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Pacheco-Sánchez D, Marín P, Molina-Fuentes Á, Marqués S. Subtle sequence differences between two interacting σ 54 -dependent regulators lead to different activation mechanisms. FEBS J 2022; 289:7582-7604. [PMID: 35816183 PMCID: PMC10084136 DOI: 10.1111/febs.16576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/08/2022] [Accepted: 07/10/2022] [Indexed: 12/13/2022]
Abstract
In the strictly anaerobic nitrate reducing bacterium Aromatoleum anaerobium, degradation of 1,3-dihydroxybenzene (1,3-DHB, resorcinol) is controlled by two bacterial enhancer-binding proteins (bEBPs), RedR1 and RedR2, which regulate the transcription of three σ54 -dependent promoters controlling expression of the pathway. RedR1 and RedR2 are identical over their length except for their N-terminal tail which differ in sequence and length (six and eight residues, respectively), a single change in their N-terminal domain (NTD), and nine non-identical residues in their C-terminal domain (CTD). Their NTD is composed of a GAF and a PAS domain connected by a linker helix. We show that each regulator is controlled by a different mechanism: whilst RedR1 responds to the classical NTD-mediated negative regulation that is released by the presence of its effector, RedR2 activity is constitutive and controlled through interaction with BtdS, an integral membrane subunit of hydroxyhydroquinone dehydrogenase carrying out the second step in 1,3-DHB degradation. BtdS sequesters the RedR2 regulator to the membrane through its NTD, where a four-Ile track in the PAS domain, interrupted by a Thr in RedR1, and the N-terminal tail are involved. The presence of 1,3-DHB, which is metabolized to hydroxybenzoquinone, releases RedR2 from the membrane. Most bEBPs assemble into homohexamers to activate transcription; we show that hetero-oligomer formation between RedR1 and RedR2 is favoured over homo-oligomers. However, either an NTD-truncated version of RedR1 or a full-length RedR2 are capable of promoter activation on their own, suggesting they should assemble into homohexamers in vivo. We show that promoter DNA behaves as an allosteric effector through binding the CTD to control ΔNTD-RedR1 multimerization and activity. Overall, the regulation of the 1,3-DHB anaerobic degradation pathway can be described as a novel mode of bEBP activation and assembly.
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Affiliation(s)
- Daniel Pacheco-Sánchez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Patricia Marín
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Águeda Molina-Fuentes
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Silvia Marqués
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Lo HY, Martínez-Lavanchy PM, Goris T, Heider J, Boll M, Kaster AK, Müller JA. IncP-type plasmids carrying genes for antibiotic resistance or for aromatic compound degradation are prevalent in sequenced Aromatoleum and Thauera strains. Environ Microbiol 2022; 24:6411-6425. [PMID: 36306376 DOI: 10.1111/1462-2920.16262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/25/2022] [Indexed: 01/12/2023]
Abstract
Self-transferable plasmids of the incompatibility group P-1 (IncP-1) are considered important carriers of genes for antibiotic resistance and other adaptive functions. In the laboratory, these plasmids have a broad host range; however, little is known about their in situ host profile. In this study, we discovered that Thauera aromatica K172T , a facultative denitrifying microorganism capable of degrading various aromatic compounds, contains a plasmid highly similar to the IncP-1 ε archetype pKJK5. The plasmid harbours multiple antibiotic resistance genes and is maintained in strain K172T for at least 1000 generations without selection pressure from antibiotics. In a subsequent search, we found additional nine IncP-type plasmids in a total of 40 sequenced genomes of the closely related genera Aromatoleum and Thauera. Six of these plasmids form a novel IncP-1 subgroup designated θ, four of which carry genes for anaerobic or aerobic degradation of aromatic compounds. Pentanucleotide sequence analyses (k-mer profiling) indicated that Aromatoleum spp. and Thauera spp. are among the most suitable hosts for the θ plasmids. Our results highlight the importance of IncP-1 plasmids for the genetic adaptation of these common facultative denitrifying bacteria and provide novel insights into the in situ host profile of these plasmids.
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Affiliation(s)
- Hao-Yu Lo
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Paula M Martínez-Lavanchy
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Tobias Goris
- Department of Molecular Toxicology, Intestinal Microbiology, German Institute of Human Nutrition, Potsdam-Rehbruecke, Germany
| | - Johann Heider
- Department of Biology, Philipps-Universität Marburg, Germany
| | - Matthias Boll
- Institute of Biology II, Albert-Ludwigs-Universität Freiburg, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Jochen A Müller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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CORRIGENDUM. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:957. [PMID: 34811935 DOI: 10.1111/1758-2229.13026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
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Xu C, Su X, Wang J, Zhang F, Shen G, Yuan Y, Yan L, Tang H, Song F, Wang W. Characteristics and functional bacteria in a microbial consortium for rice straw lignin-degrading. BIORESOURCE TECHNOLOGY 2021; 331:125066. [PMID: 33812140 DOI: 10.1016/j.biortech.2021.125066] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
The degradation of lignin is the main rate-limiting step in the bio-pulping of rice straw. A lignin-degrading bacterial consortium LDC, which can efficiently degrade lignin of reed, was screened in the early stage of our laboratory work. In present study, 7-day incubation of LDC can degrade rice straw lignin by 31.18% in mineral salt medium. The communities' structure of different incubation phases varied greatly, in which high abundance (44.78%) of Anaerocolumna was first found. The expression levels of lignin degradation enzyme class II peroxidase (AA2), vanillyl alcohol oxidase (AA4) and 1,4-benzoquinone reductase (AA6) during peak phase (48 h) were significantly up-regulated than initial phase (24 h), increasing by 112%, 165% and 67%, respectively, and 42.86% AA2 was from Thaurea; 100% AA4 was from Clostridium; 62.5% AA6 was from Pseudomonas. These provide microbial resources and data support for the industrialization of rice straw bio-pulping.
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Affiliation(s)
- Congfeng Xu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China
| | - Xin Su
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China
| | - Jinghong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China
| | - Fangzheng Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China
| | - Guinan Shen
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Yuan Yuan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Fuqiang Song
- College of Life Science, Heilongjiang University, Harbin 150080, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, People's Republic of China; Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing 163319, People's Republic of China.
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Darley PI, Hellstern J, Schink B, Philipp B. Resorcinol Hydroxylase of Azoarcus anaerobius: Molybdenum Dependence, Activity, and Heterologous Expression. Curr Microbiol 2020; 77:3385-3396. [PMID: 32915288 DOI: 10.1007/s00284-020-02186-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/25/2020] [Indexed: 12/01/2022]
Abstract
The obligately anaerobic, denitrifying bacterium Azoarcus anaerobius strain LuFRes1 grows with resorcinol (1,3-dihydroxybenzene) as sole carbon and energy source. Resorcinol is oxidized to hydroxyhydroquinone (1,2,4-trihydroxybenzene) by resorcinol hydroxylase (RH), an inducible membrane-bound enzyme. Sequence comparison places resorcinol hydroxylase into the group of anaerobic molybdopterin oxidoreductases and dimethyl sulfoxide reductase-like enzymes. In the large subunit, a molybdopterin-binding domain was predicted, and the small subunit most likely contains two [4Fe-4S] centers. Growth of molybdate-starved cells was inhibited by tungstate, and in vitro resorcinol hydroxylase activity was inhibited by arsenite and selenite that are known to inhibit molybdenum-containing enzymes. The two genes encoding resorcinol hydroxylase could be expressed in Escherichia coli but the products remained in inclusion bodies. All attempts to purify RH from A. anaerobius or to produce soluble, active RH in E. coli failed. Nevertheless, RH was produced as a C-terminally Strep-tagged protein from plasmid pSKM1 in Thauera aromatica AR1 transconjugants carrying a transposon insertion in the coding gene for the large (ΔrhL) or the small subunit (ΔrhS) of RH from cosmid R+. RH in the membrane fraction of wild-type transconjugant T. aromatica AR1/R+ showed a specific activity of 80 mU mg-1, and the specific activity of RH in the membranes of the complemented mutants was in the same range (80-95 mU mg-1). We conclude that RH of A. anaerobius is a membrane-bound molybdoenzyme consisting of two subunits which might require a further loosely bound subunit as membrane anchor.
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Affiliation(s)
- Paula I Darley
- University of Konstanz, Fachbereich Biologie, 78457, Constance, Germany.,Cambivac Ltd, Cambridge, CB22 3AT, UK
| | - Jutta Hellstern
- University of Konstanz, Fachbereich Biologie, 78457, Constance, Germany.,Novartis Pharma AG, Lichtstrasse 35, 4056, Basel, Switzerland
| | - Bernhard Schink
- University of Konstanz, Fachbereich Biologie, 78457, Constance, Germany
| | - Bodo Philipp
- University of Konstanz, Fachbereich Biologie, 78457, Constance, Germany. .,Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstr. 3, 48149, Münster, Germany.
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Tang L, Hamid Y, Zehra A, Sahito ZA, He Z, Khan MB, Feng Y, Yang X. Mechanisms of water regime effects on uptake of cadmium and nitrate by two ecotypes of water spinach (Ipomoea aquatica Forsk.) in contaminated soil. CHEMOSPHERE 2020; 246:125798. [PMID: 31927376 DOI: 10.1016/j.chemosphere.2019.125798] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/20/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
Availability of cadmium (Cd) and nitrate and their transfer to green leafy vegetables is highly dependent on physical, chemical and biochemical conditions of the soil. The phenotypic characteristics, accumulation of hazardous materials and rhizosphere properties of two ecotypes of water spinach in response to water stress were investigated. Flooding significantly enhanced plant growth and decreased Cd and nitrate concentrations in the shoot and root of both ecotypes of water spinach. Flooding extensively changed the physicochemical properties and biological processes in the rhizosphere, including increased pH and activities of urease and acid phosphatase, and decreased availability of Cd and nitrate and activity of nitrate reductase. Furthermore, flooding increased rhizosphere bacteria community diversity (including richness and evenness) and changed their community structure. Denitrifying bacteria (Clostridiales, Azoarcus and Pseudomonas), toxic metal resistant microorganisms (Rhodosporillaceae, Rhizobiales and Geobacter) were enriched in the rhizosphere under flooding conditions, and the plant growth-promoting taxa (Sphingomonadaceae) were preferentially colonized in the high accumulator (HA) rhizosphere region. These results indicated that flooding treatments result in biochemical and microbiological changes in soil, especially in the rhizosphere and reduced the availability of Cd and nitrate to plants, thus decreasing their uptake by water spinach. It is, therefore, possible to promote crop growth and reduce the accumulation of hazardous materials in vegetable crops like water spinach by controlling soil moisture conditions.
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Affiliation(s)
- Lin Tang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yasir Hamid
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Afsheen Zehra
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China; Department of Botany, Federal Urdu University of Arts, Science and Technology, Karachi, Pakistan
| | - Zulfiqar Ali Sahito
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Zhenli He
- University of Florida, Institute of Food and Agricultural Sciences, Indian River Research and Education Center, Fort Pierce, Florida, 34945, United States
| | - Muhammad Bilal Khan
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Ying Feng
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Xiaoe Yang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China.
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Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP. A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols. eLife 2020; 9:e50845. [PMID: 32067637 PMCID: PMC7028382 DOI: 10.7554/elife.50845] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Catechol dehydroxylation is a central chemical transformation in the gut microbial metabolism of plant- and host-derived small molecules. However, the molecular basis for this transformation and its distribution among gut microorganisms are poorly understood. Here, we characterize a molybdenum-dependent enzyme from the human gut bacterium Eggerthella lenta that dehydroxylates catecholamine neurotransmitters. Our findings suggest that this activity enables E. lenta to use dopamine as an electron acceptor. We also identify candidate dehydroxylases that metabolize additional host- and plant-derived catechols. These dehydroxylases belong to a distinct group of largely uncharacterized molybdenum-dependent enzymes that likely mediate primary and secondary metabolism in multiple environments. Finally, we observe catechol dehydroxylation in the gut microbiotas of diverse mammals, confirming the presence of this chemistry in habitats beyond the human gut. These results suggest that the chemical strategies that mediate metabolism and interactions in the human gut are relevant to a broad range of species and habitats.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Paola Nol Bernadino
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Michael U Luescher
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Sina Kiamehr
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Chip Le
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Jordan E Bisanz
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Peter J Turnbaugh
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Elizabeth N Bess
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
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