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Ali NS, Thakur S, Ye M, Monteil-Rivera F, Pan Y, Qin W, Yang TC. Uncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation. BMC Microbiol 2024; 24:181. [PMID: 38789935 PMCID: PMC11127350 DOI: 10.1186/s12866-024-03331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Lignin is an intricate phenolic polymer found in plant cell walls that has tremendous potential for being converted into value-added products with the possibility of significantly increasing the economics of bio-refineries. Although lignin in nature is bio-degradable, its biocatalytic conversion is challenging due to its stable complex structure and recalcitrance. In this context, an understanding of strain's genomics, enzymes, and degradation pathways can provide a solution for breaking down lignin to unlock the full potential of lignin as a dominant valuable bioresource. A gammaproteobacterial strain AORB19 has been isolated previously from decomposed wood based on its high laccase production. This work then focused on the detailed genomic and functional characterization of this strain based on whole genome sequencing, the identification of lignin degradation products, and the strain's laccase production capabilities on various agro-industrial residues. RESULTS Lignin degrading bacterial strain AORB19 was identified as Serratia quinivorans based on whole genome sequencing and core genome phylogeny. The strain comprised a total of 123 annotated CAZyme genes, including ten cellulases, four hemicellulases, five predicted carbohydrate esterase genes, and eight lignin-degrading enzyme genes. Strain AORB19 was also found to possess genes associated with metabolic pathways such as the β-ketoadipate, gentisate, anthranilate, homogentisic, and phenylacetate CoA pathways. LC-UV analysis demonstrated the presence of p-hydroxybenzaldehyde and vanillin in the culture media which constitutes potent biosignatures indicating the strain's capability to degrade lignin. Finally, the study evaluated the laccase production of Serratia AORB19 grown with various industrial raw materials, with the highest activity detected on flax seed meal (257.71 U/L), followed by pea hull (230.11 U/L), canola meal (209.56 U/L), okara (187.67 U/L), and barley malt sprouts (169.27 U/L). CONCLUSIONS The whole genome analysis of Serratia quinivorans AORB19, elucidated a repertoire of genes, pathways and enzymes vital for lignin degradation that widens the understanding of ligninolytic metabolism among bacterial lignin degraders. The LC-UV analysis of the lignin degradation products coupled with the ability of S. quinivorans AORB19 to produce laccase on diverse agro-industrial residues underscores its versatility and its potential to contribute to the economic viability of bio-refineries.
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Affiliation(s)
- Nadia Sufdar Ali
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - Subarna Thakur
- Department of Bioinformatics, University of North Bengal, Siliguri, India
| | - Mengwei Ye
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Fanny Monteil-Rivera
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada.
| | - Trent Chunzhong Yang
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- BioWise Technologies Inc, Ottawa, Canada.
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Ren X, Palmer LD. Acinetobacter Metabolism in Infection and Antimicrobial Resistance. Infect Immun 2023:e0043322. [PMID: 37191522 DOI: 10.1128/iai.00433-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Acinetobacter infections have high rates of mortality due to an increasing incidence of infections by multidrug-resistant (MDR) and extensively-drug-resistant (XDR) strains. Therefore, new therapeutic strategies for the treatment of Acinetobacter infections are urgently needed. Acinetobacter spp. are Gram-negative coccobacilli that are obligate aerobes and can utilize a wide variety of carbon sources. Acinetobacter baumannii is the main cause of Acinetobacter infections, and recent work has identified multiple strategies A. baumannii uses to acquire nutrients and replicate in the face of host nutrient restriction. Some host nutrient sources also serve antimicrobial and immunomodulatory functions. Hence, understanding Acinetobacter metabolism during infection may provide new insights into novel infection control measures. In this review, we focus on the role of metabolism during infection and in resistance to antibiotics and other antimicrobial agents and discuss the possibility that metabolism may be exploited to identify novel targets to treat Acinetobacter infections.
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Affiliation(s)
- Xiaomei Ren
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Lauren D Palmer
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
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Bearne SL, Hayden JA. Application of circular dichroism-based assays to racemases and epimerases: Recognition and catalysis of reactions of chiral substrates by mandelate racemase. Methods Enzymol 2023; 685:127-169. [PMID: 37245900 DOI: 10.1016/bs.mie.2023.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Racemases and epimerases have attracted much interest because of their astonishing ability to catalyze the rapid α-deprotonation of carbon acid substrates with high pKa values (∼13-30) leading to the formation of d-amino acids or various carbohydrate diastereomers that serve important roles in both normal physiology and pathology. Enzymatic assays to measure the initial rates of reactions catalyzed by these enzymes are discussed using mandelate racemase (MR) as an example. For MR, a convenient, rapid, and versatile circular dichroism (CD)-based assay has been used to determine the kinetic parameters accompanying the MR-catalyzed racemization of mandelate and alternative substrates. This direct, continuous assay permits real time monitoring of reaction progress, the rapid determination of initial velocities, and immediate recognition of anomalous behaviors. MR recognizes chiral substrates primarily through interactions of the phenyl ring of (R)- or (S)-mandelate with the hydrophobic R- or S-pocket at the active site, respectively. During catalysis, the carboxylate and α-hydroxyl groups of the substrate remain fixed in place through interactions with the Mg2+ ion and multiple H-bonding interactions, while the phenyl ring moves between the R- and S-pockets. The minimal requirements for the substrate appear to be the presence of a glycolate or glycolamide moiety, and a hydrophobic group of limited size that can stabilize the carbanionic intermediate through resonance or strong inductive effects. Similar CD-based assays may be applied to determine the activity of other racemases or epimerases with proper consideration of the molar ellipticity, wavelength, overall absorbance of the sample, and the light pathlength.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, Canada.
| | - Joshua A Hayden
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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Ren L, Wang G, Huang Y, Guo J, Li C, Jia Y, Chen S, Zhou JL, Hu H. Phthalic acid esters degradation by a novel marine bacterial strain Mycolicibacterium phocaicum RL-HY01: Characterization, metabolic pathway and bioaugmentation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148303. [PMID: 34118676 DOI: 10.1016/j.scitotenv.2021.148303] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 05/12/2023]
Abstract
Phthalic acid esters (PAEs) are one of the most widely used plasticizers and the well-studied environmental pollutants with endocrine disrupting properties. Investigation about PAEs in terrestrial ecosystem has been extensively conducted while the fate of PAEs in marine environment remains underexplored. In this study, a novel di-(2-ethylhexyl) phthalate (DEHP) degrading marine bacterial strain, Mycolicibacterium phocaicum RL-HY01, was isolated and characterized from intertidal sediments. Strain RL-HY01 could utilize a range of PAE plasticizers as sole carbon source for growth. The effects of different environmental factors on the degradation of PAEs were evaluated and the results indicated that strain RL-HY01 could efficiently degrade PAEs under a wide range of pH (5.0 to 9.0), temperature (20 °C to 40 °C) and salinity (below 10%). Specifically, when Tween-80 was added as solubilizing agent, strain RL-HY01 could rapidly degrade DEHP and achieve complete degradation of DEHP (50 mg/L) in 48 h. The kinetics of DEHP degradation by RL-HY01 were well fitted with the modified Gompertz model. The metabolic intermediates of DEHP by strain RL-HY01 were identified by ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis and then the metabolic pathway of DEHP was deduced. DEHP was transformed into di-ethyl phthalate (DEP) via β-oxidation and then DEP was hydrolyzed into phthalic acid (PA) by de-esterification. PA was further transformed into gentisate via salicylic acid and further utilized for cell growth. Bioaugmentation of strain RL-HY01 with marine samples was performed to evaluate its application potential and the results suggested that strain RL-HY01 could accelerate the elimination of DEHP in marine samples. The results have advanced our understanding of the fate of PAEs in marine ecosystem and identified an efficient bioremediation strategy for PAEs-polluted marine sites.
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Affiliation(s)
- Lei Ren
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, China; College of Coastal Agricultural Sciences, School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Guan Wang
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, China; College of Coastal Agricultural Sciences, School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yongxiang Huang
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, China; College of Coastal Agricultural Sciences, School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jianfu Guo
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, China; College of Coastal Agricultural Sciences, School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Chengyong Li
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, China; College of Coastal Agricultural Sciences, School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yang Jia
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Lab for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
| | - Sha Chen
- Hunan Key Laboratory of Biomass Fiber Functional Materials, School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China
| | - John L Zhou
- Centre for Green Technology, University of Technology Sydney, 15 Broadway, NSW 2007, Australia
| | - Hanqiao Hu
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, China; College of Coastal Agricultural Sciences, School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China.
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Feng M, Zhou J, Yu X, Wang H, Guo Y, Mao W. Bioremediation of triphenyl phosphate by Pycnoporus sanguineus: Metabolic pathway, proteomic mechanism and biotoxicity assessment. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:125983. [PMID: 33975170 DOI: 10.1016/j.jhazmat.2021.125983] [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: 01/20/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
So far, no information about the biodegradability of TPhP by white rot fungi has previously been made available, herein, Pycnoporus sanguineus was used as the representative to investigate the potential of white rot fungi in TPhP bioremediation. The results suggested that the biodegradation efficiency of 5 mg/L TPhP by P. sanguineus was 62.84% when pH was adjusted to 6 and initial glucose concentration was 5 g/L. Seven biodegradation products were identified, indicating that TPhP was biotransformed through oxidative cleavage, hydroxylation and methylation. The proteomic analysis revealed that cytochrome P450s, aromatic compound dioxygenase, oxidizing species-generating enzymes, methyltransferases and MFS general substrate transporters might occupy important roles in TPhP biotransformation. Carboxylesterase and glutathione S-transferase were induced to resist TPhP stress. The biotreatment by P. sanguineus contributed to a remarkable decrease of TPhP biotoxicity. Bioaugmentation with P. sanguineus could efficiently promote TPhP biodegradation in the water-sediment system due to the cooperation between P. sanguineus and some putative indigenous degraders, including Sphingobium, Burkholderia, Mycobacterium and Methylobacterium. Overall, this study provided the first insights into the degradation pathway, mechanism and security risk assessment of TPhP biodegradation by P. sanguineus and verified the feasibility of utilizing this fungus for TPhP bioremediation applications.
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Affiliation(s)
- Mi Feng
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, College of Environmental Science and Engineering, Guilin 541004, Guangxi, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Jiahua Zhou
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, College of Environmental Science and Engineering, Guilin 541004, Guangxi, China
| | - Xiaolong Yu
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Hao Wang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, College of Environmental Science and Engineering, Guilin 541004, Guangxi, China
| | - Yushuo Guo
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, College of Environmental Science and Engineering, Guilin 541004, Guangxi, China
| | - Wei Mao
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, College of Environmental Science and Engineering, Guilin 541004, Guangxi, China
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Hubloher JJ, Zeidler S, Lamosa P, Santos H, Averhoff B, Müller V. Trehalose-6-phosphate-mediated phenotypic change in Acinetobacter baumannii. Environ Microbiol 2020; 22:5156-5166. [PMID: 32618111 DOI: 10.1111/1462-2920.15148] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022]
Abstract
The stress protectant trehalose is synthesized in Acinetobacter baumannii from UPD-glucose and glucose-6-phosphase via the OtsA/OtsB pathway. Previous studies proved that deletion of otsB led to a decreased virulence, the inability to grow at 45°C and a slight reduction of growth at high salinities indicating that trehalose is the cause of these phenotypes. We have questioned this conclusion by producing ∆otsA and ∆otsBA mutants and studying their phenotypes. Only deletion of otsB, but not deletion of otsA or otsBA, led to growth impairments at high salt and high temperature. The intracellular concentrations of trehalose and trehalose-6-phosphate were measured by NMR or enzymatic assay. Interestingly, none of the mutants accumulated trehalose any more but the ∆otsB mutant with its defect in trehalose-6-phosphate phosphatase activity accumulated trehalose-6-phosphate. Moreover, expression of otsA in a ∆otsB background under conditions where trehalose synthesis is not induced led to growth inhibition and the accumulation of trehalose-6-phosphate. Our results demonstrate that trehalose-6-phosphate affects multiple physiological activities in A. baumannii ATCC 19606.
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Affiliation(s)
- Josephine Joy Hubloher
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
| | - Sabine Zeidler
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
| | - Pedro Lamosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
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7
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Sanz D, García JL, Díaz E. Expanding the current knowledge and biotechnological applications of the oxygen-independent ortho-phthalate degradation pathway. Environ Microbiol 2020; 22:3478-3493. [PMID: 32510798 DOI: 10.1111/1462-2920.15119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 11/29/2022]
Abstract
ortho-Phthalate derives from industrially produced phthalate esters, which are massively used as plasticizers and constitute major emerging environmental pollutants. The pht pathway for the anaerobic bacterial biodegradation of o-phthalate involves its activation to phthaloyl-CoA followed by decarboxylation to benzoyl-CoA. Here, we have explored further the pht peripheral pathway in denitrifying bacteria and shown that it requires also an active transport system for o-phthalate uptake that belongs to the poorly characterized class of TAXI-TRAP transporters. The construction of a fully functional pht cassette combining both catabolic and transport genes allowed to expand the o-phthalate degradation ecological trait to heterologous hosts. Unexpectedly, the pht cassette also allowed the aerobic conversion of o-phthalate to benzoyl-CoA when coupled to a functional box central pathway. Hence, the pht pathway may constitute an evolutionary acquisition for o-phthalate degradation by bacteria that thrive either in anoxic environments or in environments that face oxygen limitations and that rely on benzoyl-CoA, rather than on catecholic central intermediates, for the aerobic catabolism of aromatic compounds. Finally, the recombinant pht cassette was used both to screen for functional aerobic box pathways in bacteria and to engineer recombinant biocatalysts for o-phthalate bioconversion into sustainable bioplastics, e.g., polyhydroxybutyrate, in plastic recycling industrial processes.
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Affiliation(s)
- David Sanz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - José L García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
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Boll M, Geiger R, Junghare M, Schink B. Microbial degradation of phthalates: biochemistry and environmental implications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:3-15. [PMID: 31364812 DOI: 10.1111/1758-2229.12787] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 05/10/2023]
Abstract
The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding PA isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the PA isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three PA CoA thioesters belong to the UbiD enzyme family that harbour a prenylated flavin mononucleotide (FMN) cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of phthaloyl-CoA decarboxylase and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate.
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Affiliation(s)
- Matthias Boll
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Robin Geiger
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Madan Junghare
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
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Van Dexter S, Boopathy R. Biodegradation of phenol by Acinetobacter tandoii isolated from the gut of the termite. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:34067-34072. [PMID: 30264343 DOI: 10.1007/s11356-018-3292-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
The diet of wood-feeding termites (WFT) consists of cellulose, hemicellulose, and lignin. Cellulose and hemicellulose are utilized by symbiotic protozoa as a carbon source. Protozoa produce acetate, which is the carbon source of the termite. Recently, the mechanisms by which lignin is modified by termites have been reported. Lignin is broken down into its phenylpropanoid monomers and phenolic compounds. Bacteria from WFT gut capable of degrading lignin metabolic products are potentially valuable for bioremediation and biofuel production. A bacterium was isolated from the gut of the WFT and identified as Acinetobacter tandoii. This bacterium was capable of utilizing phenol as the sole carbon source and was able to completely degrade phenol at the concentration of 280 mg/L. A. tandoii degraded phenol via the ortho and β-ketoadipase pathway. This bacterium is a known phenol degrader, but to our knowledge, this is the first time it was isolated and tested for phenol-degrading ability from termites.
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Affiliation(s)
- Seth Van Dexter
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, 70310, USA
| | - Raj Boopathy
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, 70310, USA.
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Schutyser W, Renders T, Van den Bosch S, Koelewijn SF, Beckham GT, Sels BF. Chemicals from lignin: an interplay of lignocellulose fractionation, depolymerisation, and upgrading. Chem Soc Rev 2018; 47:852-908. [PMID: 29318245 DOI: 10.1039/c7cs00566k] [Citation(s) in RCA: 809] [Impact Index Per Article: 134.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In pursuit of more sustainable and competitive biorefineries, the effective valorisation of lignin is key. An alluring opportunity is the exploitation of lignin as a resource for chemicals. Three technological biorefinery aspects will determine the realisation of a successful lignin-to-chemicals valorisation chain, namely (i) lignocellulose fractionation, (ii) lignin depolymerisation, and (iii) upgrading towards targeted chemicals. This review provides a summary and perspective of the extensive research that has been devoted to each of these three interconnected biorefinery aspects, ranging from industrially well-established techniques to the latest cutting edge innovations. To navigate the reader through the overwhelming collection of literature on each topic, distinct strategies/topics were delineated and summarised in comprehensive overview figures. Upon closer inspection, conceptual principles arise that rationalise the success of certain methodologies, and more importantly, can guide future research to further expand the portfolio of promising technologies. When targeting chemicals, a key objective during the fractionation and depolymerisation stage is to minimise lignin condensation (i.e. formation of resistive carbon-carbon linkages). During fractionation, this can be achieved by either (i) preserving the (native) lignin structure or (ii) by tolerating depolymerisation of the lignin polymer but preventing condensation through chemical quenching or physical removal of reactive intermediates. The latter strategy is also commonly applied in the lignin depolymerisation stage, while an alternative approach is to augment the relative rate of depolymerisation vs. condensation by enhancing the reactivity of the lignin structure towards depolymerisation. Finally, because depolymerised lignins often consist of a complex mixture of various compounds, upgrading of the raw product mixture through convergent transformations embodies a promising approach to decrease the complexity. This particular upgrading approach is termed funneling, and includes both chemocatalytic and biological strategies.
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Affiliation(s)
- W Schutyser
- Center for Surface Chemistry and Catalysis, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium.
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Singh RP, Manchanda G, Li ZF, Rai AR. Insight of Proteomics and Genomics in Environmental Bioremediation. ACTA ACUST UNITED AC 2017. [DOI: 10.4018/978-1-5225-2325-3.ch003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Bioremediation of hazardous substances from environment is a major human and environmental health concern but can be managed by the microorganism due to their variety of properties that can effectively change the complexity. Microorganisms convey endogenous genetic, biochemical and physiological assets that make them superlative proxies for pollutant remediation in habitat. But, the crucial step is to degrade the complex ring structured pollutants. Interestingly, the integration of genomics and proteomics technologies that allow us to use or alter the genes and proteins of interest in a given microorganism towards a cell-free bioremediation approach. Resultantly, efforts have been finished by developing the genetically modified (Gm) microbes for the remediation of ecological contaminants. Gm microorganisms mediated bioremediation can affect the solubility, bioavailability and mobility of complex hazardous.
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Biological valorization of low molecular weight lignin. Biotechnol Adv 2016; 34:1318-1346. [DOI: 10.1016/j.biotechadv.2016.10.001] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/06/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022]
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14
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Recovery and Utilization of Lignin Monomers as Part of the Biorefinery Approach. ENERGIES 2016. [DOI: 10.3390/en9100808] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Promising approaches towards biotransformation of polycyclic aromatic hydrocarbons with Ascomycota fungi. Curr Opin Biotechnol 2016; 38:1-8. [DOI: 10.1016/j.copbio.2015.12.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 12/18/2022]
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Khemili-Talbi S, Kebbouche-Gana S, Akmoussi-Toumi S, Angar Y, Gana ML. Isolation of an extremely halophilic arhaeon Natrialba sp. C21 able to degrade aromatic compounds and to produce stable biosurfactant at high salinity. Extremophiles 2015; 19:1109-20. [PMID: 26334644 DOI: 10.1007/s00792-015-0783-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/20/2015] [Indexed: 12/30/2022]
Abstract
Natrialba sp. strain C21 was isolated from oil contaminated saline water in Ain Salah (Algeria) and has exhibited a good potential for degrading phenol (3% v/v), naphthalene (3% v/v), and pyrene (3% v/v) at high salinity with high growth, enzymatic activity and biosurfactant production. Successful metabolism of aromatic hydrocarbon compounds of the strain Natrialba sp. C21 appears to require the ortho-cleavage pathway. Indeed, assays of the key enzymes involved in the ring cleavage of catechol 1, 2-dioxygenase indicated that degradation of the phenol, naphthalene and pyrene by strain Natrialba sp. C21 was via the ortho-cleavage pathway. Cells grown on aromatic hydrocarbons displayed greater ortho-activities mainly towards catechol, while the meta-activity was very low. Besides, biosurfactants derived from the strain C21 were capable of effectively emulsifying both aromatic and aliphatic hydrocarbons and seem to be particularly promising since they have particular adaptations like the increased stability at high temperature and salinity conditions. This study clearly demonstrates for the first time that strain belonging to the genera Natrialba is able to grow at 25% (w/v) NaCl, utilizing phenol, naphthalene, and pyrene as the sole carbon sources. The results suggest that the isolated halophilic archaeon could be a good candidate for the remediation process in extreme environments polluted by aromatic hydrocarbons. Moreover, the produced biosurfactant offers a multitude of interesting potential applications in various fields of biotechnology.
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Affiliation(s)
- Souad Khemili-Talbi
- Laboratoire Conservation et Valorisation des Ressources Biologiques (VALCOR), Faculté des Sciences, Université M'Hamed Bougara de Boumerdes, Avenue de l'Indépendance, 35000, Boumerdès, Algeria.
| | - Salima Kebbouche-Gana
- Laboratoire Conservation et Valorisation des Ressources Biologiques (VALCOR), Faculté des Sciences, Université M'Hamed Bougara de Boumerdes, Avenue de l'Indépendance, 35000, Boumerdès, Algeria.
| | - Siham Akmoussi-Toumi
- Laboratoire Conservation et Valorisation des Ressources Biologiques (VALCOR), Faculté des Sciences, Université M'Hamed Bougara de Boumerdes, Avenue de l'Indépendance, 35000, Boumerdès, Algeria
| | - Yassmina Angar
- Faculté des Sciences, Université M'Hamed Bougara de Boumerdes, Avenue de l'Indépendance, 35000, Boumerdès, Algeria
| | - Mohamed Lamine Gana
- Centre de Recherche et de Développement, SONATRACH, 35000, Boumerdès, Algeria
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17
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Porter JL, Boon PLS, Murray TP, Huber T, Collyer CA, Ollis DL. Directed evolution of new and improved enzyme functions using an evolutionary intermediate and multidirectional search. ACS Chem Biol 2015; 10:611-21. [PMID: 25419863 DOI: 10.1021/cb500809f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ease with which enzymes can be adapted from their native roles and engineered to function specifically for industrial or commercial applications is crucial to enabling enzyme technology to advance beyond its current state. Directed evolution is a powerful tool for engineering enzymes with improved physical and catalytic properties and can be used to evolve enzymes where lack of structural information may thwart the use of rational design. In this study, we take the versatile and diverse α/β hydrolase fold framework, in the form of dienelactone hydrolase, and evolve it over three unique sequential evolutions with a total of 14 rounds of screening to generate a series of enzyme variants. The native enzyme has a low level of promiscuous activity toward p-nitrophenyl acetate but almost undetectable activity toward larger p-nitrophenyl esters. Using p-nitrophenyl acetate as an evolutionary intermediate, we have generated variants with altered specificity and catalytic activity up to 3 orders of magnitude higher than the native enzyme toward the larger nonphysiological p-nitrophenyl ester substrates. Several variants also possess increased stability resulting from the multidimensional approach to screening. Crystal structure analysis and substrate docking show how the enzyme active site changes over the course of the evolutions as either a direct or an indirect result of mutations.
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Affiliation(s)
- Joanne L. Porter
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Priscilla L. S. Boon
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Tracy P. Murray
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Charles A. Collyer
- School
of Molecular Bioscience, University of Sydney, Sydney, New South Wales 2006, Australia
| | - David L. Ollis
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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18
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Yamanashi T, Kim SY, Hara H, Funa N. In vitro reconstitution of the catabolic reactions catalyzed by PcaHG, PcaB, and PcaL: the protocatechuate branch of the β-ketoadipate pathway in Rhodococcus jostii RHA1. Biosci Biotechnol Biochem 2015; 79:830-5. [PMID: 25558786 DOI: 10.1080/09168451.2014.993915] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The β-ketoadipate pathway is a major pathway involved in the catabolism of the aromatic compounds in microbes. The recent progress in genome sequencing has led to a rapid accumulation of genes from the β-ketoadipate pathway in the available genetic database, yet the functions of these genes remain uncharacterized. In this study, the protocatechuate branch of the β-ketoadipate pathway of Rhodococcus jostii was reconstituted in vitro. Analysis of the reaction products of PcaHG, PcaB, and PcaL was achieved by high-performance liquid chromatography. These reaction products, β-ketoadipate enol-lactone, 3-carboxy-cis,cis-muconate, γ-carboxymuconolactone, muconolactone, and β-ketoadipate, were further characterized using LC-MS and nuclear magnetic resonance. In addition, the in vitro reaction of PcaL, a bidomain protein consisting of γ-carboxy-muconolactone decarboxylase and β-ketoadipate enol-lactone hydrolase activities, was demonstrated for the first time. This work provides a basis for analyzing the catalytic properties of enzymes involved in the growing number of β-ketoadipate pathways deposited in the genetic database.
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Affiliation(s)
- Tomoya Yamanashi
- a Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , Shizuoka , Japan
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19
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Benzoate metabolism intermediate benzoyl coenzyme A affects gentisate pathway regulation in Comamonas testosteroni. Appl Environ Microbiol 2014; 80:4051-62. [PMID: 24771026 DOI: 10.1128/aem.01146-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A previous study showed that benzoate was catabolized via a coenzyme A (CoA)-dependent epoxide pathway in Azoarcus evansii (R. Niemetz, U. Altenschmidt, S. Brucker, and G. Fuchs, Eur. J. Biochem. 227:161-168, 1995), but gentisate 1,2-dioxygenase was induced. Similarly, we found that the Comamonas testosteroni strain CNB-1 degraded benzoate via a CoA-dependent epoxide pathway and that gentisate 1,2-dioxygenase (GenA) was also induced when benzoate or 3-hydroxybenzoate served as a carbon source for growth. Genes encoding the CoA-dependent epoxide (box genes) and gentisate (gen genes) pathways were identified. Genetic disruption revealed that the gen genes were not involved in benzoate and 3-hydroxybenzoate degradation. Hence, we investigated gen gene regulation in the CNB-1 strain. The PgenA promoter, a MarR-type regulator (GenR), and the GenR binding site were identified. We found that GenR took gentisate, 3-hydroxybenzoate, and benzoyl-CoA as effectors and that binding of GenR to its target DNA sequence was prohibited when these effectors were present. In vivo studies showed that the CNB-1 mutant that lost benzoyl-CoA synthesis was not able to activate PgenA promoter, while transcription of genA was upregulated in another CNB-1 mutant that lost the ability to degrade benzoyl-CoA. The finding that benzoyl-CoA (a metabolic intermediate of benzoate degradation) and 3-hydroxybenzoate function as GenR effectors explains why GenA was induced when CNB-1 grew on benzoate or 3-hydroxybenzoate. Regulation of gentisate pathways by MarR-, LysR-, and IclR-type regulators in diverse bacterial groups is discussed in detail.
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20
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Chua JW, Hsieh JH. Oxidative bioconversion of toluene to 1,3-butadiene-1,4-dicarboxylic acid (cis,cis-muconic acid). World J Microbiol Biotechnol 2014; 6:127-43. [PMID: 24429984 DOI: 10.1007/bf01200932] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/1990] [Accepted: 02/01/1990] [Indexed: 11/30/2022]
Abstract
Pseudomonas sp. strains, isolated from soil, utilized toluene as their sole carbon source through ameta cleavage pathway. Strains metabolizing toluene through anortho cleavage pathway were selected from the wild typemeta strain. Theortho pathway strains were subjected to chemostat selection to obtain a fast-growing strain with doubling time reduced from 14 to 1.2 h. Benzoale and antibiotics enrichment selection procedures were utilized to select a blocked mutant. The blocked mutant grew on acetate as its sole carbon source and oxidatively converted toluene tocis, cis-muconic acid. Double-blocked and muconate-permeable mutants were also selected to reduce reversion frequency and to enhance muconic acid production. In shake-flask experiments, muconic acid at 3.5 g/l was obtained after 2 days of fermentation. In a 14 l fermenter, muconic acid was produced at 45 g/l in 4 days of controlled fed-batch fermentation. The oxidative bioconversion process was also demonstrated in a 1500 l fermenter.
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Affiliation(s)
- J W Chua
- Development Center for Biotechnology, 81 Chang Hsing Street, Taipei, Taiwan, ROC
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21
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Meng J, Xu J, Qin D, He Y, Xiao X, Wang F. Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. ISME JOURNAL 2013; 8:650-659. [PMID: 24108328 PMCID: PMC3930316 DOI: 10.1038/ismej.2013.174] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/30/2013] [Accepted: 08/30/2013] [Indexed: 11/15/2022]
Abstract
The Miscellaneous Crenarchaeota group (MCG) Archaea is one of the predominant archaeal groups in anoxic environments and may have significant roles in the global biogeochemical cycles. However, no isolate of MCG has been cultivated or characterized to date. In this study, we investigated the genetic organization, ecophysiological properties and evolutionary relationships of MCG archaea with other archaeal members using metagenome information and the result of gene expression experiments. A comparison of the gene organizations and similarities around the 16S rRNA genes from all available MCG fosmid and cosmid clones revealed no significant synteny among genomic fragments, demonstrating that there are large genetic variations within members of the MCG. Phylogenetic analyses of large-subunit+small-subunit rRNA, concatenated ribosomal protein genes and topoisomerases IB gene (TopoIB) all demonstrate that MCG constituted a sister lineage to the newly proposed archaeal phylum Aigarchaeota and Thaumarchaeota. Genes involved in protocatechuate degradation and chemotaxis were found in a MCG fosmid 75G8 genome fragment, suggesting that this MCG member may have a role in the degradation of aromatic compounds. Moreover, the expression of a putative 4-carboxymuconolactone decarboxylase was observed when the sediment was supplemented with protocatechuate, further supporting the hypothesis that this MCG member degrades aromatic compounds.
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Affiliation(s)
- Jun Meng
- State Key Laboratory of Microbial Metabolism and State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,3Present Address: Department of Marine Science, University of Georgia, Athens, USA
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism and State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Dan Qin
- State Key Laboratory of Microbial Metabolism and State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ying He
- State Key Laboratory of Microbial Metabolism and State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism and State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism and State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China. .,Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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22
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Simultaneous catabolism of plant-derived aromatic compounds results in enhanced growth for members of the Roseobacter lineage. Appl Environ Microbiol 2013; 79:3716-23. [PMID: 23563956 DOI: 10.1128/aem.00405-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, including Sagittula stellata E-37, utilize aromatic compounds as primary growth substrates. The genome sequence of S. stellata contains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists in S. stellata when the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (pca) and the aerobic benzoyl coenzyme A (box) pathways and the substrates known to proceed through them, p-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated that S. stellata simultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed when S. stellata was provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member, Ruegeria pomeroyi DSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.
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23
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Wang PH, Leu YL, Ismail W, Tang SL, Tsai CY, Chen HJ, Kao AT, Chiang YR. Anaerobic and aerobic cleavage of the steroid core ring structure by Steroidobacter denitrificans. J Lipid Res 2013; 54:1493-504. [PMID: 23458847 DOI: 10.1194/jlr.m034223] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aerobic degradation of steroids by bacteria has been studied in some detail. In contrast, only little is known about the anaerobic steroid catabolism. Steroidobacter denitrificans can utilize testosterone under both oxic and anoxic conditions. By conducting metabolomic investigations, we demonstrated that S. denitrificans adopts the 9,10-seco-pathway to degrade testosterone under oxic conditions. This pathway depends on the use of oxygenases for oxygenolytic ring fission. Conversely, the detected degradation intermediates under anoxic conditions suggest a novel, oxygenase-independent testosterone catabolic pathway, the 2,3-seco-pathway, which differs significantly from the aerobic route. In this anaerobic pathway, testosterone is first transformed to 1-dehydrotestosterone, which is then reduced to produce 1-testosterone followed by water addition to the C-1/C-2 double bond of 1-testosterone. Subsequently, the C-1 hydroxyl group is oxidized to produce 17-hydroxy-androstan-1,3-dione. The A-ring of this compound is cleaved by hydrolysis as evidenced by H2(18)O-incorporation experiments. Regardless of the growth conditions, testosterone is initially transformed to 1-dehydrotestosterone. This intermediate is a divergence point at which the downstream degradation pathway is governed by oxygen availability. Our results shed light into the previously unknown cleavage of the sterane ring structure without oxygen. We show that, under anoxic conditions, the microbial cleavage of steroidal core ring system begins at the A-ring.
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Affiliation(s)
- Po-Hsiang Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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24
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Krastanov A, Alexieva Z, Yemendzhiev H. Microbial degradation of phenol and phenolic derivatives. Eng Life Sci 2013. [DOI: 10.1002/elsc.201100227] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Albert Krastanov
- Department of Biotechnology; University of Food Technologies; Plovdiv; Bulgaria
| | - Zlatka Alexieva
- Institute of Microbiology; Bulgarian Academy of Sciences; Sofia; Bulgaria
| | - Husein Yemendzhiev
- Department of Water Technology; University “Prof. Asen Zlatarov”; Burgas; Bulgaria
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25
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Gröning JAD, Roth C, Kaschabek SR, Sträter N, Schlömann M. Recombinant expression of a unique chloromuconolactone dehalogenase ClcF from Rhodococcus opacus 1CP and identification of catalytically relevant residues by mutational analysis. Arch Biochem Biophys 2012; 526:69-77. [PMID: 22842338 DOI: 10.1016/j.abb.2012.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 07/16/2012] [Accepted: 07/18/2012] [Indexed: 11/28/2022]
Abstract
Chloromuconolactone dehalogenase ClcF plays a unique role in 3-chlorocatechol degradation by Rhodococcus opacus 1CP by compensating the inability of its chloromuconate cycloisomerase ClcB2 to dechlorinate the chemically stable cycloisomerization product (4R,5S)-5-chloromuconolactone (5CML). High sequence similarities showed relatedness of ClcF to muconolactone isomerases (MLIs, EC 5.3.3.4) of the 3-oxoadipate pathway. Although both enzyme types share the ability to dechlorinate 5CML, comparison of kcat/Km indicated a significant extent of specialization of ClcF for dechlorination. This assumption was substantiated by an almost complete inability of ClcF to convert (4S)-muconolactone and the exclusive formation of cis-dienelactone from 5CML. Mutational analysis of ClcF by means of variants E27D, E27Q, Y50A, N52A, and A89S indicated relevance of some highly conserved residues for substrate binding and catalysis. Based on the putative isomerization mechanism of MLI, evidence was provided for a role of E27 in initial proton abstraction as well as of Y50 and N52 in substrate binding. In case of N52 substrate binding is likely to occur to the carboxylic group of 5CML as indicated by a significant change of product specificity. Expression in Escherichia coli BL21-CP(DE)-RIL followed by a three-step purification procedure with heat treatment is a convenient strategy to obtain recombinant ClcF and variants thereof.
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26
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Epoxy Coenzyme A Thioester pathways for degradation of aromatic compounds. Appl Environ Microbiol 2012; 78:5043-51. [PMID: 22582071 DOI: 10.1128/aem.00633-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aromatic compounds (biogenic and anthropogenic) are abundant in the biosphere. Some of them are well-known environmental pollutants. Although the aromatic nucleus is relatively recalcitrant, microorganisms have developed various catabolic routes that enable complete biodegradation of aromatic compounds. The adopted degradation pathways depend on the availability of oxygen. Under oxic conditions, microorganisms utilize oxygen as a cosubstrate to activate and cleave the aromatic ring. In contrast, under anoxic conditions, the aromatic compounds are transformed to coenzyme A (CoA) thioesters followed by energy-consuming reduction of the ring. Eventually, the dearomatized ring is opened via a hydrolytic mechanism. Recently, novel catabolic pathways for the aerobic degradation of aromatic compounds were elucidated that differ significantly from the established catabolic routes. The new pathways were investigated in detail for the aerobic bacterial degradation of benzoate and phenylacetate. In both cases, the pathway is initiated by transforming the substrate to a CoA thioester and all the intermediates are bound by CoA. The subsequent reactions involve epoxidation of the aromatic ring followed by hydrolytic ring cleavage. Here we discuss the novel pathways, with a particular focus on their unique features and occurrence as well as ecological significance.
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27
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Abstract
Aromatic compounds are both common growth substrates for microorganisms and prominent environmental pollutants. The crucial step in their degradation is overcoming the resonance energy that stabilizes the ring structure. The classical strategy for degradation comprises an attack by oxygenases that hydroxylate and finally cleave the ring with the help of activated molecular oxygen. Here, we describe three alternative strategies used by microorganisms to degrade aromatic compounds. All three of these methods involve the use of CoA thioesters and ring cleavage by hydrolysis. However, these strategies are based on different ring activation mechanisms that consist of either formation of a non-aromatic ring-epoxide under oxic conditions, or reduction of the aromatic ring under anoxic conditions using one of two completely different systems.
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28
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Bains J, Leon R, Temke KG, Boulanger MJ. Elucidating the reaction mechanism of the benzoate oxidation pathway encoded aldehyde dehydrogenase from Burkholderia xenovorans LB400. Protein Sci 2011; 20:1048-59. [PMID: 21495107 DOI: 10.1002/pro.639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/04/2011] [Accepted: 04/07/2011] [Indexed: 11/09/2022]
Abstract
Oxidation of cis-3,4-dehydroadipyl-CoA semialdehyde to cis-3,4-dehydroadipyl-CoA by the aldehyde dehydrogenase, ALDH(C) (EC.1.2.1.77), is an essential step in the metabolism of benzoate in Burkholderia xenovorans LB400. In a previous study, we established a structural blueprint for this novel group of ALDH enzymes. Here, we build significantly on this initial work and propose a detailed reaction mechanism for ALDH(C) based on comprehensive structural and functional investigations of active site residues. Kinetic analyses reveal essential roles for C296 as the nucleophile and E257 as the associated general base. Structural analyses of E257Q and C296A variants suggest a dynamic charge repulsion relationship between E257 and C296 that contributes to the inherent flexibility of E257 in the native enzyme, which is further regulated by E496 and E167. A proton relay network anchored by E496 and supported by E167 and K168 serves to reset E257 for the second catalytic step. We also propose that E167, which is unique to ALDH(C) and its homologs, serves a critical role in presenting the catalytic water to the newly reset E257 such that the enzyme can proceed with deacylation and product release. Collectively, the reaction mechanism proposed for ALDH(C) promotes a greater understanding of these novel ALDH enzymes, the ALDH super-family in general, and benzoate degradation in B. xenovorans LB400.
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Affiliation(s)
- Jasleen Bains
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W3P6, Canada
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Abstract
This reminiscence is a celebration of my good fortune in family, biological and scientific. The biological family into which I was born gave me a strong start, although not entirely in the direction I took. I swerved from an anticipated career in medical practice into continuing delight in those who became my scientific family in microbiology. The families changed, yet they continued to give me strength and inspiration. In my youth, I was gently guided by mentors who gave me freedom to explore where curiosity beckoned. I hope I repaid this gift to my laboratory colleagues who enlightened me over the years. I learned much from my students, and my horizons were extended by industrial scientists. It has been my particular good fortune to learn the workings of microorganisms and microbiologists as editor of Journal of Bacteriology for a decade, as editor-in-chief of Applied and Environmental Microbiology for a decade, and as editor of Annual Review of Microbiology for a quarter of a century.
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Affiliation(s)
- L. Nicholas Ornston
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103
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30
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Bains J, Leon R, Boulanger MJ. Structural and biophysical characterization of BoxC from Burkholderia xenovorans LB400: a novel ring-cleaving enzyme in the crotonase superfamily. J Biol Chem 2009; 284:16377-16385. [PMID: 19369256 DOI: 10.1074/jbc.m900226200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mineralization of aromatic compounds by microorganisms relies on a structurally and functionally diverse group of ring-cleaving enzymes. The recently discovered benzoate oxidation pathway in Burkholderia xenovorans LB400 encodes a novel such ring-cleaving enzyme, termed BoxC, that catalyzes the conversion of 2,3-dihydro-2,3-dihydroxybenzoyl-CoA to 3,4-dehydroadipyl-CoA without the requirement for molecular oxygen. Sequence analysis indicates that BoxC is a highly divergent member of the crotonase superfamily and nearly double the size of the average superfamily member. The structure of BoxC determined to 1.5 A resolution reveals an intriguing structural demarcation. A highly divergent region in the C terminus probably serves as a structural scaffold for the conserved N terminus that encompasses the active site and, in conjunction with a conserved C-terminal helix, mediates dimer formation. Isothermal titration calorimetry and molecular docking simulations contribute to a detailed view of the active site, resulting in a compelling mechanistic model where a pair of conserved glutamate residues (Glu146 and Glu168) work in tandem to deprotonate the dihydroxylated ring substrate, leading to cleavage. A final deformylation step incorporating a water molecule and Cys111 as a general base completes the formation of 3,4-dehydroadipyl-CoA product. Overall, this study establishes the basis for BoxC as one of the most divergent members of the crotonase superfamily and provides the first structural insight into the mechanism of this novel class of ring-cleaving enzymes.
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Affiliation(s)
- Jasleen Bains
- From the Departments of Biochemistry and Microbiology, Victoria, British Columbia V8W 3P6, Canada
| | - Rafael Leon
- Chemistry, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Martin J Boulanger
- From the Departments of Biochemistry and Microbiology, Victoria, British Columbia V8W 3P6, Canada.
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32
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Gosling A, Zachariou M, Straffon M. Purification and characterisation of a 4-hydroxy benzaldehyde dehydrogenase cloned from Acinetobacter baylyi. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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de Berardinis V, Vallenet D, Castelli V, Besnard M, Pinet A, Cruaud C, Samair S, Lechaplais C, Gyapay G, Richez C, Durot M, Kreimeyer A, Le Fèvre F, Schächter V, Pezo V, Döring V, Scarpelli C, Médigue C, Cohen GN, Marlière P, Salanoubat M, Weissenbach J. A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol Syst Biol 2008; 4:174. [PMID: 18319726 PMCID: PMC2290942 DOI: 10.1038/msb.2008.10] [Citation(s) in RCA: 236] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 01/22/2008] [Indexed: 11/17/2022] Open
Abstract
We have constructed a collection of single-gene deletion mutants for all dispensable genes of the soil bacterium Acinetobacter baylyi ADP1. A total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. This essentiality data set is 88% consistent with the Escherichia coli data set inferred from the Keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as essential in Pseudomonas aeruginosa are also essential in ADP1. Several strategies were undertaken to investigate ADP1 metabolism by (1) searching for discrepancies between our essentiality data and current metabolic knowledge, (2) comparing this essentiality data set to those from other organisms, (3) systematic phenotyping of the mutant collection on a variety of carbon sources (quinate, 2-3 butanediol, glucose, etc.). This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches.
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Time-resolved fluorescence analysis of the mobile flavin cofactor in p-hydroxybenzoate hydroxylase. J CHEM SCI 2007. [DOI: 10.1007/s12039-007-0019-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Papazi A, Kotzabasis K. Bioenergetic strategy of microalgae for the biodegradation of phenolic compounds—Exogenously supplied energy and carbon sources adjust the level of biodegradation. J Biotechnol 2007; 129:706-16. [PMID: 17403549 DOI: 10.1016/j.jbiotec.2007.02.021] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2006] [Revised: 02/10/2007] [Accepted: 02/19/2007] [Indexed: 10/23/2022]
Abstract
The biodegradation of phenolic compounds by microalgae seems to be not a simple feature of a particular organism, but mostly a bioenergetic process depending on the growth conditions, especially on the exogenously supplied energy (carbon and light) sources. By using chlorophyll fluorescence induction measurements to estimate the molecular structure and function of the photosynthetic apparatus and therefore the tolerance/sensitivity of microalgae incubated with phenols, it can be assumed that, at least in low concentrations, phenol have no toxic effects on the cultures and can be used as alternative carbon source in them. Halophenols (chlorophenols, bromophenols and iodophenols) are quite toxic for the microalgal cultures. In halophenols the first step of the biodegradation is the split of the halogen substituent (dehalogenation). This is strongly determined by the bond dissociation energy of the corresponding substituent and therefore the energetic requirement for the biodegradation of halophenols increases following the sequence: iodophenol<bromophenol<chlorophenol. Additionally, the meta-position of the halogen on the phenol ring needs more energy than the ortho- and the para-one. These are possible explanations of the fact that the biodegradation of halophenols needs additional energy sources that can be exogenously supplied as organic carbon (glucose) or inorganic carbon (CO(2)).
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Affiliation(s)
- Aikaterini Papazi
- Department of Biology, University of Crete, Heraklion, Crete, Greece
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36
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Janke D, Fritsche W. Mikrobielle Dechlorierung von Pesticiden und anderen Umweltchemikalien. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/jobm.19780180509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Adams E. Catalytic aspects of enzymatic racemization. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 44:69-138. [PMID: 5862 DOI: 10.1002/9780470122891.ch3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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38
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Halak S, Lehtiö L, Basta T, Bürger S, Contzen M, Stolz A, Goldman A. Structure and function of the 3-carboxy-cis,cis-muconate lactonizing enzyme from the protocatechuate degradative pathway of Agrobacterium radiobacter S2. FEBS J 2006; 273:5169-82. [PMID: 17054713 DOI: 10.1111/j.1742-4658.2006.05512.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
3-carboxy-cis,cis-muconate lactonizing enzymes participate in the protocatechuate branch of the 3-oxoadipate pathway of various aerobic bacteria. The gene encoding a 3-carboxy-cis,cis-muconate lactonizing enzyme (pcaB1S2) was cloned from a gene cluster involved in protocatechuate degradation by Agrobacterium radiobacter strain S2. This gene encoded for a 3-carboxy-cis,cis-muconate lactonizing enzyme of 353 amino acids - significantly smaller than all previously studied 3-carboxy-cis,cis-muconate lactonizing enzymes. This enzyme, ArCMLE1, was produced in Escherichia coli and shown to convert not only 3-carboxy-cis,cis-muconate but also 3-sulfomuconate. ArCMLE1 was purified as a His-tagged enzyme variant, and the basic catalytic constants for the conversion of 3-carboxy-cis,cis-muconate and 3-sulfomuconate were determined. In contrast, Agrobacterium tumefaciens 3-carboxy-cis,cis-muconate lactonizing enzyme 1 could not, despite 87% sequence identity to ArCMLE1, use 3-sulfomuconate as substrate. The crystal structure of ArCMLE1 was determined at 2.2 A resolution. Consistent with the sequence, it showed that the C-terminal domain, present in all other members of the fumarase II family, is missing in ArCMLE1. Nonetheless, both the tertiary and quaternary structures, and the structure of the active site, are similar to those of Pseudomonas putida 3-carboxy-cis,cis-muconate lactonizing enzyme. One principal difference is that ArCMLE1 contains an Arg, as opposed to a Trp, in the active site. This indicates that activation of the carboxylic nucleophile by a hydrophobic environment is not required for lactonization, unlike earlier proposals [Yang J, Wang Y, Woolridge EM, Arora V, Petsko GA, Kozarich JW & Ringe D (2004) Biochemistry43, 10424-10434]. We identified citrate and isocitrate as noncompetitive inhibitors of ArCMLE1, and found a potential binding pocket for them on the enzyme outside the active site.
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Affiliation(s)
- Sad Halak
- Institut für Mikrobiologie, Universität Stuttgart, Germany
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Ito K, Arai R, Fusatomi E, Kamo-Uchikubo T, Kawaguchi SI, Akasaka R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S. Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD. Protein Sci 2006; 15:1187-92. [PMID: 16597838 PMCID: PMC2242516 DOI: 10.1110/ps.062148506] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
TTHA0727 is a conserved hypothetical protein from Thermus thermophilus HB8, with a molecular mass of 12.6 kDa. TTHA0727 belongs to the carboxymuconolactone decarboxylase (CMD) family (Pfam 02627). A sequence comparison with its homologs suggested that TTHA0727 is a distinct protein from alkylhydroperoxidase AhpD and gamma-carboxymuconolactone decarboxylase in the CMD family. Here we report the 1.9 A crystal structure of TTHA0727 (PDB ID: 2CWQ) determined by the multiwavelength anomalous dispersion method. The TTHA0727 monomer structure consists of seven alpha-helices (alpha1-alpha7) and one short 3(10)-helix. The crystal structure and the analytical ultracentrifugation revealed that TTHA0727 forms a hexameric ring structure in solution. The electrostatic potential distribution on the solvent-accessible surface of the TTHA0727 hexamer showed that positively charged regions exist on the side of the ring structure, suggesting that TTHA0727 interacts with some negatively charged molecules. A structural homology search revealed that the structure of three alpha-helices (alpha4-alpha6) is remarkably conserved, suggesting that it is the common structural motif for the CMD family proteins. In addition, the nine residues of the N-terminal tag bound to the cleft region between alpha1 and alpha3 in chains A and B of TTHA0727, implying that this region is the putative binding/active site for some small molecules.
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Affiliation(s)
- Kaori Ito
- Protein Research Group, RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan
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40
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Amir S, Hafidi M, Lemee L, Merlina G, Guiresse M, Pinelli E, Revel JC, Bailly JR, Ambles A. Structural characterization of humic acids, extracted from sewage sludge during composting, by thermochemolysis–gas chromatography–mass spectrometry. Process Biochem 2006. [DOI: 10.1016/j.procbio.2005.07.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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41
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Gescher J, Eisenreich W, Wörth J, Bacher A, Fuchs G. Aerobic benzoyl-CoA catabolic pathway in Azoarcus evansii: studies on the non-oxygenolytic ring cleavage enzyme. Mol Microbiol 2005; 56:1586-600. [PMID: 15916608 DOI: 10.1111/j.1365-2958.2005.04637.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel aerobic benzoate pathway has recently been discovered in various bacteria in which benzoate is first converted to benzoyl-CoA. The further downstream steps are associated with the gene products of the benzoate oxidation gene cluster (box) on the Azoarcus evansii chromosome. Benzoyl-CoA is oxidized to 2,3-dihydro-2,3-dihydroxybenzoyl-CoA (benzoyl-CoA dihydrodiol) by benzoyl-CoA oxygenase/reductase BoxBA in the presence of molecular oxygen. This study identified the next, ring cleaving step catalysed by BoxC. The boxC gene was expressed in a recombinant Escherichia coli strain as a fusion protein with maltose binding protein (BoxC(mal)) and the wild type as well as the recombinant proteins were purified and studied. BoxC catalyses the reaction 2,3-dihydro-2,3-dihydroxybenzoyl-CoA + H(2)O --> 3,4-dehydroadipyl-CoA semialdehyde + HCOOH. This is supported by the following results. Assays containing [ring-(13)C(6)]benzoyl-CoA, benzoyl-CoA oxygenase/reductase, BoxC(mal) protein, NADPH and semicarbazide were analysed directly by NMR spectroscopy and mass spectrometry. The products were identified as the semicarbazone of [2,3,4,5,6-(13)C(5)]3,4-dehydroadipyl-CoA semialdehyde; the missing one-carbon unit being formate. The same reaction mixture without semicarbazide yielded a mixture of the hydrate of [2,3,4,5,6-(13)C(5)]3,4-dehydroadipyl-CoA semialdehyde and [2,3,4,5,6-(13)C(5)]4,5-dehydroadipyl-CoA semialdehyde. BoxC, a 122 kDa homodimeric enzyme (61 kDa subunits), is termed benzoyl-CoA-dihydrodiol lyase. It contains domains characteristic for enoyl-CoA hydratases/isomerases, besides a large central domain with no significant similarity to sequences in the database. The purified protein did not require divalent metals, molecular oxygen or any cosubstrates or coenzymes for activity. The complex reaction is part of a widely distributed new principle of aerobic aromatic metabolism in which all intermediates are coenzyme A thioesters and the actual ring-cleavage reaction does not require molecular oxygen.
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Affiliation(s)
- Johannes Gescher
- Institut für Biologie II, Mikrobiologie, Fakultät für Biologie, Universität Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
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Dal S, Trautwein G, Gerischer U. Transcriptional organization of genes for protocatechuate and quinate degradation from Acinetobacter sp. strain ADP1. Appl Environ Microbiol 2005; 71:1025-34. [PMID: 15691962 PMCID: PMC546756 DOI: 10.1128/aem.71.2.1025-1034.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quinate and protocatechuate are both abundant plant products and can serve, along with a large number of other aromatic or hydroaromatic compounds, as growth substrates for Acinetobacter sp. strain ADP1. The respective genes are part of the chromosomal dca-pca-qui-pob-hca cluster encoding these pathways. The adjacent pca and qui gene clusters, which encode enzymes for protocatechuate breakdown via the beta-ketoadipate pathway and for the conversion of quinate or shikimate to protocatechuate, respectively, have the same direction of transcription and are both expressed inducibly in response to protocatechuate. The pca genes are governed by the transcriptional activator-repressor PcaU. The mechanism governing qui gene expression was previously unknown. Here we report data suggesting the existence of a large 14-kb primary transcript covering the pca and qui genes. The area between the pca and qui genes contains no promoter activity, whereas a weak, constitutive promoter was identified upstream of quiA (quiAp). The 5' end of the quiA transcript was mapped. Northern blot analysis allowed the identification of a 12-kb transcript spanning pcaI to quiX. An analysis of the pca and qui gene transcripts in a strain missing the structural gene promoter pcaIp led to the identification of two pcaIp-independent transcripts (4 and 2.4 kb). The 2.4-kb transcript makes up about 25% of the total transcript abundance of quiA, and thus the majority of transcription of the last gene of the area is also driven by pcaIp. This report strongly supports the organization of the pca and qui genes as a pca-qui operon and, furthermore, suggests that PcaU is the regulator governing its expression.
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Affiliation(s)
- Süreyya Dal
- Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany.
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43
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Zaar A, Gescher J, Eisenreich W, Bacher A, Fuchs G. New enzymes involved in aerobic benzoate metabolism in Azoarcus evansii. Mol Microbiol 2004; 54:223-38. [PMID: 15458418 DOI: 10.1111/j.1365-2958.2004.04263.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new principle of aerobic aromatic metabolism has been postulated, which is in contrast to the known pathways. In various bacteria the aromatic substrate benzoate is first converted to its coenzyme A (CoA) thioester, benzoyl-CoA, which is subsequently attacked by an oxygenase, followed by a non-oxygenolytic fission of the ring. We provide evidence for this hypothesis and show that benzoyl-CoA conversion in the bacterium Azoarcus evansii requires NADPH, O(2) and two protein components, BoxA and BoxB. BoxA is a homodimeric 46 kDa iron-sulphur-flavoprotein, which acts as reductase. In the absence of BoxB, BoxA catalyses the benzoyl-CoA stimulated artificial transfer of electrons from NADPH to O(2) via free FADH(2) to produce H(2)O(2). Physiologically, BoxA uses NADPH to reduce BoxB, a monomeric 55 kDa iron-protein that acts as benzoyl-CoA oxygenase. The product of benzoyl-CoA oxidation was identified by NMR spectroscopy as its dihydrodiol derivative, 2,3-dihydro-2,3-dihydroxybenzoyl-CoA. This suggests that BoxBA act as a benzoyl-CoA dioxygenase/reductase. Unexpectedly, benzoyl-CoA transformation by BoxBA was greatly stimulated when another enoyl-CoA hydratase/isomerase-like protein, BoxC, was added that catalysed the further transformation of the dihydrodiol product formed from benzoyl-CoA. The benzoyl-CoA oxygenase system has very low similarity to known (di)oxygenase systems and is the first member of a new enzyme family.
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Affiliation(s)
- Annette Zaar
- Institut für Biologie II, Mikrobiologie, Universität Freiburg, Schänzlestr.1, D-79104 Freiburg, Germany
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Müller WEG, Grebenjuk VA, Thakur NL, Thakur AN, Batel R, Krasko A, Müller IM, Breter HJ. Oxygen-controlled bacterial growth in the sponge Suberites domuncula: toward a molecular understanding of the symbiotic relationships between sponge and bacteria. Appl Environ Microbiol 2004; 70:2332-41. [PMID: 15066829 PMCID: PMC383090 DOI: 10.1128/aem.70.4.2332-2341.2004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sponges (phylum Porifera), known to be the richest producers among the metazoans of bioactive secondary metabolites, are assumed to live in a symbiotic relationship with microorganisms, especially bacteria. Until now, the molecular basis of the mutual symbiosis, the exchange of metabolites for the benefit of the other partner, has not been understood. We show with the demosponge Suberites domuncula as a model that the sponge expresses under optimal aeration conditions the enzyme tyrosinase, which synthesizes diphenols from monophenolic compounds. The cDNA isolated was used as a probe to determine the steady-state level of gene expression. The gene expression level parallels the level of specific activity in sponge tissue, indicating that without aeration the tyrosinase level drops drastically; this effect is reversible. The SB2 bacterium isolated from the sponge surface grew well in M9 minimal salt medium supplemented with the dihydroxylated aromatic compound protocatechuate; this carbon source supported growth more than did glucose. From the SB2 bacterium the protocatechuate gene cluster was cloned and sequenced. This cluster comprises all genes coding for enzymes involved in the conversion of protocatechuate to acetyl coenzyme A. Expression is strongly induced if the bacteria are cultivated on M9-protocatechuate medium; the genes pcaQ (encoding the putative transcriptional activator of the pca operon) and pcaDC were used for quantitative PCR analyses. We conclude that metabolites, in this case diphenols, which might be produced by the sponge S. domuncula are utilized by the sponge surface-associated bacterium for energy generation. This rationale will help to further uncover the symbiotic pathways between sponges and their associated "nonculturable" microorganisms; our approach is flanked by the establishment of an EST (expressed sequence tags) database in our laboratory.
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Affiliation(s)
- Werner E G Müller
- Institut für Physiologische Chemie, Abteilung Angewandte Molekularbiologie, Universität Mainz, D-55099 Mainz, Germany.
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45
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Meyer AF, Lipson DA, Martin AP, Schadt CW, Schmidt SK. Molecular and metabolic characterization of cold-tolerant alpine soil Pseudomonas sensu stricto. Appl Environ Microbiol 2004; 70:483-9. [PMID: 14711678 PMCID: PMC321299 DOI: 10.1128/aem.70.1.483-489.2004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alpine soils undergo dramatic temporal changes in their microclimatic properties, suggesting that the bacteria there encounter uncommon shifting selection gradients. Pseudomonads constitute important members of the alpine soil community. In order to characterize the alpine Pseudomonas community and to assess the impact of shifting selection on this community, we examined the ability of cold-tolerant Pseudomonas isolates to grow on a variety of carbon sources, and we determined their phylogenetic relationships based on 16S ribosomal DNA sequencing. We found a high prevalence of Pseudomonas in our soil samples, and isolates from these soils exhibited extensive metabolic diversity. In addition, our data revealed that many of our isolates form a unique cold-adapted clade, representatives of which are also found in the Swedish tundra and Antarctica. Our data also show a lack of concordance between the metabolic properties and 16S phylogeny, indicating that the metabolic diversity of these organisms cannot be predicted by phylogeny.
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Affiliation(s)
- A F Meyer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
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Vetting MW, Wackett LP, Que L, Lipscomb JD, Ohlendorf DH. Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. J Bacteriol 2004; 186:1945-58. [PMID: 15028678 PMCID: PMC374394 DOI: 10.1128/jb.186.7.1945-1958.2004] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2003] [Accepted: 12/04/2003] [Indexed: 11/20/2022] Open
Abstract
The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Molecular Biology and Biophysics, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Gescher J, Zaar A, Mohamed M, Schägger H, Fuchs G. Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii. J Bacteriol 2002; 184:6301-15. [PMID: 12399500 PMCID: PMC151953 DOI: 10.1128/jb.184.22.6301-6315.2002] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new pathway for aerobic benzoate oxidation has been postulated for Azoarcus evansii and for a Bacillus stearothermophilus-like strain. Benzoate is first transformed into benzoyl coenzyme A (benzoyl-CoA), which subsequently is oxidized to 3-hydroxyadipyl-CoA and then to 3-ketoadipyl-CoA; all intermediates are CoA thioesters. The genes coding for this benzoate-induced pathway were investigated in the beta-proteobacterium A. evansii. They were identified on the basis of N-terminal amino acid sequences of purified benzoate metabolic enzymes and of benzoate-induced proteins identified on two-dimensional gels. Fifteen genes probably coding for the benzoate pathway were found to be clustered on the chromosome. These genes code for the following functions: a putative ATP-dependent benzoate transport system, benzoate-CoA ligase, a putative benzoyl-CoA oxygenase, a putative isomerizing enzyme, a putative ring-opening enzyme, enzymes for beta-oxidation of CoA-activated intermediates, thioesterase, and lactone hydrolase, as well as completely unknown enzymes belonging to new protein families. An unusual putative regulator protein consists of a regulator protein and a shikimate kinase I-type domain. A deletion mutant with a deletion in one gene (boxA) was unable to grow with benzoate as the sole organic substrate, but it was able to grow with 3-hydroxybenzoate and adipate. The data support the proposed pathway, which postulates operation of a new type of ring-hydroxylating dioxygenase acting on benzoyl-CoA and nonoxygenolytic ring cleavage. A beta-oxidation-like metabolism of the ring cleavage product is thought to lead to 3-ketoadipyl-CoA, which finally is cleaved into succinyl-CoA and acetyl-CoA.
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Affiliation(s)
- Johannes Gescher
- Mikrobiologie, Institut Biologie II, Universität Freiburg, Germany
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Martins MAM, Queiroz MJ, Silvestre AJD, Lima N. Relationship of chemical structures of textile dyes on the pre-adaptation medium and the potentialities of their biodegradation by Phanerochaete chrysosporium. Res Microbiol 2002; 153:361-8. [PMID: 12234010 DOI: 10.1016/s0923-2508(02)01332-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Azo dye derivatives of azobenzene constitute the largest group of dyes used in the textile industry and possess recalcitrant chemical groups, such as those of azo and sulphonic acid. Some microorganisms are able to degrade these aromatic compounds. In the present work, decolourisation of culture media containing azo dyes by the ligninolytic fungus Phanerochaete chrysosporium was achieved under nitrogen-limited conditions. The dyes used in the study are derivatives of meta- or para-aminosulphonic or aminobenzoic acids and include in their structures groups such as guaiacol or syringol, which are bioaccessible to the lignin degrading fungus P. chrysosporium. The aim of this study was to pre-adapt the microorganism to the structure of the dyes and to establish the relationships of the chemical structure of the dye present in the pre-adaptation medium with the chemical structure of the dye to be degraded. The azo dye used in the pre-adaptation medium that gave the best overall decolourisation performance was a meta-aminosulphonic acid and guaiacol derivative. The azo dye derivative of a meta-aminobenzoic acid and syringol showed a better performance in the decolourisation assays. Preliminary GC-MS studies indicated the formation of a nitroso substituted catechol metabolite, a precursor of aromatic ring cleavage, which was confirmed to occur by an enzymatic assay. The presence of this type of metabolite allows the establishment of a possible metabolic pathway towards mineralisation.
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Nanny MA, Ratasuk N. Characterization and comparison of hydrophobic neutral and hydrophobic acid dissolved organic carbon isolated from three municipal landfill leachates. WATER RESEARCH 2002; 36:1572-1584. [PMID: 11996346 DOI: 10.1016/s0043-1354(01)00359-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The acid-precipitated (AP) and acid-soluble (AS) fractions of the combined hydrophobic neutral and hydrophobic acid dissolved organic carbon (DOC) were isolated from leachate collected from three municipal landfills of different age and redox conditions. The AP and the AS combined hydrophobic neutral and hydrophobic acid DOC comprised 6-15% and 51-66%, respectively, of the leachate nonpurgable organic carbon. Elemental analysis, infra-red spectroscopy, 13C CP-MAS nuclear magnetic resonance spectroscopy and dipolar dephasing experiments, and thermochemolysis gas chromatography/mass spectrometry results showed that the AP and AS fractions of hydrophobic neutral and hydrophobic acid DOC are highly aliphatic, with linear and branching moieties, and less oxidized than most terrestrial and aquatic humic substances. Very little, if any, polysaccharide or cellulose, lignin, or cutin components comprise these fractions. It is hypothesized that a majority of the organic carbon in these fractions originates highly branched, cyclic aliphatic organic compounds.
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Affiliation(s)
- Mark A Nanny
- School of Civil Engineering and Environmental Science, University of Oklahoma, Norman 73019, USA.
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Williams GM, Pickup RW, Thornton SF, Lerner DN, Mallinson HE, Moore Y, White C. Biogeochemical characterisation of a coal tar distillate plume. JOURNAL OF CONTAMINANT HYDROLOGY 2001; 53:175-197. [PMID: 11820470 DOI: 10.1016/s0169-7722(01)00166-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The distillation of acidified coal tars for up to 50 years has given rise to a phenol plume approximately 500 m long, 50 m deep and containing up to 15 g l(-1) dissolved organic carbon (DOC) in the Triassic Sandstones aquifer. A conceptual biogeochemical model based on chemical and microbiological analysis of groundwater samples has been developed as a preliminary to more detailed studies of the controls on natural attenuation. While the development of redox zones and the production of methane and carbon dioxide provide evidence of natural attenuation, it appears that degradation is slow. The existence of sulphate in the plume indicates that this electron acceptor has not been depleted and that consequently methanogenesis is probably limited. Based on a simple estimate of sulphate input concentration, a half-life of about 15 years has been estimated for sulphate reduction. Geochemical modelling predicts that increased alkalinity within the plume has not led to carbonate precipitation, and thus within the limits of accuracy of the measurement, alkalinity may reflect the degree of biodegradation. This implies a loss of around 18% of the DOC over a 30-year period. Despite limited degradation, microbial studies show that there are diverse microbial communities in the aquifer with the potential for both anaerobic and aerobic biodegradation. Microbial activity was found to be greatest at the leading edge of the plume where DOC concentrations are 60 mg l(-1) or less, but activity could still be observed in more contaminated samples even though cells could not be cultured. The study suggests that degradation may be limited by the high phenol concentrations within the core of the plume, but that once diluted by dispersion, natural attenuation may proceed. More detailed studies to confirm these initial findings are identified and form the basis of associated papers.
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Affiliation(s)
- G M Williams
- British Geological Surrey, Keyworth, Nottingham, UK.
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