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Gao J, Ali MY, Kamaraj Y, Zhang Z, Weike L, Sethupathy S, Zhu D. A comprehensive review on biological funnel mechanism in lignin valorization: Pathways and enzyme dynamics. Microbiol Res 2024; 287:127835. [PMID: 39032264 DOI: 10.1016/j.micres.2024.127835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/17/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Lignin, a significant byproduct of the paper and pulp industry, is attracting interest due to its potential utilization in biomaterial-based sectors and biofuel production. Investigating biological methods for converting lignin into valuable products is crucial for effective utilization and has recently gained growing attention. Several microorganisms effectively decomposed low molecular weight lignins, transforming them into intermediate compounds via upper and lower metabolic pathways. This review focuses on assessing bacterial metabolic pathways involved in the breakdown of lignin into aromatic compounds and their subsequent utilization by different bacteria through various metabolic pathways. Understanding these pathways is essential for developing efficient synthetic metabolic systems to valorize lignin and obtain valuable industrial aromatic chemicals. The concept of "biological funneling," which involves examining key enzymes, their interactions, and the complex metabolic pathways associated with lignin conversion, is crucial in lignin valorization. By manipulating lignin metabolic pathways and utilizing biological routes, many aromatic compounds can be synthesized within cellular factories. Although there is insufficient evidence regarding the complete metabolism of polyaromatic hydrocarbons by particular microorganisms, understanding lignin-degrading enzymes, regulatory mechanisms, and interactions among various enzyme systems is essential for optimizing lignin valorization. This review highlights recent advancements in lignin valorization, bio-funneling, multi-omics, and analytical characterization approaches for aromatic utilization. It provides up-to-date information and insights into the latest research findings and technological innovations. The review offers valuable insights into the future potential of biological routes for lignin valorization.
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Affiliation(s)
- Jiayue Gao
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Mohamed Yassin Ali
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China; Department of Biochemistry, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
| | - Yoganathan Kamaraj
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Zhenghao Zhang
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Li Weike
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
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Qin J, Qi X, Li Y, Tang Z, Zhang X, Ru S, Xiong JQ. Bisphenols can promote antibiotic resistance by inducing metabolic adaptations and natural transformation. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134149. [PMID: 38554512 DOI: 10.1016/j.jhazmat.2024.134149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024]
Abstract
Whether bisphenols, as plasticizers, can influence bacterial uptake of antibiotic resistance genes (ARGs) in natural environment, as well as the underlying mechanism remains largely unknown. Our results showed that four commonly used bisphenols (bisphenol A, S, F, and AF) at their environmental relative concentrations can significantly promote transmission of ARGs by 2.97-3.56 times in Acinetobacter baylyi ADP1. Intriguingly, we observed ADP1 acquired resistance by integrating plasmids uptake and cellular metabolic adaptations other than through reactive oxygen species mediated pathway. Metabolic adaptations including upregulation of capsules polysaccharide biosynthesis and intracellularly metabolic enzymes, which enabled formation of thicker capsules for capturing free plasmids, and degradation of accumulated compounds. Simultaneously, genes encoding DNA uptake and translocation machinery were incorporated to enhance natural transformation of antibiotic resistance carrying plasmids. We further exposed aquatic fish to bisphenols for 120 days to monitor their long-term effects in aquatic environment, which showed that intestinal bacteria communities were dominated by a drug resistant microbiome. Our study provides new insight into the mechanism of enhanced natural transformation of ARGs by bisphenols, and highlights the investigations for unexpectedly-elevated antibiotic-resistant risks by structurally related environmental chemicals.
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Affiliation(s)
- Jingyu Qin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; School of Life Sciences, Department of Immunology and Microbiology, Department of Chemical Biology, Southern University of Science and Technology, No. 1088, Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong, China
| | - Xin Qi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yuejiao Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhuyun Tang
- School of Life Sciences, Department of Immunology and Microbiology, Department of Chemical Biology, Southern University of Science and Technology, No. 1088, Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong, China
| | - Xiaona Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shaoguo Ru
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Jiu-Qiang Xiong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Augustiniene E, Kutraite I, Valanciene E, Matulis P, Jonuskiene I, Malys N. Transcription factor-based biosensors for detection of naturally occurring phenolic acids. N Biotechnol 2023; 78:1-12. [PMID: 37714511 DOI: 10.1016/j.nbt.2023.09.004] [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: 01/09/2023] [Revised: 06/09/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Phenolic acids including hydroxybenzoic and hydroxycinnamic acids are secondary plant and fungal metabolites involved in many physiological processes offering health and dietary benefits. They are often utilised as precursors for production of value-added compounds. The limited availability of synthetic biology tools, such as whole-cell biosensors suitable for monitoring the dynamics of phenolic acids intracellularly and extracellularly, hinders the capabilities to develop high-throughput screens to study their metabolism and forward engineering. Here, by applying a multi-genome approach, we have identified phenolic acid-inducible gene expression systems composed of transcription factor-inducible promoter pairs responding to eleven different phenolic acids. Subsequently, they were used for the development of whole-cell biosensors based on model bacterial hosts, such as Escherichia coli, Cupriavidus necator and Pseudomonas putida. The dynamics and range of the biosensors were evaluated by establishing their response and sensitivity landscapes. The specificity and previously uncharacterised interactions between transcription factor and its effector(s) were identified by a screen of twenty major phenolic acids. To exemplify applicability, we utilise a protocatechuic acid-biosensor to identify enzymes with enhanced activity for conversion of p-hydroxybenzoate to protocatechuate. Transcription factor-based biosensors developed in this study will advance the analytics of phenolic acids and expedite research into their metabolism.
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Affiliation(s)
- Ernesta Augustiniene
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Ingrida Kutraite
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Egle Valanciene
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Paulius Matulis
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Ilona Jonuskiene
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania
| | - Naglis Malys
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania; Department of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology, Radvilenu st. 19, LT-50254 Kaunas, Lithuania.
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Rogowska-van der Molen MA, Berasategui-Lopez A, Coolen S, Jansen RS, Welte CU. Microbial degradation of plant toxins. Environ Microbiol 2023; 25:2988-3010. [PMID: 37718389 DOI: 10.1111/1462-2920.16507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Plants produce a variety of secondary metabolites in response to biotic and abiotic stresses. Although they have many functions, a subclass of toxic secondary metabolites mainly serve plants as deterring agents against herbivores, insects, or pathogens. Microorganisms present in divergent ecological niches, such as soil, water, or insect and rumen gut systems have been found capable of detoxifying these metabolites. As a result of detoxification, microbes gain growth nutrients and benefit their herbivory host via detoxifying symbiosis. Here, we review current knowledge on microbial degradation of toxic alkaloids, glucosinolates, terpenes, and polyphenols with an emphasis on the genes and enzymes involved in breakdown pathways. We highlight that the insect-associated microbes might find application in biotechnology and become targets for an alternative microbial pest control strategy.
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Affiliation(s)
- Magda A Rogowska-van der Molen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Aileen Berasategui-Lopez
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Baden-Württemberg, Germany
- Amsterdam Institute for Life and Environment, Section Ecology and Evolution, Vrije Universiteit, Amsterdam, The Netherlands
| | - Silvia Coolen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Robert S Jansen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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Bianco F, Race M, Papirio S, Esposito G. Phenanthrene removal from a spent sediment washing solution in a continuous-flow stirred-tank reactor. ENVIRONMENTAL RESEARCH 2023; 228:115889. [PMID: 37054831 DOI: 10.1016/j.envres.2023.115889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023]
Abstract
The issue of polycyclic aromatic hydrocarbons (PAHs) is widespread in marine sediments involving ecological systems and human health. Sediment washing (SW) has proven to be the most effective remediation approach for sediments polluted by PAHs, such as phenanthrene (PHE). However, SW still raises waste handling concerns due to a considerable amount of effluents generated downstream. In this context, the biological treatment of a PHE- and ethanol-containing spent SW solution can represent a highly efficient and environmentally-friendly strategy, but its knowledge is still scarce in scientific literature and no studies have so far been conducted in continuous mode. Therefore, a synthetic PHE-polluted SW solution was biologically treated in a 1 L aerated continuous-flow stirred-tank reactor for 129 days by evaluating the effect of different pH values, aeration flowrates and hydraulic retention times as operating parameters over five successive phases. A PHE removal efficiency of up to 75-94% was achieved by an acclimated PHE-degrading consortium mainly composed of Proteobacteria, Bacteroidota and Firmicutes phyla through biodegradation following the adsorption mechanism. PHE biodegradation, mainly occurring via the benzoate route due to the presence of PAH-related-degrading functional genes and a phthalate accumulation up to 46 mg/L, was also accompanied by a reduction of dissolved organic carbon and ammonia nitrogen above 99% in the treated SW solution.
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Affiliation(s)
- Francesco Bianco
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043, Cassino, Italy.
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043, Cassino, Italy
| | - Stefano Papirio
- Department of Civil, Architectural and Environmental Engineering, University of Napoli Federico II, Via Claudio 21, 80125, Napoli, Italy
| | - Giovanni Esposito
- Department of Civil, Architectural and Environmental Engineering, University of Napoli Federico II, Via Claudio 21, 80125, Napoli, Italy
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Li YX, Lin W, Han YH, Wang YQ, Wang T, Zhang H, Zhang Y, Wang SS. Biodegradation of p-hydroxybenzoic acid in Herbaspirillum aquaticum KLS-1 isolated from tailing soil: Characterization and molecular mechanism. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131669. [PMID: 37236108 DOI: 10.1016/j.jhazmat.2023.131669] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/09/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The wide distribution of p-hydroxybenzoic acid (PHBA) in the environments has attracted great concerns due to its potential risks to organisms. Bioremediation is considered a green way to remove PHBA from environment. Here, a new PHBA-degrading bacterium Herbaspirillum aquaticum KLS-1was isolated and its PHBA degradation mechanisms were fully evaluated. Results showed that strain KLS-1 could utilize PHBA as the sole carbon source and completely degrade 500 mg/L PHBA within 18 h. The optimal conditions for bacterial growth and PHBA degradation were pH values of 6.0-8.0, temperatures of 30 °C-35 °C, shaking speed of 180 rpm, Mg2+ concentration of 2.0 mM and Fe2+ concentration of 1.0 mM. Draft genome sequencing and functional gene annotations identified three operons (i.e., pobRA, pcaRHGBD and pcaRIJ) and several free genes possibly participating in PHBA degradation. The key genes pobA, ubiA, fadA, ligK and ubiG involved in the regulation of protocatechuate and ubiquinone (UQ) metabolisms were successfully amplified in strain KLS-1 at mRNA level. Our data suggested that PHBA could be degraded by strain KLS-1 via the protocatechuate ortho-/meta-cleavage pathway and UQ biosynthesis pathway. This study has provided a new PHBA-degrading bacterium for potential bioremediation of PHBA pollution.
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Affiliation(s)
- Yi-Xi Li
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Wei Lin
- College of Life Science, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Yong-He Han
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China.
| | - Yao-Qiang Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Tao Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Hong Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Yong Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Shan-Shan Wang
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
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Bhandari R, Sanz-Saez A, Leisner CP, Potnis N. Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere. ISME COMMUNICATIONS 2023; 3:24. [PMID: 36973329 PMCID: PMC10043289 DOI: 10.1038/s43705-023-00232-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance or response to these stresses. We evaluated the impact of elevated tropospheric ozone (O3), individually and in combination with Xanthomonas perforans infection, under open-top chamber field conditions on overall disease outcome on resistant and susceptible pepper cultivars, and their associated microbiome structure, function, and interaction network across the growing season. Pathogen infection resulted in a distinct microbial community structure and functions on the susceptible cultivar, while concurrent O3 stress did not further alter the community structure, and function. However, O3 stress exacerbated the disease severity on resistant cultivar. This altered diseased severity was accompanied by enhanced heterogeneity in associated Xanthomonas population counts, although no significant shift in overall microbiota density, microbial community structure, and function was evident. Microbial co-occurrence networks under simultaneous O3 stress and pathogen challenge indicated a shift in the most influential taxa and a less connected network, which may reflect the altered stability of interactions among community members. Increased disease severity on resistant cultivar may be explained by such altered microbial co-occurrence network, indicating the altered microbiome-associated prophylactic shield against pathogens under elevated O3. Our findings demonstrate that microbial communities respond distinctly to individual and simultaneous stressors, in this case, O3 stress and pathogen infection, and can play a significant role in predicting how plant-pathogen interactions would change in the face of climate change.
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Affiliation(s)
- Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Alvaro Sanz-Saez
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA.
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Kutraite I, Malys N. Development and Application of Whole-Cell Biosensors for the Detection of Gallic Acid. ACS Synth Biol 2023; 12:533-543. [PMID: 36724292 PMCID: PMC9942251 DOI: 10.1021/acssynbio.2c00537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Gallic acid is a prevalent secondary plant metabolite distinguished as one of the most effective free-radical scavengers among phenolic acids. This compound is also known for its cytotoxic, anti-inflammatory, and antimicrobial activities. Bulk quantities of gallic acid are conventionally produced by acid hydrolysis of tannins, a costly and environmentally hazardous process. With the aim to develop more sustainable approaches, microbial bioproduction strategies have been attempted recently. To advance synthetic biology and metabolic engineering of microorganisms for gallic acid production, we characterize here a transcription factor-based inducible system PpGalR/PPP_RS13150 that responds to the extracellular gallic acid in a dose-dependent manner in Pseudomonas putida KT2440. Surprisingly, this compound does not mediate induction when PpGalR/PPP_RS13150 is used in non-native host background. We show that the activation of the inducible system requires gallate dioxygenase activity encoded by galA gene. The 4-oxalomesaconic acid, an intermediate of gallic acid-metabolism, is identified as the effector molecule that interacts with the transcription factor GalR mediating activation of gene expression. Introduction of galA gene along galR enables development of biosensors suitable for detection and monitoring of gallic acid extracellularly using non-native hosts such as E. coli and C. necator. Moreover, the P. putida-based biosensor's applicability is demonstrated by detecting and measuring gallic acid in extracts of Camellia sinensis leaves. This study reports the strategy, which can be applied for developing gallic acid biosensors using bacterial species outside Pseudomonas genus.
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Affiliation(s)
- Ingrida Kutraite
- Bioprocess
Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų Street 19, LT-50254Kaunas, Lithuania
| | - Naglis Malys
- Bioprocess
Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų Street 19, LT-50254Kaunas, Lithuania,Department
of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų Street 19, LT-50254Kaunas, Lithuania,
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Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids. Microorganisms 2022; 11:microorganisms11010078. [PMID: 36677370 PMCID: PMC9867520 DOI: 10.3390/microorganisms11010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Rieske-type two-component vanillate O-demethylases (VanODs) catalyze conversion of the lignin-derived monomer vanillate into protocatechuate in several bacterial species. Currently, VanODs have received attention because of the demand of effective lignin valorization technologies, since these enzymes own the potential to catalyze methoxy group demethylation of distinct lignin monomers. In this work, we identified a phylogenetically divergent VanOD from Rhodococcus ruber R1, only distantly related to previously described homologues and whose presence, along with a 3-hydroxybenzoate/gentisate pathway, correlated with the ability to grow on other meta-methoxylated aromatics, such as 3-methoxybenzoate and 5-methoxysalicylate. The complementation of catabolic abilities by heterologous expression in a host strain unable to grow on vanillate, and subsequent resting cell assays, suggest that the vanAB genes of R1 strain encode a proficient VanOD acting on different vanillate-like substrates; and also revealed that a methoxy group in the meta position and a carboxylic acid moiety in the aromatic ring are key for substrate recognition. Phylogenetic analysis of the oxygenase subunit of bacterial VanODs revealed three divergent groups constituted by homologues found in Proteobacteria (Type I), Actinobacteria (Type II), or Proteobacteria/Actinobacteria (Type III) in which the R1 VanOD is placed. These results suggest that VanOD from R1 strain, and its type III homologues, expand the range of methoxylated aromatics used as substrates by bacteria.
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From degrader to producer: reversing the gallic acid metabolism of Pseudomonas putida KT2440. Int Microbiol 2022; 26:243-255. [PMID: 36357545 PMCID: PMC9649394 DOI: 10.1007/s10123-022-00282-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/18/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
Abstract
Gallic acid is a powerful antioxidant with multiple therapeutic applications, usually obtained from the acidic hydrolysis of tannins produced by many plants. As this process generates a considerable amount of toxic waste, the use of tannases or tannase-producing microorganisms has become a greener alternative over the last years. However, their high costs still impose some barriers for industrial scalability, requiring solutions that could be both greener and cost-effective. Since Pseudomonas putida KT2440 is a powerful degrader of gallic acid, its metabolism offers pathways that can be engineered to produce it from cheap and renewable carbon sources, such as the crude glycerol generated in biodiesel units. In this study, a synthetic operon with the heterologous genes aroG4, quiC and pobA* was developed and expressed in P. putida, based on an in silico analysis of possible metabolic routes, resulting in no production. Then, the sequences pcaHG and galTAPR were deleted from the genome of this strain to avoid the degradation of gallic acid and its main intermediate, the protocatechuic acid. This mutant was transformed with the vector containing the synthetic operon and was finally able to convert glycerol into gallic acid. Production assays in shaker showed a final concentration of 346.7 ± 0.004 mg L-1 gallic acid after 72 h.
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Park M, Darwish AG, Elhag RI, Tsolova V, Soliman KFA, El-Sharkawy I. A multi-locus genome-wide association study reveals the genetics underlying muscadine antioxidant in berry skin. FRONTIERS IN PLANT SCIENCE 2022; 13:969301. [PMID: 35991419 PMCID: PMC9386419 DOI: 10.3389/fpls.2022.969301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Muscadine berries display enhanced nutraceutical value due to the accumulation of distinctive phytochemical constituents with great potential antioxidant activity. Such nutritional and health merits are not only restricted to muscadine, but muscadine berries accumulate higher amounts of bioactive polyphenolics compared with other grape species. For the genetic study of the antioxidant trait in muscadine, a multi-locus genome-wide association study (GWAS) with 350 muscadine genotypes and 1,283 RNase H2 enzyme-dependent amplicon sequencing (rhAmpSeq) markers was performed. Phenotyping was conducted with several antioxidant-related traits, including total phenolic content (TPC), total flavonoid content (TFC), 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity, and FRAP antioxidant assay in muscadine berry skin. The correlation coefficient analysis revealed that the TPC, and DPPH/FRAP activities were significantly correlated. Through the GWAS analysis, 12 QTNs were identified from the four traits, of which six were pleiotropic QTNs. Two pleiotropic QTNs, chr2_14464718 and chr4_16491374, were commonly identified from the TPC and DPPH/FRAP activities. Co-located genes with the two pleiotropic QTNs were isolated, and two candidate genes were identified with transcriptome analysis. UDP-glycosyltransferase and 4-hydroxy-4-methyl-2-oxoglutarate aldolase were the candidate genes that are positively and negatively correlated to the quantitative property of traits, respectively. These results are the first genetic evidence of the quantitative property of antioxidants in muscadine and provide genetic resources for breeding antioxidant-rich cultivars for both Muscadinia and Euvitis species.
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Affiliation(s)
- Minkyu Park
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Ahmed G. Darwish
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
- Department of Biochemistry, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Rashid I. Elhag
- College of Science and Technology, Florida A&M University, Tallahassee, FL, United States
| | - Violeta Tsolova
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Karam F. A. Soliman
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
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12
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Liu H, Liu ZH, Zhang RK, Yuan JS, Li BZ, Yuan YJ. Bacterial conversion routes for lignin valorization. Biotechnol Adv 2022; 60:108000. [DOI: 10.1016/j.biotechadv.2022.108000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 12/12/2022]
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13
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Li M, Miao H, Li Y, Wang F, Xu J. Protein Engineering of an Artificial P450BM3 Peroxygenase System Enables Highly Selective O-Demethylation of Lignin Monomers. Molecules 2022; 27:molecules27103120. [PMID: 35630597 PMCID: PMC9143554 DOI: 10.3390/molecules27103120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
The O-demethylation of lignin monomers, which has drawn substantial attention recently, is critical for the formation of phenols from aromatic ethers. The P450BM3 peroxygenase system was recently found to enable the O-demethylation of different aromatic ethers with the assistance of dual-functional small molecules (DFSM), but these prepared mutants only have either moderate O-demethylation activity or moderate selectivity, which hinders their further application. In this study, we improve the system by introducing different amino acids into the active site of P450BM3, and these amino acids with different side chains impacted the catalytic ability of enzymes due to their differences in size, polarity, and hydrophobicity. Among the prepared mutants, the combination of V78A/F87A/T268I/A264G and Im-C6-Phe efficiently catalyzed the O-demethylation of guaiacol (TON = 839) with 100% selectivity. Compared with NADPH-dependent systems, we offer an economical and practical bioconversion avenue.
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Affiliation(s)
- Maosheng Li
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China;
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
| | - Hengmin Miao
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
| | - Yanqing Li
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
| | - Fang Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao 266071, China; (H.M.); (Y.L.); (F.W.)
- Correspondence: ; Tel.: +86-13869828530
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14
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Mueller J, Willett H, Feist AM, Niu W. Engineering Pseudomonas putida for Improved Utilization of Syringyl Aromatics. Biotechnol Bioeng 2022; 119:2541-2550. [PMID: 35524438 PMCID: PMC9378539 DOI: 10.1002/bit.28131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/22/2022] [Accepted: 05/01/2022] [Indexed: 11/08/2022]
Abstract
Lignin is a largely untapped source for the bioproduction of value‐added chemicals. Pseudomonas putida KT2440 has emerged as a strong candidate for bioprocessing of lignin feedstocks due to its resistance to several industrial solvents, broad metabolic capabilities, and genetic amenability. Here we demonstrate the engineering of P. putida for the ability to metabolize syringic acid, one of the major products that comes from the breakdown of the syringyl component of lignin. The rational design was first applied for the construction of strain Sy‐1 by overexpressing a native vanillate demethylase. Subsequent adaptive laboratory evolution (ALE) led to the generation of mutations that achieved robust growth on syringic acid as a sole carbon source. The best mutant showed a 30% increase in the growth rate over the original engineered strain. Genomic sequencing revealed multiple mutations repeated in separate evolved replicates. Reverse engineering of mutations identified in agmR, gbdR, fleQ, and the intergenic region of gstB and yadG into the parental strain recaptured the improved growth of the evolved strains to varied extent. These findings thus reveal the ability of P. putida to utilize lignin more fully as a feedstock and make it a more economically viable chassis for chemical production.
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Affiliation(s)
- Joshua Mueller
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Howard Willett
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.,The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
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15
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Hemati A, Nazari M, Asgari Lajayer B, Smith DL, Astatkie T. Lignocellulosics in plant cell wall and their potential biological degradation. Folia Microbiol (Praha) 2022; 67:671-681. [PMID: 35508797 DOI: 10.1007/s12223-022-00974-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/23/2022] [Indexed: 11/29/2022]
Abstract
Lignocellulosic materials are composed of three main structural polymers: hemicellulose, cellulose, and lignin. Cellulose is a long chain molecule of glucose requiring a small number of enzymes for degradation due to its simple structure while lignin is a complex polymer of phenylpropane making its biochemical decomposition difficult. Under anaerobic conditions, lignocellulose breakdown is much easier and more rapid than aerobic conditions. Various studies have been carried out to estimate the rate of degradation of lignocellulosic materials. Microorganisms play a key role in the degradation of lignocellulosic materials because they produce a variety of hydrolytic enzymes including cellulase, proteases, xylanases, lipases, laccase, and phosphatases during the degradation of lignocellulosic materials. Based on the body of literature, microorganismal activity can provide useful information about the process of organic matter decomposition.
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Affiliation(s)
- Arash Hemati
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mahtab Nazari
- Department of Plant Sciences, Macdonald Campus/McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Behnam Asgari Lajayer
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Donald L Smith
- Department of Plant Sciences, Macdonald Campus/McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Tess Astatkie
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada.
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16
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Mutanda I, Sun J, Jiang J, Zhu D. Bacterial membrane transporter systems for aromatic compounds: Regulation, engineering, and biotechnological applications. Biotechnol Adv 2022; 59:107952. [PMID: 35398204 DOI: 10.1016/j.biotechadv.2022.107952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/20/2022] [Accepted: 04/02/2022] [Indexed: 12/13/2022]
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17
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Zhao L, Brugel S, Ramasamy KP, Andersson A. Response of Coastal Shewanella and Duganella Bacteria to Planktonic and Terrestrial Food Substrates. Front Microbiol 2022; 12:726844. [PMID: 35250896 PMCID: PMC8888917 DOI: 10.3389/fmicb.2021.726844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Global warming scenarios indicate that in subarctic regions, the precipitation will increase in the future. Coastal bacteria will thus receive increasing organic carbon sources from land runoff. How such changes will affect the function and taxonomic composition of coastal bacteria is poorly known. We performed a 10-day experiment with two isolated bacteria: Shewanella baltica from a seaside location and Duganella sp. from a river mouth, and provided them with a plankton and a river extract as food substrate. The bacterial growth and carbon consumption were monitored over the experimental period. Shewanella and Duganella consumed 40% and 30% of the plankton extract, respectively, while the consumption of the river extract was low for both bacteria, ∼1%. Shewanella showed the highest bacterial growth efficiency (BGE) (12%) when grown on plankton extract, while when grown on river extract, the BGE was only 1%. Duganella showed low BGE when grown on plankton extract (< 1%) and slightly higher BGE when grown on river extract (2%). The cell growth yield of Duganella was higher than that of Shewanella when grown on river extract. These results indicate that Duganella is more adapted to terrestrial organic substrates with low nutritional availability, while Shewanella is adapted to eutrophied conditions. The different growth performance of the bacteria could be traced to genomic variations. A closely related genome of Shewanella was shown to harbor genes for the sequestration of autochthonously produced carbon substrates, while Duganella contained genes for the degradation of relatively refractive terrestrial organic matter. The results may reflect the influence of environmental drivers on bacterial community composition in natural aquatic environments. Elevated inflows of terrestrial organic matter to coastal areas in subarctic regions would lead to increased occurrence of bacteria adapted to the degradation of complex terrestrial compounds with a low bioavailability.
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Affiliation(s)
- Li Zhao
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Sonia Brugel
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Kesava Priyan Ramasamy
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
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18
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Weiland F, Kohlstedt M, Wittmann C. Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry. Metab Eng 2021; 71:13-41. [PMID: 34864214 DOI: 10.1016/j.ymben.2021.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.
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Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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19
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Tsagogiannis E, Vandera E, Primikyri A, Asimakoula S, Tzakos AG, Gerothanassis IP, Koukkou AI. Characterization of Protocatechuate 4,5-Dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and In Situ Reaction Monitoring in the NMR Tube. Int J Mol Sci 2021; 22:9647. [PMID: 34502555 PMCID: PMC8431788 DOI: 10.3390/ijms22179647] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
The current study aims at the functional and kinetic characterization of protocatechuate (PCA) 4,5-dioxygenase (PcaA) from Pseudarthrobacter phenanthrenivorans Sphe3. This is the first single subunit Type II dioxygenase characterized in Actinobacteria. RT-PCR analysis demonstrated that pcaA and the adjacent putative genes implicated in the PCA meta-cleavage pathway comprise a single transcriptional unit. The recombinant PcaA is highly specific for PCA and exhibits Michaelis-Menten kinetics with Km and Vmax values of 21 ± 1.6 μM and 44.8 ± 4.0 U × mg-1, respectively, in pH 9.5 and at 20 °C. PcaA also converted gallate from a broad range of substrates tested. The enzymatic reaction products were identified and characterized, for the first time, through in situ biotransformation monitoring inside an NMR tube. The PCA reaction product demonstrated a keto-enol tautomerization, whereas the gallate reaction product was present only in the keto form. Moreover, the transcriptional levels of pcaA and pcaR (gene encoding a LysR-type regulator of the pathway) were also determined, showing an induction when cells were grown on PCA and phenanthrene. Studying key enzymes in biodegradation pathways is significant for bioremediation and for efficient biocatalysts development.
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Affiliation(s)
- Epameinondas Tsagogiannis
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
| | - Elpiniki Vandera
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
| | - Alexandra Primikyri
- Laboratory of Organic Chemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (A.G.T.); (I.P.G.)
| | - Stamatia Asimakoula
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
| | - Andreas G. Tzakos
- Laboratory of Organic Chemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (A.G.T.); (I.P.G.)
| | - Ioannis P. Gerothanassis
- Laboratory of Organic Chemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (A.G.T.); (I.P.G.)
| | - Anna-Irini Koukkou
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
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20
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Arentshorst M, Falco MD, Moisan MC, Reid ID, Spaapen TOM, van Dam J, Demirci E, Powlowski J, Punt PJ, Tsang A, Ram AFJ. Identification of a Conserved Transcriptional Activator-Repressor Module Controlling the Expression of Genes Involved in Tannic Acid Degradation and Gallic Acid Utilization in Aspergillus niger. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:681631. [PMID: 37744122 PMCID: PMC10512348 DOI: 10.3389/ffunb.2021.681631] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/23/2021] [Indexed: 09/26/2023]
Abstract
Tannic acid, a hydrolysable gallotannin present in plant tissues, consists of a central glucose molecule esterified with gallic acid molecules. Some microorganisms, including several Aspergillus species, can metabolize tannic acid by releasing gallic acid residues from tannic acid by secreting tannic acid specific esterases into the medium. The expression of these so-called tannases is induced by tannic acid or gallic acid. In this study, we identified a conserved transcriptional activator-repressor module involved in the regulation of predicted tannases and other genes involved in gallic acid metabolism. The transcriptional activator-repressor module regulating tannic acid utilization resembles the transcriptional activator-repressor modules regulating galacturonic acid and quinic acid utilization. Like these modules, the Zn(II)2Cys6 transcriptional activator (TanR) and the putative repressor (TanX) are located adjacent to each other. Deletion of the transcriptional activator (ΔtanR) results in inability to grow on gallic acid and severely reduces growth on tannic acid. Deletion of the putative repressor gene (ΔtanX) results in the constitutive expression of tannases as well as other genes with mostly unknown function. Known microbial catabolic pathways for gallic acid utilization involve so-called ring cleavage enzymes, and two of these ring cleavage enzymes show increased expression in the ΔtanX mutant. However, deletion of these two genes, and even deletion of all 17 genes encoding potential ring cleavage enzymes, did not result in a gallic acid non-utilizing phenotype. Therefore, in A. niger gallic acid utilization involves a hitherto unknown pathway. Transcriptome analysis of the ΔtanX mutant identified several genes and gene clusters that were significantly induced compared to the parental strain. The involvement of a selection of these genes and gene clusters in gallic acid utilization was examined by constructing gene deletion mutants and testing their ability to grow on gallic acid. Only the deletion of a gene encoding an FAD-dependent monooxygenase (NRRL3_04659) resulted in a strain that was unable to grow on gallic acid. Metabolomic studies showed accumulation of gallic acid in the ΔNRRL3_04659 mutant suggesting that this predicted monooxygenase is involved in the first step of gallic acid metabolism and is likely responsible for oxidation of the aromatic ring.
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Affiliation(s)
- Mark Arentshorst
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Marie-Claude Moisan
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Ian D. Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Tessa O. M. Spaapen
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Jisca van Dam
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Ebru Demirci
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Justin Powlowski
- Department of Chemistry & Biochemistry, Concordia University, Montreal, QC, Canada
| | - Peter J. Punt
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Utrecht, Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Arthur F. J. Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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21
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Notonier S, Werner AZ, Kuatsjah E, Dumalo L, Abraham PE, Hatmaker EA, Hoyt CB, Amore A, Ramirez KJ, Woodworth SP, Klingeman DM, Giannone RJ, Guss AM, Hettich RL, Eltis LD, Johnson CW, Beckham GT. Metabolism of syringyl lignin-derived compounds in Pseudomonas putida enables convergent production of 2-pyrone-4,6-dicarboxylic acid. Metab Eng 2021; 65:111-122. [PMID: 33741529 DOI: 10.1016/j.ymben.2021.02.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022]
Abstract
Valorization of lignin, an abundant component of plant cell walls, is critical to enabling the lignocellulosic bioeconomy. Biological funneling using microbial biocatalysts has emerged as an attractive approach to convert complex mixtures of lignin depolymerization products to value-added compounds. Ideally, biocatalysts would convert aromatic compounds derived from the three canonical types of lignin: syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H). Pseudomonas putida KT2440 (hereafter KT2440) has been developed as a biocatalyst owing in part to its native catabolic capabilities but is not known to catabolize S-type lignin-derived compounds. Here, we demonstrate that syringate, a common S-type lignin-derived compound, is utilized by KT2440 only in the presence of another energy source or when vanAB was overexpressed, as syringate was found to be O-demethylated to gallate by VanAB, a two-component monooxygenase, and further catabolized via extradiol cleavage. Unexpectedly, the specificity (kcat/KM) of VanAB for syringate was within 25% that for vanillate and O-demethylation of both substrates was well-coupled to O2 consumption. However, the native KT2440 gallate-cleaving dioxygenase, GalA, was potently inactivated by 3-O-methylgallate. To engineer a biocatalyst to simultaneously convert S-, G-, and H-type monomers, we therefore employed VanAB from Pseudomonas sp. HR199, which has lower activity for 3MGA, and LigAB, an extradiol dioxygenase able to cleave protocatechuate and 3-O-methylgallate. This strain converted 93% of a mixture of lignin monomers to 2-pyrone-4,6-dicarboxylate, a promising bio-based chemical. Overall, this study elucidates a native pathway in KT2440 for catabolizing S-type lignin-derived compounds and demonstrates the potential of this robust chassis for lignin valorization.
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Affiliation(s)
- Sandra Notonier
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Allison Z Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Eugene Kuatsjah
- Department of Microbiology and Immunology, BioProducts Institute, and the Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Linda Dumalo
- Department of Microbiology and Immunology, BioProducts Institute, and the Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Paul E Abraham
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - E Anne Hatmaker
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Caroline B Hoyt
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Antonella Amore
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Kelsey J Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Sean P Woodworth
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Dawn M Klingeman
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Richard J Giannone
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Adam M Guss
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Robert L Hettich
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, BioProducts Institute, and the Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
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22
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Wada A, Prates ÉT, Hirano R, Werner AZ, Kamimura N, Jacobson DA, Beckham GT, Masai E. Characterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromatics. Metab Eng 2021; 64:167-179. [PMID: 33549838 DOI: 10.1016/j.ymben.2021.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/10/2020] [Accepted: 01/30/2021] [Indexed: 11/18/2022]
Abstract
Pseudomonas putida KT2440 (hereafter KT2440) is a well-studied platform bacterium for the production of industrially valuable chemicals from heterogeneous mixtures of aromatic compounds obtained from lignin depolymerization. KT2440 can grow on lignin-related monomers, such as ferulate (FA), 4-coumarate (4CA), vanillate (VA), 4-hydroxybenzoate (4HBA), and protocatechuate (PCA). Genes associated with their catabolism are known, but knowledge about the uptake systems remains limited. In this work, we studied the KT2440 transporters of lignin-related monomers and their substrate selectivity. Based on the inhibition by protonophores, we focused on five genes encoding aromatic acid/H+ symporter family transporters categorized into major facilitator superfamily that uses the proton motive force. The mutants of PP_1376 (pcaK) and PP_3349 (hcnK) exhibited significantly reduced growth on PCA/4HBA and FA/4CA, respectively, while no change was observed on VA for any of the five gene mutants. At pH 9.0, the conversion of these compounds by hcnK mutant (FA/4CA) and vanK mutant (VA) was dramatically reduced, revealing that these transporters are crucial for the uptake of the anionic substrates at high pH. Uptake assays using 14C-labeled substrates in Escherichia coli and biosensor-based assays confirmed that PcaK, HcnK, and VanK have ability to take up PCA, FA/4CA, and VA/PCA, respectively. Additionally, analyses of the predicted protein structures suggest that the size and hydropathic properties of the substrate-binding sites of these transporters determine their substrate preferences. Overall, this study reveals that at physiological pH, PcaK and HcnK have a major role in the uptake of PCA/4HBA and FA/4CA, respectively, and VanK is a VA/PCA transporter. This information can contribute to the engineering of strains for the efficient conversion of lignin-related monomers to value-added chemicals.
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Affiliation(s)
- Ayumu Wada
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Érica T Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ryo Hirano
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Allison Z Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.
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Wang Y, Zhang W, Zhang Z, Wang W, Xu S, He X. Isolation, identification and characterization of phenolic acid-degrading bacteria from soil. J Appl Microbiol 2020; 131:208-220. [PMID: 33270328 DOI: 10.1111/jam.14956] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 11/22/2020] [Accepted: 11/29/2020] [Indexed: 11/29/2022]
Abstract
AIMS To isolate, identify and characterize phenolic acid-degrading bacteria and reduce plant growth inhibition caused by phenolic acids. METHODS AND RESULTS A total of 11 bacterial isolates with high phthalic acid (PA)-degrading ability were obtained using mineral salt medium (MSM) medium containing PA as sole carbon source. These isolates were identified as Arthrobacter globiformis, Pseudomonas putida and Pseudomonas hunanensis by sequence analyses of the 16S rRNA gene. Among them, five Pseudomonas strains could also effectively degrade ferulic acid (FA), p-hydroxybenzoic acid (PHBA) and syringic acid (SA) in MSM solution. P. putida strain 7 and P. hunanensis strain 10 showed highly efficient degradation of PA, SA, FA and PHBA, and could reduce their inhibition of lily, watermelon, poplar and strawberry seedling growth in soils respectively. These two strains could promote plant growth in soil with phenolic acids. CONCLUSIONS In this study, bacterial strains with highly efficient phenolic acid-degrading abilities could not only effectively reduce the autotoxicity of phenolic acids on plants but also were able to promote plant growth in soil with phenolic acids. SIGNIFICANCE AND IMPACT OF THE STUDY In this study, Pseudomonas can promote plant growth while degrading phenolic acids. Our results provide new choices for the biological removal of autotoxins.
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Affiliation(s)
- Y Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China.,College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - W Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China.,College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Z Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - W Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, China
| | - S Xu
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China.,College of Landscape Architecture, Beijing University of Agriculture, Beijing, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, China
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Mpofu E, Chakraborty J, Suzuki-Minakuchi C, Okada K, Kimura T, Nojiri H. Biotransformation of Monocyclic Phenolic Compounds by Bacillus licheniformis TAB7. Microorganisms 2019; 8:microorganisms8010026. [PMID: 31877822 PMCID: PMC7022639 DOI: 10.3390/microorganisms8010026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 01/23/2023] Open
Abstract
Bacillus licheniformis strain TAB7 is a bacterium used as a commercial deodorizing agent for compost in Japan. In this work, its ability to biotransform the following monocyclic phenolic compounds was assessed: ferulate, vanillate, p-coumarate, caffeate, protocatechuate, syringate, vanillin, and cinnamate (a precursor for some phenolic compounds). These compounds are abundant in composting material and are reported to have allelopathic properties. They come from sources such as plant material decomposition or agro-industrial waste. Biotransformation assays were carried out in LB supplemented with 0.2 mg/mL of an individual phenolic compound and incubated for up to 15 days followed by extraction and HPLC analysis. The results showed that TAB7 could biotransform ferulate, caffeate, p-coumarate, vanillate, protocatechuate, and vanillin. It, however, had a poor ability to transform cinnamate and syringate. LC-MS/MS analysis showed that ferulate was transformed into 4-vinylguaiacol as the final product, while caffeate was transformed into 4-ethylcatechol. TAB7 genome analysis suggested that, while TAB7 may not mineralize phenolic compounds, it harbored genes possibly encoding phenolic acid decarboxylase, vanillate decarboxylase, and some protocatechuate degradation pathway enzymes, which are involved in the catabolism of phenolic compounds known to have negative allelopathy on some plants. The results thus suggested that TAB7 can reduce such phenolic compounds in compost.
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Affiliation(s)
- Enock Mpofu
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Joydeep Chakraborty
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazunori Okada
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiaki Kimura
- Agriculture and Biotechnology Business Division, Toyota Motor Corporation, 1099 Marune, Kurozasa-cho, Miyoshi-shi, Aichi 470-0201, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence: ; Tel.: +81-3-5841-3067
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25
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Ravi K, García-Hidalgo J, Brink DP, Skyvell M, Gorwa-Grauslund MF, Lidén G. Physiological characterization and sequence analysis of a syringate-consuming Actinobacterium. BIORESOURCE TECHNOLOGY 2019; 285:121327. [PMID: 30991184 DOI: 10.1016/j.biortech.2019.121327] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/05/2019] [Accepted: 04/06/2019] [Indexed: 06/09/2023]
Abstract
Hardwood lignin is made of up to 75% syringyl-units and the bioconversion of syringate and syringaldehyde is therefore of considerable interest for biological valorization of lignin. In the current study, we have isolated a syringate-consuming bacterium identified as Microbacterium sp. RG1 and characterized its growth on several lignin model compounds. Growth was observed on syringate, 3-O-methylgallate, vanillate, 4-hydroxybenzoate, ferulate and p-coumarate. Toxic aromatic aldehydes such as vanillin and syringaldehyde were converted to their respective alcohols/acids which were eventually consumed with a maximum specific uptake rate of 0.02 and 0.1 mmol (gCDW h)-1 respectively. The isolate was further subjected to whole genome sequencing and putative genes related to the metabolism of syringyl-compounds were mapped for the first time in a Gram-positive bacterium. These findings will be of high significance when designing future host microorganisms and bioprocesses for the efficient valorization of pre-treated lignin feedstocks.
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Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Javier García-Hidalgo
- Division of Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Daniel P Brink
- Division of Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Martin Skyvell
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Division of Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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26
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Igeño MI, Macias D, Blasco R. A Case of Adaptive Laboratory Evolution (ALE): Biodegradation of Furfural by Pseudomonas pseudoalcaligenes CECT 5344. Genes (Basel) 2019; 10:genes10070499. [PMID: 31261932 PMCID: PMC6678421 DOI: 10.3390/genes10070499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a nitrogen source at alkaline pH. Genome sequencing of this strain allowed the detection of genes related to the utilization of furfurals as a carbon and energy source. Furfural and 5-(hydroxymethyl) furfural (HMF) are byproducts of sugars production during the hydrolysis of lignocellulosic biomass. Since they inhibit the yeast fermentation to obtain bioethanol from sugars, the biodegradation of these compounds has attracted certain scientific interest. P. pseudoalcaligenes was able to use furfuryl alcohol, furfural and furoic acid as carbon sources, but after a lag period of several days. Once adapted, the evolved strain (R1D) did not show any more prolonged lag phases. The transcriptomic analysis (RNA-seq) of R1D revealed a non-conservative punctual mutation (L261R) in BN5_2307, a member of the AraC family of activators, modifying the charge of the HTH region of the protein. The inactivation of the mutated gene in the evolved strain by double recombination reverted to the original phenotype. Although the bacterium did not assimilate HMF, it transformed it into value-added building blocks for the chemical industry. These results could be used to improve the production of cost-effective second-generation biofuels from agricultural wastes.
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Affiliation(s)
- M Isabel Igeño
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, 10003 Caceres, Spain
- Meat and Meat Products Research Institute (IProCar), BioMic Research Group, Universidad de Extremadura, 10003 Caceres, Spain
| | - Daniel Macias
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, 10003 Caceres, Spain
| | - Rafael Blasco
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, 10003 Caceres, Spain.
- Meat and Meat Products Research Institute (IProCar), BioMic Research Group, Universidad de Extremadura, 10003 Caceres, Spain.
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27
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Enabling microbial syringol conversion through structure-guided protein engineering. Proc Natl Acad Sci U S A 2019; 116:13970-13976. [PMID: 31235604 PMCID: PMC6628648 DOI: 10.1073/pnas.1820001116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbial conversion of aromatic compounds is an emerging and promising strategy for valorization of the plant biopolymer lignin. A critical and often rate-limiting reaction in aromatic catabolism is O-aryl-demethylation of the abundant aromatic methoxy groups in lignin to form diols, which enables subsequent oxidative aromatic ring-opening. Recently, a cytochrome P450 system, GcoAB, was discovered to demethylate guaiacol (2-methoxyphenol), which can be produced from coniferyl alcohol-derived lignin, to form catechol. However, native GcoAB has minimal ability to demethylate syringol (2,6-dimethoxyphenol), the analogous compound that can be produced from sinapyl alcohol-derived lignin. Despite the abundance of sinapyl alcohol-based lignin in plants, no pathway for syringol catabolism has been reported to date. Here we used structure-guided protein engineering to enable microbial syringol utilization with GcoAB. Specifically, a phenylalanine residue (GcoA-F169) interferes with the binding of syringol in the active site, and on mutation to smaller amino acids, efficient syringol O-demethylation is achieved. Crystallography indicates that syringol adopts a productive binding pose in the variant, which molecular dynamics simulations trace to the elimination of steric clash between the highly flexible side chain of GcoA-F169 and the additional methoxy group of syringol. Finally, we demonstrate in vivo syringol turnover in Pseudomonas putida KT2440 with the GcoA-F169A variant. Taken together, our findings highlight the significant potential and plasticity of cytochrome P450 aromatic O-demethylases in the biological conversion of lignin-derived aromatic compounds.
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28
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Lubbers RJM, Dilokpimol A, Visser J, Mäkelä MR, Hildén KS, de Vries RP. A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi. Biotechnol Adv 2019; 37:107396. [PMID: 31075306 DOI: 10.1016/j.biotechadv.2019.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Abstract
Aromatic compounds derived from lignin are of great interest for renewable biotechnical applications. They can serve in many industries e.g. as biochemical building blocks for bioplastics or biofuels, or as antioxidants, flavor agents or food preservatives. In nature, lignin is degraded by microorganisms, which results in the release of homocyclic aromatic compounds. Homocyclic aromatic compounds can also be linked to polysaccharides, tannins and even found freely in plant biomass. As these compounds are often toxic to microbes already at low concentrations, they need to be degraded or converted to less toxic forms. Prior to ring cleavage, the plant- and lignin-derived aromatic compounds are converted to seven central ring-fission intermediates, i.e. catechol, protocatechuic acid, hydroxyquinol, hydroquinone, gentisic acid, gallic acid and pyrogallol through complex aromatic metabolic pathways and used as energy source in the tricarboxylic acid cycle. Over the decades, bacterial aromatic metabolism has been described in great detail. However, the studies on fungal aromatic pathways are scattered over different pathways and species, complicating a comprehensive view of fungal aromatic metabolism. In this review, we depicted the similarities and differences of the reported aromatic metabolic pathways in fungi and bacteria. Although both microorganisms share the main conversion routes, many alternative pathways are observed in fungi. Understanding the microbial aromatic metabolic pathways could lead to metabolic engineering for strain improvement and promote valorization of lignin and related aromatic compounds.
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Affiliation(s)
- Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Kristiina S Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
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29
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High-Quality Draft Genome Sequence of Pseudomonas reidholzensis Strain CCOS 865 T. Microbiol Resour Announc 2019; 8:MRA01502-18. [PMID: 30687835 PMCID: PMC6346167 DOI: 10.1128/mra.01502-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 11/20/2022] Open
Abstract
We have sequenced and assembled the genome of Pseudomonas reidholzensis CCOS 865T, which was isolated in 2014 from forest soil. Members of the genus Pseudomonas play important roles in environmental systems and are utilized in many biotechnological processes. We have sequenced and assembled the genome of Pseudomonas reidholzensis CCOS 865T, which was isolated in 2014 from forest soil. Members of the genus Pseudomonas play important roles in environmental systems and are utilized in many biotechnological processes. The genome of this species may provide an important resource for the discovery of novel enzyme activities.
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30
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Rapid, Parallel Identification of Catabolism Pathways of Lignin-Derived Aromatic Compounds in Novosphingobium aromaticivorans. Appl Environ Microbiol 2018; 84:AEM.01185-18. [PMID: 30217841 DOI: 10.1128/aem.01185-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/05/2018] [Indexed: 11/20/2022] Open
Abstract
Transposon mutagenesis is a powerful technique in microbial genetics for the identification of genes in uncharacterized pathways. Recently, the throughput of transposon mutagenesis techniques has been dramatically increased through the combination of DNA barcoding and high-throughput sequencing. Here, we show that when applied to catabolic pathways, barcoded transposon libraries can be used to distinguish redundant pathways, decompose complex pathways into substituent modules, discriminate between enzyme homologs, and rapidly identify previously hypothetical enzymes in an unbiased genome-scale search. We used this technique to identify two genes, desC and desD, which are involved in the degradation of the lignin-derived aromatic compound sinapic acid in the nonmodel bacterium Novosphingobium aromaticivorans We show that DesC is a methyl esterase acting on an intermediate formed during sinapic acid catabolism, providing the last enzyme in a proposed catabolic pathway. This approach will be particularly useful in the identification of complete pathways suitable for heterologous expression in metabolic engineering.IMPORTANCE The identification of the genes involved in specific biochemical transformations is a key step in predicting microbial function from nucleic acid sequences and in engineering microbes to endow them with new functions. We have shown that new techniques for transposon mutagenesis can dramatically simplify this process and enable the rapid identification of genes in uncharacterized pathways. These techniques provide the necessary scale to fully elucidate complex biological networks such as those used to degrade mixtures of lignin-derived aromatic compounds.
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31
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Zhang R, Li C, Wang J, Yan Y. Microbial Ligninolysis: Toward a Bottom-Up Approach for Lignin Upgrading. Biochemistry 2018; 58:1501-1510. [DOI: 10.1021/acs.biochem.8b00920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Jian Wang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
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Esteban-Torres M, Santamaría L, Cabrera-Rubio R, Plaza-Vinuesa L, Crispie F, de Las Rivas B, Cotter P, Muñoz R. A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid. Appl Environ Microbiol 2018; 84:e01558-18. [PMID: 30054365 PMCID: PMC6146992 DOI: 10.1128/aem.01558-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022] Open
Abstract
The human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota were Firmicutes (74.6%), Proteobacteria (17.6%), and Actinobacteria (7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera, Anaerostipes and Klebsiella accounted for the majority of reads (40%). The usefulness of the HTS-lpdC method was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCE Despite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives of Bacteroidetes The presence of functional gallate decarboxylases was demonstrated in representative Proteobacteria and Firmicutes strains from the human microbiota, an observation that could be of considerable relevance to the in vivo production of pyrogallol, a physiologically important bioactive compound.
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Affiliation(s)
- María Esteban-Torres
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Laura Santamaría
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
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DdvK, a Novel Major Facilitator Superfamily Transporter Essential for 5,5'-Dehydrodivanillate Uptake by Sphingobium sp. Strain SYK-6. Appl Environ Microbiol 2018; 84:AEM.01314-18. [PMID: 30120118 DOI: 10.1128/aem.01314-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/02/2018] [Indexed: 12/28/2022] Open
Abstract
The microbial conversion of lignin-derived aromatics is a promising strategy for the industrial utilization of this large biomass resource. However, efficient application requires an elucidation of the relevant transport and catabolic pathways. In Sphingobium sp. strain SYK-6, most of the enzyme genes involved in 5,5'-dehydrodivanillate (DDVA) catabolism have been characterized, but the transporter has not yet been identified. Here, we identified SLG_07710 (ddvK) and SLG_07780 (ddvR), genes encoding a putative major facilitator superfamily (MFS) transporter and MarR-type transcriptional regulator, respectively. A ddvK mutant of SYK-6 completely lost the capacity to grow on and convert DDVA. DdvR repressed the expression of the DDVA O-demethylase oxygenase component gene (ligXa), while DDVA acted as the gene inducer. A DDVA uptake assay was developed by employing this DdvR-controlled ligXa transcriptional regulatory system. A Sphingobium japonicum UT26S transformant expressing ddvK acquired DDVA uptake capacity, indicating that ddvK encodes the DDVA transporter. DdvK, probably requiring the proton motive force, was suggested to be a novel MFS transporter on the basis of the amino acid sequence similarity. Subsequently, we evaluated the effects of ddvK overexpression on the production of the DDVA metabolite 2-pyrone-4,6-dicarboxylate (PDC), a building block of functional polymers. A SYK-6 mutant of the PDC hydrolase gene (ligI) cultured in DDVA accumulated PDC via 5-carboxyvanillate and grew by utilizing 4-carboxy-2-hydroxypenta-2,4-dienoate. The introduction of a ddvK-expression plasmid into a ligI mutant increased the growth rate in DDVA and the amounts of DDVA converted and PDC produced after 48 h by 1.35- and 1.34-fold, respectively. These results indicate that enhanced transporter gene expression can improve metabolite production from lignin derivatives.IMPORTANCE The bioengineering of bacteria to selectively transport and metabolize natural substrates into specific metabolites is a valuable strategy for industrial-scale chemical production. The uptake of many substrates into cells requires specific transport systems, and so the identification and characterization of transporter genes are essential for industrial applications. A number of bacterial major facilitator superfamily transporters of aromatic acids have been identified and characterized, but many transporters of lignin-derived aromatic acids remain unidentified. The efficient conversion of lignin, an abundant but unutilized aromatic biomass resource, to value-added metabolites using microbial catabolism requires the characterization of transporters for lignin-derived aromatics. In this study, we identified the transporter gene responsible for the uptake of 5,5'-dehydrodivanillate, a lignin-derived biphenyl compound, in Sphingobium sp. strain SYK-6. In addition to characterizing its function, we applied this transporter gene to the production of a value-added metabolite from 5,5'-dehydrodivanillate.
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Mori K, Kamimura N, Masai E. Identification of the protocatechuate transporter gene in Sphingobium sp. strain SYK-6 and effects of overexpression on production of a value-added metabolite. Appl Microbiol Biotechnol 2018; 102:4807-4816. [DOI: 10.1007/s00253-018-8988-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 11/28/2022]
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35
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Hogancamp TN, Raushel FM. Functional Annotation of LigU as a 1,3-Allylic Isomerase during the Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway from the Soil Bacterium Sphingobium sp. SYK-6. Biochemistry 2018; 57:2837-2845. [DOI: 10.1021/acs.biochem.8b00295] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tessily N. Hogancamp
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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Microbial dynamics and metabolite changes in Chinese Rice Wine fermentation from sorghum with different tannin content. Sci Rep 2018; 8:4639. [PMID: 29545525 PMCID: PMC5854674 DOI: 10.1038/s41598-018-23013-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 03/05/2018] [Indexed: 01/21/2023] Open
Abstract
Chinese rice wine (CRW) is the oldest kind of wine in China and is mainly fermented by wheat Qu and yeast with rice, millet, etc. This gives CRW a unique quality, but the flavor components are complex. Its formation is related to microorganisms, but the link between CRW and microorganisms is poorly understood. Here, we used two kinds of sorghum (JZ22 and JB3, of which JZ22 has a higher tannin content) as the raw materials to brew and determined the structural and functional dynamics of the microbiota by metagenomics and flavor analyses. We detected 106 (JZ22) and 109 (JB3) volatile flavor compounds and 8 organic acids. By correlation analysis, we established 687 (JZ22) and 496 (JB3) correlations between the major flavor compounds and microbes. In JZ22, Blautia, Collinsella, Bifidobacterium, Faecalibacterium and Prevotella had the most correlations with flavor production. In JB3, the top 5 genera were Stenotrophomonas, Bdellovibrio, Solibacillus, Sulfuritalea and Achromobacter. In addition, more esters were detected, and more microorganisms correlated with ester generation in JZ22. This study provides a new idea for the micro ecological diversity of CRW fermented with sorghum. This is of significance for improving the quality and broadening the CRW varieties.
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Kosuru RY, Aashique M, Fathima A, Roy A, Bera S. Revealing the dual role of gallic acid in modulating ampicillin sensitivity of Pseudomonas aeruginosa biofilms. Future Microbiol 2018; 13:297-312. [DOI: 10.2217/fmb-2017-0132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aim: To understand the effects of gallic acid (GA) on ampicillin (Amp) sensitive or resistant strain of Pseudomonas sp. and also in modulating the corresponding biofilms. Methodology: The cell viability was determined by broth dilution, dry weight and CFU assays. Biofilm formation was measured by crystal violet assay while oxygen consumption rate was measured to verify the metabolic status of the cells. The membrane damage and drug efflux/accumulation were studied by fluorimetric assays. Results: GA transformed the Amp resistant cells, both planktonic and biofilms, into highly sensitive one by inducing membrane damage and enhancing accumulation of drug, whereas the Amp sensitive cells gained resistance against Amp. Conclusion: Use of GA as an antimicrobial compound should be analyzed more critically depending on the drug dosages, drug sensitivity as well as types of bacterial strains being studied.
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Affiliation(s)
- Rekha Yamini Kosuru
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
| | - Md Aashique
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
| | - Aisha Fathima
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
| | - Amrita Roy
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
| | - Soumen Bera
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
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Kamimura N, Takahashi K, Mori K, Araki T, Fujita M, Higuchi Y, Masai E. Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:679-705. [PMID: 29052962 DOI: 10.1111/1758-2229.12597] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/26/2017] [Accepted: 10/03/2017] [Indexed: 05/21/2023]
Abstract
Lignin is the most abundant phenolic polymer; thus, its decomposition by microorganisms is fundamental to carbon cycling on earth. Lignin breakdown is initiated by depolymerization catalysed by extracellular oxidoreductases secreted by white-rot basidiomycetous fungi. On the other hand, bacteria play a predominant role in the mineralization of lignin-derived heterogeneous low-molecular-weight aromatic compounds. The outline of bacterial catabolic pathways for lignin-derived bi- and monoaryls are typically composed of the following sequential steps: (i) funnelling of a wide variety of lignin-derived aromatics into vanillate and syringate, (ii) O demethylation of vanillate and syringate to form catecholic derivatives and (iii) aromatic ring-cleavage of the catecholic derivatives to produce tricarboxylic acid cycle intermediates. Knowledge regarding bacterial catabolic systems for lignin-derived aromatic compounds is not only important for understanding the terrestrial carbon cycle but also valuable for promoting the shift to a low-carbon economy via biological lignin valorisation. This review summarizes recent progress in bacterial catabolic systems for lignin-derived aromatic compounds, including newly identified catabolic pathways and genes for decomposition of lignin-derived biaryls, transcriptional regulation and substrate uptake systems. Recent omics approaches on catabolism of lignin-derived aromatic compounds are also described.
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Affiliation(s)
- Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Kenji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Kosuke Mori
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Takuma Araki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Masaya Fujita
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Yudai Higuchi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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Whole community transcriptome of a sequencing batch reactor transforming 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one (NTO). Biodegradation 2017; 29:71-88. [DOI: 10.1007/s10532-017-9814-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/13/2017] [Indexed: 10/18/2022]
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Pawitwar SS, Nadar VS, Kandegedara A, Stemmler TL, Rosen BP, Yoshinaga M. Biochemical Characterization of ArsI: A Novel C-As Lyase for Degradation of Environmental Organoarsenicals. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11115-11125. [PMID: 28936873 PMCID: PMC5870903 DOI: 10.1021/acs.est.7b03180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Organoarsenicals such as the methylarsenical methylarsenate (MAs(V)) and aromatic arsenicals including roxarsone (4-hydroxy-3-nitrobenzenearsenate or Rox(V)) have been extensively used as an herbicide and growth enhancers in animal husbandry, respectively. They undergo environmental degradation to more toxic inorganic arsenite (As(III)) that contaminates crops and drinking water. We previously identified a bacterial gene (arsI) responsible for aerobic demethylation of methylarsenite (MAs(III)). The gene product, ArsI, is an Fe(II)-dependent extradiol dioxygenase that cleaves the carbon-arsenic (C-As) bond in MAs(III) and in trivalent aromatic arsenicals. The objective of this study was to elucidate the ArsI mechanism. Using isothermal titration calorimetry, we determined the dissociation constants and ligand-to-protein stoichiometry of ArsI for Fe(II), MAs(III), and aromatic phenylarsenite. Using a combination of methods including chemical modification, site-directed mutagenesis, and fluorescent spectroscopy, we demonstrated that amino acid residues predicted to participate in Fe(II)-binding (His5-His62-Glu115) and substrate binding (Cys96-Cys97) are involved in catalysis. Finally, the products of Rox(III) degradation were identified as As(III) and 2-nitrohydroquinone, demonstrating that ArsI is a dioxygenase that incorporates one oxygen atom from dioxygen into the carbon and the other to the arsenic to catalyze cleavage of the C-As bond. These results augment our understanding of the mechanism of this novel C-As lyase.
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Affiliation(s)
- Shashank S. Pawitwar
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Venkadesh S. Nadar
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Ashoka Kandegedara
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan 48201, United States
| | - Timothy L. Stemmler
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan 48201, United States
| | - Barry P. Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Masafumi Yoshinaga
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
- Corresponding Author: Phone: 305-348-1489; fax: 305-348-0651; ; http://orcid.org/0000-0002-7243-1761
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de Oliveira EF, Cossu A, Tikekar RV, Nitin N. Enhanced Antimicrobial Activity Based on a Synergistic Combination of Sublethal Levels of Stresses Induced by UV-A Light and Organic Acids. Appl Environ Microbiol 2017; 83:e00383-17. [PMID: 28363964 PMCID: PMC5440697 DOI: 10.1128/aem.00383-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/27/2017] [Indexed: 01/15/2023] Open
Abstract
The reduction of microbial load in food and water systems is critical for their safety and shelf life. Conventionally, physical processes such as heat or light are used for the rapid inactivation of microbes, while natural compounds such as lactic acid may be used as preservatives after the initial physical process. This study demonstrates the enhanced and rapid inactivation of bacteria based on a synergistic combination of sublethal levels of stresses induced by UV-A light and two food-grade organic acids. A reduction of 4.7 ± 0.5 log CFU/ml in Escherichia coli O157:H7 was observed using a synergistic combination of UV-A light, gallic acid (GA), and lactic acid (LA), while the individual treatments and the combination of individual organic acids with UV-A light resulted in a reduction of less than 1 log CFU/ml. Enhanced inactivation of bacteria on the surfaces of lettuce and spinach leaves was also observed based on the synergistic combination. Mechanistic investigations suggested that the treatment with a synergistic combination of GA plus LA plus UV-A (GA+LA+UV-A) resulted in significant increases in membrane permeability and intracellular thiol oxidation and affected the metabolic machinery of E. coli In addition, the antimicrobial activity of the synergistic combination of GA+LA+UV-A was effective only against metabolically active E. coli O157:H7. In summary, this study illustrates the potential of simultaneously using a combination of sublethal concentrations of natural antimicrobials and a low level of physical stress in the form of UV-A light to inactivate bacteria in water and food systems.IMPORTANCE There is a critical unmet need to improve the microbial safety of the food supply, while retaining optimal nutritional and sensory properties of food. Furthermore, there is a need to develop novel technologies that can reduce the impact of food processing operations on energy and water resources. Conventionally, physical processes such as heat and light are used for inactivating microbes in food products, but these processes often significantly reduce the sensory and nutritional properties of food and are highly energy intensive. This study demonstrates that the combination of two natural food-grade antimicrobial agents with a sublethal level of physical stress in the form of UV-A light can greatly increase microbial load inactivation. In addition, this report elucidates the potential mechanisms for this synergistic interaction among physical and chemical stresses. Overall, these results provide a novel approach to develop antimicrobial solutions for food and water systems.
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Affiliation(s)
- Erick F de Oliveira
- Department of Food Science and Technology, University of California, Davis, Davis, California, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil
| | - Andrea Cossu
- Department of Food Science and Technology, University of California, Davis, Davis, California, USA
| | - Rohan V Tikekar
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Nitin Nitin
- Department of Food Science and Technology, University of California, Davis, Davis, California, USA
- Department of Biological and Agricultural Engineering, University of California, Davis, Davis, California, USA
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42
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Reverón I, Jiménez N, Curiel JA, Peñas E, López de Felipe F, de Las Rivas B, Muñoz R. Differential Gene Expression by Lactobacillus plantarum WCFS1 in Response to Phenolic Compounds Reveals New Genes Involved in Tannin Degradation. Appl Environ Microbiol 2017; 83:e03387-16. [PMID: 28115379 PMCID: PMC5359502 DOI: 10.1128/aem.03387-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/13/2017] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus plantarum is a lactic acid bacterium that can degrade food tannins by the successive action of tannase and gallate decarboxylase enzymes. In the L. plantarum genome, the gene encoding the catalytic subunit of gallate decarboxylase (lpdC, or lp_2945) is only 6.5 kb distant from the gene encoding inducible tannase (L. plantarumtanB [tanBLp ], or lp_2956). This genomic context suggests concomitant activity and regulation of both enzymatic activities. Reverse transcription analysis revealed that subunits B (lpdB, or lp_0271) and D (lpdD, or lp_0272) of the gallate decarboxylase are cotranscribed, whereas subunit C (lpdC, or lp_2945) is cotranscribed with a gene encoding a transport protein (gacP, or lp_2943). In contrast, the tannase gene is transcribed as a monocistronic mRNA. Investigation of knockout mutations of genes located in this chromosomal region indicated that only mutants of the gallate decarboxylase (subunits B and C), tannase, GacP transport protein, and TanR transcriptional regulator (lp_2942) genes exhibited altered tannin metabolism. The expression profile of genes involved in tannin metabolism was also analyzed in these mutants in the presence of methyl gallate and gallic acid. It is noteworthy that inactivation of tanR suppresses the induction of all genes overexpressed in the presence of methyl gallate and gallic acid. This transcriptional regulator was also induced in the presence of other phenolic compounds, such as kaempferol and myricetin. This study complements the catalog of L. plantarum expression profiles responsive to phenolic compounds, which enable this bacterium to adapt to a plant food environment.IMPORTANCELactobacillus plantarum is a bacterial species frequently found in the fermentation of vegetables when tannins are present. L. plantarum strains degrade tannins to the less-toxic pyrogallol by the successive action of tannase and gallate decarboxylase enzymes. The genes encoding these enzymes are located close to each other in the chromosome, suggesting concomitant regulation. Proteins involved in tannin metabolism and regulation, such GacP (gallic acid permease) and TanR (tannin transcriptional regulator), were identified by differential gene expression in knockout mutants with mutations in genes from this region. This study provides insights into the highly coordinated mechanisms that enable L. plantarum to adapt to plant food fermentations.
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Affiliation(s)
- Inés Reverón
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN-CSIC, Madrid, Spain
| | - Natalia Jiménez
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN-CSIC, Madrid, Spain
| | - José Antonio Curiel
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN-CSIC, Madrid, Spain
| | - Elena Peñas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN-CSIC, Madrid, Spain
| | - Félix López de Felipe
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN-CSIC, Madrid, Spain
| | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN-CSIC, Madrid, Spain
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN-CSIC, Madrid, Spain
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Techer D, Milla S, Fontaine P, Viot S, Thomas M. Influence of waterborne gallic and pelargonic acid exposures on biochemical and reproductive parameters in the zebrafish (Danio rerio). ENVIRONMENTAL TOXICOLOGY 2017; 32:227-240. [PMID: 26677111 DOI: 10.1002/tox.22228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/26/2015] [Indexed: 06/05/2023]
Abstract
Gallic and pelargonic acids are biologically derived substances receiving a growing interest as eco-friendly biocides with potential applications in freshwater system management. However, some data gaps remain to address their chronic ecotoxicity issue, particularly for fish. This work aimed at investigating the sublethal effects of a long-term waterborne exposure of zebrafish to these compounds. Mature fish were exposed to gallic or pelargonic acid at the concentrations of 0, 0.05, 0.5 and 5 mg/L during one month under semi-static conditions. Fecundity, hatching rate and median hatching time were regularly evaluated. Circulating sex hormone levels (11 ketotestosterone -11 KT, 17 βestradiol -E2-), plasma vitellogenin (Vtg), and gonad histology were monitored in males and females after exposure. Lactate dehydrogenase (LDH), total glutathione peroxydase (GPx) and glutathione-S transferase (GST) activities were assessed as enzymatic biomarkers of exposure in fish liver. Significant increases of GPx activity were reported in females exposed to both type of chemicals regardless the contamination level. Moreover, 5 mg/L gallic acid induced a decrease in 11-KT levels for males. For fish exposed to pelargonic acid, decreases in circulating hormone levels were reported respectively at 0.05 and 5 mg/L for 11-KT in males, and at 0.5 mg/L for E2 in females. However, no histological alteration in gonads neither significant variation in reproductive performances were detected following zebrafish exposure to gallic or pelargonic acid. Additional investigations concerning the mode of application and the environmental fate of these substances may warrant their further use in freshwater systems at concentrations compatible with biocidal/allelochemical effects. © 2015 Wiley Periodicals, Inc. Environ Toxicol 32: 227-240, 2017.
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Affiliation(s)
- Didier Techer
- UR AFPA, USC INRA 340, Campus Victor Grignard, Université De Lorraine, Boulevard Des Aiguillettes, BP 239, 54506, Vandœuvre-lès-Nancy Cedex, France
| | - Sylvain Milla
- UR AFPA, USC INRA 340, Campus Victor Grignard, Université De Lorraine, Boulevard Des Aiguillettes, BP 239, 54506, Vandœuvre-lès-Nancy Cedex, France
| | - Pascal Fontaine
- UR AFPA, USC INRA 340, Campus Victor Grignard, Université De Lorraine, Boulevard Des Aiguillettes, BP 239, 54506, Vandœuvre-lès-Nancy Cedex, France
| | - Sandrine Viot
- UR AFPA, USC INRA 340, Campus Victor Grignard, Université De Lorraine, Boulevard Des Aiguillettes, BP 239, 54506, Vandœuvre-lès-Nancy Cedex, France
| | - Marielle Thomas
- UR AFPA, USC INRA 340, Campus Victor Grignard, Université De Lorraine, Boulevard Des Aiguillettes, BP 239, 54506, Vandœuvre-lès-Nancy Cedex, France
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44
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Antimicrobial effect of synergistic interaction between UV-A light and gallic acid against Escherichia coli O157:H7 in fresh produce wash water and biofilm. INNOV FOOD SCI EMERG 2016. [DOI: 10.1016/j.ifset.2016.07.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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45
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Belda E, van Heck RGA, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins dos Santos VAP, de Lorenzo V, Danchin A, Médigue C. The revisited genome ofPseudomonas putidaKT2440 enlightens its value as a robust metabolicchassis. Environ Microbiol 2016; 18:3403-3424. [DOI: 10.1111/1462-2920.13230] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/16/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Eugeni Belda
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- Institut Pasteur, Unit of Insect Vector Genetics and Genomics, Department of Parasitology and Mycology; 28, rue du Dr. Roux, Paris, Cedex 15 75724 France
| | - Ruben G. A. van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Maria José Lopez-Sanchez
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Stéphane Cruveiller
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Valérie Barbe
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute, National Sequencing Center; 2 rue Gaston Crémieux 91057 Evry France
| | - Claire Fraser
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine; Baltimore MD USA
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
- School of Biology, Newcastle University; Newcastle upon Tyne NE1 7RU UK
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Anne Morgat
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics; Geneva CH-1206 Switzerland
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - David Vallenet
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Zoé Rouy
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University; Dreijenplein 10, Building number 316 6703 HB Wageningen The Netherlands
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin 3 28049 Madrid Spain
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière; Paris France
| | - Claudine Médigue
- Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism; 2 rue Gaston Crémieux 91057 Evry France
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Mazurkewich S, Brott AS, Kimber MS, Seah SYK. Structural and Kinetic Characterization of the 4-Carboxy-2-hydroxymuconate Hydratase from the Gallate and Protocatechuate 4,5-Cleavage Pathways of Pseudomonas putida KT2440. J Biol Chem 2016; 291:7669-86. [PMID: 26867578 PMCID: PMC4817193 DOI: 10.1074/jbc.m115.682054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 02/03/2016] [Indexed: 11/06/2022] Open
Abstract
The bacterial catabolism of lignin and its breakdown products is of interest for applications in industrial processing of ligno-biomass. The gallate degradation pathway ofPseudomonas putidaKT2440 requires a 4-carboxy-2-hydroxymuconate (CHM) hydratase (GalB), which has a 12% sequence identity to a previously identified CHM hydratase (LigJ) fromSphingomonassp. SYK-6. The structure of GalB was determined and found to be a member of the PIG-LN-acetylglucosamine deacetylase family; GalB is structurally distinct from the amidohydrolase fold of LigJ. LigJ has the same stereospecificity as GalB, providing an example of convergent evolution for catalytic conversion of a common metabolite in bacterial aromatic degradation pathways. Purified GalB contains a bound Zn(2+)cofactor; however the enzyme is capable of using Fe(2+)and Co(2+)with similar efficiency. The general base aspartate in the PIG-L deacetylases is an alanine in GalB; replacement of the alanine with aspartate decreased the GalB catalytic efficiency for CHM by 9.5 × 10(4)-fold, and the variant enzyme did not have any detectable hydrolase activity. Kinetic analyses and pH dependence studies of the wild type and variant enzymes suggested roles for Glu-48 and His-164 in the catalytic mechanism. A comparison with the PIG-L deacetylases led to a proposed mechanism for GalB wherein Glu-48 positions and activates the metal-ligated water for the hydration reaction and His-164 acts as a catalytic acid.
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Affiliation(s)
- Scott Mazurkewich
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ashley S Brott
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Matthew S Kimber
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Stephen Y K Seah
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Sudarsan S, Blank LM, Dietrich A, Vielhauer O, Takors R, Schmid A, Reuss M. Dynamics of benzoate metabolism in Pseudomonas putida KT2440. Metab Eng Commun 2016; 3:97-110. [PMID: 29468117 PMCID: PMC5779716 DOI: 10.1016/j.meteno.2016.03.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/29/2016] [Accepted: 03/14/2016] [Indexed: 12/26/2022] Open
Abstract
Soil microorganisms mineralize lignin-derived aromatic carbon sources using oxidative catabolic pathways, such as the β-ketoadipate pathway. Although this aromatic pathway is one of the best-studied pathways in biochemistry, the complete pathway, including its regulation by aromatic carbon sources, has not been integrated into the metabolic network. In particular, information about the in vivo operation (e.g., kinetics and flux capacity) of the pathway is lacking. In this contribution, we use kinetic modeling and thermodynamic analysis to evaluate the in vivo operation of this key aromatic multi-step pathway. The resulting ab initio deterministic model of benzoate degradation via the β-ketoadipate (ortho-cleavage) pathway in Pseudomonas putida KT2440 is presented. The kinetic model includes mechanistic rate expressions for the enzymes and transport processes. The design and experimental validation of the model are driven by data generated from short-term perturbation experiments in a benzoate-limited continuous culture. The results of rigorous modeling of the in vivo dynamics provide strong support for flux regulation by the benzoate transporter and the enzymes forming and cleaving catechol. Revisiting the β-ketoadipate pathway might be valuable for applications in different fields, such as biochemistry and metabolic engineering, that use lignin monomers as a carbon source. We describe a kinetic model for the β-ketoadipate pathway. Short term metabolic responses were tracked on metabolite level by rapid sampling. The model captures steady state and dynamic conditions of the β-ketoadipate pathway. Thermodynamic analysis revealed regulation points of the pathway. The results are discussed in the context of metabolic network operation.
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Affiliation(s)
- Suresh Sudarsan
- Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology Department, RWTH Aachen University, 52074 Aachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology Department, RWTH Aachen University, 52074 Aachen, Germany
| | - Alexander Dietrich
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Oliver Vielhauer
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Andreas Schmid
- Department Solar Materials, Helmholtz Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany
| | - Matthias Reuss
- Stuttgart Research Center Systems Biology, University of Stuttgart, Nobelstrasse 15, 70569 Stuttgart, Germany
- Corresponding author.
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48
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Geiser E, Przybilla SK, Friedrich A, Buckel W, Wierckx N, Blank LM, Bölker M. Ustilago maydis produces itaconic acid via the unusual intermediate trans-aconitate. Microb Biotechnol 2015; 9:116-26. [PMID: 26639528 PMCID: PMC4720413 DOI: 10.1111/1751-7915.12329] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/18/2015] [Accepted: 09/24/2015] [Indexed: 11/28/2022] Open
Abstract
Itaconic acid is an important biomass‐derived chemical building block but has also recently been identified as a metabolite produced in mammals, which has antimicrobial activity. The biosynthetic pathway of itaconic acid has been elucidated in the ascomycetous fungus Aspergillus terreus and in human macrophages. In both organisms itaconic acid is generated by decarboxylation of the tricarboxylic acid (TCA) cycle intermediate cis‐aconitate. Here, we show that the basidiomycetous fungus Ustilago maydis uses an alternative pathway and produces itaconic acid via trans‐aconitate, the thermodynamically favoured isomer of cis‐aconitate. We have identified a gene cluster that contains all genes involved in itaconic acid formation. Trans‐aconitate is generated from cis‐aconitate by a cytosolic aconitate‐Δ‐isomerase (Adi1) that belongs to the PrpF family of proteins involved in bacterial propionate degradation. Decarboxylation of trans‐aconitate is catalyzed by a novel enzyme, trans‐aconitate decarboxylase (Tad1). Tad1 displays significant sequence similarity with bacterial 3‐carboxy‐cis,cis‐muconate lactonizing enzymes (CMLE). This suggests that U. maydis has evolved an alternative biosynthetic pathway for itaconate production using the toxic intermediate trans‐aconitate. Overexpression of a pathway‐specific transcription factor (Ria1) or a mitochondrial tricarboxylic acid transporter (Mtt1) resulted in a twofold increase in itaconate yield. Therefore, our findings offer new strategies for biotechnological production of this valuable biomass‐derived chemical.
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Affiliation(s)
- Elena Geiser
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Sandra K Przybilla
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, D-35032, Marburg, Germany
| | - Alexandra Friedrich
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, D-35032, Marburg, Germany
| | - Wolfgang Buckel
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, D-35032, Marburg, Germany
| | - Nick Wierckx
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Lars M Blank
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Michael Bölker
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, D-35032, Marburg, Germany.,LOEWE Center for Synthetic Microbiology (SYNMIKRO), Hans-Meerwein-Straße, D-35032, Marburg, Germany
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49
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Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TYS, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol 2015; 6:1118. [PMID: 26528266 PMCID: PMC4604316 DOI: 10.3389/fmicb.2015.01118] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/28/2015] [Indexed: 12/13/2022] Open
Abstract
The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.
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Affiliation(s)
- Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Alisha G Campbell
- Department of Natural Sciences, Northwest Missouri State University Maryville, MO, USA
| | - Sagar M Utturkar
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Se-Ran Jun
- Joint Institute for Computational Sciences, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Rebecca E Parales
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Watumesa A Tan
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife and Conservation Biology, Colorado State University Fort Collins, CO, USA
| | - Tse-Yuan S Lu
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - David W Ussery
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Department of Microbiology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
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50
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Luu RA, Kootstra JD, Nesteryuk V, Brunton CN, Parales JV, Ditty JL, Parales RE. Integration of chemotaxis, transport and catabolism inPseudomonas putidaand identification of the aromatic acid chemoreceptor PcaY. Mol Microbiol 2015; 96:134-47. [DOI: 10.1111/mmi.12929] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Rita A. Luu
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Joshua D. Kootstra
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Vasyl Nesteryuk
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Ceanne N. Brunton
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Juanito V. Parales
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
| | - Jayna L. Ditty
- Department of Biology; University of St. Thomas; St. Paul MN USA
| | - Rebecca E. Parales
- Department of Microbiology and Molecular Genetics; College of Biological Sciences; University of California; Davis CA USA
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