201
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Ponomareva EG, Kupryashina MA, Shelud’ko AV, Petrova LP, Vetchinkina EP, Katsy EI, Nikitina VE. Phenol Oxidase Activity of Azospirillum brasilense Sp245 Mutants with Modified Motility and Azospirillum brasilense Sp7 Phase Variants with Different Plasmid Composition. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718020091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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202
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Lopez-Ordonez T, Flores-López CA, Montejo-Lopez R, Cruz-Hernandez A, Conners EE. Cultivable Bacterial Diversity in the Gut of the Chagas Disease Vector Triatoma dimidiata: Identification of Possible Bacterial Candidates for a Paratransgenesis Approach. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2017.00174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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203
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Entwistle EM, Zak DR, Argiroff WA. Anthropogenic N deposition increases soil C storage by reducing the relative abundance of lignolytic fungi. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1288] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elizabeth M. Entwistle
- School of Natural Resources & Environment University of Michigan Ann Arbor Michigan 48109 USA
| | - Donald R. Zak
- School of Natural Resources & Environment University of Michigan Ann Arbor Michigan 48109 USA
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan 48109 USA
| | - William A. Argiroff
- School of Natural Resources & Environment University of Michigan Ann Arbor Michigan 48109 USA
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204
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Bilal M, Iqbal HM, Hu H, Wang W, Zhang X. Metabolic engineering and enzyme-mediated processing: A biotechnological venture towards biofuel production – A review. RENEWABLE & SUSTAINABLE ENERGY REVIEWS 2018. [DOI: 10.1016/j.rser.2017.09.070] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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205
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Isolation of the (+)-Pinoresinol-Mineralizing Pseudomonas sp. Strain SG-MS2 and Elucidation of Its Catabolic Pathway. Appl Environ Microbiol 2018; 84:AEM.02531-17. [PMID: 29222099 DOI: 10.1128/aem.02531-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/28/2017] [Indexed: 11/20/2022] Open
Abstract
Pinoresinol is a dimer of two β-β'-linked coniferyl alcohol molecules. It is both a plant defense molecule synthesized through the shikimic acid pathway and a representative of several β-β-linked dimers produced during the microbial degradation of lignin in dead plant material. Until now, little has been known about the bacterial catabolism of such dimers. Here we report the isolation of the efficient (+)-pinoresinol-mineralizing Pseudomonas sp. strain SG-MS2 and its catabolic pathway. Degradation of pinoresinol in this strain is inducible and proceeds via a novel oxidative route, which is in contrast to the previously reported reductive transformation by other bacteria. Based on enzyme assays and bacterial growth, cell suspension, and resting cell studies, we provide conclusive evidence that pinoresinol degradation in strain SG-MS2 is initiated by benzylic hydroxylation, generating a hemiketal via a quinone methide intermediate, which is then hydrated at the benzylic carbon by water. The hemiketal, which stays in equilibrium with the corresponding keto alcohol, undergoes an aryl-alkyl cleavage to generate a lactone and 2-methoxyhydroquinone. While the fate of 2-methoxyhydroquinone is not investigated further, it is assumed to be assimilated by ring cleavage. The lactone is further metabolized via two routes, namely, lactone ring cleavage and benzylic hydroxylation via a quinone methide intermediate, as described above. The resulting hemiketal again exists in equilibrium with a keto alcohol. Our evidence suggests that both routes of lactone metabolism lead to vanillin and vanillic acid, which we show can then be mineralized by strain SG-MS2.IMPORTANCE The oxidative catabolism of (+)-pinoresinol degradation elucidated here is fundamentally different from the reductive cometabolism reported for two previously characterized bacteria. Our findings open up new opportunities to use lignin for the biosynthesis of vanillin, a key flavoring agent in foods, beverages, and pharmaceuticals, as well as various new lactones. Our work also has implications for the study of new pinoresinol metabolites in human health. The enterodiol and enterolactone produced through reductive transformation of pinoresinol by gut microbes have already been associated with decreased risks of cancer and cardiovascular diseases. The metabolites from oxidative metabolism we find here also deserve attention in this respect.
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206
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Hooda R, Bhardwaj NK, Singh P. Brevibacillus parabrevis MTCC 12105: a potential bacterium for pulp and paper effluent degradation. World J Microbiol Biotechnol 2018; 34:31. [DOI: 10.1007/s11274-018-2414-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 01/23/2018] [Indexed: 01/14/2023]
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207
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Sun Z, Fridrich B, de Santi A, Elangovan S, Barta K. Bright Side of Lignin Depolymerization: Toward New Platform Chemicals. Chem Rev 2018; 118:614-678. [PMID: 29337543 PMCID: PMC5785760 DOI: 10.1021/acs.chemrev.7b00588] [Citation(s) in RCA: 739] [Impact Index Per Article: 123.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Indexed: 11/28/2022]
Abstract
Lignin, a major component of lignocellulose, is the largest source of aromatic building blocks on the planet and harbors great potential to serve as starting material for the production of biobased products. Despite the initial challenges associated with the robust and irregular structure of lignin, the valorization of this intriguing aromatic biopolymer has come a long way: recently, many creative strategies emerged that deliver defined products via catalytic or biocatalytic depolymerization in good yields. The purpose of this review is to provide insight into these novel approaches and the potential application of such emerging new structures for the synthesis of biobased polymers or pharmacologically active molecules. Existing strategies for functionalization or defunctionalization of lignin-based compounds are also summarized. Following the whole value chain from raw lignocellulose through depolymerization to application whenever possible, specific lignin-based compounds emerge that could be in the future considered as potential lignin-derived platform chemicals.
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Affiliation(s)
- Zhuohua Sun
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Bálint Fridrich
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Alessandra de Santi
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Saravanakumar Elangovan
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Katalin Barta
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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208
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Oxidative rearrangement of (+)-sesamin by CYP92B14 co-generates twin dietary lignans in sesame. Nat Commun 2017; 8:2155. [PMID: 29255253 PMCID: PMC5735135 DOI: 10.1038/s41467-017-02053-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/02/2017] [Indexed: 11/09/2022] Open
Abstract
(+)-Sesamin, (+)-sesamolin, and (+)-sesaminol glucosides are phenylpropanoid-derived specialized metabolites called lignans, and are rich in sesame (Sesamum indicum) seed. Despite their renowned anti-oxidative and health-promoting properties, the biosynthesis of (+)-sesamolin and (+)-sesaminol remained largely elusive. Here we show that (+)-sesamolin deficiency in sesame is genetically associated with the deletion of four C-terminal amino acids (Del4C) in a P450 enzyme CYP92B14 that constitutes a novel clade separate from sesamin synthase CYP81Q1. Recombinant CYP92B14 converts (+)-sesamin to (+)-sesamolin and, unexpectedly, (+)-sesaminol through an oxygenation scheme designated as oxidative rearrangement of α-oxy-substituted aryl groups (ORA). Intriguingly, CYP92B14 also generates (+)-sesaminol through direct oxygenation of the aromatic ring. The activity of CYP92B14 is enhanced when co-expressed with CYP81Q1, implying functional coordination of CYP81Q1 with CYP92B14. The discovery of CYP92B14 not only uncovers the last steps in sesame lignan biosynthesis but highlights the remarkable catalytic plasticity of P450s that contributes to metabolic diversity in nature.
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209
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Park SY, Yang D, Ha SH, Lee SY. Metabolic Engineering of Microorganisms for the Production of Natural Compounds. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700190] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seon Young Park
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Shin Hee Ha
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
- BioProcess Engineering Research Center; KAIST; Daejeon 34141 Republic of Korea
- BioInformatics Research Center; KAIST; Daejeon 34141 Republic of Korea
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210
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Nelson CE, Attia MA, Rogowski A, Morland C, Brumer H, Gardner JG. Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification. Environ Microbiol 2017; 19:5025-5039. [PMID: 29052930 DOI: 10.1111/1462-2920.13959] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/27/2017] [Accepted: 10/08/2017] [Indexed: 12/16/2022]
Abstract
Lignocellulose degradation is central to the carbon cycle and renewable biotechnologies. The xyloglucan (XyG), β(1→3)/β(1→4) mixed-linkage glucan (MLG) and β(1→3) glucan components of lignocellulose represent significant carbohydrate energy sources for saprophytic microorganisms. The bacterium Cellvibrio japonicus has a robust capacity for plant polysaccharide degradation, due to a genome encoding a large contingent of Carbohydrate-Active enZymes (CAZymes), many of whose specific functions remain unknown. Using a comprehensive genetic and biochemical approach, we have delineated the physiological roles of the four C. japonicus glycoside hydrolase family 3 (GH3) members on diverse β-glucans. Despite high protein sequence similarity and partially overlapping activity profiles on disaccharides, these β-glucosidases are not functionally equivalent. Bgl3A has a major role in MLG and sophorose utilization, and supports β(1→3) glucan utilization, while Bgl3B underpins cellulose utilization and supports MLG utilization. Bgl3C drives β(1→3) glucan utilization. Finally, Bgl3D is the crucial β-glucosidase for XyG utilization. This study not only sheds the light on the metabolic machinery of C. japonicus, but also expands the repertoire of characterized CAZymes for future deployment in biotechnological applications. In particular, the precise functional analysis provided here serves as a reference for informed bioinformatics on the genomes of other Cellvibrio and related species.
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Affiliation(s)
- Cassandra E Nelson
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, USA
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.,Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Carl Morland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.,Department of Chemistry, University of British Columbia, Vancouver, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.,Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, USA
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211
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Ligaba-Osena A, Hankoua B, DiMarco K, Pace R, Crocker M, McAtee J, Nagachar N, Tien M, Richard TL. Reducing biomass recalcitrance by heterologous expression of a bacterial peroxidase in tobacco (Nicotiana benthamiana). Sci Rep 2017; 7:17104. [PMID: 29213132 PMCID: PMC5719049 DOI: 10.1038/s41598-017-16909-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 10/25/2017] [Indexed: 11/13/2022] Open
Abstract
Commercial scale production of biofuels from lignocellulosic feed stocks has been hampered by the resistance of plant cell walls to enzymatic conversion, primarily owing to lignin. This study investigated whether DypB, the lignin-degrading peroxidase from Rodococcus jostii, depolymerizes lignin and reduces recalcitrance in transgenic tobacco (Nicotiana benthamiana). The protein was targeted to the cytosol or the ER using ER-targeting and retention signal peptides. For each construct, five independent transgenic lines were characterized phenotypically and genotypically. Our findings reveal that expression of DypB in the cytosol and ER does not affect plant development. ER-targeting increased protein accumulation, and extracts from transgenic leaves showed higher activity on classic peroxidase substrates than the control. Intriguingly, in situ DypB activation and subsequent saccharification released nearly 200% more fermentable sugars from transgenic lines than controls, which were not explained by variation in initial structural and non-structural carbohydrates and lignin content. Pyrolysis-GC-MS analysis showed more reduction in the level of lignin associated pyrolysates in the transgenic lines than the control primarily when the enzyme is activated prior to pyrolysis, consistent with increased lignin degradation and improved saccharification. The findings reveal for the first time that accumulation and in situ activation of a peroxidase improves biomass digestibility.
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Affiliation(s)
- Ayalew Ligaba-Osena
- College of Agriculture and Related Sciences, Delaware State University, 1200 N DuPont Highway, Dover, DE, 19901, USA
| | - Bertrand Hankoua
- College of Agriculture and Related Sciences, Delaware State University, 1200 N DuPont Highway, Dover, DE, 19901, USA.
| | - Kay DiMarco
- Agricultural and Biological Engineering, Pennsylvania State University, 111 Research Unit A, University Park, Pennsylvania, PA, 16802, USA
| | - Robert Pace
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY, 40511, USA
| | - Mark Crocker
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY, 40511, USA
| | - Jesse McAtee
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Nivedita Nagachar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 305 South Frear Laboratory, University Park, Pennsylvania, PA, 16802, USA
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 305 South Frear Laboratory, University Park, Pennsylvania, PA, 16802, USA
| | - Tom L Richard
- Agricultural and Biological Engineering, Pennsylvania State University, 111 Research Unit A, University Park, Pennsylvania, PA, 16802, USA
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212
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Transcriptome analysis of Pseudomonas sp. from subarctic tundra soil: pathway description and gene discovery for humic acids degradation. Folia Microbiol (Praha) 2017; 63:315-323. [PMID: 29196950 DOI: 10.1007/s12223-017-0573-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Although humic acids (HA) are involved in many biological processes in soils and thus their ecological importance has received much attention, the degradative pathways and corresponding catalytic genes underlying the HA degradation by bacteria remain unclear. To unveil those uncertainties, we analyzed transcriptomes extracted from Pseudomonas sp. PAMC 26793 cells time-dependently induced in the presence of HA in a lab flask. Out of 6288 genes, 299 (microarray) and 585 (RNA-seq) were up-regulated by > 2.0-fold in HA-induced cells, compared with controls. A significant portion (9.7% in microarray and 24.1% in RNA-seq) of these genes are predicted to function in the transport and metabolism of small molecule compounds, which could result from microbial HA degradation. To further identify lignin (a surrogate for HA)-degradative genes, 6288 protein sequences were analyzed against carbohydrate-active enzyme database and a self-curated list of putative lignin degradative genes. Out of 19 genes predicted to function in lignin degradation, several genes encoding laccase, dye-decolorizing peroxidase, vanillate O-demethylase oxygenase and reductase, and biphenyl 2,3-dioxygenase were up-regulated > 2.0-fold in RNA-seq. This induction was further confirmed by qRT-PCR, validating the likely involvement of these genes in the degradation of HA.
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213
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Ece S, Lambertz C, Fischer R, Commandeur U. Heterologous expression of a Streptomyces cyaneus laccase for biomass modification applications. AMB Express 2017; 7:86. [PMID: 28439850 PMCID: PMC5403781 DOI: 10.1186/s13568-017-0387-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 11/24/2022] Open
Abstract
Laccases are used for the conversion of biomass into fermentable sugars but it is difficult to produce high yields of active laccases in heterologous expression systems. We overcame this challenge by expressing Streptomyces cyaneus CECT 3335 laccase in Escherichia coli (ScLac) and we achieved a yield of up to 104 mg L-1 following purification by one-step affinity chromatography. Stability and activity assays using simple lignin model substrates showed that the purified enzyme preparation was active over a broad pH range and at high temperatures, suggesting it would be suitable for biomass degradation. The reusability of ScLac was also demonstrated by immobilizing the enzyme on agarose beads with a binding yield of 33%, and by the synthesis of cross-linked enzyme aggregates with an initial activity recovery of 72%.
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Affiliation(s)
- Selin Ece
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Camilla Lambertz
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Rainer Fischer
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Forckenbeckstrasse 6, 52074 Aachen, Germany
| | - Ulrich Commandeur
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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214
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Ceballos SJ, Yu C, Claypool JT, Singer SW, Simmons BA, Thelen MP, Simmons CW, VanderGheynst JS. Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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215
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Falade AO, Eyisi OA, Mabinya LV, Nwodo UU, Okoh AI. Peroxidase production and ligninolytic potentials of fresh water bacteria Raoultella ornithinolytica and Ensifer adhaerens. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2017; 16:12-17. [PMID: 29062721 PMCID: PMC5645169 DOI: 10.1016/j.btre.2017.10.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 09/11/2017] [Accepted: 10/06/2017] [Indexed: 12/01/2022]
Abstract
Interest in novel ligninolytic bacteria has remained topical due to, in part, the maneuverability of the bacterial genome. Conversely, the fungal genome lacks the dexterity for similar maneuverability thus, posing challenges in the fungal enzyme yield optimization process. Some impact of this situation includes the inability to commercialize the bio-catalytic process of lignin degradation by fungi. Consequently, this study assessed some fresh water bacteria isolates for ligninolytic and peroxidase properties through the utilization and degradation of model lignin compounds (guaiacol and veratryl alcohol) and the decolourization of selected ligninolytic indicator dyes; Azure B (AZB), Remazol Brilliant Blue R (RBBR) and Congo Red (CR). Bacterial strains with appreciable ligninolytic and peroxidase production potentials were identified through 16S rDNA sequence analysis and the nucleotide sequences deposited in the GenBank. About 5 isolates were positive for the degradation of both guaiacol (GA) and veratryl alcohol (VA) thus, accounting for about 17% of the test isolates. Similarly, AZB, RBBR and CR were respectively decolorized by 3, 2 and 5 bacterial strains thus, accounting for 10%, 7% and 17% of the test isolates. Two of the test bacterial strains were able to decolourize AZB, RBBR and CR respectively and these bacterial strains were identified as Raoultella ornithinolytica OKOH-1 and Ensifer adhaerens NWODO-2 with respective accession numbers as KX640917 and KX640918. Upon quantitation of the peroxidase activities; 5250 ± 0.00 U/L was recorded against Raoultella ornithinolytica OKOH-1 and 5833 ± 0.00 U/L against Ensifer adhaerens NWODO-2. The ligninolytic and dye decolourization properties of Raoultella ornithinolytica OKOH-1 and Ensifer adhaerens NWODO-2 marks for novelty particularly, as dyes with arene substituents were decolourized. Consequently, the potentials for the industrial applicability of these test bacterial strains abound as there is a dearth of information on organisms with such potentials.
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Affiliation(s)
- Ayodeji O. Falade
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
| | - Onyedikachi A.L. Eyisi
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
| | - Leonard V. Mabinya
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
| | - Uchechukwu U. Nwodo
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
| | - Anthony I. Okoh
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa
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216
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Niu H, Yang W, Zhuang K, Chen X, Chen Y, Liu D, Wu J, Zhu C, Ying H. Screening of promoters from Arthrobacter sp. CGMCC 3584 using a green fluorescent protein reporter system. World J Microbiol Biotechnol 2017; 33:208. [DOI: 10.1007/s11274-017-2375-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/29/2017] [Indexed: 11/29/2022]
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217
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Janusz G, Pawlik A, Sulej J, Swiderska-Burek U, Jarosz-Wilkolazka A, Paszczynski A. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol Rev 2017; 41:941-962. [PMID: 29088355 PMCID: PMC5812493 DOI: 10.1093/femsre/fux049] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/12/2017] [Indexed: 12/11/2022] Open
Abstract
Extensive research efforts have been dedicated to describing degradation of wood, which is a complex process; hence, microorganisms have evolved different enzymatic and non-enzymatic strategies to utilize this plentiful plant material. This review describes a number of fungal and bacterial organisms which have developed both competitive and mutualistic strategies for the decomposition of wood and to thrive in different ecological niches. Through the analysis of the enzymatic machinery engaged in wood degradation, it was possible to elucidate different strategies of wood decomposition which often depend on ecological niches inhabited by given organism. Moreover, a detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion. Through analysis of genomics and secretomic data, it was possible to underline the probable importance of certain wood-degrading enzymes produced by different fungal organisms, potentially giving them advantage in their ecological niches. The paper highlights different fungal strategies of wood degradation, which possibly correlates to the number of genes coding for secretory enzymes. Furthermore, investigation of the evolution of wood-degrading organisms has been described.
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Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Pawlik
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Justyna Sulej
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Urszula Swiderska-Burek
- Department of Botany and Mycology, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Jarosz-Wilkolazka
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Andrzej Paszczynski
- School of Food Science, Food Research Center, Room 103, University of Idaho, Moscow, ID 83844, USA
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218
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López-Loveira E, Ariganello F, Medina MS, Centrón D, Candal R, Curutchet G. Degradation alternatives for a commercial fungicide in water: biological, photo-Fenton, and coupled biological photo-Fenton processes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:25634-25644. [PMID: 27640058 DOI: 10.1007/s11356-016-7602-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
Imazalil (IMZ) is a widely used fungicide for the post-harvest treatment of citrus, classified as "likely to be carcinogenic in humans" for EPA, that can be only partially removed by conventional biological treatment. Consequently, specific or combined processes should be applied to prevent its release to the environment. Biological treatment with adapted microorganism consortium, photo-Fenton, and coupled biological photo-Fenton processes were tested as alternatives for the purification of water containing high concentration of the fungicide and the coadjutants present in the commercial formulation. IMZ-resistant consortium with the capacity to degrade IMZ in the presence of a C-rich co-substrate was isolated from sludge coming from a fruit packaging company wastewater treatment plant. This consortium was adapted to resist and degrade the organics present in photo-Fenton-oxidized IMZ water solution. Bacteria colonies from the consortia were isolated and identified. The effect of H2O2 initial concentration and dosage on IMZ degradation rate, average oxidation state (AOS), organic acid concentration, oxidation, and mineralization percentage after photo-Fenton process was determined. The application of biological treatment to the oxidized solutions notably decreased the total organic carbon (TOC) in solution. The effect of the oxidation degree, limited by H2O2 concentration and dosage, on the percentage of mineralization obtained after the biological treatment was determined and explained in terms of changes in AOS. The concentration of H2O2 necessary to eliminate IMZ by photo-Fenton and to reduce TOC and chemical oxygen demand (COD) by biological treatment, in order to allow the release of the effluents to rivers with different flows, was estimated.
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Affiliation(s)
- Elsa López-Loveira
- 3iA-UNSAM, Instituto de Investigación e Ingeniería Ambiental, CONICET, Universidad Nacional de San Martín, Campus Miguelete, Av. 25 de mayo y Francia, B1650HMP General San Martín, Provincia de Buenos Aires, Argentina
| | - Federico Ariganello
- 3iA-UNSAM, Instituto de Investigación e Ingeniería Ambiental, CONICET, Universidad Nacional de San Martín, Campus Miguelete, Av. 25 de mayo y Francia, B1650HMP General San Martín, Provincia de Buenos Aires, Argentina
| | - María Sara Medina
- 3iA-UNSAM, Instituto de Investigación e Ingeniería Ambiental, CONICET, Universidad Nacional de San Martín, Campus Miguelete, Av. 25 de mayo y Francia, B1650HMP General San Martín, Provincia de Buenos Aires, Argentina
| | - Daniela Centrón
- IMPAM-UBA, Laboratorio de Investigaciones en Mecanismos y Resistencias a Antibióticos, CONICET, Universidad Nacional de Buenos Aires, Paraguay 2155, C1121ABG, Ciudad de Buenos Aires, Argentina
| | - Roberto Candal
- 3iA-UNSAM, Instituto de Investigación e Ingeniería Ambiental, CONICET, Universidad Nacional de San Martín, Campus Miguelete, Av. 25 de mayo y Francia, B1650HMP General San Martín, Provincia de Buenos Aires, Argentina.
| | - Gustavo Curutchet
- 3iA-UNSAM, Instituto de Investigación e Ingeniería Ambiental, CONICET, Universidad Nacional de San Martín, Campus Miguelete, Av. 25 de mayo y Francia, B1650HMP General San Martín, Provincia de Buenos Aires, Argentina
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219
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Yang CX, Wang T, Gao LN, Yin HJ, Lü X. Isolation, identification and characterization of lignin-degrading bacteria from Qinling, China. J Appl Microbiol 2017; 123:1447-1460. [PMID: 28801977 DOI: 10.1111/jam.13562] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 07/19/2017] [Accepted: 08/01/2017] [Indexed: 11/30/2022]
Abstract
AIMS Lignin is an aromatic heteropolymer forming a physical barrier and it is a big challenge in biomass utilization. This paper first investigated lignin-degradation bacteria from rotten wood in Qinling Mountain. METHODS AND RESULTS Nineteen potential strains were selected and ligninolytic enzyme activities were determined over 84 h. Strains that had higher enzyme activities were selected. Further, the biodegradation of wheat straw lignin and alkali lignin was evaluated indicating that Burkholderia sp. H1 had the highest capability. It was confirmed by gel permeation chromatography and field emission scanning electron microscope that alkali lignin was depolymerized into small fragments. The degraded products were analysed using gas chromatography-mass spectrometry. The total ion chromatograph of products treated for 7 days showed the formation of aromatic compounds, an important intermediate from lignin degradation. Interestingly, they disappeared in 15 days while the aldehyde and ester compounds increased. CONCLUSIONS The results suggest that the lignin-degrading bacteria are abundant in rotten wood and strain H1 has high potential to break down lignin. SIGNIFICANCE AND IMPACT OF THE STUDY The diversity of lignin-degrading bacteria in Qinling Mountain is revealed. The study of Burkholderia sp. H1 expands the range of bacteria for lignin degradation and provides novel bacteria for application to lignocellulosic biomass.
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Affiliation(s)
- C-X Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
| | - T Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
| | - L-N Gao
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
| | - H-J Yin
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
| | - X Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Shaanxi Province, China
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220
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Pinder AP, Panter I, Abbott GD, Keely BJ. Deterioration of the Hanson Logboat: chemical and imaging assessment with removal of polyethylene glycol conserving agent. Sci Rep 2017; 7:13697. [PMID: 29057970 PMCID: PMC5651872 DOI: 10.1038/s41598-017-14057-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/04/2017] [Indexed: 11/09/2022] Open
Abstract
The state of preservation of wood in two samples from the Hanson Logboat, currently on display in Derby Museum and Art Gallery, was analysed using elemental analysis (EA), pyrolysis–gas chromatography/flame ionisation detection (Py-GC/FID), pyrolysis–gas chromatography/mass spectrometry (Py–GC/MS) and scanning electron microscopy (SEM). The samples were collected in 2003, after the boat had undergone conservation, and in 2011 after the condition of the boat began to deteriorate. Solvent extraction enabled removal of polyethylene glycol, with which the wood had been impregnated during conservation, allowing the degradation of the cellulose and lignin polymeric components of the woods to be assessed. Elemental compositions (C, H, N, O, S), Py–GC/FID, Py-GC/MS and SEM imaging reveal extensive degradation of the wood polymers during the eight year period since conservation.
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Affiliation(s)
- Adam P Pinder
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Ian Panter
- York Archaeological Trust, 47 Aldwark, York, YO1 7BX, UK
| | - Geoffrey D Abbott
- School of Civil Engineering and Geosciences, Drummond Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Brendan J Keely
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
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221
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Kuatsjah E, Chan ACK, Kobylarz MJ, Murphy MEP, Eltis LD. The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the α/β-hydrolase superfamily. J Biol Chem 2017; 292:18290-18302. [PMID: 28935670 DOI: 10.1074/jbc.m117.797696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/15/2017] [Indexed: 01/27/2023] Open
Abstract
Strain SYK-6 of the bacterium Sphingobium sp. catabolizes lignin-derived biphenyl via a meta-cleavage pathway. In this pathway, LigY is proposed to catalyze the hydrolysis of the meta-cleavage product (MCP) 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoate. Here, we validated this reaction by identifying 5-carboxyvanillate and 4-carboxy-2-hydroxypenta-2,4-dienoate as the products and determined the kcat and kcat/Km values as 9.3 ± 0.6 s-1 and 2.5 ± 0.2 × 107 m-1 s-1, respectively. Sequence analyses and a 1.9 Å resolution crystal structure established that LigY belongs to the amidohydrolase superfamily, unlike previously characterized MCP hydrolases, which are serine-dependent enzymes of the α/β-hydrolase superfamily. The active-site architecture of LigY resembled that of α-amino-β-carboxymuconic-ϵ-semialdehyde decarboxylase, a class III amidohydrolase, with a single zinc ion coordinated by His-6, His-8, His-179, and Glu-282. Interestingly, we found that LigY lacks the acidic residue proposed to activate water for hydrolysis in other class III amidohydrolases. Moreover, substitution of His-223, a conserved residue proposed to activate water in other amidohydrolases, reduced the kcat to a much lesser extent than what has been reported for other amidohydrolases, suggesting that His-223 has a different role in LigY. Substitution of Arg-72, Tyr-190, Arg-234, or Glu-282 reduced LigY activity over 100-fold. On the basis of these results, we propose a catalytic mechanism involving substrate tautomerization, substrate-assisted activation of water for hydrolysis, and formation of a gem-diol intermediate. This last step diverges from what occurs in serine-dependent MCP hydrolases. This study provides insight into C-C-hydrolyzing enzymes and expands the known range of reactions catalyzed by the amidohydrolase superfamily.
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Affiliation(s)
| | - Anson C K Chan
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Marek J Kobylarz
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E P Murphy
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- From the Genome Science and Technology Program and .,the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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222
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Shrestha R, Huang G, Meekins DA, Geisbrecht BV, Li P. Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects. ACS Catal 2017; 7:6352-6364. [PMID: 29308295 PMCID: PMC5751952 DOI: 10.1021/acscatal.7b01861] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are a family of H2O2-dependent heme peroxidases, which have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been uncovered for the B-class ElDyP from Enterobacter lignolyticus. Its structure revealed that a water molecule acts as the sixth axial ligand with two channels at diameters of ~3.0 and 8.0 Å leading to the heme center. A conformational change of ERS* to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs' bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type ElDyP with D2O2 at pH 3.5 suggested that cmpd 0 deprotonation by the distal aspartate is rate-limiting in the formation of cmpd I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with cmpd I instead of the free enzyme. The significant inverse sKIEs of kcat/KM and kERS* suggested that the aquo release in DyPs is mechanistically important and may explain the enzyme's adoption of two-electron reduction for cmpd I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining DyPs' acidic pH optimum. The kinetic mechanism of D143H-ElDyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs' lignolytic activity.
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Affiliation(s)
- Ruben Shrestha
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Gaochao Huang
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - David A. Meekins
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Ping Li
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
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223
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Tian JH, Pourcher AM, Bize A, Wazeri A, Peu P. Impact of wet aerobic pretreatments on cellulose accessibility and bacterial communities in rape straw. BIORESOURCE TECHNOLOGY 2017; 237:31-38. [PMID: 28411050 DOI: 10.1016/j.biortech.2017.03.142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
A new pretreatment method of lignocellulosic biomass was explored by using a wet aerobic process with an alkaline lignin and a mineral salt solution. This treatment significantly improved structural modification of rape straw used as substrate model in this study. Change in cellulose accessibility to cellulase of rape straw rose up to six fold within the first days of this pretreatment without generated significant modification of van Soest lignocellulose fractionation. The biological pretreatment apply to rape straw induced a high microbial activity revealed by quantitative PCR and sequencing techniques, suggesting that bacteria including Xanthomonadales and Sphingobacteriales may be involved in this lignocellulosic biomass transformation. Moreover, results of this work demonstrate that the endogenous microbial community associated with rape straw plays a key role in its alteration.
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Affiliation(s)
- Jiang-Hao Tian
- IRSTEA, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France
| | - Anne-Marie Pourcher
- IRSTEA, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France
| | - Ariane Bize
- IRSTEA, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, CS 10030, F-92761 Antony, France
| | - Alaa Wazeri
- Egypt-Japan University of Science and Technology (E-JUST), Environmental Engineering Department, P.O. Box 179, New Borg El-Arab City 21934, Alexandria, Egypt
| | - Pascal Peu
- IRSTEA, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France.
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224
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Luo L, Meng H, Gu JD. Microbial extracellular enzymes in biogeochemical cycling of ecosystems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 197:539-549. [PMID: 28419976 DOI: 10.1016/j.jenvman.2017.04.023] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/23/2017] [Accepted: 04/08/2017] [Indexed: 06/07/2023]
Abstract
Extracellular enzymes, primarily produced by microorganisms, affect ecosystem processes because of their essential roles in degradation, transformation and mineralization of organic matter. Extracellular enzymes involved in the cycling of carbon (C), nitrogen (N) and phosphorus (P) have been widely investigated in many different ecosystems, and several enzymes have been recognized as key components in regulating C storage and nutrient cycling. In this review, it was the first time to summarize the specific extracellular enzymes related to C storage and nutrient cycling for better understanding the important role of microbial extracellular enzymes in biogeochemical cycling of ecosystems. Subsequently, ecoenzymatic stoichiometry - the relative ratio of extracellular enzyme, has been reviewed and further provided a new perspective for understanding biogeochemical cycling of ecosystems. Finally, the new insights of using microbial extracellular enzyme in indicating biogeochemical cycling and then protecting ecosystems have been suggested.
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Affiliation(s)
- Ling Luo
- College of Environmental Sciences, Sichuan Agricultural University, Huimin Road, 611130 Chengdu, P.R. China; Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, P.R. China.
| | - Han Meng
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, P.R. China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, P.R. China.
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225
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Akita H, Kimura ZI, Yusoff MZM, Nakashima N, Hoshino T. Identification and characterization of Burkholderia multivorans CCA53. BMC Res Notes 2017; 10:249. [PMID: 28683814 PMCID: PMC5501517 DOI: 10.1186/s13104-017-2565-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 06/26/2017] [Indexed: 01/30/2023] Open
Abstract
Objective A lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp. CCA53. Results Multilocus sequence typing (MLST) analysis based on fragments of the atpD, gltD, gyrB, lepA, recA and trpB gene sequences was performed to identify Burkholderia sp. CCA53. The MLST analysis revealed that Burkholderia sp. CCA53 was tightly clustered with B. multivorans ATCC BAA-247T. The quinone and cellular fatty acid profiles, carbon source utilization, growth temperature and pH were consistent with the characteristics of B. multivorans species. Burkholderia sp. CCA53 was therefore identified as B. multivorans CCA53.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.
| | - Zen-Ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima, 737-8506, Japan
| | - Mohd Zulkhairi Mohd Yusoff
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.,Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan.,Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tamotsu Hoshino
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
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226
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Lai CMT, Chua HB, Danquah MK, Saptoro A. Isolation of Thermophilic Lignin Degrading Bacteria from Oil-Palm Empty Fruit Bunch (EFB) Compost. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1757-899x/206/1/012016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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227
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Gui H, Purahong W, Hyde KD, Xu J, Mortimer PE. The Arbuscular Mycorrhizal Fungus Funneliformis mosseae Alters Bacterial Communities in Subtropical Forest Soils during Litter Decomposition. Front Microbiol 2017; 8:1120. [PMID: 28676797 PMCID: PMC5476864 DOI: 10.3389/fmicb.2017.01120] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/01/2017] [Indexed: 12/25/2022] Open
Abstract
Bacterial communities and arbuscular mycorrhizal fungi (AMF) co-occur in the soil, however, the interaction between these two groups during litter decomposition remains largely unexplored. In order to investigate the effect of AMF on soil bacterial communities, we designed dual compartment microcosms, where AMF (Funneliformis mosseae) was allowed access (AM) to, or excluded (NM) from, a compartment containing forest soil and litterbags. Soil samples from this compartment were analyzed at 0, 90, 120, 150, and 180 days. For each sample, Illumina sequencing was used to assess any changes in the soil bacterial communities. We found that most of the obtained operational taxonomic units (OTUs) from both treatments belonged to the phylum of Proteobacteria, Acidobacteria, and Actinobacteria. The community composition of bacteria at phylum and class levels was slightly influenced by both time and AMF. In addition, time and AMF significantly affected bacterial genera (e.g., Candidatus Solibacter, Dyella, Phenylobacterium) involved in litter decomposition. Opposite to the bacterial community composition, we found that overall soil bacterial OTU richness and diversity are relatively stable and were not significantly influenced by either time or AMF inoculation. OTU richness at phylum and class levels also showed consistent results with overall bacterial OTU richness. Our study provides new insight into the influence of AMF on soil bacterial communities at the genus level.
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Affiliation(s)
- Heng Gui
- Key laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- World Agroforestry Centre, East and Central AsiaKunming, China
- Centre of Excellence in Fungal Research, Mae Fah Luang UniversityChiang Rai, Thailand
- School of Science, Mae Fah Luang UniversityChiang Rai, Thailand
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental ResearchHalle, Germany
| | - Kevin D. Hyde
- Centre of Excellence in Fungal Research, Mae Fah Luang UniversityChiang Rai, Thailand
- School of Science, Mae Fah Luang UniversityChiang Rai, Thailand
| | - Jianchu Xu
- Key laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- World Agroforestry Centre, East and Central AsiaKunming, China
| | - Peter E. Mortimer
- Key laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- World Agroforestry Centre, East and Central AsiaKunming, China
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228
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Delignification and enhanced gas release from soil containing lignocellulose by treatment with bacterial lignin degraders. J Appl Microbiol 2017; 123:159-171. [DOI: 10.1111/jam.13470] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 01/14/2023]
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229
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Wang W, Zhang C, Sun X, Su S, Li Q, Linhardt RJ. Efficient, environmentally-friendly and specific valorization of lignin: promising role of non-radical lignolytic enzymes. World J Microbiol Biotechnol 2017; 33:125. [DOI: 10.1007/s11274-017-2286-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/16/2017] [Indexed: 12/11/2022]
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230
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Smith CC, Srygley RB, Healy F, Swaminath K, Mueller UG. Spatial Structure of the Mormon Cricket Gut Microbiome and its Predicted Contribution to Nutrition and Immune Function. Front Microbiol 2017; 8:801. [PMID: 28553263 PMCID: PMC5427142 DOI: 10.3389/fmicb.2017.00801] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/19/2017] [Indexed: 01/24/2023] Open
Abstract
The gut microbiome of insects plays an important role in their ecology and evolution, participating in nutrient acquisition, immunity, and behavior. Microbial community structure within the gut is heavily influenced by differences among gut regions in morphology and physiology, which determine the niches available for microbes to colonize. We present a high-resolution analysis of the structure of the gut microbiome in the Mormon cricket Anabrus simplex, an insect known for its periodic outbreaks in the western United States and nutrition-dependent mating system. The Mormon cricket microbiome was dominated by 11 taxa from the Lactobacillaceae, Enterobacteriaceae, and Streptococcaceae. While most of these were represented in all gut regions, there were marked differences in their relative abundance, with lactic-acid bacteria (Lactobacillaceae) more common in the foregut and midgut and enteric (Enterobacteriaceae) bacteria more common in the hindgut. Differences in community structure were driven by variation in the relative prevalence of three groups: a Lactobacillus in the foregut, Pediococcus lactic-acid bacteria in the midgut, and Pantoea agglomerans, an enteric bacterium, in the hindgut. These taxa have been shown to have beneficial effects on their hosts in insects and other animals by improving nutrition, increasing resistance to pathogens, and modulating social behavior. Using PICRUSt to predict gene content from our 16S rRNA sequences, we found enzymes that participate in carbohydrate metabolism and pathogen defense in other orthopterans. These were predominately represented in the hindgut and midgut, the most important sites for nutrition and pathogen defense. Phylogenetic analysis of 16S rRNA sequences from cultured isolates indicated low levels of divergence from sequences derived from plants and other insects, suggesting that these bacteria are likely to be exchanged between Mormon crickets and the environment. Our study shows strong spatial variation in microbiome community structure, which influences predicted gene content and thus the potential of the microbiome to influence host function.
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Affiliation(s)
- Chad C Smith
- Department of Integrative Biology, University of Texas at Austin, AustinTX, USA
| | - Robert B Srygley
- Northern Plains Agricultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, SidneyMT, USA
| | - Frank Healy
- Department of Biology, Trinity University, San AntonioTX, USA
| | | | - Ulrich G Mueller
- Department of Integrative Biology, University of Texas at Austin, AustinTX, USA
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231
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Influences of Media Compositions on Characteristics of Isolated Bacteria Exhibiting Lignocellulolytic Activities from Various Environmental Sites. Appl Biochem Biotechnol 2017; 183:931-942. [PMID: 28405916 DOI: 10.1007/s12010-017-2474-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 04/05/2017] [Indexed: 02/08/2023]
Abstract
Efficient isolation of lignocellulolytic bacteria is essential for the utilization of lignocellulosic biomass. In this study, bacteria with cellulolytic, xylanolytic, and lignolytic activities were isolated from environmental sites such as mountain, wetland, and mudflat using isolation media containing the combination of lignocellulose components (cellulose, xylan, and lignin). Eighty-nine isolates from the isolation media were characterized by analyzing taxonomic ranks and cellulolytic, xylanolytic, and lignolytic activities. Most of the cellulolytic bacteria showed multienzymatic activities including xylanolytic activity. The isolation media without lignin were efficient in isolating bacteria exhibiting multienzymatic activities even including lignolytic activity, whereas a lignin-containing medium was effective to isolate bacteria exhibiting lignolytic activity only. Multienzymatic activities were mainly observed in Bacillus and Streptomyces, while Burkholderia was the most abundant genus with lignolytic activity only. This study provides insight into isolation medium for efficient isolation of lignocellulose-degrading microorganisms.
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232
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Anacleto LR, Roberto MM, Marin-Morales MA. Toxicological effects of the waste of the sugarcane industry, used as agricultural fertilizer, on the test system Allium cepa. CHEMOSPHERE 2017; 173:31-42. [PMID: 28104478 DOI: 10.1016/j.chemosphere.2017.01.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 12/14/2016] [Accepted: 01/05/2017] [Indexed: 06/06/2023]
Abstract
Sugarcane is cultivated in tropical countries for sugar and ethanol production. In Brazil, this culture is among the most profitable with a production of 658.7 million tons/harvest. Sugarcane filter cake (SCFC) is a waste rich in organic matter and micronutrients, but also contains toxic metals. As it has been used as fertilizer and there is not enough knowledge about its environmental impacts, this work assessed the genotoxicogenetic effects of raw SCFC and associations with soil and sugarcane bagasse (SCB), by Allium cepa tests. Six associations of SCFC + soil and five associations of SCFC + soil + SCB were tested at three moments of degradation: initial (T0), 3 and 6 months (T1 and T2). Genotoxicogenetic assays were performed with solid substrates of these associations and with their respective aqueous extracts. Chemical analysis showed a decrease in metals, total organic carbon and nitrogen after 6 months of biodegradation, complying with Brazilian laws. In general, the combination of SCFC + soil + SCB was better than using only SCFC. T0 solubilized samples of different associations composed by highest quantities of SCFC inhibited the MI and induced CA without presenting mutagenicity (except for 75%-SCFC + soil + SCB). T1 samples showed more cytotoxicity than T0 samples, and also presented genotoxic and mutagenic effects. Solid substrate and solubilized associations of SCFC + soil + SCB of T2 samples had no toxicity. These results suggest 6 months of biodegradation and the SCB adding as effective to reduce toxicogenetic effects induced by SCFC. Also, small proportions of SCFC interfered less on the A. cepa test-system when compared with those containing high quantities of residue.
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Affiliation(s)
- Leonardo Ramos Anacleto
- Universidade Estadual Paulista (Unesp), Departamento de Biologia, Instituto de Biociências, Rio Claro, São Paulo, Brazil
| | - Matheus Mantuanelli Roberto
- Universidade Estadual Paulista (Unesp), Departamento de Biologia, Instituto de Biociências, Rio Claro, São Paulo, Brazil; Centro Universitário Hermínio Ometto (UNIARARAS), Araras, São Paulo, Brazil
| | - Maria Aparecida Marin-Morales
- Universidade Estadual Paulista (Unesp), Departamento de Biologia, Instituto de Biociências, Rio Claro, São Paulo, Brazil.
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233
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Carbon Source-Dependent Inducible Metabolism of Veratryl Alcohol and Ferulic Acid in Pseudomonas putida CSV86. Appl Environ Microbiol 2017; 83:AEM.03326-16. [PMID: 28188206 DOI: 10.1128/aem.03326-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/02/2017] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas putida CSV86 degrades lignin-derived metabolic intermediates, viz, veratryl alcohol, ferulic acid, vanillin, and vanillic acid, as the sole sources of carbon and energy. Strain CSV86 also degraded lignin sulfonate. Cell respiration, enzyme activity, biotransformation, and high-pressure liquid chromatography (HPLC) analyses suggest that veratryl alcohol and ferulic acid are metabolized to vanillic acid by two distinct carbon source-dependent inducible pathways. Vanillic acid was further metabolized to protocatechuic acid and entered the central carbon pathway via the β-ketoadipate route after ortho ring cleavage. Genes encoding putative enzymes involved in the degradation were found to be present at fer, ver, and van loci. The transcriptional analysis suggests a carbon source-dependent cotranscription of these loci, substantiating the metabolic studies. Biochemical and quantitative real-time (qRT)-PCR studies revealed the presence of two distinct O-demethylases, viz, VerAB and VanAB, involved in the oxidative demethylation of veratric acid and vanillic acid, respectively. This report describes the various steps involved in metabolizing lignin-derived aromatic compounds at the biochemical level and identifies the genes involved in degrading veratric acid and the arrangement of phenylpropanoid metabolic genes as three distinct inducible transcription units/operons. This study provides insight into the bacterial degradation of lignin-derived aromatics and the potential of P. putida CSV86 as a suitable candidate for producing valuable products.IMPORTANCEPseudomonas putida CSV86 metabolizes lignin and its metabolic intermediates as a carbon source. Strain CSV86 displays a unique property of preferential utilization of aromatics, including for phenylpropanoids over glucose. This report unravels veratryl alcohol metabolism and genes encoding veratric acid O-demethylase, hitherto unknown in pseudomonads, thereby providing new insight into the metabolic pathway and gene pool for lignin degradation in bacteria. The biochemical and genetic characterization of phenylpropanoid metabolism makes it a prospective system for its application in producing valuable products, such as vanillin and vanillic acid, from lignocellulose. This study supports the immense potential of P. putida CSV86 as a suitable candidate for bioremediation and biorefinery.
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234
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Huang G, Shrestha R, Jia K, Geisbrecht BV, Li P. Enantioselective Synthesis of Dilignol Model Compounds and Their Stereodiscrimination Study with a Dye-Decolorizing Peroxidase. Org Lett 2017; 19:1820-1823. [PMID: 28326791 DOI: 10.1021/acs.orglett.7b00587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A four-step enantioselective approach was developed to synthesize anti (1R,2S)-1a and (1S,2R)-1b containing a β-O-4 linkage in good yields. A significant difference was observed for the apparent binding affinities of four stereospecific lignin model compounds with TcDyP by surface plasmon resonance, which was not translated into a significant difference in enzyme activities. The discrepancy may be attributed to the conformational change involving a loop widely present in DyPs upon H2O2 binding.
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Affiliation(s)
- Gaochao Huang
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ruben Shrestha
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Brian V Geisbrecht
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ping Li
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
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235
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Ravi K, García-Hidalgo J, Gorwa-Grauslund MF, Lidén G. Conversion of lignin model compounds by Pseudomonas putida KT2440 and isolates from compost. Appl Microbiol Biotechnol 2017; 101:5059-5070. [PMID: 28299400 PMCID: PMC5486835 DOI: 10.1007/s00253-017-8211-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/21/2017] [Accepted: 02/26/2017] [Indexed: 11/29/2022]
Abstract
Starting from mature vegetable compost, four bacterial strains were selected using a lignin-rich medium. 16S ribosomal RNA identification of the isolates showed high score similarity with Pseudomonas spp. for three out of four isolates. Further characterization of growth on mixtures of six selected lignin model compounds (vanillin, vanillate, 4-hydroxybenzoate, p-coumarate, benzoate, and ferulate) was carried out with three of the Pseudomonas isolates and in addition with the strain Pseudomonas putida KT2440 from a culture collection. The specific growth rates on benzoate, p-coumarate, and 4-hydroxybenzoate were considerably higher (0.26–0.27 h−1) than those on ferulate and vanillate (0.21 and 0.22 h−1), as were the uptake rates. There was no direct growth of P. putida KT2440 on vanillin, but instead, vanillin was rapidly converted into vanillate at a rate of 4.87 mmol (gCDW h)−1 after which the accumulated vanillate was taken up. The growth curve reflected a diauxic growth when mixtures of the model compounds were used as carbon source. Vanillin, 4-hydroxybenzoate, and benzoate were preferentially consumed first, whereas ferulate was always the last substrate to be taken in. These results contribute to a better understanding of the aromatic metabolism of P. putida in terms of growth and uptake rates, which will be helpful for the utilization of these bacteria as cell factories for upgrading lignin-derived mixtures of aromatic molecules.
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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
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
| | - Marie F Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, 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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236
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A bacterial aromatic aldehyde dehydrogenase critical for the efficient catabolism of syringaldehyde. Sci Rep 2017; 7:44422. [PMID: 28294121 PMCID: PMC5353671 DOI: 10.1038/srep44422] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/07/2017] [Indexed: 01/18/2023] Open
Abstract
Vanillin and syringaldehyde obtained from lignin are essential intermediates for the production of basic chemicals using microbial cell factories. However, in contrast to vanillin, the microbial conversion of syringaldehyde is poorly understood. Here, we identified an aromatic aldehyde dehydrogenase (ALDH) gene responsible for syringaldehyde catabolism from 20 putative ALDH genes of Sphingobium sp. strain SYK-6. All these genes were expressed in Escherichia coli, and nine gene products, including previously characterized BzaA, BzaB, and vanillin dehydrogenase (LigV), exhibited oxidation activities for syringaldehyde to produce syringate. Among these genes, SLG_28320 (desV) and ligV were most highly and constitutively transcribed in the SYK-6 cells. Disruption of desV in SYK-6 resulted in a significant reduction in growth on syringaldehyde and in syringaldehyde oxidation activity. Furthermore, a desV ligV double mutant almost completely lost its ability to grow on syringaldehyde. Purified DesV showed similar kcat/Km values for syringaldehyde (2100 s−1·mM−1) and vanillin (1700 s−1·mM−1), whereas LigV substantially preferred vanillin (8800 s−1·mM−1) over syringaldehyde (1.4 s−1·mM−1). These results clearly demonstrate that desV plays a major role in syringaldehyde catabolism. Phylogenetic analyses showed that DesV-like ALDHs formed a distinct phylogenetic cluster separated from the vanillin dehydrogenase cluster.
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237
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Jackson CA, Couger MB, Prabhakaran M, Ramachandriya KD, Canaan P, Fathepure BZ. Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass. J Appl Microbiol 2017; 122:940-952. [PMID: 28092137 DOI: 10.1111/jam.13401] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this work was to isolate novel lignin-degrading organisms. METHODS AND RESULTS Several pure cultures of bacteria that degrade lignin were isolated from bacterial consortia developed from decaying biomass. Among the isolates, Rhizobium sp. strain YS-1r (closest relative of Rhizobium petrolearium strain SL-1) was explored for its lignin-degrading ability. Microcosm studies showed that strain YS-1r was able to degrade a variety of lignin monomers, dimers and also native lignin in switchgrass and alfalfa. The isolate demonstrated lignin peroxidase (LiP) activity when grown on alkali lignin, p-anisoin, switchgrass or alfalfa, and only negligible activity was measured in glucose-grown cells suggesting inducible nature of the LiP activity. Analysis of the strain YS-1r genome revealed the presence of a variety of genes that code for various lignin-oxidizing, H2 O2 -producing as well as polysaccharide-hydrolysing enzymes. CONCLUSIONS This study shows both the genomic and physiological capability of bacteria in the genus Rhizobium to metabolize lignin and lignin-like compounds. This is the first detailed report on the lignocellulose-degrading ability of a Rhizobium species and thus this study expands the role of alpha-proteobacteria in the degradation of lignin. SIGNIFICANCE AND IMPACT OF THE STUDY The organism's ability to degrade lignin is significant since Rhizobia are widespread in soil, water and plant rhizospheres and some fix atmospheric nitrogen and also have the ability to degrade aromatic hydrocarbons.
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Affiliation(s)
- C A Jackson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M Prabhakaran
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - K D Ramachandriya
- Department of Biosystems and Agricultural Engineering, Oklahoma State University, Stillwater, OK, USA
| | - P Canaan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - B Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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238
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Enhanced delignification of steam-pretreated poplar by a bacterial laccase. Sci Rep 2017; 7:42121. [PMID: 28169340 PMCID: PMC5294454 DOI: 10.1038/srep42121] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/05/2017] [Indexed: 11/09/2022] Open
Abstract
The recalcitrance of woody biomass, particularly its lignin component, hinders its sustainable transformation to fuels and biomaterials. Although the recent discovery of several bacterial ligninases promises the development of novel biocatalysts, these enzymes have largely been characterized using model substrates: direct evidence for their action on biomass is lacking. Herein, we report the delignification of woody biomass by a small laccase (sLac) from Amycolatopsis sp. 75iv3. Incubation of steam-pretreated poplar (SPP) with sLac enhanced the release of acid-precipitable polymeric lignin (APPL) by ~6-fold, and reduced the amount of acid-soluble lignin by ~15%. NMR spectrometry revealed that the APPL was significantly syringyl-enriched relative to the original material (~16:1 vs. ~3:1), and that sLac preferentially oxidized syringyl units and altered interunit linkage distributions. sLac's substrate preference among monoaryls was also consistent with this observation. In addition, sLac treatment reduced the molar mass of the APPL by over 50%, as determined by gel-permeation chromatography coupled with multi-angle light scattering. Finally, sLac acted synergistically with a commercial cellulase cocktail to increase glucose production from SPP ~8%. Overall, this study establishes the lignolytic activity of sLac on woody biomass and highlights the biocatalytic potential of bacterial enzymes.
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239
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Xu J, Wei Y, Jia H, Xiao L, Gong D. A new perspective on studying burial environment before archaeological excavation: analyzing bacterial community distribution by high-throughput sequencing. Sci Rep 2017; 7:41691. [PMID: 28169321 PMCID: PMC5294632 DOI: 10.1038/srep41691] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/23/2016] [Indexed: 02/01/2023] Open
Abstract
Burial conditions play a crucial role in archaeological heritage preservation. Especially, the microorganisms were considered as the leading causes which incurred degradation and vanishment of historic materials. In this article, we analyzed bacterial diversity and community structure from M1 of Wangshanqiao using 16 S rRNA gene amplicon sequencing. The results indicated that microbial communities in burial conditions were diverse among four different samples. The samples from the robber hole varied most obviously in community structure both in Alpha and Beta diversity. In addition, the dominant phylum in different samples were Proteobacteria, Actinobacteria and Bacteroidetes, respectively. Moreover, the study implied that historical materials preservation conditions had connections with bacterial community distribution. At the genus level, Acinetobacter might possess high ability in degrading organic culture heritage in burial conditions, while Bacteroides were associated closely with favorable preservation conditions. This method contributes to fetch information which would never recover after excavation, and it will help to explore microbial degradation on precious organic culture heritage and further our understanding of archaeological burial environment. The study also indicates that robbery has a serious negative impact on burial remains.
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Affiliation(s)
- Jinjin Xu
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei, 230026 China
| | - Yanfei Wei
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei, 230026 China.,Jingzhou Preservation Centre of Cultural Relics, Jingzhou, 434020 China
| | | | - Lin Xiao
- Chengdu Institute of Cultural Relics and Archaeology, Chengdu, 610000 China
| | - Decai Gong
- Department of History of Science and Scientific Archaeology, University of Science and Technology of China, Hefei, 230026 China
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240
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Pornsuwan S, Maenpuen S, Kamutira P, Watthaisong P, Thotsaporn K, Tongsook C, Juttulapa M, Nijvipakul S, Chaiyen P. 3,4-Dihydroxyphenylacetate 2,3-dioxygenase from Pseudomonas aeruginosa: An Fe(II)-containing enzyme with fast turnover. PLoS One 2017; 12:e0171135. [PMID: 28158217 PMCID: PMC5291488 DOI: 10.1371/journal.pone.0171135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/15/2017] [Indexed: 11/18/2022] Open
Abstract
3,4-dihydroxyphenylacetate (DHPA) dioxygenase (DHPAO) from Pseudomonas aeruginosa (PaDHPAO) was overexpressed in Escherichia coli and purified to homogeneity. As the enzyme lost activity over time, a protocol to reactivate and conserve PaDHPAO activity has been developed. Addition of Fe(II), DTT and ascorbic acid or ROS scavenging enzymes (catalase or superoxide dismutase) was required to preserve enzyme stability. Metal content and activity analyses indicated that PaDHPAO uses Fe(II) as a metal cofactor. NMR analysis of the reaction product indicated that PaDHPAO catalyzes the 2,3-extradiol ring-cleavage of DHPA to form 5-carboxymethyl-2-hydroxymuconate semialdehyde (CHMS) which has a molar absorptivity of 32.23 mM-1cm-1 at 380 nm and pH 7.5. Steady-state kinetics under air-saturated conditions at 25°C and pH 7.5 showed a Km for DHPA of 58 ± 8 μM and a kcat of 64 s-1, indicating that the turnover of PaDHPAO is relatively fast compared to other DHPAOs. The pH-rate profile of the PaDHPAO reaction shows a bell-shaped plot that exhibits a maximum activity at pH 7.5 with two pKa values of 6.5 ± 0.1 and 8.9 ± 0.1. Study of the effect of temperature on PaDHPAO activity indicated that the enzyme activity increases as temperature increases up to 55°C. The Arrhenius plot of ln(k’cat) versus the reciprocal of the absolute temperature shows two correlations with a transition temperature at 35°C. Two activation energy values (Ea) above and below the transition temperature were calculated as 42 and 14 kJ/mol, respectively. The data imply that the rate determining steps of the PaDHPAO reaction at temperatures above and below 35°C may be different. Sequence similarity network analysis indicated that PaDHPAO belongs to the enzyme clusters that are largely unexplored. As PaDHPAO has a high turnover number compared to most of the enzymes previously reported, understanding its biochemical and biophysical properties should be useful for future applications in biotechnology.
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Affiliation(s)
- Soraya Pornsuwan
- Department of Chemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Philaiwarong Kamutira
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Pratchaya Watthaisong
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kittisak Thotsaporn
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Chanakan Tongsook
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Maneerat Juttulapa
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sarayut Nijvipakul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
- * E-mail:
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Guo P, Han T, Zhang L, Li S, Ma D, Du Y. Changes of soil bacterial activities and functions after different N additions in a temperate forest. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:3853-3860. [PMID: 27900719 DOI: 10.1007/s11356-016-8141-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
It has been shown that different nitrogen (N) addition led to various influences on soil microbial activities in forest ecosystems; however, the changes of bacteria were still unclear. In this work, inorganic N (NH4NO3) and organic N (urea and glycine) were fertilized with different ratios (5:0, 1:4, 3:2, 2:3, and 1:4) on temperate forest soils, while fungicide (cycloheximide) was simultaneously added on half of each treatment to inhibit fungal activities (leaving only bacteria). After a 3-year field experiment, soil samples were harvested, then microbial enzymatic activities involved in carbon (C), and N and phosphorus (P) cycles were determined. Under laboratory conditions, four purified bacteria which were isolated from sample site had been inoculated in sterilized soils under different N types and enzymatic activities were assayed after 90-day incubation. The results showed that cellulase and polyphenol oxidase activities of non-fungicide-added treatments increased after N addition and greater organic N accelerated the increases. However, these enzymatic activities of fungicide-added treatments were not significantly influenced by N addition and N types. It may be due to the insufficient ability of bacteria to synthesize enough enzymes to decompose complex organic C (such as cellulose and lignin) into available compound, although N-limitation was alleviated. Alkaline phosphatase activities increased after N addition in both non-fungicide-added and fungicide-added treatments, and the acceleration on bacterial alkaline phosphatase activities was even greater. Furthermore, organic N showed at least 2.5 times promotion on bacteria alkaline phosphatase than those of inorganic N, which indicated greater alleviation of bacterial P-limitation after the addition of organic N. All the results indicated that soil bacteria may be seriously limited by soil available C but become the dominant decomposer of the complex P compounds after N addition, particularly greater organic N.
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Affiliation(s)
- Peng Guo
- Hebei College of Industry and Technology, Hongqi Street 626, Shijiazhuang, 050091, China.
| | - Tiwen Han
- Hebei College of Industry and Technology, Hongqi Street 626, Shijiazhuang, 050091, China
| | - Li Zhang
- Hebei College of Industry and Technology, Hongqi Street 626, Shijiazhuang, 050091, China
| | - Shushan Li
- Hebei College of Industry and Technology, Hongqi Street 626, Shijiazhuang, 050091, China
| | - Dongzhu Ma
- Hebei College of Industry and Technology, Hongqi Street 626, Shijiazhuang, 050091, China
| | - Yuhan Du
- Hebei College of Industry and Technology, Hongqi Street 626, Shijiazhuang, 050091, China
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242
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Falade AO, Nwodo UU, Iweriebor BC, Green E, Mabinya LV, Okoh AI. Lignin peroxidase functionalities and prospective applications. Microbiologyopen 2017; 6:e00394. [PMID: 27605423 PMCID: PMC5300883 DOI: 10.1002/mbo3.394] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/18/2016] [Accepted: 06/28/2016] [Indexed: 11/18/2022] Open
Abstract
Ligninolytic extracellular enzymes, including lignin peroxidase, are topical owing to their high redox potential and prospective industrial applications. The prospective applications of lignin peroxidase span through sectors such as biorefinery, textile, energy, bioremediation, cosmetology, and dermatology industries. The litany of potentials attributed to lignin peroxidase is occasioned by its versatility in the degradation of xenobiotics and compounds with both phenolic and non-phenolic constituents. Over the years, ligninolytic enzymes have been studied however; research on lignin peroxidase seems to have been lagging when compared to other ligninolytic enzymes which are extracellular in nature including laccase and manganese peroxidase. This assertion becomes more pronounced when the application of lignin peroxidase is put into perspective. Consequently, a succinct documentation of the contemporary functionalities of lignin peroxidase and, some prospective applications of futuristic relevance has been advanced in this review. Some articulated applications include delignification of feedstock for ethanol production, textile effluent treatment and dye decolourization, coal depolymerization, treatment of hyperpigmentation, and skin-lightening through melanin oxidation. Prospective application of lignin peroxidase in skin-lightening functions through novel mechanisms, hence, it holds high value for the cosmetics sector where it may serve as suitable alternative to hydroquinone; a potent skin-lightening agent whose safety has generated lots of controversy and concern.
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Affiliation(s)
- Ayodeji O. Falade
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Uchechukwu U. Nwodo
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Benson C. Iweriebor
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Ezekiel Green
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Leonard V. Mabinya
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Anthony I. Okoh
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
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Mar BD, Kulik HJ. Depolymerization Pathways for Branching Lignin Spirodienone Units Revealed with ab Initio Steered Molecular Dynamics. J Phys Chem A 2017; 121:532-543. [PMID: 28005362 DOI: 10.1021/acs.jpca.6b11414] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lignocellulosic biomass is an abundant, rich source of aromatic compounds, but direct utilization of raw lignin has been hampered by both the high heterogeneity and variability of linking bonds in this biopolymer. Ab initio steered molecular dynamics (AISMD) has emerged both as a fruitful direct computational screening approach to identify products that occur through mechanical depolymerization (i.e., in sonication or ball-milling) and as a sampling approach. By varying the direction of force and sampling over 750 AISMD trajectories, we identify numerous possible pathways through which lignin depolymerization may occur in pyrolysis or through catalytic depolymerization as well. Here, we present eight unique major depolymerization pathways discovered via AISMD for the recently characterized spirodienone lignin branching linkage that may comprise around 10% weight of all lignin in some softwoods. We extract representative trajectories from AISMD and carry out reaction pathway analysis to identify energetically favorable pathways for lignin depolymerization. Importantly, we identify dynamical effects that could not be observed through more traditional calculations of bond dissociation energies. Such effects include thermodynamically favorable recovery of aromaticity in the dienone ring that leads to near-barrierless subsequent ether cleavage and hydrogen-bonding effects that stabilize newly formed radicals. Some of the most stable spirodienone fragments that reside at most 1 eV above the reactant structure are formed with only 2 eV barriers for C-C bond cleavage, suggesting key targets for catalyst design to drive targeted depolymerization of lignin.
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Affiliation(s)
- Brendan D Mar
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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244
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Rais D, Zibek S. Biotechnological and Biochemical Utilization of Lignin. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:469-518. [PMID: 28540404 DOI: 10.1007/10_2017_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This chapter provides an overview of the biosynthesis and structure of lignin. Moreover, examples of the commercial use of lignin and its promising future implementation are briefly described. Many applications are still hampered by the properties of technical lignins. Thus, the major challenge is the conversion of lignins into suitable building blocks or aromatics in order to open up new avenues for the usage of this renewable raw material. This chapter focuses on details about natural lignin degradation by fungi and bacteria, which harbor potential tools for lignin degradation and modification, which might help to develop eco-efficient processes for lignin utilization.
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Affiliation(s)
| | - Susanne Zibek
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
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245
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Chaplin AK, Wilson MT, Worrall JAR. Kinetic characterisation of a dye decolourising peroxidase from Streptomyces lividans: new insight into the mechanism of anthraquinone dye decolourisation. Dalton Trans 2017; 46:9420-9429. [DOI: 10.1039/c7dt01144j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A dye decolourising haem peroxidase fromStreptomyces lividansdecolourises the anthraquinone dye RB19 through a disproportionation mechanism.
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246
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Duwe A, Tippkötter N, Ulber R. Lignocellulose-Biorefinery: Ethanol-Focused. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:177-215. [PMID: 29071401 DOI: 10.1007/10_2016_72] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development prospects of the world markets for petroleum and other liquid fuels are diverse and partly contradictory. However, comprehensive changes for the energy supply of the future are essential. Notwithstanding the fact that there are still very large deposits of energy resources from a geological point of view, the finite nature of conventional oil reserves is indisputable. To reduce our dependence on oil, the EU, the USA, and other major economic zones rely on energy diversification. For this purpose, alternative materials and technologies are being sought, and is most obvious in the transport sector. The objective is to progressively replace fossil fuels with renewable and more sustainable fuels. In this respect, biofuels have a pre-eminent position in terms of their capability of blending with fossil fuels and being usable in existing cars without substantial modification. Ethanol can be considered as the primary renewable liquid fuel. In this chapter enzymes, micro-organisms, and processes for ethanol production based on renewable resources are described.
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Affiliation(s)
- A Duwe
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany.
| | - N Tippkötter
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany
| | - R Ulber
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany
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247
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Zhu D, Zhang P, Xie C, Zhang W, Sun J, Qian WJ, Yang B. Biodegradation of alkaline lignin by Bacillus ligniniphilus L1. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:44. [PMID: 28239416 PMCID: PMC5320714 DOI: 10.1186/s13068-017-0735-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/14/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Lignin is the most abundant aromatic biopolymer in the biosphere and it comprises up to 30% of plant biomass. Although lignin is the most recalcitrant component of the plant cell wall, still there are microorganisms able to decompose it or degrade it. Fungi are recognized as the most widely used microbes for lignin degradation. However, bacteria have also been known to be able to utilize lignin as a carbon or energy source. Bacillus ligniniphilus L1 was selected in this study due to its capability to utilize alkaline lignin as a single carbon or energy source and its excellent ability to survive in extreme environments. RESULTS To investigate the aromatic metabolites of strain L1 decomposing alkaline lignin, GC-MS analysis was performed and fifteen single phenol ring aromatic compounds were identified. The dominant absorption peak included phenylacetic acid, 4-hydroxy-benzoicacid, and vanillic acid with the highest proportion of metabolites resulting in 42%. Comparison proteomic analysis was carried out for further study showed that approximately 1447 kinds of proteins were produced, 141 of which were at least twofold up-regulated with alkaline lignin as the single carbon source. The up-regulated proteins contents different categories in the biological functions of protein including lignin degradation, ABC transport system, environmental response factors, protein synthesis, assembly, etc. CONCLUSIONS GC-MS analysis showed that alkaline lignin degradation of strain L1 produced 15 kinds of aromatic compounds. Comparison proteomic data and metabolic analysis showed that to ensure the degradation of lignin and growth of strain L1, multiple aspects of cells metabolism including transporter, environmental response factors, and protein synthesis were enhanced. Based on genome and proteomic analysis, at least four kinds of lignin degradation pathway might be present in strain L1, including a Gentisate pathway, the benzoic acid pathway and the β-ketoadipate pathway. The study provides an important basis for lignin degradation by bacteria.
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Affiliation(s)
- Daochen Zhu
- School of Environment and safty Engineering, Jiangsu University, Zhenjiang, Jiangsu China
- State Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, Guangdong China
| | - Peipei Zhang
- School of Environment and safty Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Changxiao Xie
- School of Environment and safty Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Weimin Zhang
- State Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, Guangdong China
| | - Jianzhong Sun
- School of Environment and safty Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Bin Yang
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA 99354 USA
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248
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The degradation of coniferyl alcohol and the complementary production of chlorogenic acids in the growth culture of Streptomyces albogriseolus KF977548 isolated from decaying wood residues. Process Biochem 2017. [DOI: 10.1016/j.procbio.2016.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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249
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De la Cruz-Barrón M, Cruz-Mendoza A, Navarro-Noya YE, Ruiz-Valdiviezo VM, Ortíz-Gutiérrez D, Ramírez-Villanueva DA, Luna-Guido M, Thierfelder C, Wall PC, Verhulst N, Govaerts B, Dendooven L. The Bacterial Community Structure and Dynamics of Carbon and Nitrogen when Maize (Zea mays L.) and Its Neutral Detergent Fibre Were Added to Soil from Zimbabwe with Contrasting Management Practices. MICROBIAL ECOLOGY 2017; 73:135-152. [PMID: 27538875 DOI: 10.1007/s00248-016-0807-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Abstract
Water infiltration, soil carbon content, aggregate stability and yields increased in conservation agriculture practices compared to conventionally ploughed control treatments at the Henderson research station near Mazowe (Zimbabwe). How these changes in soil characteristics affect the bacterial community structure and the bacteria involved in the degradation of applied organic material remains unanswered. Soil was sampled from three agricultural systems at Henderson, i.e. (1) conventional mouldboard ploughing with continuous maize (conventional tillage), (2) direct seeding with a Fitarelli jab planter and continuous maize (direct seeding with continuous maize) and (3) direct seeding with a Fitarelli jab planter with rotation of maize sunn hemp (direct seeding with crop rotation). Soil was amended with young maize plants or their neutral detergent fibre (NDF) and incubated aerobically for 56 days, while C and N mineralization and the bacterial community structure were monitored. Bacillus (Bacillales), Micrococcaceae (Actinomycetales) and phylotypes belonging to the Pseudomonadales were first degraders of the applied maize plants. At day 3, Streptomyces (Actinomycetales), Chitinophagaceae ([Saprospirales]) and Dyella (Xanthomonadales) participated in the degradation of the applied maize and at day 7 Oxalobacteraceae (Burkholderiales). Phylotypes belonging to Halomonas (Oceanospirillales) were the first degraders of NDF and were replaced by Phenylobacterium (Caulobacterales) and phylotypes belonging to Pseudomonadales at day 3. Afterwards, similar bacterial groups were favoured by application of NDF as they were by the application of maize plants, but there were also clear differences. Phylotypes belonging to the Micrococcaceae and Bacillus did not participate in the degradation of NDF or its metabolic products, while phylotypes belonging to the Acidobacteriaceae participated in the degradation of NDF but not in that of maize plants. It was found that agricultural practices had a limited effect on the bacterial community structure, but application of organic material altered it substantially.
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Affiliation(s)
| | | | - Yendi E Navarro-Noya
- Cátedras CONACYT-Universidad Autónoma de Tlaxcala, Av. Universidad 1, C.P., 90062, Tlaxcala, Mexico
| | | | | | | | - Marco Luna-Guido
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, Mexico
| | - Cristian Thierfelder
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Patrick C Wall
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Bram Govaerts
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, Mexico.
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250
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McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD. Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase. Proc Natl Acad Sci U S A 2016; 113:14324-14329. [PMID: 27911781 PMCID: PMC5167157 DOI: 10.1073/pnas.1608917113] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stilbenes are diphenyl ethene compounds produced naturally in a wide variety of plant species and some bacteria. Stilbenes are also derived from lignin during kraft pulping. Stilbene cleavage oxygenases (SCOs) cleave the central double bond of stilbenes, forming two phenolic aldehydes. Here, we report the structure of an SCO. The X-ray structure of NOV1 from Novosphingobium aromaticivorans was determined in complex with its substrate resveratrol (1.89 Å), its product vanillin (1.75 Å), and without any bound ligand (1.61 Å). The enzyme is a seven-bladed β-propeller with an iron cofactor coordinated by four histidines. In all three structures, dioxygen is observed bound to the iron in a side-on fashion. These structures, along with EPR analysis, allow us to propose a mechanism in which a ferric-superoxide reacts with substrate activated by deprotonation of a phenol group at position 4 of the substrate, which allows movement of electron density toward the central double bond and thus facilitates reaction with the ferric superoxide electrophile. Correspondingly, NOV1 cleaves a wide range of other stilbene-like compounds with a 4'-OH group, offering potential in processing some solubilized fragments of lignin into monomer aromatic compounds.
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Affiliation(s)
- Ryan P McAndrew
- Joint BioEnergy Institute, Emeryville, CA 94608;
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Noppadon Sathitsuksanoh
- Joint BioEnergy Institute, Emeryville, CA 94608
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Chemical Engineering, University of Louisville, Louisville, KY 40292
- Conn Center for Renewable Energy Research, University of Louisville, Louisville, KY 40292
| | - Michael M Mbughuni
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706
| | - Richard A Heins
- Joint BioEnergy Institute, Emeryville, CA 94608
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551
| | - Jose H Pereira
- Joint BioEnergy Institute, Emeryville, CA 94608
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Anthe George
- Joint BioEnergy Institute, Emeryville, CA 94608
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551
| | - Kenneth L Sale
- Joint BioEnergy Institute, Emeryville, CA 94608
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551
| | - Brian G Fox
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA 94608;
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, CA 94720
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