator that also regulates l-2-HG metabolism. The identification of CsiR as a regulator that responds to l-2-HG could help in the discovery and investigation of other regulatory proteins involved in l-2-HG catabolism.
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Affiliation(s)
- Manman Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Department of Radiobiology, Institute of Radiation Medicine of Chinese Academy of Medical Science & Peking Union Medical College, Tianjin, People's Republic of China
| | - Zhaoqi Kang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Xiaoting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Shiting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Dan Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Yidong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Abstract
The family Geobacteraceae, with its only valid genus Geobacter, comprises deltaproteobacteria ubiquitous in soil, sediments, and subsurface environments where metal reduction is an active process. Research for almost three decades has provided novel insights into environmental processes and biogeochemical reactions not previously known to be carried out by microorganisms. At the heart of the environmental roles played by Geobacter bacteria is their ability to integrate redox pathways and regulatory checkpoints that maximize growth efficiency with electron donors derived from the decomposition of organic matter while respiring metal oxides, particularly the often abundant oxides of ferric iron. This metabolic specialization is complemented by versatile metabolic reactions, respiratory chains, and sensory networks that allow specific members to adaptively respond to environmental cues to integrate organic and inorganic contaminants in their oxidative and reductive metabolism, respectively. Thus, Geobacteraceae are important members of the microbial communities that degrade hydrocarbon contaminants under iron-reducing conditions and that contribute, directly or indirectly, to the reduction of radionuclides, toxic metals, and oxidized species of nitrogen. Their ability to produce conductive pili as nanowires for discharging respiratory electrons to solid-phase electron acceptors and radionuclides, or for wiring cells in current-harvesting biofilms highlights the unique physiological traits that make these organisms attractive biological platforms for bioremediation, bioenergy, and bioelectronics application. Here we review some of the most notable physiological features described in Geobacter species since the first model representatives were recovered in pure culture. We provide a historical account of the environmental research that has set the foundation for numerous physiological studies and the laboratory tools that had provided novel insights into the role of Geobacter in the functioning of microbial communities from pristine and contaminated environments. We pay particular attention to latest research, both basic and applied, that has served to expand the field into new directions and to advance interdisciplinary knowledge. The electrifying physiology of Geobacter, it seems, is alive and well 30 years on.
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Wagner AO, Prem EM, Markt R, Kaufmann R, Illmer P. Formation of phenylacetic acid and phenylpropionic acid under different overload conditions during mesophilic and thermophilic anaerobic digestion. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:26. [PMID: 30787959 PMCID: PMC6368962 DOI: 10.1186/s13068-019-1370-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/03/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Substrate spectra for anaerobic digestion have been broadened in the past decade, inter alia, due to the application of different pretreatment strategies and now include materials rich in lignocellulose, protein, and/or fat. The application of these substrates, however, also entails risks regarding the formation of undesired by-products, among which phenolic compounds are known to accumulate under unfavorable digestion conditions. METHODS Different states of overload were simulated in batch experiments while reviewing the generation of phenyl acids out of different lab-use substrates in order to evaluate the impact on biogas and methane production as well as some additional process performance parameters under defined laboratory conditions. Investigations were conducted under both mesophilic and thermophilic conditions. RESULTS It could be shown that the tested input materials led to the formation of phenyl acids in a substrate-dependent manner with the formation itself being less temperature driven. Once formed, the formation of phenyl acids turned out to be a reversible process. CONCLUSIONS Although a mandatory negative impact of phenyl acids per se on the anaerobic digestion process in general and the methanogenesis process in particular could not be proven, phenyl acids, however, seem to play an important role in the microbial response to overloaded biogas systems.
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Affiliation(s)
- Andreas Otto Wagner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Eva Maria Prem
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Rüdiger Kaufmann
- Department of Ecology, Universität Innsbruck, Sternwartestr. 15/Technikerstraße 25/5, 6020 Innsbruck, Austria
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
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9
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Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat Commun 2018; 9:4999. [PMID: 30479325 PMCID: PMC6258724 DOI: 10.1038/s41467-018-07418-0] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/31/2018] [Indexed: 12/16/2022] Open
Abstract
Microbes in Guaymas Basin (Gulf of California) hydrothermal sediments thrive on hydrocarbons and sulfur and experience steep, fluctuating temperature and chemical gradients. The functional capacities of communities inhabiting this dynamic habitat are largely unknown. Here, we reconstructed 551 genomes from hydrothermally influenced, and nearby cold sediments belonging to 56 phyla (40 uncultured). These genomes comprise 22 unique lineages, including five new candidate phyla. In contrast to findings from cold hydrocarbon seeps, hydrothermal-associated communities are more diverse and archaea dominate over bacteria. Genome-based metabolic inferences provide first insights into the ecological niches of these uncultured microbes, including methane cycling in new Crenarchaeota and alkane utilization in ANME-1. These communities are shaped by a high biodiversity, partitioning among nitrogen and sulfur pathways and redundancy in core carbon-processing pathways. The dynamic sediments select for distinctive microbial communities that stand out by expansive biodiversity, and open up new physiological perspectives into hydrothermal ecosystem function. The diversity and function of microbes inhabiting hydrothermal areas is a topic of active interest in marine microbiology. Here, the authors assemble genomes from Guaymas Basin hydrothermal sediments and describe the metabolic roles of the bacterial community, which includes five new bacterial candidate phyla
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Jochum LM, Schreiber L, Marshall IPG, Jørgensen BB, Schramm A, Kjeldsen KU. Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment. Front Microbiol 2018; 9:2038. [PMID: 30233524 PMCID: PMC6129605 DOI: 10.3389/fmicb.2018.02038] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.
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Affiliation(s)
- Lara M Jochum
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Ian P G Marshall
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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11
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Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving L-2-hydroxyglutarate. Nat Commun 2018; 9:2114. [PMID: 29844506 PMCID: PMC5974017 DOI: 10.1038/s41467-018-04513-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/04/2018] [Indexed: 11/09/2022] Open
Abstract
Glutarate is a five carbon platform chemical produced during the catabolism of L-lysine. It is known that it can be catabolized through the glutaryl-CoA dehydrogenation pathway. Here, we discover that Pseudomonas putida KT2440 has an additional glutarate catabolic pathway involving L-2-hydroxyglutarate (L-2-HG), an abnormal metabolite produced from 2-ketoglutarate (2-KG). In this pathway, CsiD, a Fe2+/2-KG-dependent glutarate hydroxylase, is capable of converting glutarate into L-2-HG, and LhgO, an L-2-HG oxidase, can catalyze L-2-HG into 2-KG. We construct a recombinant strain that lacks both glutarate catabolic pathways. It can produce glutarate from L-lysine with a yield of 0.85 mol glutarate/mol L-lysine. Thus, L-2-HG anabolism and catabolism is a metabolic alternative to the glutaryl-CoA dehydrogenation pathway in P. putida KT2440; L-lysine can be both ketogenic and glucogenic.
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A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways. Sci Rep 2018. [PMID: 29540736 PMCID: PMC5852087 DOI: 10.1038/s41598-018-22617-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.
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Weyrauch P, Zaytsev AV, Stephan S, Kocks L, Schmitz OJ, Golding BT, Meckenstock RU. Conversion of cis-2-carboxycyclohexylacetyl-CoA in the downstream pathway of anaerobic naphthalene degradation. Environ Microbiol 2017; 19:2819-2830. [PMID: 28574200 DOI: 10.1111/1462-2920.13806] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/29/2022]
Abstract
The cyclohexane derivative cis-2-(carboxymethyl)cyclohexane-1-carboxylic acid [(1R,2R)-/(1S,2S)-2-(carboxymethyl)cyclohexane-1-carboxylic acid] has previously been identified as metabolite in the pathway of anaerobic degradation of naphthalene by sulfate-reducing bacteria. We tested the corresponding CoA esters of isomers and analogues of this compound for conversion in cell free extracts of the anaerobic naphthalene degraders Desulfobacterium strain N47 and Deltaproteobacterium strain NaphS2. Conversion was only observed for the cis-isomer, verifying that this is a true intermediate and not a dead-end product. Mass-spectrometric analyses confirmed that conversion is performed by an acyl-CoA dehydrogenase and a subsequent hydratase yielding an intermediate with a tertiary hydroxyl-group. We propose that a novel kind of ring-opening lyase is involved in the further catabolic pathway proceeding via pimeloyl-CoA. In contrast to degradation pathways of monocyclic aromatic compounds where ring-cleavage is achieved via hydratases, this lyase might represent a new ring-opening strategy for the degradation of polycyclic compounds. Conversion of the potential downstream metabolites pimeloyl-CoA and glutaryl-CoA was proved in cell free extracts, yielding 2,3-dehydropimeloyl-CoA, 3-hydroxypimeloyl-CoA, 3-oxopimeloyl-CoA, glutaconyl-CoA, crotonyl-CoA, 3-hydroxybutyryl-CoA and acetyl-CoA as observable intermediates. This indicates a link to central metabolism via β-oxidation, a non-decarboxylating glutaryl-CoA dehydrogenase and a subsequent glutaconyl-CoA decarboxylase.
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Affiliation(s)
- Philip Weyrauch
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andrey V Zaytsev
- School of Chemistry, Newcastle University, Newcastle, UK.,Health and Life Sciences, Northumberland University, Newcastle, UK
| | - Susanne Stephan
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Lena Kocks
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Oliver J Schmitz
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
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Ghattas AK, Fischer F, Wick A, Ternes TA. Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment. WATER RESEARCH 2017; 116:268-295. [PMID: 28347952 DOI: 10.1016/j.watres.2017.02.001] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 05/22/2023]
Abstract
Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.
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Affiliation(s)
- Ann-Kathrin Ghattas
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Ferdinand Fischer
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Arne Wick
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany.
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15
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Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation. Sci Rep 2017; 7:40101. [PMID: 28067254 PMCID: PMC5220378 DOI: 10.1038/srep40101] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/30/2016] [Indexed: 01/15/2023] Open
Abstract
The Candidate Phyla Radiation (CPR) is a large group of bacteria, the scale of which approaches that of all other bacteria. CPR organisms are inferred to depend on other community members for many basic cellular building blocks and all appear to be obligate anaerobes. To date, there has been no evidence for any significant respiratory capacity in an organism from this radiation. Here we report a curated draft genome for 'Candidatus Parcunitrobacter nitroensis' a member of the Parcubacteria (OD1) superphylum of the CPR. The genome encodes versatile energy pathways, including fermentative and respiratory capacities, nitrogen and fatty acid metabolism, as well as the first complete electron transport chain described for a member of the CPR. The sequences of all of these enzymes are highly divergent from sequences found in other organisms, suggesting that these capacities were not recently acquired from non-CPR organisms. Although the wide respiration-based repertoire points to a different lifestyle compared to other CPR bacteria, we predict similar obligate dependence on other organisms or the microbial community. The results substantially expand the known metabolic potential of CPR bacteria, although sequence comparisons indicate that these capacities are very rare in members of this radiation.
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Boll M, Kung JW, Ermler U, Martins BM, Buckel W. Fermentative Cyclohexane Carboxylate Formation in Syntrophus aciditrophicus. J Mol Microbiol Biotechnol 2016; 26:165-79. [PMID: 26959729 DOI: 10.1159/000440881] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Short-chain fatty acids such as acetic, propionic, butyric or lactic acids are typical primary fermentation products in the anaerobic feeding chain. Fifteen years ago, a novel fermentation type was discovered in the obligately anaerobic Deltaproteobacterium Syntrophus aciditrophicus. During fermentative growth with crotonate and/or benzoate, acetate is formed in the oxidative branch and cyclohexane carboxylate in the reductive branch. In both cases cyclohexa-1,5-diene-1-carboxyl-CoA (Ch1,5CoA) is a central intermediate that is either formed by a class II benzoyl-CoA reductase (fermentation of benzoate) or by reverse reactions of the benzoyl-CoA degradation pathway (fermentation of crotonate). Here, we summarize the current knowledge of the enzymology involved in fermentations yielding cyclohexane carboxylate as an excreted product. The characteristic enzymes involved are two acyl-CoA dehydrogenases specifically acting on Ch1,5CoA and cyclohex-1-ene-1-carboxyl-CoA. Both enzymes are also employed during the syntrophic growth of S. aciditrophicus with cyclohexane carboxylate as the carbon source in coculture with a methanogen. An investigation of anabolic pathways in S. aciditrophicus revealed a rather unusual pathway for glutamate synthesis involving a Re-citrate synthase. Future work has to address the unresolved question concerning which components are involved in reoxidation of the NADH formed in the oxidative branch of the unique cyclohexane carboxylate fermentation pathway in S. aciditrophicus.
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Affiliation(s)
- Matthias Boll
- Mikrobiologie, Fakultx00E4;t fx00FC;r Biologie, Albert-Ludwigs-Universitx00E4;t Freiburg, Freiburg, Germany
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17
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Meckenstock RU, Boll M, Mouttaki H, Koelschbach JS, Cunha Tarouco P, Weyrauch P, Dong X, Himmelberg AM. Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:92-118. [DOI: 10.1159/000441358] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.
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18
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Schürmann M, Meijers R, Schneider TR, Steinbüchel A, Cianci M. 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7(T): crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1360-72. [PMID: 26057676 PMCID: PMC4461206 DOI: 10.1107/s1399004715006616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/01/2015] [Indexed: 01/19/2023]
Abstract
3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase (AcdDPN7; EC 3.13.1.4) was identified during investigation of the 3,3'-dithiodipropionic acid (DTDP) catabolic pathway in the betaproteobacterium Advenella mimigardefordensis strain DPN7(T). DTDP is an organic disulfide and a precursor for the synthesis of polythioesters (PTEs) in bacteria, and is of interest for biotechnological PTE production. AcdDPN7 catalyzes sulfur abstraction from 3SP-CoA, a key step during the catabolism of DTDP. Here, the crystal structures of apo AcdDPN7 at 1.89 Å resolution and of its complex with the CoA moiety from the substrate analogue succinyl-CoA at 2.30 Å resolution are presented. The apo structure shows that AcdDPN7 belongs to the acyl-CoA dehydrogenase superfamily fold and that it is a tetramer, with each subunit containing one flavin adenine dinucleotide (FAD) molecule. The enzyme does not show any dehydrogenase activity. Dehydrogenase activity would require a catalytic base (Glu or Asp residue) at either position 246 or position 366, where a glutamine and a glycine are instead found, respectively, in this desulfinase. The positioning of CoA in the crystal complex enabled the modelling of a substrate complex containing 3SP-CoA. This indicates that Arg84 is a key residue in the desulfination reaction. An Arg84Lys mutant showed a complete loss of enzymatic activity, suggesting that the guanidinium group of the arginine is essential for desulfination. AcdDPN7 is the first desulfinase with an acyl-CoA dehydrogenase fold to be reported, which underlines the versatility of this enzyme scaffold.
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Affiliation(s)
- Marc Schürmann
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory Hamburg Unit, EMBL, Notkestrasse 85, 22603 Hamburg, Germany
| | - Thomas R. Schneider
- European Molecular Biology Laboratory Hamburg Unit, EMBL, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Michele Cianci
- European Molecular Biology Laboratory Hamburg Unit, EMBL, Notkestrasse 85, 22603 Hamburg, Germany
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Leroy B, De Meur Q, Moulin C, Wegria G, Wattiez R. New insight into the photoheterotrophic growth of the isocytrate lyase-lacking purple bacterium Rhodospirillum rubrum on acetate. MICROBIOLOGY-SGM 2015; 161:1061-1072. [PMID: 25737481 DOI: 10.1099/mic.0.000067] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/27/2015] [Indexed: 11/18/2022]
Abstract
Purple non-sulfur bacteria are well known for their metabolic versatility. One of these bacteria, Rhodospirillum rubrum S1H, has been selected by the European Space Agency to ensure the photoheterotrophic assimilation of volatile fatty acids in its regenerative life support system, MELiSSA. Here, we combined proteomic analysis with bacterial growth analysis and enzymatic activity assays in order to better understand acetate photoassimilation. In this isocitrate lyase-lacking organism, the assimilation of two-carbon compounds cannot occur through the glyoxylate shunt, and the citramalate cycle has been proposed to fill this role, while, in Rhodobacter sphaeroides, the ethylmalonyl-CoA pathway is used for acetate assimilation. Using proteomic analysis, we were able to identify and quantify more than 1700 unique proteins, representing almost one-half of the theoretical proteome of the strain. Our data reveal that a pyruvate : ferredoxin oxidoreductase (NifJ) could be used for the direct assimilation of acetyl-CoA through pyruvate, potentially representing a new redox-balancing reaction. We additionally propose that the ethylmalonyl-CoA pathway could also be involved in acetate assimilation by the examined strain, since specific enzymes of this pathway were all upregulated and activity of crotonyl-CoA reductase/carboxylase was increased in acetate conditions. Surprisingly, we also observed marked upregulation of glutaryl-CoA dehydrogenase, which could be a component of a new pathway for acetate photoassimilation. Finally, our data suggest that citramalate could be an intermediate of the branched-chain amino acid biosynthesis pathway, which is activated during acetate assimilation, rather than a metabolite of the so-called citramalate cycle.
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Affiliation(s)
- B Leroy
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, 7000 Mons, Belgium
| | - Q De Meur
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, 7000 Mons, Belgium
| | - C Moulin
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, 7000 Mons, Belgium
| | - G Wegria
- Biotech Materia Nova, Parc Initialis, Avenue Copernic 1, 7000 Mons, Belgium
| | - R Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 20, 7000 Mons, Belgium
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20
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Estelmann S, Boll M. Glutaryl-coenzyme A dehydrogenase from Geobacter metallireducens - interaction with electron transferring flavoprotein and kinetic basis of unidirectional catalysis. FEBS J 2014; 281:5120-31. [PMID: 25223645 DOI: 10.1111/febs.13051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/04/2014] [Accepted: 09/12/2014] [Indexed: 11/28/2022]
Abstract
Glutaryl-CoA dehydrogenases (GDHs) are FAD containing acyl-CoA dehydrogenases that usually catalyze the dehydrogenation and decarboxylation of glutaryl-CoA to crotonyl-CoA with an electron transferring flavoprotein (ETF) acting as natural electron acceptor. In anaerobic bacteria, GDHs play an important role in the benzoyl-CoA degradation pathway of monocyclic aromatic compounds. In the present study, we identified, purified and characterized the benzoate-induced BamOP as the electron accepting ETF of GDH (BamM) from the Fe(III)-respiring Geobacter metallireducens. The BamOP heterodimer contained FAD and AMP as cofactors. In the absence of an artificial electron acceptor, at pH values above 8, the BamMOP-components catalyzed the expected glutaryl-CoA oxidation to crotonyl-CoA and CO2 ; however, at pH values below 7, the redox-neutral glutaryl-CoA conversion to butyryl-CoA and CO2 became the dominant reaction. This previously unknown, strictly ETF-dependent coupled glutaryl-CoA oxidation/crotonyl-CoA reduction activity was facilitated by an unexpected two-electron transfer between FAD(BamM) and FAD(BamOP) , as well as by the similar redox potentials of the two FAD cofactors in the substrate-bound state. The strict order of electron/proton transfer and C-C-cleavage events including transient charge-transfer complexes did not allow an energetic coupling of electron transfer and decarboxylation. This explains why it was difficult to release the glutaconyl-CoA intermediate from reduced GDH. Moreover, it provides a kinetic rational for the apparent inability of BamM to catalyze the reverse reductive crotonyl-CoA carboxylation, even under thermodynamically favourable conditions. For this reason reductive crotonyl-CoA carboxylation, a key reaction in C2-assimilation via the ethylmalonyl-CoA pathway, is accomplished by a different crotonyl-CoA carboxylase/reductase via a covalent NADPH/ene-adduct.
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Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily. J Bacteriol 2013; 196:882-93. [PMID: 24317404 DOI: 10.1128/jb.01265-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In a previous study, the essential role of 3-sulfinopropionyl coenzyme A (3SP-CoA) desulfinase acyl-CoA dehydrogenase (Acd) in Advenella mimigardefordensis strain DPN7(T) (AcdDPN7) during degradation of 3,3'-dithiodipropionic acid (DTDP) was elucidated. DTDP is a sulfur-containing precursor substrate for biosynthesis of polythioesters (PTEs). AcdDPN7 showed high amino acid sequence similarity to acyl-CoA dehydrogenases but was unable to catalyze a dehydrogenation reaction. Hence, it was investigated in the present study whether 3SP-CoA desulfinase activity is an uncommon or a widespread property within the acyl-CoA dehydrogenase superfamily. Therefore, proteins of the acyl-CoA dehydrogenase superfamily from Advenella kashmirensis WT001, Bacillus cereus DSM31, Cupriavidus necator N-1, Escherichia coli BL21, Pseudomonas putida KT2440, Burkholderia xenovorans LB400, Ralstonia eutropha H16, Variovorax paradoxus B4, Variovorax paradoxus S110, and Variovorax paradoxus TBEA6 were expressed in E. coli strains. All purified acyl-CoA dehydrogenases appeared as homotetramers, as revealed by size exclusion chromatography. AcdS110, AcdB4, AcdH16, and AcdKT2440 were able to dehydrogenate isobutyryl-CoA. AcdKT2440 additionally dehydrogenated butyryl-CoA and valeryl-CoA, whereas AcdDSM31 dehydrogenated only butyryl-CoA and valeryl-CoA. No dehydrogenation reactions were observed with propionyl-CoA, isovaleryl-CoA, succinyl-CoA, and glutaryl-CoA for any of the investigated acyl-CoA dehydrogenases. Only AcdTBEA6, AcdN-1, and AcdLB400 desulfinated 3SP-CoA and were thus identified as 3SP-CoA desulfinases within the acyl-CoA dehydrogenase family, although none of these three Acds dehydrogenated any of the tested acyl-CoA thioesters. No appropriate substrates were identified for AcdBL21 and AcdWT001. Spectrophotometric assays provided apparent Km and Vmax values for active substrates and indicated the applicability of phylogenetic analyses to predict the substrate range of uncharacterized acyl-CoA dehydrogenases. Furthermore, C. necator N-1 was found to utilize 3SP as the sole source of carbon and energy.
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Kung JW, Seifert J, von Bergen M, Boll M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J Bacteriol 2013; 195:3193-200. [PMID: 23667239 PMCID: PMC3697644 DOI: 10.1128/jb.00322-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/07/2013] [Indexed: 11/20/2022] Open
Abstract
The strictly anaerobic Syntrophus aciditrophicus is a fermenting deltaproteobacterium that is able to degrade benzoate or crotonate in the presence and in the absence of a hydrogen-consuming partner. During growth in pure culture, both substrates are dismutated to acetate and cyclohexane carboxylate. In this work, the unknown enzymes involved in the late steps of cyclohexane carboxylate formation were studied. Using enzyme assays monitoring the oxidative direction, a cyclohex-1-ene-1-carboxyl-CoA (Ch1CoA)-forming cyclohexanecarboxyl-CoA (ChCoA) dehydrogenase was purified and characterized from S. aciditrophicus and after heterologous expression of its gene in Escherichia coli. In addition, a cyclohexa-1,5-diene-1-carboxyl-CoA (Ch1,5CoA)-forming Ch1CoA dehydrogenase was characterized after purification of the heterologously expressed gene. Both enzymes had a native molecular mass of 150 kDa and were composed of a single, 40- to 45-kDa subunit; both contained flavin adenine dinucleotide (FAD) as a cofactor. While the ChCoA dehydrogenase was competitively inhibited by Ch1CoA in the oxidative direction, Ch1CoA dehydrogenase further converted the product Ch1,5CoA to benzoyl-CoA. The results obtained suggest that Ch1,5CoA is a common intermediate in benzoate and crotonate fermentation that serves as an electron-accepting substrate for the two consecutively operating acyl-CoA dehydrogenases characterized in this work. In the case of benzoate fermentation, Ch1,5CoA is formed by a class II benzoyl-CoA reductase; in the case of crotonate fermentation, Ch1,5CoA is formed by reversing the reactions of the benzoyl-CoA degradation pathway that are also employed during the oxidative (degradative) branch of benzoate fermentation.
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Affiliation(s)
- Johannes W. Kung
- Microbiology, Institute of Biology II, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jana Seifert
- Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany
- Helmholtz Centre for Environmental Research, Department of Metabolomics, Leipzig, Germany
| | - Matthias Boll
- Microbiology, Institute of Biology II, University of Freiburg, Freiburg im Breisgau, Germany
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Schürmann M, Deters A, Wübbeler JH, Steinbüchel A. A novel 3-sulfinopropionyl coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis strain DPN7T acting as a key enzyme during catabolism of 3,3'-dithiodipropionic acid is a member of the acyl-CoA dehydrogenase superfamily. J Bacteriol 2013; 195:1538-51. [PMID: 23354747 PMCID: PMC3624521 DOI: 10.1128/jb.02105-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/17/2013] [Indexed: 01/28/2023] Open
Abstract
3-Sulfinopropionyl coenzyme A (3SP-CoA) desulfinase (AcdDPN7) is a new desulfinase that catalyzes the sulfur abstraction from 3SP-CoA in the betaproteobacterium Advenella mimigardefordensis strain DPN7(T). During investigation of a Tn5::mob-induced mutant defective in growth on 3,3'-dithiodipropionate (DTDP) and also 3-sulfinopropionate (3SP), the transposon insertion was mapped to an open reading frame with the highest homology to an acyl-CoA dehydrogenase (Acd) from Burkholderia phenoliruptrix strain BR3459a (83% identical and 91% similar amino acids). An A. mimigardefordensis Δacd mutant was generated and verified the observed phenotype of the Tn5::mob-induced mutant. For enzymatic studies, AcdDPN7 was heterologously expressed in Escherichia coli BL21(DE3)/pLysS by using pET23a::acdDPN7. The purified protein is yellow and contains a noncovalently bound flavin adenine dinucleotide (FAD) cofactor, as verified by high-performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-ESI-MS) analyses. Size-exclusion chromatography revealed a native molecular mass of about 173 kDa, indicating a homotetrameric structure (theoretically 179 kDa), which is in accordance with other members of the acyl-CoA dehydrogenase superfamily. In vitro assays unequivocally demonstrated that the purified enzyme converted 3SP-CoA into propionyl-CoA and sulfite (SO3(2-)). Kinetic studies of AcdDPN7 revealed a Vmax of 4.19 μmol min(-1) mg(-1), an apparent Km of 0.013 mM, and a kcat/Km of 240.8 s(-1) mM(-1) for 3SP-CoA. However, AcdDPN7 is unable to perform a dehydrogenation, which is the usual reaction catalyzed by members of the acyl-CoA dehydrogenase superfamily. Comparison to other known desulfinases showed a comparably high catalytic efficiency of AcdDPN7 and indicated a novel reaction mechanism. Hence, AcdDPN7 encodes a new desulfinase based on an acyl-CoA dehydrogenase (EC 1.3.8.x) scaffold. Concomitantly, we identified the gene product that is responsible for the final desulfination step during catabolism of 3,3'-dithiodipropionate (DTDP), a sulfur-containing precursor substrate for biosynthesis of polythioesters.
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Affiliation(s)
- Marc Schürmann
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Anika Deters
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Bozinovski D, Herrmann S, Richnow HH, Bergen M, Seifert J, Vogt C. Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing. FEMS Microbiol Ecol 2012; 81:134-44. [DOI: 10.1111/j.1574-6941.2012.01334.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/08/2012] [Accepted: 02/09/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Dragana Bozinovski
- Department of Proteomics; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | | | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | | | - Jana Seifert
- Department of Proteomics; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
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Wu L, Qiao Y, Gao J, Deng G, Yu W, Chen G, Li D. Functional characterization of rat glutaryl-CoA dehydrogenase and its comparison with straight-chain acyl-CoA dehydrogenase. Bioorg Med Chem Lett 2011; 21:6667-73. [PMID: 21974953 DOI: 10.1016/j.bmcl.2011.09.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/13/2011] [Accepted: 09/16/2011] [Indexed: 11/17/2022]
Abstract
Glutaryl-CoA dehydrogenase catalyzes the oxidative decarboxylation of the γ-carboxylate of the substrate, glutaryl-CoA, to yield crotonyl-CoA and CO(2). The enzyme is a member of the acyl-CoA dehydrogenase (ACD) family of flavoproteins. In the present study, the catalytic properties of this enzyme, including its substrate specificity, isomerase activity, and interactions with inhibitors, were systematically studied. Our results indicated that the enzyme has its catalytic properties very similar to those of short-chain and medium-chain acyl-CoA dehydrogenase except its additional decarboxylation reaction. Therefore, the inhibitors of fatty acid oxidation targeting straight chain acyl-CoA dehydrogenase could also function as inhibitors for amino acid metabolism of lysine, hydroxylysine, and tryptophan.
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Affiliation(s)
- Long Wu
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, PR China
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26
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Begley DW, Davies DR, Hartley RC, Hewitt SN, Rychel AL, Myler PJ, Van Voorhis WC, Staker BL, Stewart LJ. Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1060-9. [PMID: 21904051 PMCID: PMC3169403 DOI: 10.1107/s1744309111014436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/17/2011] [Indexed: 11/10/2022]
Abstract
Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.
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Affiliation(s)
- Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA.
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27
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Schaarschmidt J, Wischgoll S, Hofmann HJ, Boll M. Conversion of a decarboxylating to a non-decarboxylating glutaryl-coenzyme A dehydrogenase by site-directed mutagenesis. FEBS Lett 2011; 585:1317-21. [PMID: 21477586 DOI: 10.1016/j.febslet.2011.03.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 03/30/2011] [Accepted: 03/31/2011] [Indexed: 11/26/2022]
Abstract
Glutaryl-coenzyme A (CoA) dehydrogenases (GDHs) are acyl-CoA dehydrogenases, which usually dehydrogenate and decarboxylate the substrate to crotonyl-CoA. In some anaerobic bacteria, non-decarboxylating GDHs exist that release glutaconyl-CoA (2,3-dehydroglutaryl-CoA) without decarboxylation. The differing mechanisms of decarboxylating and non-decarboxylating GDHs were investigated by site-directed mutagenesis of the gene coding for the crotonyl-CoA-forming GDH from Geobacter metallireducens. Exchange of single amino acids involved in substrate carboxylate binding impaired the decarboxylation step, resulting in relative glutaconyl-CoA:crotonyl-CoA formation rates of 1:1 (S97A) or 13:1 (Y370A). The total amount of glutaconyl-CoA formed was maximal in the Y370V+S97A double mutant. The results obtained indicate that an invariant deprotonated Tyr plays a crucial role for optimizing the leaving group potential of CO(2) in decarboxylating GDHs.
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28
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Lovley DR, Ueki T, Zhang T, Malvankar NS, Shrestha PM, Flanagan KA, Aklujkar M, Butler JE, Giloteaux L, Rotaru AE, Holmes DE, Franks AE, Orellana R, Risso C, Nevin KP. Geobacter: the microbe electric's physiology, ecology, and practical applications. Adv Microb Physiol 2011; 59:1-100. [PMID: 22114840 DOI: 10.1016/b978-0-12-387661-4.00004-5] [Citation(s) in RCA: 384] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.
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Affiliation(s)
- Derek R Lovley
- Department of Microbiology and Environmental Biotechnology Center, University of Massachusetts, Amherst, Massachusetts, USA
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29
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Aklujkar M, Young ND, Holmes D, Chavan M, Risso C, Kiss HE, Han CS, Land ML, Lovley DR. The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments. BMC Genomics 2010; 11:490. [PMID: 20828392 PMCID: PMC2996986 DOI: 10.1186/1471-2164-11-490] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 09/09/2010] [Indexed: 12/05/2022] Open
Abstract
Background Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. Geobacter bemidjiensis, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to Geobacter species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of G. bemidjiensis compared to non-subsurface Geobacter species. Results Annotation of the genome sequence of G. bemidjiensis indicates several differences in metabolism compared to previously sequenced non-subsurface Geobacteraceae, which will be useful for in silico metabolic modeling of subsurface bioremediation processes involving Geobacter species. Pathways can now be predicted for the use of various carbon sources such as propionate by G. bemidjiensis. Additional metabolic capabilities such as carbon dioxide fixation and growth on glucose were predicted from the genome annotation. The presence of different dicarboxylic acid transporters and two oxaloacetate decarboxylases in G. bemidjiensis may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that G. bemidjiensis is known or predicted to utilize as an electron donor and carbon source, the genome suggests that this species may be able to detoxify other aromatic pollutants without degrading them. Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which makes it the first Geobacter species identified as having a vitamin requirement. Several features of the genome indicated that G. bemidjiensis has enhanced abilities to respire, detoxify and avoid oxygen. Conclusion Overall, the genome sequence of G. bemidjiensis offers surprising insights into the metabolism and physiology of Geobacteraceae in subsurface environments, compared to non-subsurface Geobacter species, such as the ability to disproportionate fumarate, more efficient oxidation of propionate, enhanced responses to oxygen stress, and dependence on the environment for a vitamin requirement. Therefore, an understanding of the activity of Geobacter species in the subsurface is more likely to benefit from studies of subsurface isolates such as G. bemidjiensis than from the non-subsurface model species studied so far.
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Affiliation(s)
- Muktak Aklujkar
- University of Massachusetts Amherst, Amherst, MA 01003, USA.
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30
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Wischgoll S, Demmer U, Warkentin E, Günther R, Boll M, Ermler U. Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme a dehydrogenases. Biochemistry 2010; 49:5350-7. [PMID: 20486657 DOI: 10.1021/bi100317m] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Glutaryl-coenzyme A dehydrogenases (GDHs) involved in amino acid degradation were thought to catalyze both the dehydrogenation and decarboxylation of glutaryl-coenzyme A to crotonyl-coenzyme A and CO(2). Recently, a structurally related but nondecarboxylating, glutaconyl-coenzyme A-forming GDH was characterized in the obligately anaerobic bacteria Desulfococcus multivorans (GDH(Des)) which conserves the free energy of decarboxylation by a Na(+)-pumping glutaconyl-coenzyme A decarboxylase. To understand the distinct catalytic behavior of the two GDH types on an atomic basis, we determined the crystal structure of GDH(Des) with and without glutaconyl-coenzyme A bound at 2.05 and 2.1 A resolution, respectively. The decarboxylating and nondecarboxylating capabilities are provided by complex structural changes around the glutaconyl carboxylate group, the key factor being a Tyr --> Val exchange strictly conserved between the two GDH types. As a result, the interaction between the glutaconyl carboxylate and the guanidinium group of a conserved arginine is stronger in GDH(Des) (short and planar bidentate hydrogen bond) than in the decarboxylating human GDH (longer and monodentate hydrogen bond), which is corroborated by molecular dynamics studies. The identified structural changes prevent decarboxylation (i) by strengthening the C4-C5 bond of glutaconyl-coenzyme A, (ii) by reducing the leaving group potential of CO(2), and (iii) by increasing the distance between the C4 atom (negatively charged in the dienolate transition state) and the adjacent glutamic acid.
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Affiliation(s)
- Simon Wischgoll
- Institute of Biochemistry, University of Leipzig, Leipzig, Germany
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Identification of the Geobacter metallireducens bamVW two-component system, involved in transcriptional regulation of aromatic degradation. Appl Environ Microbiol 2009; 76:383-5. [PMID: 19915033 DOI: 10.1128/aem.02255-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Regulation of aromatic degradation in obligate anaerobes was studied in the Fe(III)-respiring model organism Geobacter metallireducens GS-15. A two-component system and a sigma54-dependent promoter were identified that are both involved in the regulation of the gene coding for benzoate-coenzyme A ligase, catalyzing the initial step of benzoate degradation.
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Tetralin-induced and ThnR-regulated aldehyde dehydrogenase and beta-oxidation genes in Sphingomonas macrogolitabida strain TFA. Appl Environ Microbiol 2009; 76:110-8. [PMID: 19897762 DOI: 10.1128/aem.01846-09] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new cluster of genes has been found downstream of the previously identified thnA2 gene. The gene products are similar to nonacylating aldehyde dehydrogenases (ThnG) and to proteins representing a complete beta-oxidation pathway (ThnH to ThnP). ThnG has a nonacylating NAD-dependent pimelic semialdehyde dehydrogenase activity that renders pimelic acid a seven-carbon dicarboxylic acid. For further metabolism via beta-oxidation, pimelic acid could be acylated by a constitutive acyl coenzyme A (acyl-CoA) ligase found in Sphingomonas macrogolitabida strain TFA or by ThnH, which would transfer CoA from a previously acylated molecule. The first round of beta-oxidation is expected to render glutaryl-CoA and acetyl-CoA. Glutaryl-CoA dehydrogenase (ThnN) would catalyze the oxidation and decarboxylation of glutaryl-CoA and yield crotonyl-CoA, which enters the central metabolism via acetyl-CoA. Mutagenesis studies have shown that these genes are not essential for growth on tetralin or fatty acids, although a thnG disruption mutant showed threefold less pimelic semialdehyde dehydrogenase activity. Transcriptional analysis indicated that these genes are induced by tetralin, subjected to catabolite repression, and regulated by the same regulatory factors previously identified to regulate other thn structural genes. In the present study, transcription initiation upstream of thnH and thnM has been detected by primer extension analysis, and putative promoters were identified by sequence analysis. In addition, binding of the activator ThnR to its putative binding sites at the PH and PM promoter regions has been characterized. These results provide a complete characterization of the biodegradation pathway of tetralin to central metabolites and describe the transcriptional organization of the thn operons in S. macrogolitabida strain TFA.
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Aklujkar M, Krushkal J, DiBartolo G, Lapidus A, Land ML, Lovley DR. The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens. BMC Microbiol 2009; 9:109. [PMID: 19473543 PMCID: PMC2700814 DOI: 10.1186/1471-2180-9-109] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 05/27/2009] [Indexed: 12/12/2022] Open
Abstract
Background The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. Results The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second putative succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE) regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes. Conclusion The genomic evidence suggests that metabolism, physiology and regulation of gene expression in G. metallireducens may be dramatically different from other Geobacteraceae.
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Affiliation(s)
- Muktak Aklujkar
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA.
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