351
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Shah V, Dobiásová P, Baldrian P, Nerud F, Kumar A, Seal S. Influence of iron and copper nanoparticle powder on the production of lignocellulose degrading enzymes in the fungus Trametes versicolor. JOURNAL OF HAZARDOUS MATERIALS 2010; 178:1141-5. [PMID: 20185234 DOI: 10.1016/j.jhazmat.2010.01.141] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 01/27/2010] [Accepted: 01/28/2010] [Indexed: 05/20/2023]
Abstract
White rot fungi are one of the key group of microorganisms that help to enrich the soil via degradation of wood. In the current communication, influence of iron and copper nanoparticles on the production of lignocellulolytic enzymes by Trametes versicolor have been investigated. The production of enzymes in the presence of the two nanoparticles was compared to that of ferrous and cupric ions respectively. Results show that both the tested nanoparticles alter the production profile of the lignocellulolytic enzymes when compared to the control set. The production of laccase was not influenced by iron nanoparticles but was effected by copper nanoparticles within 24h of incubation. Both the nanoparticles decreased the production of beta-glucosidase, beta-xylosidase and cellobiohydrolase significantly. However, the production profile of Mn-peroxidase and remained statistically similar to that of control when the organism was incubated with iron and copper nanoparticles. The production profiles were also different when one compares the ionic form of metals and the nanoparticles, suggesting different mechanism of action of the particles on the organism. The difference in the production profile was not growth related as no significant difference was recorded for either form of iron and copper on the growth of T. versicolor.
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Affiliation(s)
- Vishal Shah
- Department of Biology, Dowling College, 150 Idle Hour Blvd., Oakdale, NY 11769, USA.
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352
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One-step purification and characterization of a β-1,4-glucosidase from a newly isolated strain of Stereum hirsutum. Appl Microbiol Biotechnol 2010; 87:2107-16. [DOI: 10.1007/s00253-010-2668-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 05/04/2010] [Accepted: 05/05/2010] [Indexed: 11/27/2022]
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353
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Kellner H, Zak DR, Vandenbol M. Fungi unearthed: transcripts encoding lignocellulolytic and chitinolytic enzymes in forest soil. PLoS One 2010; 5:e10971. [PMID: 20532045 PMCID: PMC2881045 DOI: 10.1371/journal.pone.0010971] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 05/14/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Fungi are the main organisms responsible for the degradation of biopolymers such as lignin, cellulose, hemicellulose, and chitin in forest ecosystems. Soil surveys largely target fungal diversity, paying less attention to fungal activity. METHODOLOGY/PRINCIPAL FINDINGS Here we have focused on the organic horizon of a hardwood forest dominated by sugar maple that spreads widely across Eastern North America. The sampling site included three plots receiving normal atmospheric nitrogen deposition and three that received an extra 3 g nitrogen m(2) y(1) in form of sodium nitrate pellets since 1994, which led to increased accumulation of organic matter in the soil. Our aim was to assess, in samples taken from all six plots, transcript-level expression of fungal genes encoding lignocellulolytic and chitinolytic enzymes. For this we collected RNA from the forest soil, reverse-transcribed it, and amplified cDNAs of interest, using both published primer pairs as well as 23 newly developed ones. We thus detected transcript-level expression of 234 genes putatively encoding 26 different groups of fungal enzymes, notably major ligninolytic and diverse aromatic-oxidizing enzymes, various cellulose- and hemicellulose-degrading glycoside hydrolases and carbohydrate esterases, enzymes involved in chitin breakdown, N-acetylglucosamine metabolism, and cell wall degradation. Among the genes identified, 125 are homologous to known ascomycete genes and 105 to basidiomycete genes. Transcripts corresponding to all 26 enzyme groups were detected in both control and nitrogen-supplemented plots. CONCLUSIONS/SIGNIFICANCE Many of these enzyme groups are known to be important in soil turnover processes, but the contribution of some is probably underestimated. Our data highlight the importance of ascomycetes, as well as basidiomycetes, in important biogeochemical cycles. In the nitrogen-supplemented plots, we have detected no transcript-level gap likely to explain the observed increased carbon storage, which is more likely due to community changes and perhaps transcriptional and/or post-transcriptional down-regulation of relevant genes.
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Affiliation(s)
- Harald Kellner
- Unité de Biologie Animale et Microbienne, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium.
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354
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Joo AR, Jeya M, Lee KM, Lee KM, Moon HJ, Kim YS, Lee JK. Production and characterization of β-1,4-glucosidase from a strain of Penicillium pinophilum. Process Biochem 2010. [DOI: 10.1016/j.procbio.2010.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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355
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Hadacek F, Bachmann G, Engelmeier D, Chobot V. Hormesis and a Chemical Raison D'être for Secondary Plant Metabolites. Dose Response 2010; 9:79-116. [PMID: 21431080 PMCID: PMC3057638 DOI: 10.2203/dose-response.09-028.hadacek] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In plants, accumulation in specific compartments and huge structural diversity of secondary metabolites is one trait that is not understood yet. By exploring the diverse abiotic and biotic interactions of plants above- and belowground, we provide examples that are characterized by nonlinear effects of the secondary metabolites. We propose that redox chemistry, specifically the reduction of reactive oxygen species (ROS) and, in their absence, reduction of molecular oxygen by the identical secondary metabolite, is an important component of the hormetic effects caused by these compounds. This is illustrated for selected phenols, terpenoids, and alkaloids. The redox reactions are modulated by the variable availability of transition metals that serve as donors of electrons in a Fenton reaction mode. Low levels of ROS stimulate growth, cell differentiation, and stress resistance; high levels induce programmed cell death. We propose that provision of molecules that can participate in this redox chemistry is the raison d'être for secondary metabolites. In this context, the presence or absence of functional groups in the molecule is more essential than the whole structure. Accordingly, there exist no constraints that limit structural diversity. Redox chemistry is ubiquitous, from the atmosphere to the soil.
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Affiliation(s)
- Franz Hadacek
- Department of Chemical Ecology and Ecosystem Research, Faculty of Life Sciences, University of Vienna, Austria
| | - Gert Bachmann
- Department of Chemical Ecology and Ecosystem Research, Faculty of Life Sciences, University of Vienna, Austria
| | - Doris Engelmeier
- Department of Chemical Ecology and Ecosystem Research, Faculty of Life Sciences, University of Vienna, Austria
| | - Vladimir Chobot
- Department of Chemical Ecology and Ecosystem Research, Faculty of Life Sciences, University of Vienna, Austria
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356
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Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium. Appl Environ Microbiol 2010; 76:3599-610. [PMID: 20400566 DOI: 10.1128/aem.00058-10] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellulose degradation by brown rot fungi, such as Postia placenta, is poorly understood relative to the phylogenetically related white rot basidiomycete, Phanerochaete chrysosporium. To elucidate the number, structure, and regulation of genes involved in lignocellulosic cell wall attack, secretome and transcriptome analyses were performed on both wood decay fungi cultured for 5 days in media containing ball-milled aspen or glucose as the sole carbon source. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), a total of 67 and 79 proteins were identified in the extracellular fluids of P. placenta and P. chrysosporium cultures, respectively. Viewed together with transcript profiles, P. chrysosporium employs an array of extracellular glycosyl hydrolases to simultaneously attack cellulose and hemicelluloses. In contrast, under these same conditions, P. placenta secretes an array of hemicellulases but few potential cellulases. The two species display distinct expression patterns for oxidoreductase-encoding genes. In P. placenta, these patterns are consistent with an extracellular Fenton system and include the upregulation of genes involved in iron acquisition, in the synthesis of low-molecular-weight quinones, and possibly in redox cycling reactions.
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357
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Fujii K, Sugimura T, Nakatake K. Ascomycetes with cellulolytic, amylolytic, pectinolytic, and mannanolytic activities inhabiting dead beech (Fagus crenata) trees. Folia Microbiol (Praha) 2010; 55:29-34. [PMID: 20336501 DOI: 10.1007/s12223-010-0005-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 09/03/2009] [Indexed: 11/30/2022]
Abstract
It is generally accepted that dead tree decomposition is performed mainly by delignifying basidiomycetes. While ascomycetes have been reported to inhabit dead tree bark, their contribution to dead tree decomposition is still unclear. Here, we isolated five bark-inhabiting ascomycetes possessing cellulolytic activity from dead beech tree and assessed their polysaccharolytic activities. When cultivated in a medium containing filter paper as a sole carbon source, three strains degraded >40 % of the filter paper in a 4-week cultivation and the others degraded 15-30 % of the paper. The degraders possessed amylolytic, pectinolytic, and mannanolytic activities as well as cellulolytic activity, implying that they play an important role in dead tree decomposition after delignification by basidiomycetes. Phylogenetic analysis based on large subunit ribosomal DNA (lsu-DNA) sequences implied that the isolates belonged to Penicillium or Amorphotheca.
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Affiliation(s)
- K Fujii
- Department of Agriculture, Yamaguchi University, Yoshida, Yamaguchi 7538511, Japan.
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358
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Mahajan S, Master ER. Proteomic characterization of lignocellulose-degrading enzymes secreted by Phanerochaete carnosa grown on spruce and microcrystalline cellulose. Appl Microbiol Biotechnol 2010; 86:1903-14. [PMID: 20306191 DOI: 10.1007/s00253-010-2516-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 02/19/2010] [Accepted: 02/20/2010] [Indexed: 11/29/2022]
Abstract
Proteins secreted by the white-rot, softwood-degrading fungus Phanerochaete carnosa during growth on cellulose and spruce were analyzed using tandem mass spectrometry and de novo sequencing. Homology-driven proteomics was applied to compare P. carnosa peptide sequences to proteins in Phanerochaete chrysosporium using MS BLAST and non-gapped alignment. In this way, 665 and 365 peptides from cellulose and spruce cultivations, respectively, were annotated. Predicted activities included endoglucanases from glycoside hydrolase (GH) families 5, 16, and 61, cellobiohydrolases from GH6 and GH7, GH3 beta-glucosidases, xylanases from GH10 and GH11, GH2 beta-mannosidases, and debranching hemicellulases from GH43 and CE15. Peptides corresponding to glyoxal oxidases, peroxidases, and glycopeptides that could participate in lignin degradation were also detected. Overall, predicted activities detected in extracellular filtrates of cellulose and spruce cultures were similar, suggesting that the adaptation of P. carnosa to growth on lignocellulose might result from fine tuning the expression of similar enzyme families.
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Affiliation(s)
- Sonam Mahajan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
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359
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Identification of a dehydrogenase required for lactose metabolism in Caulobacter crescentus. Appl Environ Microbiol 2010; 76:3004-14. [PMID: 20190087 DOI: 10.1128/aem.02085-09] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Caulobacter crescentus, which thrives in freshwater environments with low nutrient levels, serves as a model system for studying bacterial cell cycle regulation and organelle development. We examined its ability to utilize lactose (i) to gain insight into the metabolic capacities of oligotrophic bacteria and (ii) to obtain an additional genetic tool for studying this model organism, aiming to eliminate the basal enzymatic activity that hydrolyzes the chromogenic substrate 5-bromo-4-chloro-3-indolyl-beta-d-galactopyranoside (X-gal). Using a previously isolated transposon mutant, we identified a gene, lacA, that is required for growth on lactose as the sole carbon source and for turning colonies blue in the presence of X-gal. LacA, which contains a glucose-methanol-choline (GMC) oxidoreductase domain, has homology to the flavin subunit of Pectobacterium cypripedii's gluconate dehydrogenase. Sequence comparisons indicated that two genes near lacA, lacB and lacC, encode the other subunits of the membrane-bound dehydrogenase. In addition to lactose, all three lac genes are involved in the catabolism of three other beta-galactosides (lactulose, lactitol, and methyl-beta-d-galactoside) and two glucosides (salicin and trehalose). Dehydrogenase assays confirmed that the lac gene products oxidize lactose, salicin, and trehalose. This enzymatic activity is inducible, and increased lac expression in the presence of lactose and salicin likely contributes to the induction. Expression of lacA also depends on the presence of the lac genes, implying that the dehydrogenase participates in induction. The involvement of a dehydrogenase suggests that degradation of lactose and other sugars in C. crescentus may resemble a proposed pathway in Agrobacterium tumefaciens.
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360
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Estimation of Treatment Time for Microbial Preprocessing of Biomass. Appl Biochem Biotechnol 2010; 162:1414-22. [DOI: 10.1007/s12010-010-8917-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 01/17/2010] [Indexed: 11/26/2022]
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361
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Liu Y, Yoshida M, Kurakata Y, Miyazaki T, Igarashi K, Samejima M, Fukuda K, Nishikawa A, Tonozuka T. Crystal structure of a glycoside hydrolase family 6 enzyme, CcCel6C, a cellulase constitutively produced by Coprinopsis cinerea. FEBS J 2010; 277:1532-42. [DOI: 10.1111/j.1742-4658.2010.07582.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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362
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363
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364
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Chobot V, Hadacek F. Iron and its complexation by phenolic cellular metabolites: from oxidative stress to chemical weapons. PLANT SIGNALING & BEHAVIOR 2010; 5:4-8. [PMID: 20592800 PMCID: PMC2835949 DOI: 10.4161/psb.5.1.10197] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Accepted: 09/28/2009] [Indexed: 05/20/2023]
Abstract
Iron is a transition metal that forms chelates and complexes with various organic compounds, also with phenolic plant secondary metabolites. The ligands of iron affect the redox potential of iron. Electrons may be transferred either to hydroxyl radicals, hydrogen peroxide or molecular oxygen. In the first case, oxidative stress is decreased, in the latter two cases, oxidative stress is increased. This milieu-dependent mode of action may explain the non-linear mode of action of juglone and other secondary metabolites. Attention to this phenomenon may help to explain idiosyncratic and often nonlinear effects that result in biological assays. Current chemical assays are discussed that help to explore these aspects of redox chemistry.
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Affiliation(s)
- Vladimir Chobot
- Department of Chemical Ecology and Ecosystem Research, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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365
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Dashtban M, Schraft H, Qin W. Fungal bioconversion of lignocellulosic residues; opportunities & perspectives. Int J Biol Sci 2009; 5:578-95. [PMID: 19774110 PMCID: PMC2748470 DOI: 10.7150/ijbs.5.578] [Citation(s) in RCA: 324] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 08/02/2009] [Indexed: 11/28/2022] Open
Abstract
The development of alternative energy technology is critically important because of the rising prices of crude oil, security issues regarding the oil supply, and environmental issues such as global warming and air pollution. Bioconversion of biomass has significant advantages over other alternative energy strategies because biomass is the most abundant and also the most renewable biomaterial on our planet. Bioconversion of lignocellulosic residues is initiated primarily by microorganisms such as fungi and bacteria which are capable of degrading lignocellulolytic materials. Fungi such as Trichoderma reesei and Aspergillus niger produce large amounts of extracellular cellulolytic enzymes, whereas bacterial and a few anaerobic fungal strains mostly produce cellulolytic enzymes in a complex called cellulosome, which is associated with the cell wall. In filamentous fungi, cellulolytic enzymes including endoglucanases, cellobiohydrolases (exoglucanases) and beta-glucosidases work efficiently on cellulolytic residues in a synergistic manner. In addition to cellulolytic/hemicellulolytic activities, higher fungi such as basidiomycetes (e.g. Phanerochaete chrysosporium) have unique oxidative systems which together with ligninolytic enzymes are responsible for lignocellulose degradation. This review gives an overview of different fungal lignocellulolytic enzymatic systems including extracellular and cellulosome-associated in aerobic and anaerobic fungi, respectively. In addition, oxidative lignocellulose-degradation mechanisms of higher fungi are discussed. Moreover, this paper reviews the current status of the technology for bioconversion of biomass by fungi, with focus on mutagenesis, co-culturing and heterologous gene expression attempts to improve fungal lignocellulolytic activities to create robust fungal strains.
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Affiliation(s)
- Mehdi Dashtban
- 1. Biorefining Research Initiative, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
- 2. Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
| | - Heidi Schraft
- 2. Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
| | - Wensheng Qin
- 1. Biorefining Research Initiative, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
- 2. Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
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366
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Baldrian P. Ectomycorrhizal fungi and their enzymes in soils: is there enough evidence for their role as facultative soil saprotrophs? Oecologia 2009; 161:657-60. [PMID: 19685081 DOI: 10.1007/s00442-009-1433-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Accepted: 07/28/2009] [Indexed: 10/20/2022]
Abstract
Although ectomycorrhizal (ECM) fungi are generally regarded as dependent upon the supply of carbon from their plant hosts, some recent papers have postulated a role for these fungi in the saprotrophic acquisition of carbon from soil. This theory was mainly based on the increase in enzymatic activity during periods of low photosynthate supply from tree hosts and emergence of the theory has led to a question about the overall influence of saprotrophy by ECM fungi on soil carbon turnover. However, I argue here that there is still not enough evidence to confirm this proposed function. My argument is based on inference from several lines of observation and concern over several aspects of the past studies. First, ECM fungi mainly inhabit deeper soil horizons, in which the availability of carbon compounds with positive energetic value is low. Second, the ability of ECM fungi to produce ligninolytic enzymes and cellulases is much weaker than that of saprotrophic basidiomycetes. This is most apparent in the low copy abundance of corresponding genes in the sequenced genomes of ECM species Laccaria bicolor and Amanita bisporigenes compared to the saprotrophic species Galerina marginata. I offer alternative hypotheses to explain the past observations of increased enzyme activity during starvation periods. These include, the induction of autolytic processes in ECM fungal mycelia or an attack on the host tissues to support escape from a dying root and to allow for a search for new hosts.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, v.v.i., Vídenská 1083, 14220 Praha 4, Czech Republic.
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367
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Chobot V, Huber C, Trettenhahn G, Hadacek F. (+/-)-catechin: chemical weapon, antioxidant, or stress regulator? J Chem Ecol 2009; 35:980-96. [PMID: 19701725 PMCID: PMC2746304 DOI: 10.1007/s10886-009-9681-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 07/23/2009] [Accepted: 08/06/2009] [Indexed: 01/23/2023]
Abstract
(+/-)-Catechin is a flavan-3-ol that occurs in the organs of many plant species, especially fruits. Health-beneficial effects have been studied extensively, and notable toxic effects have not been found. In contrast, (+/-)-catechin has been implicated as a 'chemical weapon' that is exuded by the roots of Centaurea stoebe, an invasive knapweed of northern America. Recently, this hypothesis has been rejected based on (+/-)-catechin's low phytotoxicity, instability at pH levels higher than 5, and poor recovery from soil. In the current study, (+/-)-catechin did not inhibit the development of white and black mustard to an extent that was comparable to the highly phytotoxic juglone, a naphthoquinone that is allegedly responsible for the allelopathy of the walnut tree. At high stress levels, caused by sub-lethal methanol concentrations in the medium, and a 12 h photoperiod, (+/-)-catechin even attenuated growth retardation. A similar effect was observed when (+/-)-catechin was assayed for brine shrimp mortality. Higher concentrations reduced the mortality caused by toxic concentrations of methanol. Further, when (+/-)-catechin was tested in variants of the deoxyribose degradation assay, it was an efficient scavenger of reactive oxygen species (ROS) when they were present in higher concentrations. This antioxidant effect was enhanced when iron was chelated directly by (+/-)-catechin. Conversely, if iron was chelated to EDTA, pro-oxidative effects were demonstrated at higher concentrations; in this case (+/-)-catechin reduced molecular oxygen and iron to reagents required by the Fenton reaction to produce hydroxyl radicals. A comparison of cyclic voltammograms of (+/-)-catechin with the phytotoxic naphthoquinone juglone indicated similar redox-cycling properties for both compounds although juglone required lower electrochemical potentials to enter redox reactions. In buffer solutions, (+/-)-catechin remained stable at pH 3.6 (vacuole) and decomposed at pH 7.4 (cytoplasm) after 24 h. The results support the recent rejection of the hypothesis that (+/-)-catechin may serve as a 'chemical weapon' for invasive plants. Instead, accumulation and exudation of (+/-)-catechin may help plants survive periods of stress.
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Affiliation(s)
- Vladimir Chobot
- Department of Chemical Ecology and Ecosystem Research, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | - Christoph Huber
- Department of Physical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Guenter Trettenhahn
- Department of Physical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Franz Hadacek
- Department of Chemical Ecology and Ecosystem Research, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
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368
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Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in decaying wood. ISME JOURNAL 2009; 3:1218-21. [DOI: 10.1038/ismej.2009.64] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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369
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Abstract
To move our economy onto a sustainable basis, it is essential that we find a replacement for fossil carbon as a source of liquid fuels and chemical industry feedstocks. Lignocellulosic biomass, available in enormous quantities, is the only feasible replacement. Many micro-organisms are capable of rapid and efficient degradation of biomass, employing a battery of specialized enzymes, but do not produce useful products. Attempts to transfer biomass-degrading capability to industrially useful organisms by heterologous expression of one or a few biomass-degrading enzymes have met with limited success. It seems probable that an effective biomass-degradation system requires the synergistic action of a large number of enzymes, the individual and collective actions of which are poorly understood. By offering the ability to combine any number of transgenes in a modular, combinatorial way, synthetic biology offers a new approach to elucidating the synergistic action of combinations of biomass-degrading enzymes in vivo and may ultimately lead to a transferable biomass-degradation system. Also, synthetic biology offers the potential for assembly of novel product-formation pathways, as well as mechanisms for increased solvent tolerance. Thus, synthetic biology may finally lead to cheap and effective processes for conversion of biomass to useful products.
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370
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Joo AR, Jeya M, Lee KM, Sim WI, Kim JS, Kim IW, Kim YS, Oh DK, Gunasekaran P, Lee JK. Purification and characterization of a β-1,4-glucosidase from a newly isolated strain of Fomitopsis pinicola. Appl Microbiol Biotechnol 2009; 83:285-94. [DOI: 10.1007/s00253-009-1861-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 01/05/2009] [Accepted: 01/06/2009] [Indexed: 11/30/2022]
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371
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Abstract
In an effort to prevent forest fires after the clear cutting of plantation forests, fungi capable of degrading lignocelluloses were isolated to make a fertilizer from the logging waste. Seventy five fungal species were isolated from fruiting bodies and mycelia in plantation forests of South and North Sumatera, Indonesia. Sixty three of the fungi were identified based on the appearance and morphological characteristics of their fruiting bodies and mycelia, as Pycnoporus sanguineus, Dacryopinax spathularia, Schizophyllum commune, Polyporus sp. and Trametes sp. Twenty fungi were categorized as white-rot fungi and 12 as brown-rot fungi. Moreover, isolates 371, 368, 265, 346, 345 and 338 were selected using indicators and tested for the ability to degrade lignin and holo-cellulose in mangium wood meal over 1 to 4 weeks. Results showed that the 6 fungi could degrade lignin and holo-cellulose in wood meal. An increase in incubation time tended to decrease the amounts of lignin and holo-cellulose. Isolate 371 was found to be best at degrading lignin and holo-cellulose in mangium wood meal.
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372
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Induction of extracellular hydroxyl radical production by white-rot fungi through quinone redox cycling. Appl Environ Microbiol 2009; 75:3944-53. [PMID: 19376892 DOI: 10.1128/aem.02137-08] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A simple strategy for the induction of extracellular hydroxyl radical (OH) production by white-rot fungi is presented. It involves the incubation of mycelium with quinones and Fe(3+)-EDTA. Succinctly, it is based on the establishment of a quinone redox cycle catalyzed by cell-bound dehydrogenase activities and the ligninolytic enzymes (laccase and peroxidases). The semiquinone intermediate produced by the ligninolytic enzymes drives OH production by a Fenton reaction (H(2)O(2) + Fe(2+) --> OH + OH(-) + Fe(3+)). H(2)O(2) production, Fe(3+) reduction, and OH generation were initially demonstrated with two Pleurotus eryngii mycelia (one producing laccase and versatile peroxidase and the other producing just laccase) and four quinones, 1,4-benzoquinone (BQ), 2-methoxy-1,4-benzoquinone (MBQ), 2,6-dimethoxy-1,4-benzoquinone (DBQ), and 2-methyl-1,4-naphthoquinone (menadione [MD]). In all cases, OH radicals were linearly produced, with the highest rate obtained with MD, followed by DBQ, MBQ, and BQ. These rates correlated with both H(2)O(2) levels and Fe(3+) reduction rates observed with the four quinones. Between the two P. eryngii mycelia used, the best results were obtained with the one producing only laccase, showing higher OH production rates with added purified enzyme. The strategy was then validated in Bjerkandera adusta, Phanerochaete chrysosporium, Phlebia radiata, Pycnoporus cinnabarinus, and Trametes versicolor, also showing good correlation between OH production rates and the kinds and levels of the ligninolytic enzymes expressed by these fungi. We propose this strategy as a useful tool to study the effects of OH radicals on lignin and organopollutant degradation, as well as to improve the bioremediation potential of white-rot fungi.
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373
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Tomsovský M, Popelárová P, Baldrian P. Production and regulation of lignocellulose-degrading enzymes of Poria-like wood-inhabiting basidiomycetes. Folia Microbiol (Praha) 2009; 54:74-80. [PMID: 19330548 DOI: 10.1007/s12223-009-0011-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 10/15/2008] [Indexed: 10/21/2022]
Abstract
The wood-decomposing fungal species Antrodia macra, A. pulvinascens, Ceriporiopsis aneirina, C. resinascens and Dichomitus albidofuscus were determined for production of laccase (LAC), Mn peroxidase (MnP), lignin peroxidase (LiP), endo-l,4-P-beta-glucanase, endo-l,4-beta-xylanase, cellobiohydrolase, 1,4-beta-glucosidase and 1,4-beta-xylosidase. The results confirmed the brown-rot mode of Antrodia spp. which did not produce the activity of LAC and MnP. The remaining species performed detectable activity of both enzymes while no strain produced LiP. Significant inhibition of LAC production by high nitrogen was found in all white-rot species while only MnP of D. albidofuscus was regulated in the same way. The endoglucanase and endoxylanase activities of white-rotting species were inhibited by glucose in the medium while those of Antrodia spp. were not influenced by glucose concentration. The regulation of enzyme activity and bio-mass production can vary even within a single fungal genus.
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Affiliation(s)
- M Tomsovský
- Mendel University of Agriculture and Forestry in Brno, Czech Republic.
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374
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Ortiz de Orué Lucana D, Groves MR. The three-component signalling system HbpS-SenS-SenR as an example of a redox sensing pathway in bacteria. Amino Acids 2009; 37:479-86. [PMID: 19259771 DOI: 10.1007/s00726-009-0260-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 01/30/2009] [Indexed: 01/06/2023]
Abstract
The two-component system SenS-SenR and the extracellular HbpS protein of the cellulose degrader Streptomyces reticuli have been shown to act in concert as a novel system which detects redox stress. In vivo and in vitro experiments have led to the hypothesis that HbpS binds and degrades heme, communicating the extracellular presence of heme and oxidative stress to the membrane-embedded sensor histidine kinase SenS via a bound iron. The response regulator SenR would then up-regulate downstream signalling cascades, leading to the appropriate gene expression levels for bacterial survival in an oxidative environment. Sequence analysis has shown that homologs of HbpS and SenS-SenR exist in a number of ecologically and medically relevant bacterial species, suggesting the existence of a previously undescribed bacterial oxidative stress-response pathway common to both Gram-negative and Gram-positive bacteria. The presented report reviews the current knowledge of the function of this novel protein family consisting of an accessory protein and its cognate two-component system, which could be more properly described as a three-component system.
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375
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Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci U S A 2009; 106:1954-9. [PMID: 19193860 DOI: 10.1073/pnas.0809575106] [Citation(s) in RCA: 369] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative beta-1-4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H(2)O(2). These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H(2)O(2) react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost.
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376
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Courty PE, Hoegger PJ, Kilaru S, Kohler A, Buée M, Garbaye J, Martin F, Kües U. Phylogenetic analysis, genomic organization, and expression analysis of multi-copper oxidases in the ectomycorrhizal basidiomycete Laccaria bicolor. THE NEW PHYTOLOGIST 2009; 182:736-750. [PMID: 19243515 DOI: 10.1111/j.1469-8137.2009.02774.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In forest soils, ectomycorrhizal and saprotrophic Agaricales differ in their strategies for carbon acquisition, but share common gene families encoding multi-copper oxidases (MCOs). These enzymes are involved in the oxidation of a variety of soil organic compounds. The MCO gene family of the ectomycorrhizal fungus Laccaria bicolor is composed of 11 genes divided into two distinct subfamilies corresponding to laccases (lcc) sensu stricto (lcc1 to lcc9), sharing a high sequence homology with the coprophilic Coprinopsis cinerea laccase genes, and to ferroxidases (lcc10 and lcc11) that are not present in C. cinerea. The fet3-like ferroxidase genes lcc10 and lcc11 in L. bicolor are each arranged in a mirrored tandem orientation with an ftr gene coding for an iron permease. Unlike C. cinerea, L. bicolor has no sid1/sidA gene for siderophore biosynthesis. Transcript profiling using whole-genome expression arrays and quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) revealed that some transcripts were very abundant in ectomycorrhizas (lcc3 and lcc8), in fruiting bodies (lcc7) or in the free-living mycelium grown on agar medium (lcc9 and lcc10), suggesting a specific function of these MCOs. The amino acid composition of the MCO substrate binding sites suggests that L. bicolor MCOs interact with substrates different from those of saprotrophic fungi.
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Affiliation(s)
- P E Courty
- UMR 1136 INRA-Nancy Université, Interactions Arbres/Microorganisms, INRA-Nancy, 54280 Champenoux, France
- Botanical Institute, University of Basel, CH-4056 Basel, Switzerland
| | - P J Hoegger
- Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University, D-37077 Göttingen, Germany
| | - S Kilaru
- Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University, D-37077 Göttingen, Germany
| | - A Kohler
- UMR 1136 INRA-Nancy Université, Interactions Arbres/Microorganisms, INRA-Nancy, 54280 Champenoux, France
| | - M Buée
- UMR 1136 INRA-Nancy Université, Interactions Arbres/Microorganisms, INRA-Nancy, 54280 Champenoux, France
| | - J Garbaye
- UMR 1136 INRA-Nancy Université, Interactions Arbres/Microorganisms, INRA-Nancy, 54280 Champenoux, France
| | - F Martin
- UMR 1136 INRA-Nancy Université, Interactions Arbres/Microorganisms, INRA-Nancy, 54280 Champenoux, France
| | - U Kües
- Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University, D-37077 Göttingen, Germany
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377
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Romero E, Ferreira P, Martínez AT, Martínez MJ. New oxidase from Bjerkandera arthroconidial anamorph that oxidizes both phenolic and nonphenolic benzyl alcohols. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:689-97. [PMID: 19110079 DOI: 10.1016/j.bbapap.2008.11.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 11/17/2008] [Accepted: 11/18/2008] [Indexed: 11/15/2022]
Abstract
A new flavooxidase is described from a Bjerkandera arthroconidial anamorph. Its physicochemical characteristics, a monomeric enzyme containing non-covalently bound flavin adenine dinucleotide (FAD), and several catalytic properties, such as oxidation of aromatic and polyunsaturated aliphatic primary alcohols, are similar to those of Pleurotus eryngii aryl-alcohol oxidase (AAO). However, it also efficiently oxidizes phenolic benzyl and cinnamyl alcohols that are typical substrates of vanillyl-alcohol oxidase (VAO), a flavooxidase from a different family, characterized by its multimeric nature and presence of covalently-bound FAD. The enzyme also differs from P. eryngii AAO by having extremely high efficiency oxidizing chlorinated benzyl alcohols (1000-1500 s(-1) mM(-1)), a feature related to the different alcohol metabolites secreted by the Pleurotus and Bjerkandera species including chloroaromatics, and higher activity on aromatic aldehydes. What is even more intriguing is the fact that, the new oxidase is optimally active at pH 6.0 on both p-anisyl and vanillyl alcohols, suggesting a mechanism for phenolic benzyl alcohol oxidation that is different from that described in VAO, which proceeds via the substrate phenolate anion formed at basic pH. Based on the above properties, and its ADP-binding motif, partially detected after N-terminus sequencing, the new enzyme is classified as a member of the GMC (glucose-methanol-choline oxidase) oxidoreductase family oxidizing both AAO and VAO substrates.
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Affiliation(s)
- Elvira Romero
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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378
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Baldrian P. Wood-inhabiting ligninolytic basidiomycetes in soils: Ecology and constraints for applicability in bioremediation. FUNGAL ECOL 2008. [DOI: 10.1016/j.funeco.2008.02.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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