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Phylogenetic and kinetic characterization of a suite of dehydrogenases from a newly isolated bacterium, strain SG61-1L, that catalyze the turnover of guaiacylglycerol-β-guaiacyl ether stereoisomers. Appl Environ Microbiol 2015; 81:8164-76. [PMID: 26386069 PMCID: PMC4651090 DOI: 10.1128/aem.01573-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/15/2015] [Indexed: 11/20/2022] Open
Abstract
Lignin is a complex aromatic polymer found in plant cell walls that makes up 15 to 40% of plant biomass. The degradation of lignin substructures by bacteria is of emerging interest because it could provide renewable alternative feedstocks and intermediates for chemical manufacturing industries. We have isolated a bacterium, strain SG61-1L, that rapidly degrades all of the stereoisomers of one lignin substructure, guaiacylglycerol-β-guaiacyl ether (GGE), which contains a key β-O-4 linkage found in most intermonomer linkages in lignin. In an effort to understand the rapid degradation of GGE by this bacterium, we heterologously expressed and kinetically characterized a suite of dehydrogenase candidates for the first known step of GGE degradation. We identified a clade of active GGE dehydrogenases and also several other dehydrogenases outside this clade that were all able to oxidize GGE. Several candidates exhibited stereoselectivity toward the GGE stereoisomers, while others had higher levels of catalytic performance than previously described GGE dehydrogenases for all four stereoisomers, indicating a variety of potential applications for these enzymes in the manufacture of lignin-derived commodities.
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302
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Membrane-associated glucose-methanol-choline oxidoreductase family enzymes PhcC and PhcD are essential for enantioselective catabolism of dehydrodiconiferyl alcohol. Appl Environ Microbiol 2015; 81:8022-36. [PMID: 26362985 DOI: 10.1128/aem.02391-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/09/2015] [Indexed: 01/06/2023] Open
Abstract
Sphingobium sp. strain SYK-6 is able to degrade various lignin-derived biaryls, including a phenylcoumaran-type compound, dehydrodiconiferyl alcohol (DCA). In SYK-6 cells, the alcohol group of the B-ring side chain of DCA is initially oxidized to the carboxyl group to generate 3-(2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-7-methoxy-2,3-dihydrobenzofuran-5-yl) acrylic acid (DCA-C). Next, the alcohol group of the A-ring side chain of DCA-C is oxidized to the carboxyl group, and then the resulting metabolite is catabolized through vanillin and 5-formylferulate. In this study, the genes involved in the conversion of DCA-C were identified and characterized. The DCA-C oxidation activities in SYK-6 were enhanced in the presence of flavin adenine dinucleotide and an artificial electron acceptor and were induced ca. 1.6-fold when the cells were grown with DCA. Based on these observations, SLG_09480 (phcC) and SLG_09500 (phcD), encoding glucose-methanol-choline oxidoreductase family proteins, were presumed to encode DCA-C oxidases. Analyses of phcC and phcD mutants indicated that PhcC and PhcD are essential for the conversion of (+)-DCA-C and (-)-DCA-C, respectively. When phcC and phcD were expressed in SYK-6 and Escherichia coli, the gene products were mainly observed in their membrane fractions. The membrane fractions of E. coli that expressed phcC and phcD catalyzed the specific conversion of DCA-C into the corresponding carboxyl derivatives. In the oxidation of DCA-C, PhcC and PhcD effectively utilized ubiquinone derivatives as electron acceptors. Furthermore, the transcription of a putative cytochrome c gene was significantly induced in SYK-6 grown with DCA. The DCA-C oxidation catalyzed by membrane-associated PhcC and PhcD appears to be coupled to the respiratory chain.
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303
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Abstract
Litter decomposition is a keystone ecosystem process impacting nutrient cycling and productivity, soil properties, and the terrestrial carbon (C) balance, but the factors regulating decomposition rate are still poorly understood. Traditional models assume that the rate is controlled by litter quality, relying on parameters such as lignin content as predictors. However, a strong correlation has been observed between the manganese (Mn) content of litter and decomposition rates across a variety of forest ecosystems. Here, we show that long-term litter decomposition in forest ecosystems is tightly coupled to Mn redox cycling. Over 7 years of litter decomposition, microbial transformation of litter was paralleled by variations in Mn oxidation state and concentration. A detailed chemical imaging analysis of the litter revealed that fungi recruit and redistribute unreactive Mn(2+) provided by fresh plant litter to produce oxidative Mn(3+) species at sites of active decay, with Mn eventually accumulating as insoluble Mn(3+/4+) oxides. Formation of reactive Mn(3+) species coincided with the generation of aromatic oxidation products, providing direct proof of the previously posited role of Mn(3+)-based oxidizers in the breakdown of litter. Our results suggest that the litter-decomposing machinery at our coniferous forest site depends on the ability of plants and microbes to supply, accumulate, and regenerate short-lived Mn(3+) species in the litter layer. This observation indicates that biogeochemical constraints on bioavailability, mobility, and reactivity of Mn in the plant-soil system may have a profound impact on litter decomposition rates.
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304
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Picart P, de María PD, Schallmey A. From gene to biorefinery: microbial β-etherases as promising biocatalysts for lignin valorization. Front Microbiol 2015; 6:916. [PMID: 26388858 PMCID: PMC4560021 DOI: 10.3389/fmicb.2015.00916] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/21/2015] [Indexed: 11/13/2022] Open
Abstract
The set-up of biorefineries for the valorization of lignocellulosic biomass will be core in the future to reach sustainability targets. In this area, biomass-degrading enzymes are attracting significant research interest for their potential in the production of chemicals and biofuels from renewable feedstock. Glutathione-dependent β-etherases are emerging enzymes for the biocatalytic depolymerization of lignin, a heterogeneous aromatic polymer abundant in nature. They selectively catalyze the reductive cleavage of β-O-4 aryl-ether bonds which account for 45–60% of linkages present in lignin. Hence, application of β-etherases in lignin depolymerization would enable a specific lignin breakdown, selectively yielding (valuable) low-molecular-mass aromatics. Albeit β-etherases have been biochemically known for decades, only very recently novel β-etherases have been identified and thoroughly characterized for lignin valorization, expanding the enzyme toolbox for efficient β-O-4 aryl-ether bond cleavage. Given their emerging importance and potential, this mini-review discusses recent developments in the field of β-etherase biocatalysis covering all aspects from enzyme identification to biocatalytic applications with real lignin samples.
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Affiliation(s)
- Pere Picart
- Institute of Biotechnology, RWTH Aachen University , Aachen, Germany
| | | | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig , Braunschweig, Germany
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305
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Cébron A, Beguiristain T, Bongoua-Devisme J, Denonfoux J, Faure P, Lorgeoux C, Ouvrard S, Parisot N, Peyret P, Leyval C. Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13724-13738. [PMID: 25616383 DOI: 10.1007/s11356-015-4117-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/11/2015] [Indexed: 06/04/2023]
Abstract
The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the development of PAH-degrading bacteria holding Gram-negative PAH-ring hydroxylating dioxygenase, catechol-1,2-dioxygenase and catechol-2,3-dioxygenase genes. Regarding the total community structure, bacteria closely related to Thiobacillus (β-Proteobacteria) and Steroidobacter (γ-Proteobacteria) genera were favoured by wood sawdust amendment. In both soils, plant rhizospheres induced the development of fungi belonging to Ascomycota and related to Alternaria and Fusarium genera. Bacteria closely related to Luteolibacter (Verrucomicrobia) and Microbacterium (Actinobacteria) were favoured in alfalfa and ryegrass rhizosphere.
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Affiliation(s)
- Aurélie Cébron
- CNRS, LIEC UMR 7360, Faculté des Sciences et Technologies, BP 70239, 54506, Vandoeuvre-lès-Nancy Cedex, France,
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306
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Ogura T, Date Y, Tsuboi Y, Kikuchi J. Metabolic dynamics analysis by massive data integration: application to tsunami-affected field soils in Japan. ACS Chem Biol 2015; 10:1908-15. [PMID: 25997449 DOI: 10.1021/cb500609p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A new metabolic dynamics analysis approach has been developed in which massive data sets from time-series of (1)H and (13)C NMR spectra are integrated in combination with microbial variability to characterize the biomass degradation process using field soil microbial communities. On the basis of correlation analyses that revealed relationships between various metabolites and bacteria, we efficiently monitored the metabolic dynamics of saccharides, amino acids, and organic acids, by assessing time-course changes in the microbial and metabolic profiles during biomass degradation. Specific bacteria were found to support specific steps of metabolic pathways in the degradation process of biomass to short chain fatty acids. We evaluated samples from agricultural and abandoned fields contaminated by the tsunami that followed the Great East earthquake in Japan. Metabolic dynamics and activities in the biomass degradation process differed considerably between soil from agricultural and abandoned fields. In particular, production levels of short chain fatty acids, such as acetate and propionate, which were considered to be produced by soil bacteria such as Sedimentibacter sp. and Coprococcus sp., were higher in the soil from agricultural fields than from abandoned fields. Our approach could characterize soil activity based on the metabolic dynamics of microbial communities in the biomass degradation process and should therefore be useful in future investigations of the environmental effects of natural disasters on soils.
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Affiliation(s)
- Tatsuki Ogura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuuri Tsuboi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate
School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-0810, Japan
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307
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Santana RH, Catão ECP, Lopes FAC, Constantino R, Barreto CC, Krüger RH. The Gut Microbiota of Workers of the Litter-Feeding Termite Syntermes wheeleri (Termitidae: Syntermitinae): Archaeal, Bacterial, and Fungal Communities. MICROBIAL ECOLOGY 2015; 70:545-556. [PMID: 25749937 DOI: 10.1007/s00248-015-0581-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 02/03/2015] [Indexed: 06/04/2023]
Abstract
The gut microbiota of termites allows them to thrive on a variety of different materials such as wood, litter, and soil. For that reason, they play important roles in the decomposition of biomass in diverse biomes. This function is essential in the savanna, where litter-feeding termites are one of the few invertebrates active during the dry season. In this study, we describe the gut microbiota of workers (third and fourth instars) of the species Syntermes wheeleri, a litter-feeding termite from the Brazilian savanna. Results of 16S and 18S ribosomal RNA (rRNA) gene-targeted pyrosequencing using primers sets specific to each domain have revealed its bacterial, archaeal, and fungal diversities. Firmicutes accounted for more than half of the operational taxonomic units of the Bacteria domain. The most abundant fungal species were from the class Dothideomycetes of the phylum Ascomycota. The methanogenic orders Methanobacteriales, Methanosarcinales, and Methanomicrobiales of the phylum Euryarchaeota accounted for the greatest part of the Archaea detected in this termite. A comparison of the gut microbiota of the two instars revealed a difference in operational taxonomic unit (OTU) abundance but not in species richness. This description of the whole gut microbiota represents the first study to evaluate relationships among bacteria, archaea, fungi, and host in S. wheeleri.
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Affiliation(s)
- Renata Henrique Santana
- Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil
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308
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Medina J, Monreal C, Barea JM, Arriagada C, Borie F, Cornejo P. Crop residue stabilization and application to agricultural and degraded soils: A review. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 42:41-54. [PMID: 25936555 DOI: 10.1016/j.wasman.2015.04.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
Agricultural activities produce vast amounts of organic residues including straw, unmarketable or culled fruit and vegetables, post-harvest or post-processing wastes, clippings and residuals from forestry or pruning operations, and animal manure. Improper disposal of these materials may produce undesirable environmental (e.g. odors or insect refuges) and health impacts. On the other hand, agricultural residues are of interest to various industries and sectors of the economy due to their energy content (i.e., for combustion), their potential use as feedstock to produce biofuels and/or fine chemicals, or as a soil amendments for polluted or degraded soils when composted. Our objective is review new biotechnologies that could be used to manage these residues for land application and remediation of contaminated and eroded soils. Bibliographic information is complemented through a comprehensive review of the physico-chemical fundamental mechanisms involved in the transformation and stabilization of organic matter by biotic and abiotic soil components.
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Affiliation(s)
- Jorge Medina
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile; Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile
| | - Carlos Monreal
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Center, K.W. Neatby Building, Ottawa K1A0C6, Canada
| | - José Miguel Barea
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain
| | - César Arriagada
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile
| | - Fernando Borie
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile; Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile
| | - Pablo Cornejo
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile; Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco, Chile.
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309
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Hall SJ, Silver WL, Timokhin VI, Hammel KE. Lignin decomposition is sustained under fluctuating redox conditions in humid tropical forest soils. GLOBAL CHANGE BIOLOGY 2015; 21:2818-2828. [PMID: 25711691 DOI: 10.1111/gcb.12908] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
Lignin mineralization represents a critical flux in the terrestrial carbon (C) cycle, yet little is known about mechanisms and environmental factors controlling lignin breakdown in mineral soils. Hypoxia is thought to suppress lignin decomposition, yet potential effects of oxygen (O2 ) variability in surface soils have not been explored. Here, we tested the impact of redox fluctuations on lignin breakdown in humid tropical forest soils during ten-week laboratory incubations. We used synthetic lignins labeled with 13 C in either of two positions (aromatic methoxyl or propyl side chain Cβ ) to provide highly sensitive and specific measures of lignin mineralization seldom employed in soils. Four-day redox fluctuations increased the percent contribution of methoxyl C to soil respiration relative to static aerobic conditions, and cumulative methoxyl-C mineralization was statistically equivalent under static aerobic and fluctuating redox conditions despite lower soil respiration in the latter treatment. Contributions of the less labile lignin Cβ to soil respiration were equivalent in the static aerobic and fluctuating redox treatments during periods of O2 exposure, and tended to decline during periods of O2 limitation, resulting in lower cumulative Cβ mineralization in the fluctuating treatment relative to the static aerobic treatment. However, cumulative mineralization of both the Cβ - and methoxyl-labeled lignins nearly doubled in the fluctuating treatment relative to the static aerobic treatment when total lignin mineralization was normalized to total O2 exposure. Oxygen fluctuations are thought to be suboptimal for canonical lignin-degrading microorganisms. However, O2 fluctuations drove substantial Fe reduction and oxidation, and reactive oxygen species generated during abiotic Fe oxidation might explain the elevated contribution of lignin to C mineralization. Iron redox cycling provides a potential mechanism for lignin depletion in soil organic matter. Couplings between soil moisture, redox fluctuations, and lignin breakdown provide a potential link between climate variability and the biochemical composition of soil organic matter.
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Affiliation(s)
- Steven J Hall
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Whendee L Silver
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Vitaliy I Timokhin
- Department of Biochemistry, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53706, USA
| | - Kenneth E Hammel
- US Forest Products Laboratory, Madison, WI, 53726, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
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310
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Enzymatic conversion of lignin into renewable chemicals. Curr Opin Chem Biol 2015; 29:10-7. [PMID: 26121945 DOI: 10.1016/j.cbpa.2015.06.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 05/29/2015] [Accepted: 06/08/2015] [Indexed: 11/22/2022]
Abstract
The aromatic heteropolymer lignin is a major component of plant cell walls, and is produced industrially from paper/pulp manufacture and cellulosic bioethanol production. Conversion of lignin into renewable chemicals is a major unsolved problem in the development of a biomass-based biorefinery. The review describes recent developments in the understanding of bacterial enzymes for lignin breakdown, such as DyP peroxidases, bacterial laccases, and beta-etherase enzymes. The use of pathway engineering methods to construct genetically modified microbes to convert lignin to renewable chemicals (e.g. vanillin, adipic acid) via fermentation is discussed, and the search for novel applications for lignin (e.g. carbon fibre).
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311
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Environmental factors shaping the abundance and distribution of laccase-encoding bacterial community with potential phenolic oxidase capacity during composting. Appl Microbiol Biotechnol 2015; 99:9191-201. [DOI: 10.1007/s00253-015-6754-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 05/26/2015] [Accepted: 05/30/2015] [Indexed: 11/26/2022]
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312
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Mar BD, Qi HW, Liu F, Kulik HJ. Ab Initio Screening Approach for the Discovery of Lignin Polymer Breaking Pathways. J Phys Chem A 2015; 119:6551-62. [PMID: 26001164 DOI: 10.1021/acs.jpca.5b03503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The directed depolymerization of lignin biopolymers is of utmost relevance for the valorization or commercialization of biomass fuels. We present a computational and theoretical screening approach to identify potential cleavage pathways and resulting fragments that are formed during depolymerization of lignin oligomers containing two to six monomers. We have developed a chemical discovery technique to identify the chemically relevant putative fragments in eight known polymeric linkage types of lignin. Obtaining these structures is a crucial precursor to the development of any further kinetic modeling. We have developed this approach by adapting steered molecular dynamics calculations under constant force and varying the points of applied force in the molecule to diversify the screening approach. Key observations include relationships between abundance and breaking frequency, the relative diversity of potential pathways for a given linkage, and the observation that readily cleaved bonds can destabilize adjacent bonds, causing subsequent automatic cleavage.
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Affiliation(s)
| | | | - Fang Liu
- §Department of Chemistry, Stanford University, Stanford, California 94305, United States
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313
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Wuensch C, Pavkov-Keller T, Steinkellner G, Gross J, Fuchs M, Hromic A, Lyskowski A, Fauland K, Gruber K, Glueck SM, Faber K. Regioselective Enzymatic β-Carboxylation of para-Hydroxy- styrene Derivatives Catalyzed by Phenolic Acid Decarboxylases. Adv Synth Catal 2015; 357:1909-1918. [PMID: 26190963 PMCID: PMC4498466 DOI: 10.1002/adsc.201401028] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/07/2015] [Indexed: 11/17/2022]
Abstract
We report on a 'green' method for the utilization of carbon dioxide as C1 unit for the regioselective synthesis of (E)-cinnamic acids via regioselective enzymatic carboxylation of para-hydroxystyrenes. Phenolic acid decarboxylases from bacterial sources catalyzed the β-carboxylation of para-hydroxystyrene derivatives with excellent regio- and (E/Z)-stereoselectivity by exclusively acting at the β-carbon atom of the C=C side chain to furnish the corresponding (E)-cinnamic acid derivatives in up to 40% conversion at the expense of bicarbonate as carbon dioxide source. Studies on the substrate scope of this strategy are presented and a catalytic mechanism is proposed based on molecular modelling studies supported by mutagenesis of amino acid residues in the active site.
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Affiliation(s)
- Christiane Wuensch
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Tea Pavkov-Keller
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Johannes Gross
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Michael Fuchs
- Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Altijana Hromic
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Andrzej Lyskowski
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Kerstin Fauland
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Silvia M Glueck
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
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314
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Pold G, Melillo JM, DeAngelis KM. Two decades of warming increases diversity of a potentially lignolytic bacterial community. Front Microbiol 2015; 6:480. [PMID: 26042112 PMCID: PMC4438230 DOI: 10.3389/fmicb.2015.00480] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/30/2015] [Indexed: 11/13/2022] Open
Abstract
As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
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Affiliation(s)
- Grace Pold
- Microbiology Department, University of Massachusetts Amherst, MA, USA ; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, MA, USA
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315
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Ye XK, Chen Y. Kinetics study of enzymatic hydrolysis of Paulownia by dilute acid, alkali, and ultrasonic-assisted alkali pretreatments. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0490-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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316
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Plácido J, Capareda S. Ligninolytic enzymes: a biotechnological alternative for bioethanol production. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0049-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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317
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Affiliation(s)
- James Harrison
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
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318
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Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00019-15. [PMID: 25744986 PMCID: PMC4358373 DOI: 10.1128/genomea.00019-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas sp. strain YS-1p and Rhizobium sp. strain YS-1r were isolated from a lignin-degrading enrichment culture. The isolates degraded lignin-derived monomers, dimers, alkali lignin, and, to a smaller extent (3% to 5%), lignin in switch grass and alfalfa. Genome analysis revealed the presence of a variety of lignin-degrading genes.
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319
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Johnson CW, Beckham GT. Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin. Metab Eng 2015; 28:240-247. [DOI: 10.1016/j.ymben.2015.01.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/08/2015] [Accepted: 01/13/2015] [Indexed: 10/24/2022]
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320
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Mathews SL, Pawlak J, Grunden AM. Bacterial biodegradation and bioconversion of industrial lignocellulosic streams. Appl Microbiol Biotechnol 2015; 99:2939-54. [PMID: 25722022 DOI: 10.1007/s00253-015-6471-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 01/10/2023]
Abstract
Lignocellulose is a term for plant materials that are composed of matrices of cellulose, hemicellulose, and lignin. Lignocellulose is a renewable feedstock for many industries. Lignocellulosic materials are used for the production of paper, fuels, and chemicals. Typically, industry focuses on transforming the polysaccharides present in lignocellulose into products resulting in the incomplete use of this resource. The materials that are not completely used make up the underutilized streams of materials that contain cellulose, hemicellulose, and lignin. These underutilized streams have potential for conversion into valuable products. Treatment of these lignocellulosic streams with bacteria, which specifically degrade lignocellulose through the action of enzymes, offers a low-energy and low-cost method for biodegradation and bioconversion. This review describes lignocellulosic streams and summarizes different aspects of biological treatments including the bacteria isolated from lignocellulose-containing environments and enzymes which may be used for bioconversion. The chemicals produced during bioconversion can be used for a variety of products including adhesives, plastics, resins, food additives, and petrochemical replacements.
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Affiliation(s)
- Stephanie L Mathews
- Department of Plant and Microbial Biology, North Carolina State University, 4550A Thomas Hall, Campus Box 7612, Raleigh, NC, 27695, USA,
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321
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A dye-decolorizing peroxidase from Bacillus subtilis exhibiting substrate-dependent optimum temperature for dyes and β-ether lignin dimer. Sci Rep 2015; 5:8245. [PMID: 25650125 PMCID: PMC4316163 DOI: 10.1038/srep08245] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/19/2014] [Indexed: 11/17/2022] Open
Abstract
In the biorefinery using lignocellulosic biomass as feedstock, pretreatment to breakdown or loosen lignin is important step and various approaches have been conducted. For biological pretreatment, we screened Bacillus subtilis KCTC2023 as a potential lignin-degrading bacterium based on veratryl alcohol (VA) oxidation test and the putative heme-containing dye-decolorizing peroxidase was found in the genome of B. subtilis KCTC2023. The peroxidase from B. subtilis KCTC2023 (BsDyP) was capable of oxidizing various substrates and atypically exhibits substrate-dependent optimum temperature: 30°C for dyes (Reactive Blue19 and Reactive Black5) and 50°C for high redox potential substrates (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid [ABTS], VA, and veratryl glycerol-β-guaiacyl ether [VGE]) over +1.0 V vs. normal hydrogen electrode. At 50°C, optimum temperature for high redox potential substrates, BsDyP not only showed the highest VA oxidation activity (0.13 Umg−1) among the previously reported bacterial peroxidases but also successfully achieved VGE decomposition by cleaving Cα-Cβ bond in the absence of any oxidative mediator with a specific activity of 0.086 Umg−1 and a conversion rate of 53.5%. Based on our results, BsDyP was identified as the first bacterial peroxidase capable of oxidizing high redox potential lignin-related model compounds, especially VGE, revealing a previously unknown versatility of lignin degrading biocatalyst in nature.
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322
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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323
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Lin J, Chen J, He J, Chen J, Yan Q, Zhou J, Xie P. Effects of microcystin-LR on bacterial and fungal functional genes profile in rat gut. Toxicon 2015; 96:50-6. [PMID: 25617596 DOI: 10.1016/j.toxicon.2015.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/29/2014] [Accepted: 01/20/2015] [Indexed: 10/24/2022]
Abstract
The short-term exposure to microcystin-LR (MC-LR, one of the most common and toxic variants generated by toxigenic cyanobacteria) induced gut dysfunction such as generation of reactive oxygen species, cell erosion and deficient intestinal absorption of nutrients. However, till now, little is known about its impact on gut microbial community, which has been considered as necessary metabolic assistant and stresses resistant entities for the host. This study was designed to reveal the shift of microbial functional genes in the gut of rat orally gavaged with MC-LR. GeoChip detected a high diversity of bacterial and fungal genes involved in basic metabolic processes and stress resistance. The results showed that the composition of functional genes was significantly changed in rat gut after one week of exposure to MC-LR, and we found some relatively enriched genes that are involved in carbon degradation including chitin, starch and limonene metabolism, and these genes were mainly derived from fungal and bacterial pathogens. In addition, we found large amounts of significantly enriched genes relevant to degradation of the specific carbon compounds, aromatics. The dysbiosis of bacterial and fungal flora gave an implication of pathogens invasion. The enriched gene functions could be linked to acute gastroenteritis induced by MC-LR.
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Affiliation(s)
- Juan Lin
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; Graduate University of Chinese Academy of Sciences, Beijing 10049, PR China
| | - Jun Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Jun He
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; Graduate University of Chinese Academy of Sciences, Beijing 10049, PR China
| | - Jing Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; Graduate University of Chinese Academy of Sciences, Beijing 10049, PR China
| | - Qingyun Yan
- Key Laboratory of Biodiversity and Conservation of Aquatic Organisms, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
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324
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Characterisation of Dyp-type peroxidases from Pseudomonas fluorescens Pf-5: Oxidation of Mn(II) and polymeric lignin by Dyp1B. Arch Biochem Biophys 2015; 574:93-8. [PMID: 25558792 DOI: 10.1016/j.abb.2014.12.022] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 11/24/2022]
Abstract
Members of the DyP family of peroxidases in Gram-positive bacteria have recently been shown to oxidise Mn(II) and lignin model compounds. Gram-negative pseudomonads, which also show activity for lignin oxidation, also contain dyp-type peroxidase genes. Pseudomonas fluorescens Pf-5 contains three dyp-type peroxidases (35, 40 and 55kDa), each of which has been overexpressed in Escherichia coli, purified, and characterised. Each of the three enzymes shows activity for oxidation of phenol substrates, but the 35kDa Dyp1B enzyme also shows activity for oxidation of Mn(II) and Kraft lignin. Treatment of powdered lignocellulose with Dyp1B in the presence of Mn(II) and hydrogen peroxide leads to the release of a low molecular weight lignin fragment, which has been identified by mass spectrometry as a β-aryl ether lignin dimer containing one G unit and one H unit bearing a benzylic ketone. A mechanism for release of this fragment from lignin oxidation is proposed.
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325
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Chen M, Zeng G, Lai C, Li J, Xu P, Wu H. Molecular basis of laccase bound to lignin: insight from comparative studies on the interaction of Trametes versicolor laccase with various lignin model compounds. RSC Adv 2015. [DOI: 10.1039/c5ra07916k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Binding orientation of lignin model compounds in laccase.
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Affiliation(s)
- Ming Chen
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
| | - Guangming Zeng
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
| | - Cui Lai
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
| | - Jian Li
- Department of River
- Yangtze River Scientific Research Institute
- Wuhan 430010
- China
| | - Piao Xu
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
| | - Haipeng Wu
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
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326
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Transcriptional regulation of the vanillate utilization genes (vanABK Operon) of Corynebacterium glutamicum by VanR, a PadR-like repressor. J Bacteriol 2014; 197:959-72. [PMID: 25535273 DOI: 10.1128/jb.02431-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium glutamicum is able to utilize vanillate, the product of lignin degradation, as the sole carbon source. The vanillate utilization components are encoded by the vanABK operon. The vanA and vanB genes encode the subunits of vanillate O-demethylase, converting vanillate to protocatechuate, while VanK is the specific vanillate transporter. The vanABK operon is regulated by a PadR-type repressor, VanR. Heterologous gene expression and variations of the vanR open reading frame revealed that the functional VanR contains 192 residues (21 kDa) and forms a dimer, as analyzed by size exclusion chromatography. In vivo, ferulate, vanillin, and vanillate induced PvanABK in C. glutamicum, while only vanillate induced the activity of PvanABK in Escherichia coli lacking the ferulate catabolic system. Differential scanning fluorimetry verified that vanillate is the only effector of VanR. Interaction between the PvanABK DNA fragment and the VanR protein had an equilibrium dissociation constant (KD) of 15.1 ± 1.7 nM. The VanR-DNA complex had a dissociation rate constant (Kd) of (267 ± 23) × 10(-6) s(-1), with a half-life of 43.5 ± 3.6 min. DNase I footprinting localized the VanR binding site at PvanABK, extending from +9 to +45 on the coding strand. Deletion of the nucleotides +18 to +27 inside the VanR binding site rendered PvanABK constitutive. Fusion of the T7 promoter and the wild-type VanR operator, as well as its shortened versions, indicated that the inverted repeat AACTAACTAA(N4)TTAGGTATTT is the specific VanR binding site. It is proposed that the VanR-DNA complex contains two VanR dimers at the VanR operator.
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327
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Population genetic analysis of Streptomyces albidoflavus reveals habitat barriers to homologous recombination in the diversification of streptomycetes. Appl Environ Microbiol 2014; 81:966-75. [PMID: 25416769 DOI: 10.1128/aem.02925-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes.
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328
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Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez‐Valera F. Key roles for freshwater
A
ctinobacteria revealed by deep metagenomic sequencing. Mol Ecol 2014; 23:6073-90. [DOI: 10.1111/mec.12985] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Rohit Ghai
- Evolutionary Genomics Group Departamento de Producción Vegetal y Microbiología Universidad Miguel Hernández San Juan de Alicante 03550 Alicante Spain
| | - Carolina Megumi Mizuno
- Evolutionary Genomics Group Departamento de Producción Vegetal y Microbiología Universidad Miguel Hernández San Juan de Alicante 03550 Alicante Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia Burjassot E‐46100 Valencia Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia Burjassot E‐46100 Valencia Spain
| | - Francisco Rodriguez‐Valera
- Evolutionary Genomics Group Departamento de Producción Vegetal y Microbiología Universidad Miguel Hernández San Juan de Alicante 03550 Alicante Spain
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329
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Microbial enzyme systems for lignin degradation and their transcriptional regulation. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1336-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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330
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Schaller J, Hines J, Brackhage C, Bäucker E, Gessner MO. Silica decouples fungal growth and litter decomposition without changing responses to climate warming and N enrichment. Ecology 2014. [DOI: 10.1890/13-2104.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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331
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Tian JH, Pourcher AM, Bouchez T, Gelhaye E, Peu P. Occurrence of lignin degradation genotypes and phenotypes among prokaryotes. Appl Microbiol Biotechnol 2014; 98:9527-44. [PMID: 25343973 DOI: 10.1007/s00253-014-6142-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/24/2022]
Abstract
A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNA sequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.
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Affiliation(s)
- Jiang-Hao Tian
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, 35044, Rennes, France
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332
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Gall DL, Ralph J, Donohue TJ, Noguera D. A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:12454-63. [PMID: 25232892 PMCID: PMC4207535 DOI: 10.1021/es503886d] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Lignin biosynthesis occurs via radical coupling of guaiacyl and syringyl hydroxycinnamyl alcohol monomers (i.e., "monolignols") through chemical condensation with the growing lignin polymer. With each chain-extension step, monolignols invariably couple at their β-positions, generating chiral centers. Here, we report on activities of bacterial glutathione-S-transferase (GST) enzymes that cleave β-aryl ether bonds in lignin dimers that are composed of different monomeric units. Our data reveal that these sequence-related enzymes from Novosphingobium sp. strain PP1Y, Novosphingobium aromaticivorans strain DSM12444, and Sphingobium sp. strain SYK-6 have conserved functions as β-etherases, catalyzing cleavage of each of the four dimeric α-keto-β-aryl ether-linked substrates (i.e., guaiacyl-β-guaiacyl, guaiacyl-β-syringyl, syringyl-β-guaiacyl, and syringyl-β-syringyl). Although each β-etherase cleaves β-guaiacyl and β-syringyl substrates, we have found that each is stereospecific for a given β-enantiomer in a racemic substrate; LigE and LigP β-etherase homologues exhibited stereospecificity toward β(R)-enantiomers whereas LigF and its homologues exhibited β(S)-stereospecificity. Given the diversity of lignin's monomeric units and the racemic nature of lignin polymers, we propose that bacterial catabolic pathways have overcome the existence of diverse lignin-derived substrates in nature by evolving multiple enzymes with broad substrate specificities. Thus, each bacterial β-etherase is able to cleave β-guaiacyl and β-syringyl ether-linked compounds while retaining either β(R)- or β(S)-stereospecificity.
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Affiliation(s)
- Daniel L. Gall
- Department
of Civil & Environmental Engineering, University of Wisconsin, Madison, Wisconsin 53706, United States
- U.S.
Department of Energy’s Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison Wisconsin 53726, United States
- Phone: 608-265-8465; e-mail:
| | - John Ralph
- U.S.
Department of Energy’s Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison Wisconsin 53726, United States
- Department
of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Timothy J. Donohue
- U.S.
Department of Energy’s Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison Wisconsin 53726, United States
- Department
of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Daniel
R. Noguera
- Department
of Civil & Environmental Engineering, University of Wisconsin, Madison, Wisconsin 53706, United States
- U.S.
Department of Energy’s Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison Wisconsin 53726, United States
- Environmental
Chemistry and Technology Program, University
of Wisconsin, Madison, Wisconsin 53706, United States
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333
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Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R. Census-based rapid and accurate metagenome taxonomic profiling. BMC Genomics 2014; 15:918. [PMID: 25336203 PMCID: PMC4218995 DOI: 10.1186/1471-2164-15-918] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/06/2014] [Indexed: 12/04/2022] Open
Abstract
Background Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis. Results Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results. Conclusion CensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%. Windows and UNIX versions of CensuScope are available for download at https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope. CensuScope is also available through the High-performance Integrated Virtual Environment (HIVE) and can be used in conjunction with other HIVE analysis and visualization tools. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-918) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, George Washington University, Washington DC 20037, USA.
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334
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Eastman AW, Heinrichs DE, Yuan ZC. Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness. BMC Genomics 2014; 15:851. [PMID: 25280501 PMCID: PMC4209062 DOI: 10.1186/1471-2164-15-851] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 09/22/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported. RESULTS Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp. CONCLUSIONS Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.
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Affiliation(s)
| | | | - Ze-Chun Yuan
- Southern Crop Protection & Food Research Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4 T3, Canada.
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335
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Co-occurrence of bacteria and fungi and spatial partitioning during photographic materials biodeterioration. Polym Degrad Stab 2014. [DOI: 10.1016/j.polymdegradstab.2014.05.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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336
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337
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Keegan R, Lebedev A, Erskine P, Guo J, Wood SP, Hopper DJ, Rigby SEJ, Cooper JB. Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2444-54. [PMID: 25195757 PMCID: PMC4219425 DOI: 10.1107/s1399004714015053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/26/2014] [Indexed: 11/11/2022]
Abstract
The enzyme 2,4'-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. Whilst the vast majority of dioxygenases cleave within the aromatic ring of the substrate, DAD is very unusual in that it is involved in C-C bond cleavage in a substituent of the aromatic ring. There is evidence that the enzyme is a homotetramer of 20.3 kDa subunits, each containing nonhaem iron, and its sequence suggests that it belongs to the cupin family of dioxygenases. In this paper, the first X-ray structure of a DAD enzyme from the Gram-negative bacterium Alcaligenes sp. 4HAP is reported, at a resolution of 2.2 Å. The structure establishes that the enzyme adopts a cupin fold, forming dimers with a pronounced hydrophobic interface between the monomers. The catalytic iron is coordinated by three histidine residues (76, 78 and 114) within a buried active-site cavity. The iron also appears to be tightly coordinated by an additional ligand which was putatively assigned as a carbonate dianion since this fits the electron density optimally, although it might also be the product formate. The modelled carbonate is located in a position which is highly likely to be occupied by the α-hydroxyketone group of the bound substrate during catalysis. Modelling of a substrate molecule in this position indicates that it will interact with many conserved amino acids in the predominantly hydrophobic active-site pocket where it undergoes peroxide radical-mediated heterolysis.
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Affiliation(s)
- R. Keegan
- STFC Rutherford Appleton Laboratory, RAL, Harwell Oxford, Didcot OX11 0FA, England
| | - A. Lebedev
- STFC Rutherford Appleton Laboratory, RAL, Harwell Oxford, Didcot OX11 0FA, England
| | - P. Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - J. Guo
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - S. P. Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - D. J. Hopper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth SY23 3DA, Wales
| | - S. E. J. Rigby
- Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, England
| | - J. B. Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
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338
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Hu M, Zhou X, Shi Y, Lin J, Irfan M, Tao Y. Essential Role of the N- and C-terminals of Laccase from Pleurotus florida on the Laccase Activity and Stability. Appl Biochem Biotechnol 2014; 174:2007-17. [DOI: 10.1007/s12010-014-1147-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/13/2014] [Indexed: 11/30/2022]
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339
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Lignin valorization through integrated biological funneling and chemical catalysis. Proc Natl Acad Sci U S A 2014; 111:12013-8. [PMID: 25092344 DOI: 10.1073/pnas.1410657111] [Citation(s) in RCA: 422] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lignin is an energy-dense, heterogeneous polymer comprised of phenylpropanoid monomers used by plants for structure, water transport, and defense, and it is the second most abundant biopolymer on Earth after cellulose. In production of fuels and chemicals from biomass, lignin is typically underused as a feedstock and burned for process heat because its inherent heterogeneity and recalcitrance make it difficult to selectively valorize. In nature, however, some organisms have evolved metabolic pathways that enable the utilization of lignin-derived aromatic molecules as carbon sources. Aromatic catabolism typically occurs via upper pathways that act as a "biological funnel" to convert heterogeneous substrates to central intermediates, such as protocatechuate or catechol. These intermediates undergo ring cleavage and are further converted via the β-ketoadipate pathway to central carbon metabolism. Here, we use a natural aromatic-catabolizing organism, Pseudomonas putida KT2440, to demonstrate that these aromatic metabolic pathways can be used to convert both aromatic model compounds and heterogeneous, lignin-enriched streams derived from pilot-scale biomass pretreatment into medium chain-length polyhydroxyalkanoates (mcl-PHAs). mcl-PHAs were then isolated from the cells and demonstrated to be similar in physicochemical properties to conventional carbohydrate-derived mcl-PHAs, which have applications as bioplastics. In a further demonstration of their utility, mcl-PHAs were catalytically converted to both chemical precursors and fuel-range hydrocarbons. Overall, this work demonstrates that the use of aromatic catabolic pathways enables an approach to valorize lignin by overcoming its inherent heterogeneity to produce fuels, chemicals, and materials.
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340
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Vacas S, Abad-Payá M, Primo J, Navarro-Llopis V. Identification of pheromone synergists for Rhynchophorus ferrugineus trapping systems from Phoenix canariensis palm volatiles. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:6053-6064. [PMID: 24930773 DOI: 10.1021/jf502663y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Trapping systems for the red palm weevil, Rhynchophorus ferrugineus Olivier, rely on the use of natural plant odor sources to boost the attractiveness of the aggregation pheromone. The identification of the key odorants involved in attraction is essential in the development of a synthetic pheromone synergist to replace the nonstandardized use of plant material in traps. Canary Islands date palms (Phoenix canariensis) have become preferred hosts for R. ferrugineus in Europe; thus, the volatile profile of different P. canariensis plant materials, including healthy and infested tissues, is investigated in the present work by means of solid phase microextraction (SPME-GC-MS), aimed to identify pheromone synergists. The electroantennography (EAG) response of the compounds identified was recorded, as well as the preliminary field response of several EAG-active compounds. The so-called "palm esters" (ethyl acetate, ethyl propionate, ethyl butyrate, and propyl butyrate) elicit the strongest EAG responses but performed poorly in the field. Mixtures of esters and alcohols give evidence of better performance, but release rates need further optimization.
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Affiliation(s)
- Sandra Vacas
- Centro de Ecología Quı́mica Agrícola, Instituto Agroforestal del Mediterráneo, Universitat Politècnica de València, edificio 6C, 5a planta, Cmno. de Vera s/n, 46022 Valencia, Spain
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341
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Mathews SL, Pawlak JJ, Grunden AM. Isolation of Paenibacillus glucanolyticus from pulp mill sources with potential to deconstruct pulping waste. BIORESOURCE TECHNOLOGY 2014; 164:100-5. [PMID: 24841577 DOI: 10.1016/j.biortech.2014.04.093] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/14/2014] [Accepted: 04/25/2014] [Indexed: 05/24/2023]
Abstract
Black liquor is a pulping waste generated by the kraft process that has potential for downstream bioconversion. A microorganism was isolated from a black liquor sample collected from the Department of Forest Biomaterials at North Carolina State University. The organism was identified as Paenibacillus glucanolyticus using 16S rRNA sequence analysis and was shown to be capable of growth on black liquor as the sole carbon source based on minimal media growth studies. Minimal media growth curves demonstrated that this facultative anaerobic microorganism can degrade black liquor as well as cellulose, hemicellulose, and lignin. Gas chromatography-mass spectrometry was used to identify products generated by P. glucanolyticus when it was grown anaerobically on black liquor. Fermentation products which could be converted into high-value chemicals such as succinic, propanoic, lactic, and malonic acids were detected.
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Affiliation(s)
- Stephanie L Mathews
- Department of Plant and Microbial Biology, 4550A Thomas Hall, Campus Box 7612, North Carolina State University, Raleigh, NC 27695, USA; Department of Forest Biomaterials, Biltmore Hall, Campus Box 8005, North Carolina State University, Raleigh, NC 27695, USA.
| | - Joel J Pawlak
- Department of Forest Biomaterials, Biltmore Hall, Campus Box 8005, North Carolina State University, Raleigh, NC 27695, USA.
| | - Amy M Grunden
- Department of Plant and Microbial Biology, 4550A Thomas Hall, Campus Box 7612, North Carolina State University, Raleigh, NC 27695, USA.
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342
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Majumdar S, Lukk T, Solbiati JO, Bauer S, Nair SK, Cronan JE, Gerlt JA. Roles of Small Laccases from Streptomyces in Lignin Degradation. Biochemistry 2014; 53:4047-58. [DOI: 10.1021/bi500285t] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sudipta Majumdar
- Institute
for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tiit Lukk
- Institute
for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jose O. Solbiati
- Institute
for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stefan Bauer
- Energy
Biosciences Institute, University of California, Berkeley, California 94720, United States
| | - Satish K. Nair
- Institute
for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - John E. Cronan
- Institute
for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - John A. Gerlt
- Institute
for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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343
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Jurado M, López MJ, Suárez-Estrella F, Vargas-García MC, López-González JA, Moreno J. Exploiting composting biodiversity: study of the persistent and biotechnologically relevant microorganisms from lignocellulose-based composting. BIORESOURCE TECHNOLOGY 2014; 162:283-293. [PMID: 24759645 DOI: 10.1016/j.biortech.2014.03.145] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 06/03/2023]
Abstract
The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. This work analyzes the identity of microbial community that persists throughout lignocellulose-based composting, evaluates their metabolic activities and studies the capability of selected isolates for composting bioaugmentation. Bacterial species of the phyla Firmicutes, Actinobacteria and Proteobacteria and fungi of the phylum Ascomycota were ubiquitous throughout the composting. The species Arthrobacter russicus, Microbacterium gubbeenense, Ochrocladosporium frigidarii and Cladosporium lignicola are detected for the first time in this ecosystem. In addition, several bacterial and fungal isolates exhibited a wide range of metabolic capabilities such as polymers (lignocellulose, protein, lipids, pectin and starch) breakdown and phosphate-solubilization that may find many biotechnological applications. In particular, Streptomyces albus BM292, Gibellulopsis nigrescens FM1397 and FM1411, Bacillus licheniformis BT575, Bacillus smithii AT907 and Alternaria tenuissima FM1385 exhibited a great potential as inoculants for composting bioaugmentation.
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Affiliation(s)
- Macarena Jurado
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence ceiA3, 04120 Almeria, Spain
| | - María J López
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence ceiA3, 04120 Almeria, Spain.
| | - Francisca Suárez-Estrella
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence ceiA3, 04120 Almeria, Spain
| | - María C Vargas-García
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence ceiA3, 04120 Almeria, Spain
| | - Juan A López-González
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence ceiA3, 04120 Almeria, Spain
| | - Joaquín Moreno
- Unit of Microbiology, Department of Biology and Geology, CITE II-B, University of Almeria, Agrifood Campus of International Excellence ceiA3, 04120 Almeria, Spain
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344
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Latif H, Zeidan AA, Nielsen AT, Zengler K. Trash to treasure: production of biofuels and commodity chemicals via syngas fermenting microorganisms. Curr Opin Biotechnol 2014; 27:79-87. [DOI: 10.1016/j.copbio.2013.12.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 11/27/2013] [Accepted: 12/02/2013] [Indexed: 01/01/2023]
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345
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Oligonucleotide primers for specific detection of actinobacterial laccases from superfamilies I and K. Antonie van Leeuwenhoek 2014; 106:391-8. [PMID: 24846052 DOI: 10.1007/s10482-014-0193-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/08/2014] [Indexed: 02/04/2023]
Abstract
Although many putative laccase-like genes have been assigned to members of the phylum Actinobacteria, few of the related enzymes have been characterized so far. It is noteworthy, however, that this small number of enzymes has presented properties with industrial relevance. This observation, combined with the recognized biotechnological potential and the capability of this phylum to degrade recalcitrant soil polymers, has attracted attention for bioprospective approaches. In the present work, we have designed and tested primers that were specific for detection of sub-groups of laccase-like genes within actinomycetes, which corresponded to the superfamilies I and K from the classification presented by the laccase and multicopper oxidase engineering database. The designed primers have amplified laccase-like gene fragments from actinomycete isolates that were undetectable by primers available from the literature. Furthermore, phylogenetic alignments suggest that some of these fragments may belong to new laccases-like proteins, and thus emphasize the benefits of designing subgroup-specific primers.
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346
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Ragauskas AJ, Beckham GT, Biddy MJ, Chandra R, Chen F, Davis MF, Davison BH, Dixon RA, Gilna P, Keller M, Langan P, Naskar AK, Saddler JN, Tschaplinski TJ, Tuskan GA, Wyman CE. Lignin Valorization: Improving Lignin Processing in the Biorefinery. Science 2014; 344:1246843. [DOI: 10.1126/science.1246843] [Citation(s) in RCA: 2410] [Impact Index Per Article: 241.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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347
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Nacke H, Fischer C, Thürmer A, Meinicke P, Daniel R. Land use type significantly affects microbial gene transcription in soil. MICROBIAL ECOLOGY 2014; 67:919-930. [PMID: 24553913 DOI: 10.1007/s00248-014-0377-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/29/2014] [Indexed: 06/03/2023]
Abstract
Soil microorganisms play an essential role in sustaining biogeochemical processes and cycling of nutrients across different land use types. To gain insights into microbial gene transcription in forest and grassland soil, we isolated mRNA from 32 sampling sites. After sequencing of generated complementary DNA (cDNA), a total of 5,824,229 sequences could be further analyzed. We were able to assign nonribosomal cDNA sequences to all three domains of life. A dominance of bacterial sequences, which were affiliated to 25 different phyla, was found. Bacterial groups capable of aromatic compound degradation such as Phenylobacterium and Burkholderia were detected in significantly higher relative abundance in forest soil than in grassland soil. Accordingly, KEGG pathway categories related to degradation of aromatic ring-containing molecules (e.g., benzoate degradation) were identified in high abundance within forest soil-derived metatranscriptomic datasets. The impact of land use type forest on community composition and activity is evidently to a high degree caused by the presence of wood breakdown products. Correspondingly, bacterial groups known to be involved in lignin degradation and containing ligninolytic genes such as Burkholderia, Bradyrhizobium, and Azospirillum exhibited increased transcriptional activity in forest soil. Higher solar radiation in grassland presumably induced increased transcription of photosynthesis-related genes within this land use type. This is in accordance with high abundance of photosynthetic organisms and plant-infecting viruses in grassland.
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Affiliation(s)
- Heiko Nacke
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
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348
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Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S, Gilbert J, Schnecker J, Wild B, Hannisdal B, Maerz J, Lashchinskiy N, Čapek P, Šantrůčková H, Gentsch N, Shibistova O, Guggenberger G, Richter A, Torsvik VL, Schleper C, Urich T. Distinct microbial communities associated with buried soils in the Siberian tundra. THE ISME JOURNAL 2014; 8:841-53. [PMID: 24335828 PMCID: PMC3960545 DOI: 10.1038/ismej.2013.219] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/21/2013] [Accepted: 11/06/2013] [Indexed: 01/22/2023]
Abstract
Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze-thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.
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Affiliation(s)
- Antje Gittel
- Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
- Austrian Polar Research Institute, Vienna, Austria
| | - Jiří Bárta
- Department of Ecosystems Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Iva Kohoutová
- Department of Ecosystems Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Robert Mikutta
- Institut für Bodenkunde, Leibniz Universität Hannover, Hannover, Germany
| | - Sarah Owens
- Institute of Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
- Computation Institute, University of Chicago, Chicago, IL, USA
| | - Jack Gilbert
- Institute of Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Jörg Schnecker
- Austrian Polar Research Institute, Vienna, Austria
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Birgit Wild
- Austrian Polar Research Institute, Vienna, Austria
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Bjarte Hannisdal
- Department of Earth Science, Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Joeran Maerz
- Division of Ecosystem Modelling, Institute of Coastal Research, Helmholtz Zentrum Geesthacht, Geesthacht, Germany
| | - Nikolay Lashchinskiy
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Petr Čapek
- Department of Ecosystems Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Hana Šantrůčková
- Department of Ecosystems Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Norman Gentsch
- Institut für Bodenkunde, Leibniz Universität Hannover, Hannover, Germany
| | - Olga Shibistova
- Institut für Bodenkunde, Leibniz Universität Hannover, Hannover, Germany
- VN Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Akademgorodok, Russia
| | - Georg Guggenberger
- Institut für Bodenkunde, Leibniz Universität Hannover, Hannover, Germany
| | - Andreas Richter
- Austrian Polar Research Institute, Vienna, Austria
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Vigdis L Torsvik
- Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Christa Schleper
- Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
- Austrian Polar Research Institute, Vienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Tim Urich
- Austrian Polar Research Institute, Vienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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349
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Xie S, Syrenne R, Sun S, Yuan JS. Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel--from systems biology to synthetic design. Curr Opin Biotechnol 2014; 27:195-203. [PMID: 24657913 DOI: 10.1016/j.copbio.2014.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 12/24/2022]
Abstract
Efficient degradation and utilization of lignocellulosic biomass remains a challenge for sustainable and affordable biofuels. Various natural biomass utilization systems (NBUS) evolved the capacity to combat the recalcitrance of plant cell walls. The study of these NBUS could enable the development of efficient and cost-effective biocatalysts, microorganisms, and bioprocesses for biofuels and bioproducts. Here, we reviewed the recent research progresses for several NBUS, ranging from single cell microorganisms to consortiums such as cattle rumen and insect guts. These studies aided the discovery of biomass-degrading enzymes and the elucidation of the evolutionary and functional relevance in these systems. In particular, advances in the next generation 'omics' technologies offered new opportunities to explore NBUS in a high-throughput manner. Systems biology helped to facilitate the rapid biocatalyst discovery and detailed mechanism analysis, which could in turn guide the reverse design of engineered microorganisms and bioprocesses for cost-effective and efficient biomass conversion.
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Affiliation(s)
- Shangxian Xie
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States
| | - Ryan Syrenne
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States; Molecular & Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, United States
| | - Su Sun
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States
| | - Joshua S Yuan
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States.
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Lapkin A, Adou E, Mlambo BN, Chemat S, Suberu J, Collis AE, Clark A, Barker G. Integrating medicinal plants extraction into a high-value biorefinery: An example of Artemisia annua L. CR CHIM 2014. [DOI: 10.1016/j.crci.2013.10.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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