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Civzele A, Stipniece-Jekimova AA, Mezule L. Fungal Ligninolytic Enzymes and Their Application in Biomass Lignin Pretreatment. J Fungi (Basel) 2023; 9:780. [PMID: 37504768 PMCID: PMC10381709 DOI: 10.3390/jof9070780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023] Open
Abstract
Lignocellulosic biomass is a significant source of sustainable fuel and high-value chemical production. However, due to the complex cross-linked three-dimensional network structure, lignin is highly rigid to degradation. In natural environments, the degradation is performed by wood-rotting fungi. The process is slow, and thus, the use of lignin degradation by fungi has not been regarded as a feasible technology in the industrial lignocellulose treatment. Fungi produce a wide variety of ligninolytic enzymes that can be directly introduced in industrial processing of lignocellulose. Within this study, screening of ligninolytic enzyme production using decolorization of ABTS and Azure B dyes was performed for 10 fungal strains with potentially high enzyme production abilities. In addition to standard screening methods, media containing lignin and hay biomass as carbon sources were used to determine the change in enzyme production depending on the substrate. All selected fungi demonstrated the ability to adapt to a carbon source limitation; however, four strains indicated the ability to secrete ligninolytic enzymes in all experimental conditions-Irpex lacteus, Pleurotus dryinus, Bjerkandera adusta, and Trametes versicolor-respectively displayed a 100%, 82.7%, 82.7%, and 55% oxidation of ABTS on lignin-containing media and 100%, 87.9%, 78%, and 70% oxidation of ABTS on hay-containing media after 168 h of incubation. As a result, the most potent strains of fungi were selected to produce lignocellulose-degrading enzymes and to demonstrate their potential application in biological lignocellulose pretreatment.
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Affiliation(s)
- Anna Civzele
- Water Research and Environmental Biotechnology Laboratory, Water Systems and Biotechnology Institute, Faculty of Civil Engineering, Riga Technical University, LV-1048 Riga, Latvia
| | - Alise Anna Stipniece-Jekimova
- Water Research and Environmental Biotechnology Laboratory, Water Systems and Biotechnology Institute, Faculty of Civil Engineering, Riga Technical University, LV-1048 Riga, Latvia
| | - Linda Mezule
- Water Research and Environmental Biotechnology Laboratory, Water Systems and Biotechnology Institute, Faculty of Civil Engineering, Riga Technical University, LV-1048 Riga, Latvia
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An X, Zhong B, Chen G, An W, Xia X, Li H, Lai F, Zhang Q. Evaluation of bioremediation and detoxification potentiality for papermaking black liquor by a new isolated thermophilic and alkali-tolerant Serratia sp. AXJ-M. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124285. [PMID: 33189463 DOI: 10.1016/j.jhazmat.2020.124285] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
There is a great need for efficiently treating papermaking black liquor because it can seriously pollute both soil and water ecosystems. In this study, the Plackett-Burman (PB) experimental design combined with response surface methodology (RSM) was used for improving the biodegradation efficiency of lignin by a new isolated thermophilic and alkali-tolerant strain Serratia sp. AXJ-M, and the results showed that a biodegradation efficiency of 70.5% was achieved under optimal culture conditions. The bacterium with ligninolytic activities significantly decreased target the parameters (color 80%, lignin 60%, phenol 95%, BOD 80% and COD 80%). The control and treated samples were analyzed by gas chromatography-mass spectrometer (GC-MS), which showed that the concentrations of a majority of low-molecular-weight compounds were decreased after biological treatment. Furthermore, toxicological, genotoxicity and phytotoxicity studies have supported the detoxification by the bacterium of black liquor. Finally, the genome sequence of the thermophilic, alkali-tolerant and lignin-degrading bacterium AXJ-M was completed, and the genetic basis of the thermophilic and alkali-resistant properties of AXJ-M was preliminarily revealed. The dyp-type peroxidase was first reported to have the potential to catalyze lignin degradation structurally. These findings suggest that Serratia sp. AXJ-M may be potentially useful for bioremediation applications for papermaking black liquor.
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Affiliation(s)
- Xuejiao An
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Bin Zhong
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Guotao Chen
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Weijuan An
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Xiang Xia
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Hanguang Li
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Fenju Lai
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Qinghua Zhang
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China; Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang 330045, PR China.
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Zhang K, Gu L, Zhang Y, Liu Z, Li X. Dinactin from a new producer, Streptomyces badius gz-8, and its antifungal activity against the rubber anthracnose fungus Colletotrichum gloeosporioides. Microbiol Res 2020; 240:126548. [PMID: 32653809 DOI: 10.1016/j.micres.2020.126548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 10/23/2022]
Abstract
Colletotrichum gloeosporioides is a main cause of rubber anthracnose, which results in very large losses for the natural rubber industry. In this study, an actinomycete strain gz-8 was isolated and had strong antagonistic activity against C. gloeosporioides, with an inhibition rate of 72.5 %. Strain gz-8 was identified as Streptomyces badius. Three active compounds were separated from S. badius gz-8 and identified as feigrisolide B, feigrisolide C and dinactin according to the mass spectrometry and NMR-spectra results. In the three compounds, dinactin exhibited the best antifungal activity against C. gloeosporioides, with an EC50 value of 2.55 μg/mL, and its minimum inhibitory concentration was 44 μg/mL. Dinactin had broad inhibitory activities against nine other pathogenic fungi, and it also had an obvious control effect on rubber anthracnose comparable to that of chlorothalonil. Dinactin could inhibit the conidiogenesis and spore germination of C. gloeosporioides. This report will contribute to understanding the antifungal activity of dinactin against C. gloeosporioides.
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Affiliation(s)
- Kai Zhang
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Liushuang Gu
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Yuefeng Zhang
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Zhiqiang Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China.
| | - Xiaoyu Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China.
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Brink DP, Ravi K, Lidén G, Gorwa-Grauslund MF. Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. Appl Microbiol Biotechnol 2019; 103:3979-4002. [PMID: 30963208 PMCID: PMC6486533 DOI: 10.1007/s00253-019-09692-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 12/18/2022]
Abstract
Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.
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Affiliation(s)
- Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
| | - Krithika Ravi
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
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Asina F, Brzonova I, Voeller K, Kozliak E, Kubátová A, Yao B, Ji Y. Biodegradation of lignin by fungi, bacteria and laccases. BIORESOURCE TECHNOLOGY 2016; 220:414-424. [PMID: 27598570 DOI: 10.1016/j.biortech.2016.08.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 05/24/2023]
Abstract
Indulin AT biodegradation by basidiomycetous fungi, actinobacteria and commercial laccases was evaluated using a suite of chemical analysis methods. The extent of microbial degradation was confirmed by novel thermal carbon analysis (TCA), as the treatments altered the carbon desorption and pyrolysis temperature profiles in supernatants. Laccase treatments caused only minor changes, though with increases occurring in the 850°C and char precursor fractions. After fungal treatments, lignin showed a similar change in the TCA profile, along with a gradual decrease of the total carbon, signifying lignin mineralization (combined with polymerization). By contrast, bacteria produced phenolic monomers without their further catabolism. After 54days of cultivation, a 20wt% weight loss was observed only for fungi, Coriolus versicolor, corroborating the near-80% carbon mass balance closure obtained by TCA. Compositional changes in lignin as a result of biodegradation were confirmed by thermal desorption (TD)-pyrolysis-GC-MS validating the carbon fractionation obtained by TCA.
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Affiliation(s)
- Fnu Asina
- Department of Chemical Engineering, University of North Dakota, Grand Forks, ND, USA
| | - Ivana Brzonova
- Department of Chemical Engineering, University of North Dakota, Grand Forks, ND, USA
| | - Keith Voeller
- Department of Chemistry, University of North Dakota, Grand Forks, ND, USA
| | - Evguenii Kozliak
- Department of Chemistry, University of North Dakota, Grand Forks, ND, USA
| | - Alena Kubátová
- Department of Chemistry, University of North Dakota, Grand Forks, ND, USA
| | - Bin Yao
- Department of Chemistry and Applied Biological Sciences, South Dakota School of Mine and Technology, Rapid City, SD, USA
| | - Yun Ji
- Department of Chemical Engineering, University of North Dakota, Grand Forks, ND, USA.
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Shi Y, Chai L, Tang C, Yang Z, Zheng Y, Chen Y, Jing Q. Biochemical investigation of kraft lignin degradation by Pandoraea sp. B-6 isolated from bamboo slips. Bioprocess Biosyst Eng 2013; 36:1957-65. [PMID: 23877715 PMCID: PMC3825317 DOI: 10.1007/s00449-013-0972-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/09/2013] [Indexed: 11/30/2022]
Abstract
Kraft lignin (KL) is the major pollutant in black liquor. The bacterial strain Pandoraea sp. B-6 was able to degrade KL without any co-substrate under high alkaline conditions. At least 38.2 % of chemical oxygen demand and 41.6 % of color were removed in 7 days at concentrations from 1 to 6 g L(-1). The optimum pH for KL degradation was 10 and the optimum temperature was 30 °C. The greatest activities of 2,249.2 U L(-1) for manganese peroxidase and 1,120.6 U L(-1) for laccase were detected on the third and fifth day at pH 10, respectively. Many small molecules, such as cinnamic acid, ferulic acid, 2-hydroxy benzyl alcohol, and vanillyl methyl ketone, were formed during the period of KL degradation based on GC-MS analysis. These results indicate that this strain has great potential for biotreatment of black liquor.
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Affiliation(s)
- Yan Shi
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
| | - Liyuan Chai
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
- Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Changsha, 410017 People’s Republic of China
| | - Chongjian Tang
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
- Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Changsha, 410017 People’s Republic of China
| | - Zhihui Yang
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
- Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Changsha, 410017 People’s Republic of China
| | - Yu Zheng
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
| | - Yuehui Chen
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
| | - Qingxiu Jing
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017 Hunan People’s Republic of China
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Musengi A, Khan N, Le Roes-Hill M, Pletschke B, Burton S. Increasing the scale of peroxidase production by Streptomyces
sp. strain BSII#1. J Appl Microbiol 2013; 116:554-62. [PMID: 24176016 DOI: 10.1111/jam.12380] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/15/2013] [Accepted: 10/27/2013] [Indexed: 11/29/2022]
Affiliation(s)
- A. Musengi
- Biocatalysis and Technical Biology Research Group; Cape Peninsula University of Technology; Bellville South Africa
| | - N. Khan
- Biocatalysis and Technical Biology Research Group; Cape Peninsula University of Technology; Bellville South Africa
| | - M. Le Roes-Hill
- Biocatalysis and Technical Biology Research Group; Cape Peninsula University of Technology; Bellville South Africa
| | - B.I. Pletschke
- Department of Biochemistry; Microbiology and Biotechnology; Faculty of Science; Rhodes University; Grahamstown South Africa
| | - S.G. Burton
- University of Pretoria; Hatfield Pretoria South Africa
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Shi Y, Chai L, Tang C, Yang Z, Zhang H, Chen R, Chen Y, Zheng Y. Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:1. [PMID: 24225035 PMCID: PMC3560178 DOI: 10.1186/1754-6834-6-1] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 12/21/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND Lignin materials are abundant and among the most important potential sources for biofuel production. Development of an efficient lignin degradation process has considerable potential for the production of a variety of chemicals, including bioethanol. However, lignin degradation using current methods is inefficient. Given their immense environmental adaptability and biochemical versatility, bacterial could be used as a valuable tool for the rapid degradation of lignin. Kraft lignin (KL) is a polymer by-product of the pulp and paper industry resulting from alkaline sulfide treatment of lignocellulose, and it has been widely used for lignin-related studies. RESULTS Beta-proteobacterium Cupriavidus basilensis B-8 isolated from erosive bamboo slips displayed substantial KL degradation capability. With initial concentrations of 0.5-6 g L-1, at least 31.3% KL could be degraded in 7 days. The maximum degradation rate was 44.4% at the initial concentration of 2 g L-1. The optimum pH and temperature for KL degradation were 7.0 and 30°C, respectively. Manganese peroxidase (MnP) and laccase (Lac) demonstrated their greatest level of activity, 1685.3 U L-1 and 815.6 U L-1, at the third and fourth days, respectively. Many small molecule intermediates were formed during the process of KL degradation, as determined using GC-MS analysis. In order to perform metabolic reconstruction of lignin degradation in this bacterium, a draft genome sequence for C. basilensis B-8 was generated. Genomic analysis focused on the catabolic potential of this bacterium against several lignin-derived compounds. These analyses together with sequence comparisons predicted the existence of three major metabolic pathways: β-ketoadipate, phenol degradation, and gentisate pathways. CONCLUSION These results confirmed the capability of C. basilensis B-8 to promote KL degradation. Whole genomic sequencing and systematic analysis of the C. basilensis B-8 genome identified degradation steps and intermediates from this bacterial-mediated KL degradation method. Our findings provide a theoretical basis for research into the mechanisms of lignin degradation as well as a practical basis for biofuel production using lignin materials.
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Affiliation(s)
- Yan Shi
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017, PR China
| | - Liyuan Chai
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017, PR China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410017, PR China
| | - Chongjian Tang
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017, PR China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410017, PR China
| | - Zhihui Yang
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017, PR China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410017, PR China
| | - Huan Zhang
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017, PR China
| | - Runhua Chen
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017, PR China
| | - Yuehui Chen
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017, PR China
| | - Yu Zheng
- School of Metallurgical Science and Engineering, Central South University, Changsha, 410017, PR China
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Santhanam N, Badri DV, Decker SR, Manter DK, Reardon KF, Vivanco JM. Lignocellulose Decomposition by Microbial Secretions. SIGNALING AND COMMUNICATION IN PLANTS 2012. [DOI: 10.1007/978-3-642-23047-9_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Microbial responses to a changing environment: implications for the future functioning of terrestrial ecosystems. FUNGAL ECOL 2011. [DOI: 10.1016/j.funeco.2011.04.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Actinobacteria isolated from termite guts as a source of novel oxidative enzymes. Antonie van Leeuwenhoek 2011; 100:589-605. [PMID: 21720857 DOI: 10.1007/s10482-011-9614-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 06/20/2011] [Indexed: 01/05/2023]
Abstract
A multi-faceted screening programme was designed to search for the oxidases, laccase, peroxidase and tyrosinase. Actinobacteria were selectively isolated from the paunch and colon region of the hindguts of the higher termite, Amitermes hastatus. The isolates were subjected to solid media assays (dye decolourization, melanin production and the utilization of indulin AT as sole carbon source) and liquid media assays. Eleven of the 39 strains had the ability to decolourize the dye RBBR, an indicator for the production of peroxidases in actinobacteria. Melanin production on ISP6 and ISP7 agar plates served as a good indicator for laccase and/or tyrosinase production and the ability of the strains to grow in the presence of indulin AT as a sole carbon source served as a good indicator of lignin peroxidase and/or general peroxidase production. Enzyme-producing strains were cultivated in liquid media and extracellular enzyme activities measured. Strains with the ability to produce oxidative enzymes under the conditions tested were identified to genus level by 16S rRNA gene analysis and compared to known oxidase producers. A strong relationship was observed between the environment sampled (termite guts where lignocellulose degradation occurs) and the dominant type of oxidative enzyme activity detected (laccases and peroxidases), which suggests the possibility of future targeted screening protocols linking the physical properties of the target enzymes with specific operational conditions required, such as lignocellulosic degradation in the preparation of biofuel feedstocks.
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Brown ME, Walker MC, Nakashige TG, Iavarone AT, Chang MCY. Discovery and characterization of heme enzymes from unsequenced bacteria: application to microbial lignin degradation. J Am Chem Soc 2011; 133:18006-9. [PMID: 21671563 DOI: 10.1021/ja203972q] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacteria and other living organisms offer a potentially unlimited resource for the discovery of new chemical catalysts, but many interesting reaction phenotypes observed at the whole organism level remain difficult to elucidate down to the molecular level. A key challenge in the discovery process is the identification of discrete molecular players involved in complex biological transformations because multiple cryptic genetic components often work in concert to elicit an overall chemical phenotype. We now report a rapid pipeline for the discovery of new enzymes of interest from unsequenced bacterial hosts based on laboratory-scale methods for the de novo assembly of bacterial genome sequences using short reads. We have applied this approach to the biomass-degrading soil bacterium Amycolatopsis sp. 75iv2 ATCC 39116 (formerly Streptomyces setonii and S. griseus 75vi2) to discover and biochemically characterize two new heme proteins comprising the most abundant members of the extracellular oxidative system under lignin-reactive growth conditions.
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Affiliation(s)
- Margaret E Brown
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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Zak DR, Holmes WE, Burton AJ, Pregitzer KS, Talhelm AF. Simulated atmospheric NO3- deposition increases soil organic matter by slowing decomposition. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2008; 18:2016-2027. [PMID: 19263894 DOI: 10.1890/07-1743.1] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Presently, there is uncertainty regarding the degree to which anthropogenic N deposition will foster C storage in the N-limited forests of the Northern Hemisphere, ecosystems which are globally important sinks for anthropogenic CO2. We constructed organic matter and N budgets for replicate northern hardwood stands (n = 4) that have received ambient (0.7-1.2 g N x m(-2) x yr(-1) and experimental NO3- deposition (ambient plus 3 g NO3(-)-N x m(-2) x yr(-1)) for a decade; we also traced the flow of a 15NO3- pulse over a six-year period. Experimental NO3- deposition had no effect on organic matter or N stored in the standing forest overstory, but it did significantly increase the N concentration (+19%) and N content (+24%) of canopy leaves. In contrast, a decade of experimental NO3- deposition significantly increased amounts of organic matter (+12%) and N (+9%) in forest floor and mineral soil, despite no increase in detritus production. A greater forest floor (Oe/a) mass under experimental NO3- deposition resulted from slower decomposition, which is consistent with previously reported declines in lignolytic activity by microbial communities exposed to experimental NO3- deposition. Tracing 15NO3- revealed that N accumulated in soil organic matter by first flowing through soil microorganisms and plants, and that the shedding of 15N-labeled leaf litter enriched soil organic matter over a six-year duration. Our results demonstrate that atmospheric NO3- deposition exerts a direct and negative effect on microbial activity in this forest ecosystem, slowing the decomposition of aboveground litter and leading to the accumulation of forest floor and soil organic matter. To the best of our knowledge, this mechanism is not represented in the majority of simulation models predicting the influence of anthropogenic N deposition on ecosystem C storage in northern forests.
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Affiliation(s)
- Donald R Zak
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, Michigan 48109, USA.
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15
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Hernandez-pérez G, Goma G, Rols JL. Biodegradability of lignosulphonate byStreptomyces viridosporusstrain T7A and a mixed natural microbial population antagonistic effects. ACTA ACUST UNITED AC 2004. [DOI: 10.1002/abio.370180115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Thomas L, Crawford DL. Cloning of clustered Streptomyces viridosporus T7A lignocellulose catabolism genes encoding peroxidase and endoglucanase and their extracellular expression in Pichia pastoris. Can J Microbiol 1998; 44:364-72. [PMID: 9674109 DOI: 10.1139/w98-010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A 4.1-kb fragment of chromosomal DNA from the lignocellulose-decomposing actinomycete Streptomyces viridosporus T7A was previously found to encode a lignin peroxidase gene. However, when cloned into Escherichia coli in pBSKS+, peroxidase activity was not expressed. When cloned in pIJ702 in Streptomyces lividans, the gene was expressed in a peroxidase positive background, owing to the production by S. lividans of its own extracellular peroxidase. To circumvent these problems, the DNA was cloned into the commercial expression vector pIC9 for extracellular expression in the yeast Pichia pastoris. Yeast transformants, however, expressed two activities, extracellular peroxidase and an extracellular endoglucanase. The enzymes were not expressed by the yeast cells alone or by yeast cells with pIC9 without the insert. Expression of the enzymes by only those transformants expressing the 4.1-kb DNA was confirmed by Western blot analyses, by nondenaturing activity gel staining, and by spectrophotometric enzyme assays of extracellular culture filtrates. Activity gel staining showed that the two activities resided in different proteins and the peroxidase expressed was similar to ALip-P3, one of the isoenzymes of lignin peroxidase of the S. viridosporus T7A wildtype. Other evidence indicated that in the transformants, the peroxidase and endoglucanase genes in the 4.1-kb insert were controlled by the methanol-inducible AOX1 yeast promoter in pIC9, since their expression was induced by methanol. In the best transformants, extracellular production of peroxidase by recombinant P. pastoris cultures was significantly higher than typically observed in S. viridosporus. The results also indicate that lignocellulose catabolism genes may be clustered on the S. viridosporus chromosome.
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Affiliation(s)
- L Thomas
- Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow 83844-3052, USA
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Ball AS, Colton J. Decolorisation of the polymeric dye Poly R byStreptomyces viridosporus T7A. J Basic Microbiol 1996. [DOI: 10.1002/jobm.3620360104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Magnuson TS, Crawford DL. Comparison of extracellular peroxidase- and esterase-deficient mutants of Streptomyces viridosporus T7A. Appl Environ Microbiol 1992; 58:1070-2. [PMID: 1315498 PMCID: PMC195385 DOI: 10.1128/aem.58.3.1070-1072.1992] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Peroxidase-deficient mutants of the lignin-degrading bacterium Streptomyces viridosporus T7A were screened for their production of acid-precipitable polymeric lignin, extracellular peroxidases and esterases, and immunoreactivities against a polyclonal antibody produced against electrophoretically purified peroxidase isoform P3 of wild-type S. viridosporus. The mutants showed diminished abilities to solubilize lignin and produce acid-precipitable polymeric lignin. Their peroxidase activities were decreased, and their esterase production patterns were altered. Western immunoblots demonstrated that the mutants produced proteins immunologically reactive with the antibody, but with different mobilities from those of wild-type proteins. These findings confirm a direct role for peroxidases in lignin solubilization. They also indicate a possible role for esterases.
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Affiliation(s)
- T S Magnuson
- Department of Bacteriology and Biochemistry, University of Idaho, Moscow
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Ball A. Degradation byStreptomyces viridosporusT7A of plant material grown under elevated CO2conditions. FEMS Microbiol Lett 1991. [DOI: 10.1111/j.1574-6968.1991.tb04586.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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The effects of various nutrients on extracellular peroxidases and acid-precipitable polymeric lignin production byStreptomyces chromofuscus A2 andS. viridosporus T7A. Appl Microbiol Biotechnol 1991. [DOI: 10.1007/bf00167919] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Ball AS, Godden B, Helvenstein P, Penninckx MJ, McCarthy AJ. Lignocarbohydrate Solubilization from Straw by Actinomycetes. Appl Environ Microbiol 1990; 56:3017-22. [PMID: 16348309 PMCID: PMC184892 DOI: 10.1128/aem.56.10.3017-3022.1990] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Actinomycetes grown on wheat straw solubilized a lignocarbohydrate fraction which could be recovered by acid precipitation. Further characterization of this product (APPL) during growth of
Streptomyces
sp. strain EC1 revealed an increase in carboxylic acid and phenolic hydroxyl content, suggesting progressive modification. This was also observed in dioxane-extracted lignin fractions of degraded straw, and some similarity was further suggested by comparative infrared spectroscopy. However, the molecular weight profile of APPL was relatively constant during growth of
Streptomyces
sp. strain EC1 on straw, while analysis of the dioxane-extracted lignin fractions appeared to show fragmentation followed by repolymerization. Lignocarbohydrate solubilization could be monitored in all cultures by routine assay of APPL-associated protein, which accounted for up to 20% of the extracellular culture protein in some cases. Interestingly, this protein fraction was found to include active hydrolytic and oxidative enzymes involved in the degradation of lignocellulose, and specific enzyme activities were often increased in the acid-insoluble fractions of culture supernatants. This was particularly important for peroxidase and veratryl oxidase activities, which could be readily detected in the acid-precipitable lignocarbohydrate complex but were virtually undetectable in untreated culture supernatants.
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Affiliation(s)
- A S Ball
- Department of Genetics & Microbiology, University of Liverpool, Liverpool L69 3BX, United Kingdom, and Unité de Physiologie et Ecologie Microbienne, Faculté des Sciences, Université Libre de Bruxelles, CERIA 1, B-1070 Brussels, Belgium
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Wang ZM, Bleakley BH, Crawford DL, Hertel G, Rafii F. Cloning and expression of a lignin peroxidase gene from Streptomyces viridosporus in Streptomyces lividans. J Biotechnol 1990; 13:131-44. [PMID: 1366423 DOI: 10.1016/0168-1656(90)90099-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A lignin peroxidase gene was cloned from Streptomyces viridosporus T7A into Streptomyces lividans TK64 in plasmid pIJ702. BglII-digested genomic DNA (4-10 kb) of S. viridosporus was shotgun-cloned into S. lividans after insertion into the melanin (mel+) gene of pIJ702. Transformants expressing pIJ702 with insert DNA were selected based upon the appearance of thiostrepton resistant (tsrr)/mel-colonies on regeneration medium. Lignin peroxidase-expressing clones were isolated from this population by screening of transformants on a tsr-poly B-411 dye agar medium. In the presence of H2O2 excreted by S. lividans, colonies of lignin peroxidase-expressing clones decolorized the dye. Among 1000 transformants screened, 2 dye-decolorizing clones were found. One, pIJ702/TK64.1 (TK64.1), was further characterized. TK64.1 expressed significant extracellular 2,4-dichlorophenol (2.4-DCP) peroxidase activity (= assay for S. viridosporus lignin peroxidase). Under the cultural conditions employed, plasmidless S. lividans TK64 had a low background level of 2.4-DCP oxidizing activity. TK64.1 excreted an extracellular peroxidase not observed in S. lividans TK64, but similar to S. viridosporus lignin peroxidase ALip-P3, as shown by activity stain assays on nondenaturing polyacrylamide gels. The gene was located on a 4 kb fragment of S. viridosporus genomic DNA. When peroxidase-encoding plasmid, pIJ702.LP, was purified and used to transform three different S. lividans strains (TK64, TK23, TK24), all transformants tested decolorized poly B-411. When grown on lignocellulose in solid state processes, genetically engineered S. lividans TK64.1 degraded the lignocellulose slightly better than did S. lividans TK64. This is the first report of the cloning of a bacterial gene coding for a lignin-degrading enzyme.
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Affiliation(s)
- Z M Wang
- Department of Bacteriology and Biochemistry, University of Idaho, Moscow
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Pasti MB, Pometto AL, Nuti MP, Crawford DL. Lignin-solubilizing ability of actinomycetes isolated from termite (Termitidae) gut. Appl Environ Microbiol 1990; 56:2213-8. [PMID: 2167628 PMCID: PMC184585 DOI: 10.1128/aem.56.7.2213-2218.1990] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The lignocellulose-degrading abilities of 11 novel actinomycete strains isolated from termite gut were determined and compared with that of the well-characterized actinomycete, Streptomyces viridosporus T7A. Lignocellulose bioconversion was followed by (i) monitoring the degradation of [14C]lignin- and [14C]cellulose-labeled phloem of Abies concolor to 14CO2 and 14C-labeled water-soluble products, (ii) determining lignocellulose, lignin, and carbohydrate losses resulting from growth on a lignocellulose substrate prepared from corn stalks (Zea mays), and (iii) quantifying production of a water-soluble lignin degradation intermediate (acid-precipitable polymeric lignin). The actinomycetes were all Streptomyces strains and could be placed into three groups, including a group of five strains that appear superior to S. viridosporus T7A in lignocellulose-degrading ability, three strains of approximately equal ability, and three strains of lesser ability. Strain A2 was clearly the superior and most effective lignocellulose decomposer of those tested. Of the assays used, total lignocellulose weight loss was most useful in determining overall bioconversion ability but not in identifying the best lignin-solubilizing strains. A screening procedure based on 14CO2 evolution from [14C-lignin]lignocellulose combined with measurement of acid-precipitable polymeric lignin yield was the most effective in identifying lignin-solubilizing strains. For the termite gut strains, the pH of the medium showed no increase after 3 weeks of growth on lignocellulose. This is markedly different from the pattern observed with S. viridosporus T7A, which raises the medium pH considerably. Production of extracellular peroxidases by the 11 strains and S. viridosporus T7A was followed for 5 days in liquid cultures.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M B Pasti
- Department of Bacteriology and Biochemistry, University of Idaho, Moscow 83843
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Chauvet JM, Lamy F. Determination of soluble lignin and proteins in the presence of each other. Anal Chim Acta 1990. [DOI: 10.1016/s0003-2670(00)82087-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ball AS, Betts WB, McCarthy AJ. Degradation of Lignin-Related Compounds by Actinomycetes. Appl Environ Microbiol 1989; 55:1642-4. [PMID: 16347959 PMCID: PMC202920 DOI: 10.1128/aem.55.6.1642-1644.1989] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evidence for activity against the lignin fraction of straw was produced for a range of actinomycete strains. Decolorization of the polymeric dye Poly R and oxidation of veratryl alcohol, indicators of ligninolytic activity in white rot fungi, and utilization of fractionated Kraft lignin and low-molecular-weight methoxylated aromatic compounds were the criteria used. The relationships between these activities and the solubilization of native lignin are discussed.
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Affiliation(s)
- A S Ball
- Department of Genetics and Microbiology, University of Liverpool, P.O. Box 147, Liverpool L69 3BX, England
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