Southern blot screening for lignin peroxidase and aryl-alcohol oxidase genes in 30 fungal species

Process optimization and scale-up production of fungal aryl alcohol oxidase from genetically modified Aspergillus nidulans in stirred-tank bioreactor

Microbial production of aryl alcohol oxidase (AAO) has attracted increasing attention due to the central role of AAO in enzymatic lignin depolymerization. However, large-scale production of AAO has not been reached because of the low yield and inefficient fermentation process. This study aims to optimize the process parameters and scale-up production of AAO using Aspergillus nidulans in a stirred-tank bioreactor. Effects of pH and dissolved oxygen on AAO production at bioreactor scale were particularly investigated. Results revealed that pH control significantly affected protein production and increasing dissolved oxygen level stimulated AAO production. The greatest AAO activity (1906 U/L) and protein concentration (1.19 g/L) were achieved in 48 h at 60% dissolved oxygen with pH controlled at 6.0. The yield and productivity (in 48 h) were 31.2 U/g maltose and 39.7 U/L/h, respectively. In addition, crude AAO was concentrated and partially purified by ultrafiltration and verified by protein identification.

Extracellular proteins of Trametes hirsuta st. 072 induced by copper ions and a lignocellulose substrate

Background

Fungi are organisms with the highest natural capacity to degrade lignocellulose substrates, which is enabled by complex systems of extracellular enzymes, whose expression and secretion depend on the characteristics of substrates and the environment.

Results

This study reports a secretome analysis for white-rot basidiomycete Trametes hirsuta cultivated on a synthetic media and a lignocellulose substrate. We demonstrate that T. hirsuta st. 072 produces multiple extracellular ligninolytic, cellulolytic, hemicellulolytic, peroxide generating, and proteolytic enzymes, as well as cerato-platanins. In contrast to other white rot species described earlier, which mostly secreted glucanases and mannosidases in response to the presence of the lignocellulose substrate, T. hirsuta expressed a spectrum of extracellular cellulolytic enzymes containing predominantly cellobiases and xylanases. As proteomic analysis could not detect lignin peroxidase (LiP) among the secreted lignin degrading enzymes, we attributed the observed extracellular LiP - like activity to the expressed versatile peroxidase (VP). An accessory enzyme, glyoxal oxidase, was found among the proteins secreted in the media during submerged cultivation of T. hirsuta both in the presence and in the absence of copper. However, aryl-alcohol oxidase (AAO) was not identified, despite the presence of AAO enzymatic activity secreted by the fungus.

The spectra of the expressed enzymes dramatically changed depending on the growth conditions. Transfer from submerged cultivation to surface cultivation with the lignocellulose substrate switched off expression of exo-β-1,3-glucanase and α-amylase and turned on secretion of endo-β-1,3-glucanase and a range of glycosidases. In addition, an aspartic peptidase started being expressed instead of family S53 protease. For the first time, we report production of cerato-platanin proteins by Trametes species. The secretion of cerato-platanins was observed only in response to contact with lignocellulose, thus indicating a specific role of these proteins in degradation of the lignocellulose substrates.

Conclusions

Our results suggest a sequential mechanism of natural substrate degradation by T. hirsuta, in which the fungus produces different sets of enzymes to digest all main components of the substrate during cultivation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0729-0) contains supplementary material, which is available to authorized users.

Amatoxins in wood-rotting Galerina marginata

Amatoxins, bicyclic octapeptide derivatives responsible for severe hepatic failure, are present in several Basidiomycota species belonging to four genera, i.e. Amanita, Conocybe, Galerina and Lepiota. DNA studies for G. autumnalis, G. marginata, G. oregonensis, G. unicolor and G. venenata (section Naucoriopsis) determined that these species are the same, supporting the concept of Galerina marginata complex. These mostly lignicolous species are designated as white-rot fungi having a broad host range and capable of degrading both hardwoods and softwoods. Twenty-seven G. marginata basidiomes taken from different sites and hosts (three sets) as well as 17 A. phalloides specimens (three sets) were collected in French locations. The 44 basidiomes were examined for amatoxins and phallotoxins using high-performance liquid chromatography. Toxinological data for the wood-rotting G. marginata and the ectomycorrhizal A. phalloides species were compared and statistically analyzed. The acidic and neutral phallotoxins were not detected in any G. marginata specimen, whereas the acidic (β-Ama) and neutral (α-Ama and γ-Ama) amanitins were found in all basidiomes from either Angiosperms or Gymnosperms hosts. The G. marginata amatoxin content varied from 78.17 to 243.61 μg.mg(-1) of fresh weight and was elevated significantly in one set out of three. The amanitin amounts from certain Galerina specimens were higher than those from some A. phalloides basidiomes. Relationship between the amanitin distribution and the chemical composition of substrate was underlined and statistically validated for the white-rot G. marginata. Changes in nutritional components from decayed host due to enzymatic systems and genetic factors as well as environmental conditions seem to play a determinant role in the amanitin profile. Variability noticed in the amanitin distribution for the white-rot G. marginata basidiomes was not observed for the ectomycorrhizal A. phalloides specimens.

Dynamics of ligninolytic enzyme production in Ganoderma applanatum depending on cultivation type

Ganoderma applanatum belongs to the group of white-rot fungi, due to a well-developed ligninolytic enzyme system. White-rot fungi have attracted great scientific attention in recent years, especially with respect to their enzymatic potential for the bioremediation of persistent pollutants. Contrary to G. lucidum, which medicinal properties, as well as ligninolytic enzyme system have been extensively studied, enzymatic system of G. applanatum has not been studied yet. Thus, the aim of this study was to analyze the dynamics of laccase, Mn-dependent peroxidase, and versatile peroxidase activity during submerged and solid state cultivation on two selected plant raw materials. Enzyme activity was determined spectrophotometrically after 7, 10 and 14 days of cultivation. The peak of laccase activity (220.14 Ul-1) was noted after 14 days of submerged wheat straw fermentation. Maximum level of Mn-dependent peroxidase (110.91 Ul-1) and versatile peroxidase (116.20 Ul-1) activity was obtained in the medium with oak sawdust after 14 days of submerged cultivation.

Biological treatment of the effluent from a bleached kraft pulp mill using basidiomycete and zygomycete fungi

Three white-rot fungi (Pleurotus sajor caju, Trametes versicolor and Phanerochaete chrysosporium) and one soft-rot fungi (Rhizopus oryzae) species confirmed their potential for future applications in the biological treatment of effluents derived from the secondary treatment of a bleached kraft pulp mill processing Eucalyptus globulus. Among the four species P. sajor caju and R. oryzae were the most effective in the biodegradation of organic compounds present in the effluent, being responsible for the reduction of relative absorbance (25-46% at 250 nm and 72-74% at 465 nm) and of chemical oxygen demand levels (74 to 81%) after 10 days of incubation. Laccase (Lac), lignin (Lip) and manganese peroxidases (MnP) expression varied among fungal species, where Lac and LiP activities were correlated with the degradation of organic compounds in the effluent treated with P. sajor caju. The first two axes of a principal component analysis explained 88.9% of the total variation among sub-samples treated with the four fungus species, after different incubation periods. All the variables measured contributed positively to the first component except for the MnP enzyme activity which was the only variable contributing negatively to the first component. Absorbances at 465 nm, LiP and Lac enzyme activities were the variables with more weight on the second component. P. sajor caju revealed to be the only species able to perform the biological treatment without promoting an increment in the toxicity of the effluent to the Vibrio fischeri, as it was assessed by the Microtox assay. The opposite was recorded for the treatments with the other three species of fungus. EC(50-5 min) values ranging between 28 and 57% (effluent concentrations) were recorded even after 10 to 13 days of treatment with P. chrysosporium, R. oryzae or with T. versicolor.

Sensitive detection of lip genes by electrochemical DNA sensor and its application in polymerase chain reaction amplicons from Phanerochaete chrysosporium

An electrochemical DNA sensor based on the sandwich hybridization recognition of target sequence of lignin peroxidase (lip) genes on a gold electrode was developed. A monolayer of thiolated capture probe was formed on a gold electrode through self-assembling. Following hybridizations with target nucleic acid and biotinylated detection probe, streptavidin-horseradish peroxidase (HRP) conjugate was applied to the electrode. The DNA conformation and surface coverage on electrode were characterized by impedance spectroscopy and square wave voltammetry. The experimental variables were optimized to maximize the hybridization efficiency, detection sensitivity and speed up the assay time. The amperometric current response to HRP-catalyzed reaction was linearly related to the natural logarithm of the target nucleic acid concentration in the range from 0.6 to 30 nM, with the correlation coefficient of 0.9722. The detection limit was 0.03 nM. Synthesized oligonucleotide as well as Phanerochaete chrysosporium lip gene fragments amplified using polymerase chain reaction and digested by restriction endonucleases were tested. The DNA sensor exhibited good precision, stability, sensitivity, and selectivity, and discriminated satisfactorily against mismatched nucleic acid samples of similar lengths.

An anamorph of the white-rot fungus Bjerkandera adusta capable of colonizing and degrading compact disc components

A Geotrichum-like fungus isolated from a biodeteriorated compact disc (CD) was able to degrade in vitro the components of different CD types. The fungal hyphae inside the CD fragments grew through the aluminium layer and produced the solubilization of this metal. Furthermore, examination of CDs by scanning electron microscopy showed that the fungus was able to destroy the pits and lands structures grooved in the polycarbonate layer, confirming degradation of this aromatic polymer. The fungus secretes aryl-alcohol oxidase and Mn2+-oxidizing peroxidase, two kinds of oxidoreductases characteristic of ligninolytic basidiomycetes. Analysis of the ITS region of ribosomal DNA, as well as the morphological characteristics, the lack of sexual forms and the profile of enzymes secreted in liquid medium identified the fungus as a Geotrichum-like anamorph of Bjerkandera adusta (Willd.) P. Karst.

Screening of basidiomycetes and xylariaceous fungi for lignin peroxidase and laccase gene-specific sequences

Lignin peroxidase and laccase gene-specific PCR primers were used to screen 38 diverse basidiomycetes and xylariaceous fungi. Lignin peroxidase gene-specific sequences were obtained for basidiomycetes only and were highly divergent. Possession of laccase genes was relatively widespread among basidiomycetes, and is shown for the first time in Xylariaceae. All sequences were highly conserved with no variation resulting in changes to predicted amino acid sequence. Those basidiomycetes shown to possess lignin peroxidase and laccase genes also produced the enzyme in vitro. Conversely none of the xylariaceous fungi shown to possess laccase genes were able to do so, whilst others decolorized Poly R yet yielded no PCR amplicons.

Fungal peroxidases: molecular aspects and applications

Peroxidases are oxidoreductases that utilize hydrogen peroxide to catalyze oxidative reactions. A large number of peroxidases have been identified in fungal species and are being characterized at the molecular level. In this manuscript we review the current knowledge on the molecular aspects of this type of enzymes. We present an overview of the research efforts undertaken in deciphering the structural basis of the catalytic properties of fungal peroxidases and discuss molecular genetics and protein homology aspects of this enzyme class. Finally, we summarize the potential biotechnological applications of these enzymes and evaluate recent advances on their expression in heterologous systems for production purposes.

Identification of genes for lignin peroxidases and manganese peroxidases in ectomycorrhizal fungi

•  Genes for ligninolytic enzymes, normally associated with white-rot fungi, are shown to be widespread in a broad taxonomic range of ectomycorrhizal (ECM) fungi. •  ECM fungi were screened for lignin peroxidase (LiP) and manganese peroxidase (MnP) genes by PCR using primers specific for known isozymes in the white-rot fungus Phanerochaete chrysosporium, with DNA sequencing used to confirm the identity of the amplified fragments. •  Genes for LiPs were detected in ECM fungi representing the orders Agaricales, Aphyllophorales, Boletales, Cantharellales, Hymenochaetales, Sclerodermatales, Stereales and Thelephorales. MnP genes were detected in only Cortinarius rotundisporus and three ECM Stereales taxa. •  The presence of genes for decomposer activities supports putative evolutionary relationships between ECM and saprotrophic fungi. Expression of the lignolytic genes may facilitate ECM fungal access to nutrients associated with dead plant material in soil and potentially a supplementary carbon supply. Strict functional boundaries between ECM and decomposer fungi may be less clear-cut than previously thought.