Expression of phanerochaete chrysosporium genes encoding lignin peroxidases, manganese peroxidases, and glyoxal oxidase in wood

Morphological growth pattern of Phanerochaete chrysosporium cultivated on different Miscanthus x giganteus biomass fractions

BACKGROUND

Solid-state fermentation is a fungal culture technique used to produce compounds and products of industrial interest. The growth behaviour of filamentous fungi on solid media is challenging to study due to the intermixity of the substrate and the growing organism. Several strategies are available to measure indirectly the fungal biomass during the fermentation such as following the biochemical production of mycelium-specific components or microscopic observation. The microscopic observation of the development of the mycelium, on lignocellulosic substrate, has not been reported. In this study, we set up an experimental protocol based on microscopy and image processing through which we investigated the growth pattern of Phanerochaete chrysosporium on different Miscanthus x giganteus biomass fractions.

RESULTS

Object coalescence, the occupied surface area, and radial expansion of the colony were measured in time. The substrate was sterilized by autoclaving, which could be considered a type of pre-treatment. The fastest growth rate was measured on the unfractionated biomass, followed by the soluble fraction of the biomass, then the residual solid fractions. The growth rate on the different fractions of the substrate was additive, suggesting that both the solid and soluble fractions were used by the fungus. Based on the FTIR analysis, there were differences in composition between the solid and soluble fractions of the substrate, but the main components for growth were always present. We propose using this novel method for measuring the very initial fungal growth by following the variation of the number of objects over time. Once growth is established, the growth can be followed by measurement of the occupied surface by the mycelium.

CONCLUSION

Our data showed that the growth was affected from the very beginning by the nature of the substrate. The most extensive colonization of the surface was observed with the unfractionated substrate containing both soluble and solid components. The methodology was practical and may be applied to investigate the growth of other fungi, including the influence of environmental parameters on the fungal growth.

Comparative characterization of glyoxal oxidase from Phanerochaete chrysosporium expressed at high levels in Pichia pastoris and Trichoderma reesei

In the secretome of Phanerochaete chrysosporium, a white-rot fungus serving as a model organism to elucidate lignocellulose deconstruction, the copper containing metalloprotein glyoxal oxidase (GLOX) is potentially involved in the crucial production of hydrogen peroxide to fuel and initiate oxidative biomass degradation by lignin-degrading peroxidases. Its ability to oxidize a variety of aldehydes and α-hydroxy carbonyls with the concomitant reduction of dioxygen to hydrogen peroxide has attracted attention for its application as green biocatalyst in different industrial fields. Here we report and compare two efficient processes for the heterologous production of GLOX from P. chrysosporium using the well-established methanolytic yeast Pichia pastoris and the filamentous fungus Trichoderma reesei as expression hosts with subsequent purification by anion exchange and hydrophobic interaction chromatography. Both processes were shown to be suitable for the production of the target protein at high levels. GLOX produced in T. reesei carries mainly Man5 glycosylation while the enzyme produced in P. pastoris exhibits the typical high-mannose type N-glycosylation. The enzyme expressed in P. pastoris showed slightly higher specific activities which correlates with the higher copper loading of 65.5 % compared to 51.9 % for the protein from T. reesei. The pH optimum for both recombinant proteins was 6.0, however, GLOX activity was found to be highly affected by different buffer species. Both enzymes showed very similar substrate affinities and turnover numbers with the highest catalytic efficiency observed for methylglyoxal. GLOX from both expression hosts is therefore a suitable enzyme for further mechanistic characterization and application studies.

Transcription of lignocellulose-decomposition associated genes, enzyme activities and production of ethanol upon bioconversion of waste substrate by Phlebia radiata

Previously identified twelve plant cell wall degradation-associated genes of the white rot fungus Phlebia radiata were studied by RT-qPCR in semi-aerobic solid-state cultures on lignocellulose waste material, and on glucose-containing reference medium. Wood-decay-involved enzyme activities and ethanol production were followed to elucidate both the degradative and fermentative processes. On the waste lignocellulose substrate, P. radiata carbohydrate-active enzyme (CAZy) genes encoding cellulolytic and hemicellulolytic activities were significantly upregulated whereas genes involved in lignin modification displayed a more complex response. Two lignin peroxidase genes were differentially expressed on waste lignocellulose compared to glucose medium, whereas three manganese peroxidase-encoding genes were less affected. On the contrary, highly significant difference was noticed for three cellulolytic genes (cbhI_1, eg1, bgl1) with higher expression levels on the lignocellulose substrate than on glucose. This indicates expression of the wood-attacking degradative enzyme system by the fungus also on the recycled, waste core board material. During the second week of cultivation, ethanol production increased on the core board to 0.24 g/L, and extracellular activities against cellulose, xylan, and lignin were detected. Sugar release from the solid lignocellulose resulted with concomitant accumulation of ethanol as fermentation product. Our findings confirm that the fungus activates its white rot decay system also on industrially processed lignocellulose adopted as growth substrate, and under semi-aerobic cultivation conditions. Thus, P. radiata is a good candidate for lignocellulose-based renewable biotechnology to make biofuels and biocompounds from materials with less value for recycling or manufacturing.

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood

Since uncertainty remains about how white rot fungi oxidize and degrade lignin in wood, it would be useful to monitor changes in fungal gene expression during the onset of ligninolysis on a natural substrate. We grew Phanerochaete chrysosporium on solid spruce wood and included oxidant-sensing beads bearing the fluorometric dye BODIPY 581/591 in the cultures. Confocal fluorescence microscopy of the beads showed that extracellular oxidation commenced 2 to 3 days after inoculation, coincident with cessation of fungal growth. Whole transcriptome shotgun sequencing (RNA-seq) analyses based on the v.2.2 P. chrysosporium genome identified 356 genes whose transcripts accumulated to relatively high levels at 96 h and were at least four times the levels found at 40 h. Transcripts encoding some lignin peroxidases, manganese peroxidases, and auxiliary enzymes thought to support their activity showed marked apparent upregulation. The data were also consistent with the production of ligninolytic extracellular reactive oxygen species by the action of manganese peroxidase-catalyzed lipid peroxidation, cellobiose dehydrogenase-catalyzed Fe(3+) reduction, and oxidase-catalyzed H2O2 production, but the data do not support a role for iron-chelating glycopeptides. In addition, transcripts encoding a variety of proteins with possible roles in lignin fragment uptake and processing, including 27 likely transporters and 18 cytochrome P450s, became more abundant after the onset of extracellular oxidation. Genes encoding cellulases showed little apparent upregulation and thus may be expressed constitutively. Transcripts corresponding to 165 genes of unknown function accumulated more than 4-fold after oxidation commenced, and some of them may merit investigation as possible contributors to ligninolysis.

Improvement of ligninolytic properties by recombinant expression of glyoxal oxidase gene in hyper lignin-degrading fungus Phanerochaete sordida YK-624

Glyoxal oxidase (GLOX) is a source of the extracellular H2O2 required for the oxidation reactions catalyzed by the ligninolytic peroxidases. In the present study, the GLOX-encoding gene (glx) of Phanerochaete chrysosporium was cloned, and bee2 promoter of P. sordida YK-624 was used to drive the expression of glx. The expression plasmid was transformed into a P. sordida YK-624 uracil auxotrophic mutant (strain UV-64), and 16 clones were obtained as GLOX-introducing transformants. These transformants showed higher GLOX activities than wild-type P. sordida YK-624 and control transformants harboring marker plasmid. RT-PCR analysis indicated that the increased GLOX activity was associated with elevated recombinant glx expression. Moreover, these transformants showed higher ligninolytic activity than control transformants. These results suggest that the ligninolytic properties of white-rot fungi can be improved by recombinant expression of glx.

Characterization of novel gene expression related to glyoxal oxidase by agro-infiltration of the leaves of accession Baihe-35-1 of Vitis pseudoreticulata involved in production of H2O2 for resistance to Erysiphe necator

Glyoxal oxidase (GLOX), an extracellular H(2)O(2)-producing enzyme, has been reported in Phanerochaete chrysosporium and Ustilago maydis. We previously isolated a grapevine GLOX gene from the highly resistant to Erysiphe necator Chinese wild Vitis pseudoreticulata accession Baihe-35-1 and designated it as VpGLOX (GenBank accession no. DQ201181). Transient expression of VpGLOX can suppress Powdery Mildew in susceptible genotype were studied. To further investigate the function of the VpGLOX gene, real-time PCR and Western blot analysis were performed to examine expression patterns at transcriptional and translational levels, respectively. The results showed that VpGLOX expression at the transcriptional level increased significantly in the disease-resistant accession Baihe-35-1 after Erysiphe necator inoculation, but no significant changes in the susceptible accession, V. pseudoreticulata accession Guangxi-2 could be observed. As evident from a Western blot analysis, VpGLOX protein increased slightly in Baihe-35-1 after E. necator inoculation, but not statistical significant difference changes in Guangxi-2. The immunolocalization via immunogold electron microscopy showed that VpGLOX was mainly located in the adaxial epidermal cell wall of E. necator-inoculated leaves of both Baihe-35-1 and Guangxi-2. Agrobacterium-mediated transient expression assays revealed that VpGLOX expression could produce H(2)O(2), which may directly play a role in defense mechanism during plant-pathogen interactions. Our results could provide further insight into the biological role of VpGLOX in the defense response against E. necator in V. pseudoreticulata.

Spatial mapping of extracellular oxidant production by a white rot basidiomycete on wood reveals details of ligninolytic mechanism

Oxidative cleavage of the recalcitrant plant polymer lignin is a crucial step in global carbon cycling, and is accomplished most efficiently by fungi that cause white rot of wood. These basidiomycetes secrete many enzymes and metabolites with proposed ligninolytic roles, and it is not clear whether all of these agents are physiologically important during attack on natural lignocellulosic substrates. One new approach to this problem is to infer properties of ligninolytic oxidants from their spatial distribution relative to the fungus on the lignocellulose. We grew Phanerochaete chrysosporium on wood sections in the presence of oxidant-sensing beads based on the ratiometric fluorescent dye BODIPY 581/591. The beads, having fixed locations relative to the fungal hyphae, enabled spatial mapping of cumulative extracellular oxidant distributions by confocal fluorescence microscopy. The results showed that oxidation gradients occurred around the hyphae, and data analysis using a mathematical reaction-diffusion model indicated that the dominant oxidant during incipient white rot had a half-life under 0.1 s. The best available hypothesis is that this oxidant is the cation radical of the secreted P. chrysosporium metabolite veratryl alcohol.

Fungal laccase, manganese peroxidase and lignin peroxidase: gene expression and regulation

Extensive research efforts have been dedicated to characterizing expression of laccases and peroxidases and their regulation in numerous fungal species. Much attention has been brought to these enzymes broad substrate specificity resulting in oxidation of a variety of organic compounds which brings about possibilities of their utilization in biotechnological and environmental applications. Research attempts have resulted in increased production of both laccases and peroxidases by the aid of heterologous and homologous expression. Through analysis of promoter regions, protein expression patterns and culture conditions manipulations it was possible to compare and identify common pathways of these enzymes' production and secretion. Although laccase and peroxidase proteins have been crystallized and thoroughly analyzed, there are still a lot of questions remaining about their evolutionary origin and the physiological functions. This review describes the present understanding of promoter sequences and correlation between the observed regulatory effects on laccase, manganese peroxidase and lignin peroxidase genes transcript levels and the presence of specific response elements.

Bioligninolysis: recent updates for biotechnological solution

Bioligninolysis involves living organisms and/or their products in degradation of lignin, which is highly resistant, plant-originated polymer having three-dimensional network of dimethoxylated (syringyl), monomethoxylated (guaiacyl), and non-methoxylated (p-hydroxyphenyl) phenylpropanoid and acetylated units. As a major repository of aromatic chemical structures on earth, lignin bears paramount significance for its removal owing to potential application of bioligninolytic systems in industrial production. Early reports illustrating the discovery and cloning of ligninolytic biocatalysts in fungi was truly a landmark in the field of enzymatic delignification. However, the enzymology for bacterial delignification is hitherto poorly understood. Moreover, the lignin-degrading bacterial genes are still unknown and need further exploration. This review deals with the current knowledge about ligninolytic enzyme families produced by fungi and bacteria, their mechanisms of action, and genetic regulation and reservations, which render them attractive candidates in biotechnological applications.

Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

BACKGROUND

Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars.However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process.

RESULTS

In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed.

CONCLUSION

The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

Expression and regulation of genes encoding lignocellulose-degrading activity in the genus Phanerochaete

As white-rot basidiomycetes, Phanerochaete species are critical to the cycling of carbon sequestered as woody biomass, and are predicted to encode many enzymes that can be harnessed to promote the conversion of lignocellulose to sugars for fermentation to fuels and chemicals. Advances in genomic, transcriptomic, and proteomic technologies have enabled detailed analyses of different Phanerochaete species and have revealed numerous enzyme families required for lignocellulose utilization, as well as insight into the regulation of corresponding genes. Recent studies of Phanerochaete are also exemplified by molecular analyses following cultivation on different wood preparations, and show substrate-dependent responses that were difficult to predict using model compounds or isolated plant polysaccharides. The aim of this mini-review is to synthesize results from studies that have applied recent advances in molecular tools to evaluate the expression and regulation of proteins that contribute to lignocellulose conversion in Phanerochaete species. The identification of proteins with as yet unknown function are also highlighted and noted as important targets for future investigation of white-rot decay.

Transcriptional effect of a calmodulin inhibitor, W-7, on the ligninolytic enzyme genes in Phanerochaete chrysosporium

We investigated the effects of a calmodulin (CaM) inhibitor, W-7, on the expression of lignin peroxidase (LiP) and manganese peroxidase (MnP) genes in Phanerochaete chrysosporium to consider the role of cam gene, which was upregulated in parallel with the total activities of LiP and MnP in our previous transcriptomic analysis. The addition of 100 μM W-7 to the fungal cultures repressed the total activities of LiP and MnP, whereas the addition of 100 μM W-5, which is a control drug of W-7, retained approximately half of them, indicating that the effect of W-7 was attributable to CaM inhibition. Real-time reverse transcription polymerase chain reaction analysis revealed that most of lip and mnp isozyme genes predicted from whole-genome data were significantly inhibited by W-7 at the transcription level (P ≤ 0.05). These results suggest that CaM has an important role for the expression of isozyme genes of LiP and MnP at the transcription level.

Rapid quantification of Salmonella typhimurium inoculated to meat products by real-time PCR

The objective of this study was to use a 5'-nuclease (TaqMan) real-time PCR method with primers and probe specific to the spaQ gene as a rapid approach to quantitatively determine Salmonella Typhimurium. The result showed that the correlation coefficient between real-time PCR estimates and bovine serum albumin (BSA) plate counts of S. Typhimurium was 0.99, independently of 10(5)-fold numbers of bystander Escherichia coli O157:H7 or total viable counts. The sensitivity of the real-time quantitative PCR assay was 10 CFU/mL for pure S. Typhimurium culture without enrichment. A known number of S. Typhimurium target cells were inoculated to dumpling fillings and chicken nuggets and DNA was extracted for real-time PCR analysis. The sensitivity was 60 CFU/g for S. Typhimurium inoculated to the food samples without any preceding procedure of enrichment. The duration of the entire experiment from DNA isolation and purification to PCR amplification was less than 12 h. This study demonstrated that real-time PCR is a rapid and reliable technique for quantifying S. Typhimurium possessing the spaQ gene in pure culture and in meat products.

Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium

The US Department of Energy has assembled a high quality draft genome of Phanerochaete chrysosporium, a white rot Basidiomycete capable of completely degrading all major components of plant cell walls including cellulose, hemicellulose and lignin. Hundreds of sequences are predicted to encode extracellular enzymes including an impressive number of oxidative enzymes potentially involved in lignocellulose degradation. Herein, we summarize the number, organization, and expression of genes encoding peroxidases, copper radical oxidases, FAD-dependent oxidases, and multicopper oxidases. Possibly relevant to extracellular oxidative systems are genes involved in posttranslational processes and a large number of hypothetical proteins.

A limiting source of organic nitrogen induces specific transcriptional responses in the extraradical structures of the endomycorrhizal fungus Glomus intraradices

The molecular bases of organic nitrogen (N) metabolism in arbuscular mycorrhizal (AM) fungi remain so far largely unexplored. To isolate genes responsive to low versus high organic N concentrations, the techniques of suppressive subtractive hybridization (SSH) and reverse Northern dot blot were performed on extraradical structures of the AM fungus Glomus intraradices grown on carrot hairy roots. This approach allowed the identification of 32 up-regulated and 2 down-regulated genes following a 48-h treatment with 2 microM of an amino acid pool (leucine, alanine, asparagine, lysine, tyrosine). The expression profile of eight genes was further confirmed by semi-quantitative and real-time RT-PCR. The majority of the sequences showed no significant similarity to proteins in databases. The other responsive genes code for putative glyoxal oxidases, transcription factors, a subunit of the 20S proteasome, a protein kinase and a Ras protein. This novel set of data indicates that G. intraradices extraradical structures perceive organic N limitation in the surrounding environment leading to a response at transcriptional level and supports the role of N as signalling molecule in AM fungi.

Structure, organization, and transcriptional regulation of a family of copper radical oxidase genes in the lignin-degrading basidiomycete Phanerochaete chrysosporium

The white rot basidiomycete Phanerochaete chrysosporium produces an array of nonspecific extracellular enzymes thought to be involved in lignin degradation, including lignin peroxidases, manganese peroxidases, and the H2O2-generating copper radical oxidase, glyoxal oxidase (GLX). Preliminary analysis of the P. chrysosporium draft genome had identified six sequences with significant similarity to GLX and designated cro1 through cro6. The predicted mature protein sequences diverge substantially from one another, but the residues coordinating copper and constituting the radical redox site are conserved. Transcript profiles, microscopic examination, and lignin analysis of inoculated thin wood sections are consistent with differential regulation as decay advances. The cro2-encoded protein was detected by liquid chromatography-tandem mass spectrometry in defined medium. The cro2 cDNA was successfully expressed in Aspergillus nidulans under the control of the A. niger glucoamylase promoter and secretion signal. The recombinant CRO2 protein had a substantially different substrate preference than GLX. The role of structurally and functionally diverse cro genes in lignocellulose degradation remains to be established.

Expression and molecular properties of a new laccase of the white rot fungus Phlebia radiata grown on wood

Laccases are phenol-oxidizing, multicopper enzymes produced by fungi, plants, insects and bacteria. Fungal laccases are involved in ecologically important processes such as decomposition of lignocellulose (wood and plant material). In this work, in order to find out the role of fungal laccases upon wood colonisation and lignin decay, we describe expression of laccase-encoding genes in the white rot basidiomycete Phlebia radiata 79, when the fungus grows on its natural substrates, that is on softwood (Alnus incana) and hardwood (Picea abies). Clones for two laccase-encoding genes, the previously described Pr-lac1 and a new gene Pr-lac2 were characterized. Pr-lac2 coding region is interrupted by 12 introns and the deduced Lac2 protein displays a higher pI value (5.8) than Lac1 (pI 3.2-3.5). Phylogenetic analysis indicates differential evolution for the two laccases, and Lac2 demonstrates the highest sequence identity with Trametes laccases (66%). Transcripts of Pr-lac1 were the most abundant both in solid-state softwood and semi-solid hardwood cultures, as analyzed by competitive RT-PCR and Northern hybridization. On spruce wood chips, Pr-lac1 and Pr-lac2 were expressed within 2-3 weeks of growth together with manganese and lignin peroxidase-encoding genes. Our results indicate wood-promoted but time-dependent regulation of expression for the two, at protein and gene level distinct P. radiata laccases.

Growth of Phanerochaete chrysosporium on diesel fuel hydrocarbons at neutral pH

Generally, the white-rot fungus Phanerochaete chrysosporium performs its biodegradative activities in liquid culture while growing on easily utilized carbon sources such as malt- or potato-extract. However, less is known about the potential of this organism to grow directly on environmental pollutants without regard to special conditions. Growth of P. chrysosporium on a middle fraction (MF) of diesel fuel at neutral pH in mineral medium under non-ligninolytic conditions was explored. After 14 d, the GC-analyzable n-alkanes of 1000 mg l(-1)MF were reduced to background, with most biodegradation occurring by day 7 when quantified relative to the biodegradation of the internal fuel biodegradation marker, pristane. Investigations with n-hexadecane and unmodified diesel fuel further confirmed these biodegradation results. Biomass production was monitored and indicated that fungal biomass was more than 10 times less than positive controls (potato dextrose broth, PDB) but that biomass increased relative to negative controls. When P. chrysosporium was incubated with diesel fuel and PDB, fuel biodegradation was delayed for at least 4d and inhibited overall through 14 d. Experiments with P. chrysosporium growing on n-hexadecane in the presence of 1 mM 1-aminobenzotriazole (ABT), an inhibitor of the cytochrome P-450 enzyme system, resulted in inhibition of biomass production relative to positive controls implicating the utilization of this enzyme system in n-alkane metabolism. Finally, when P. chrysosporium was incubated in a non-aqueous phase liquid (NAPL) mixture of polycyclic aromatic hydrocarbons (PAHs) and MF, n-alkanes and phenanthrene were degraded in 2 weeks while anthracene, chrysene and benzo[a]pyrene were not.

Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins

The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 'computational secretome,' 43% showed no significant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed significant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identified in culture filtrates by mass spectrometry (LS-MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identified in carbon-starved cultures. Beyond proteases and M6Pase, 28 specific gene products were identified including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium's extracellular enzyme systems.

Expression on wood, molecular cloning and characterization of three lignin peroxidase (LiP) encoding genes of the white rot fungus Phlebia radiata

Lignin peroxidase (LiP) is the first enzyme connected to oxidative breakdown of the aromatic plant heteropolymer lignin and related xenobiotics. However, this extracellular enzyme has been described in only a few species of wood-decaying basidiomycetous fungi. The white rot basidiomycete Phlebia radiata 79 readily produces a versatile set of lignin-oxidizing enzymes including lignin and manganese peroxidases (LiPs and MnPs) and laccases. Here we describe genomic and primary structure of two new LiP-encoding genes, Pr-lip1 and Pr-lip4, and genomic characterization for isozyme LiP3/LIII of P. radiata, encoded by the gene depicted Pr-lip3. Pr-lip1 and Pr-lip4 code for 370- and 361-amino-acid long proteins beginning with 26- and 24-amino-acid secretion pre-propeptides, respectively. Translated LiP1 and LiP4 share the highest protein sequence identity (74 and 86%) with P. radiata LiP3, and 70% identity with the one deduced LiP from Bjerkandera adusta. The three P. radiata LiP sequences form a coherent phylogenetic cluster, which is further supported by similarities within gene organization interrupted by 11-introns. To find out the significance of LiP upon fungal growth on natural lignocellulose, such as wood, we studied ligninolytic gene expression on hardwood (milled alder) and softwood (spruce chips). All the LiP-encoding genes were expressed on wood with predominance of Pr-lip3 transcript abundance, in particular on spruce wood chips, where also time-dependent expression of the multiple lip genes was observed.

Two isolates of Fusarium proliferatum from different habitats and global locations have similar abilities to degrade lignin

Two isolates of Fusarium proliferatum from different global locations and habitats mineralized several natural and synthetic lignins. MUCL 31970 was isolated from a forest soil whereas the second strain, NRRL 31071, was a wheat endophyte causing disease in stressed seedlings. Onset and the fastest rate of lignin mineralization occurred during logarithmic and early stationary-phase of culture. Reduction of glucose in the medium shortened log-growth phase and advanced the onset of mineralization for both isolates. Mineralization correlated with the detection of extracellular laccase and aryl alcohol oxidase activities. The carbon-nitrogen ratio in the medium influenced laccase isozyme production and secretion by both strains. These studies suggest that both F. proliferatum strains degrade lignin via comparable routes, despite their different habitats and saprophytic or endophytic strategies.

The Phanerochaete chrysosporium secretome: Database predictions and initial mass spectrometry peptide identifications in cellulose-grown medium

The white rot basidiomycete, Phanerochaete chrysosporium, employs an array of extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose and lignin. Towards the identification of participating enzymes, 268 likely secreted proteins were predicted using SignalP and TargetP algorithms. To assess the reliability of secretome predictions and to evaluate the usefulness of the current database, we performed shotgun LC-MS/MS on cultures grown on standard cellulose-containing medium. A total of 182 unique peptide sequences were matched to 50 specific genes, of which 24 were among the secretome subset. Underscoring the rich genetic diversity of P. chrysosporium, identifications included 32 glycosyl hydrolases. Functionally interconnected enzyme groups were recognized. For example, the multiple endoglucanases and processive exocellobiohydrolases observed quite probably attack cellulose in a synergistic manner. In addition, a hemicellulolytic system included endoxylanases, alpha-galactosidase, acetyl xylan esterase, and alpha-l-arabinofuranosidase. Glucose and cellobiose metabolism likely involves cellobiose dehydrogenase, glucose oxidase, and various inverting glycoside hydrolases, all perhaps enhanced by an epimerase. To evaluate the completeness of the current database, mass spectroscopy analysis was performed on a larger and more inclusive dataset containing all possible ORFs. This allowed identification of a previously undetected hypothetical protein and a putative acid phosphatase. The expression of several genes was supported by RT-PCR amplification of their cDNAs.

Incomplete processing of peroxidase transcripts in the lignin degrading fungus Phanerochaete chrysosporium

Phanerochaete chrysosporium has been thoroughly studied as a microbial model for lignin degradation. The enzymes lignin peroxidase (LiP) and manganese peroxidase (MnP), both encoded by several genes, play the main role in the cleavage of different lignin substructures. In this work, the expression of specific LiP and MnP transcripts in liquid medium and in a wood-containing soil system was studied by reverse transcription-PCR and subsequent cloning and sequencing of the products obtained. Splice variants of different LiP and MnP transcripts were observed in wood-containing soil incubations and in liquid cultures. The processed transcripts contained different numbers of complete introns. Since the presence of stop codons in several of these introns would prevent the synthesis of active enzyme, we propose that these transcripts arise as a result of incomplete processing rather than alternative splicing. Interestingly, analysis of splice variants from mnp genes led to the identification of a fourth actively transcribed gene coding for MnP in P. chrysosporium.

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.

Isolation and purification of pyranose 2-oxidase from Phanerochaete chrysosporium and characterization of gene structure and regulation

Pyranose 2-oxidase (POX) was recovered from Phanerochaete chrysosporium BKM-F-1767 solid substrate culture using mild extraction conditions and was purified. (13)C-nuclear magnetic resonance confirmed production of d-arabino-hexos-2-ulose (glucosone) from d-glucose with the oxidase. Peptide fingerprints generated by liquid chromatography-tandem mass spectrometry of tryptic digests and analysis of the corresponding cDNA revealed a structurally unusual sequence for the P. chrysosporium POX. Relatively high levels of pox transcript were detected under carbon-starved culture conditions but not under nutrient sufficiency. This regulation pattern is similar to that observed for lignin peroxidases, manganese peroxidases, and glyoxal oxidase of P. chrysosporium, supporting evidence that POX has a role in lignocellulose degradation.

A H2O2-producing glyoxal oxidase is required for filamentous growth and pathogenicity in Ustilago maydis

In the phytopathogenic fungus Ustilago maydis the mating-type loci control the transition from yeast-like to filamentous growth required for pathogenic development. In a large REMI (restriction enzyme mediated integration) screen, non-pathogenic mutants were isolated in a haploid strain that had been engineered to be pathogenic. In one of these mutants, which showed a specific morphological phenotype, the tagged gene, glo1 , was found to encode a product that is highly homologous to a glyoxal oxidase gene from the wood-rot fungus Phanerochaete chrysosporium. Glyoxal oxidase homologues are found in human, plant pathogenic fungi and in plants, but not in other mammals or yeasts. To confirm the function of the glo1 gene, null mutations were generated in compatible haploid U. maydis strains. In crosses null mutants were unable to generate filamentous dikaryons, and were completely non-pathogenic. Using a Glo1-overproducing strain we demonstrated that Glo1 is membrane bound, oxidizes a series of small aldehydes (< C4) and produces H2O2. The enzyme needs to be activated, presumably by auto-oxidation, to show full activity. A potential role for Glo1 during filamentous growth and pathogenic development of U. maydis is proposed.

Molecular approach for analysis of model fungal genes encoding ligninolytic peroxidases in wood-decaying soil systems

AIMS

Test the use of nondegenerated consensus polymerase chain reaction (PCR) primers targeting lip and mnp sequences to detect ligninolytic fungi in wood-decaying soil systems, avoiding the need for enrichment or isolation on traditional fungal media culture.

METHODS AND RESULTS

The PCR primers were tested with total DNA isolated from incubations of wood-soil systems inoculated or not with the white-rot fungi Phanerochaete chrysosporium, or a white-rot sample obtained from a Nothofagus forest. The PCR products for lip and mnp sequences were only obtained in soil with P. chrysosporium-colonized wood chips. In these soil samples, reverse transcription-PCR analysis of lip and mnp PCR products indicated expression of LipA, LipB, LipJ and MnP isoenzymes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first assessment of the use of consensus PCR primers for direct detection of ligninolytic peroxidase genes in wood-decaying soil systems.

Real-time quantitative PCR assay on bacterial DNA: In a model soil system and environmental samples

Real-time quantitative PCR (RTQ-PCR) was used to quantify the bacterial target DNA extracted by three commonly used DNA extraction protocols (bead mill homogenization, grinding in presence of liquid nitrogen and hot detergent SDS based enzymatic lysis). For the purpose of our study, pure culture of Bacillus cereus (model organism), sterilized soil seeded with a known amount of B. cereus (model soil system) and samples from woodland and grassland (environmental samples) were chosen to extract DNA by three different protocols. The extracted DNA was then quantified by RTQ-PCR using 16S rDNA specific universal bacterial primers. The standard curve used for the quantification by RTQ-PCR was linear and revealed a strong linear relationship (r(2)=0.9968) with a higher amplification efficiency, e5=1.02. High resolution gel electrophoresis was also carried out to observe the effect of these extraction methods on diversity analysis. For the model soil system, the liquid nitrogen method showed the highest target DNA copy number (1.3 x 10(9) copies/microl). However, for both the environmental samples, the bead beating method was found to be suitable on the basis of the high target DNA copy numbers (5.38 x 10(9) and 4.01 x 10(8) copies/ml for woodland and grassland respectively), high yield (6.4 microg/g and 1.76 microg/g of soil for woodland and grassland respectively) and different band patterns on high resolution gel electrophoresis suggesting an overall high extraction efficiency. This difference in the extraction efficiency between the model soil system and environmental samples may be attributed to different affinity of seeded and native DNA to soil particles.

Transcript analysis of genes encoding a family 61 endoglucanase and a putative membrane-anchored family 9 glycosyl hydrolase from Phanerochaete chrysosporium

Phanerochaete chrysosporium cellulase genes were cloned and characterized. The cel61A product was structurally similar to fungal endoglucanases of glycoside hydrolase family 61, whereas the cel9A product revealed similarities to Thermobifida fusca Cel9A (E4), an enzyme with both endo- and exocellulase characteristics. The fungal Cel9A is apparently a membrane-bound protein, which is very unusual for microbial cellulases. Transcript levels of both genes were substantially higher in cellulose-grown cultures than in glucose-grown cultures. These results show that P. chrysosporium possesses a wide array of conventional and unconventional cellulase genes.

Lignocellulose affects Mn2+ regulation of peroxidase transcript levels in solid-state cultures of Pleurotus ostreatus

The effect of Mn2+ amendment on peroxidase gene expression was studied during Pleurotus ostreatus growth on cotton stalks. Four peroxidase-encoding genes were expressed differentially and in a manner different from that observed in defined media. Mn2+ affects mnp3 expression even 2 h after its addition to the cultures, suggesting a direct effect of the metal ion on expression.

Differential regulation of mnp2, a new manganese peroxidase-encoding gene from the ligninolytic fungus Trametes versicolor PRL 572

A peroxidase-encoding gene, mnp2, and its corresponding cDNA were characterized from the white-rot basidiomycete Trametes versicolor PRL 572. We used quantitative reverse transcriptase-mediated PCR to identify mnp2 transcripts in nutrient-limited stationary cultures. Although mnp2 lacks upstream metal response elements (MREs), addition of MnSO(4) to cultures increased mnp2 transcript levels 250-fold. In contrast, transcript levels of an MRE-containing gene of T. versicolor, mnp1, increased only eightfold under the same conditions. Thus, the manganese peroxidase genes in T. versicolor are differentially regulated, and upstream MREs are not necessarily involved. Our results support the hypothesis that fungal and plant peroxidases arose through an ancient duplication and folding of two structural domains, since we found the mnp1 and mnp2 polypeptides to have internal homology.

Rapid, quantitative PCR monitoring of growth of Clostridium botulinum type E in modified-atmosphere-packaged fish

A rapid, quantitative PCR assay (TaqMan assay) which quantifies Clostridium botulinum type E by amplifying a 280-bp sequence from the botulinum neurotoxin type E (BoNT/E) gene is described. With this method, which uses the hydrolysis of an internal fluoregenic probe and monitors in real time the increase in the intensity of fluorescence during PCR by using the ABI Prism 7700 sequence detection system, it was possible to perform accurate and reproducible quantification of the C. botulinum type E toxin gene. The sensitivity and specificity of the assay were verified by using 6 strains of C. botulinum type E and 18 genera of 42 non-C. botulinum type E strains, including strains of C. botulinum types A, B, C, D, F, and G. In both pure cultures and modified-atmosphere-packaged fish samples (jack mackerel), the increase in amounts of C. botulinum DNA could be monitored (the quantifiable range was 10(2) to 10(8) CFU/ml or g) much earlier than toxin could be detected by mouse assay. The method was applied to a variety of seafood samples with a DNA extraction protocol using guanidine isothiocyanate. Overall, an efficient recovery of C. botulinum cells was obtained from all of the samples tested. These results suggested that quantification of BoNT/E DNA by the rapid, quantitative PCR method was a good method for the sensitive assessment of botulinal risk in the seafood samples tested.

Ligninolytic characteristics of Pleurotus ostreatus strain F6 and its monokaryotic protoplast derivative P19

A stable isolate of Pleurotus ostreatus P19 differing in some morphological and physiological characteristics from its parental wild-type strain F6 was obtained via protoplast isolation during the preparation of strains with altered ligninolytic abilities. The isolate is monokaryotic, does not form clamp-connections, and produces much higher activities of enzymes involved in lignin modification (laccase, manganese peroxidase). Cellulase activity was comparable to that of wild-type strain F6, but the xylanase activity was slightly higher in isolate P19. However, this monokaryotic derivative degrades lignin at a slightly lower rate than its parental strain F6. Electron microscopy observations of wood degradation as a function of mycelium growth were performed on three zones of birch wafers delimited according to the distance from the point of inoculation. The different stages of fungal mycelium growth showed differences in the ultrastructural patterns of the decay not only between the strains P19 and F6, but also depending on the distance from the point of inoculation. This suggests a spatio-temporally controlled secretion of enzymes along the hyphae. The enhanced ability of P19 to degrade the condensed forms of lignin in middle lamellae is correlated to its higher laccase activity.

A homokaryotic derivative of a Phanerochaete chrysosporium strain and its use in genomic analysis of repetitive elements

Analysis of complex gene families in the lignin-degrading basidiomycete Phanerochaete chrysosporium has been hampered by the dikaryotic nuclear condition. To facilitate genetic investigations in P. chrysosporium strain BKM-F-1767, we isolated a homokaryon from regenerated protoplasts. The nuclear condition was established by PCR amplification of five unlinked genes followed by probing with allele-specific oligonucleotides. Under standard nitrogen-limited culture conditions, lignin peroxidase, manganese peroxidase, and glyoxal oxidase activities of the homokaryon were equivalent to those of the parental dikaryon. We used the homokaryon to determine the genomic organization and to assess transcriptional effects of a family of repetitive elements. Previous studies had identified an insertional mutation, Pce1, within lignin peroxidase allele lipI2. The element resembled nonautonomous class II transposons and was present in multiple copies in strain BKM-F-1767. In the present study, three additional copies of the Pce1-like element were cloned and sequenced. The distribution of elements was nonrandom; all localized to the same 3.7-Mb chromosome, as assessed by segregation analysis and Southern blot analysis of the homokaryon. Reverse transcription-PCR (RT-PCR) showed that Pce1 was not spliced from the lipI2 transcript in either the homokaryon or the parental dikaryon. However, both strains had equivalent lignin peroxidase activity, suggesting that some lip genes may be redundant.

Manganese peroxidase isoenzymes produced by Pleurotus ostreatus grown on wood sawdust

The white rot basidiomycete Pleurotus ostreatus produces two manganese peroxidase (MnP) isoenzymes when grown in solid stationary conditions on poplar sawdust, whereas a lower production of these same enzymes is observed on fir sawdust. Addition of Mn(2+) to poplar culture resulted in a threefold increase of MnP activity; the same addition to fir culture was able to increase tenfold the MnP production. The two MnP isoenzymes (MnP2 and MnP3) were purified from P. ostreatus poplar culture. The isoenzymes differ in their pI values, molecular masses, and N-terminal sequences. MnP3 has the same N-terminal sequence as that of a P. ostreatus MnP previously reported. Both isoenzymes exhibit Mn(2+)-dependent and Mn(2+)-independent peroxidase activities when tested on phenolic substrates. The gene coding for the new isoenzyme MnP2 was cloned and sequenced and the promoter region analyzed. Furthermore, the chromosomal localization of all known P. ostreatus genes was determined.

Analysis of the gene family encoding lipases in Candida rugosa by competitive reverse transcription-PCR

Synthesis of multiple extracellular lipases in Candida rugosa has been demonstrated. However, it is difficult to characterize the expression spectrum of lip genes, since the sequences of the lip multigene family are very closely related. A competitive reverse transcription-PCR assay was developed to quantify the expression of lip genes. In agreement with the protein profile, the abundance of lip mRNAs was found to be (in decreasing order) lip1, lip3, lip2, lip5, and lip4. To analyze the effects of different culture conditions, the transcript concentrations for these mRNA species were normalized relative to the values for gpd, encoding glyceraldehyde-3-phosphate dehydrogenase. In relative terms, lip1 and lip3 were highly and constitutively expressed (about 10(5) molecules per microg of total RNA) whereas the other inducible lip genes, especially lip4, showed significant changes in mRNA expression under different culture conditions. These results indicate that differential transcriptional control of lip genes results in multiple forms of lipase proteins.