Hydroxyl radical generation by an extracellular low-molecular-weight substance and phenol oxidase activity during wood degradation by the white-rot basidiomycete Trametes versicolor

Microenzymes: Is There Anybody Out There?

Biological macromolecules are found in different shapes and sizes. Among these, enzymes catalyze biochemical reactions and are essential in all organisms, but is there a limit size for them to function properly? Large enzymes such as catalases have hundreds of kDa and are formed by multiple subunits, whereas most enzymes are smaller, with molecular weights of 20-60 kDa. Enzymes smaller than 10 kDa could be called microenzymes and the present literature review brings together evidence of their occurrence in nature. Additionally, bioactive peptides could be a natural source for novel microenzymes hidden in larger peptides and molecular downsizing could be useful to engineer artificial enzymes with low molecular weight improving their stability and heterologous expression. An integrative approach is crucial to discover and determine the amino acid sequences of novel microenzymes, together with their genomic identification and their biochemical biological and evolutionary functions.

Changes in bacterial communities during rice cultivation remove phenolic constraints on peatland carbon preservation

Northern peatlands contain ~30% of terrestrial carbon (C) stores, but in recent decades, 14% to 20% of the stored C has been lost because of conversion of the peatland to cropland. Microorganisms are widely acknowledged as primary decomposers, but the keystone taxa within the bacterial community regulating C loss from cultivated peatlands remain largely unknown. In this study, we investigated the bacterial taxa driving peat C mineralization during rice cultivation. Cultivation significantly decreased concentrations of soil organic C, dissolved organic C (DOC), carbohydrates, and phenolics but increased C mineralization rate (CMR). Consistent with the classic theory that phenolic inhibition creates a "latch" that reduces peat C decomposition, phenolics were highly negatively correlated with CMR in cultivated peatlands, indicating that elimination of inhibitory phenolics can accelerate soil C mineralization. Bacterial communities were significantly different following peatland cultivation, and co-occurrence diagnosis analysis revealed substantial changes in network clusters of closely connected nodes (modules) and bacterial keystone taxa. Specifically, in cultivated peatlands, bacterial modules were significantly negatively correlated with phenolics, carbohydrates, and DOC. While keystone taxa Xanthomonadales, Arthrobacter, and Bacteroidetes_vadinHA17 can regulate bacterial modules and promote carbon mineralization. Those observations indicated that changes in bacterial modules can promote phenolic decomposition and eliminate phenolic inhibition of labile C decomposition, thus accelerating soil organic C loss during rice cultivation. Overall, the study provides deeper insights into microbe-driven peat C loss during rice cultivation and highlights the crucial role of keystone bacterial taxa in the removal of phenolic constraints on peat C preservation.

Retracted and Republished from: "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola"

Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed gene expression levels of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression was observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species—aspen, pine, and spruce—under various culture conditions. We found that F. pinicola is able to modify gene expression (transcription levels) across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This study provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.

A Review on the Utilization of Lignin as a Fermentation Substrate to Produce Lignin-Modifying Enzymes and Other Value-Added Products

The lignocellulosic biomass is comprised of three major components: cellulose, hemicellulose, and lignin. Among these three, cellulose and hemicellulose were already used for the generation of simple sugars and subsequent value-added products. However, lignin is the least applied material in this regard because of its complex and highly variable nature. Regardless, lignin is the most abundant material, and it can be used to produce value-added products such as lignin-modifying enzymes (LMEs), polyhydroxyalkanoates (PHAs), microbial lipids, vanillin, muconic acid, and many others. This review explores the potential of lignin as the microbial substrate to produce such products. A special focus was given to the different types of lignin and how each one can be used in different microbial and biochemical pathways to produce intermediate products, which can then be used as the value-added products or base to make other products. This review paper will summarize the effectiveness of lignin as a microbial substrate to produce value-added products through microbial fermentations. First, basic structures of lignin along with its types and chemistry are discussed. The subsequent sections highlight LMEs and how such enzymes can enhance the value of lignin by microbial degradation. A major focus was also given to the value-added products that can be produced from lignin.

Biogenic fenton-like reaction involvement in aerobic degradation of C60 by Labrys sp. WJW

Buckminster fullerene (C₆₀), the most representative type among fullerenes, has attracted widely attentions because of its many potential applications. The increasing application of fullerene and limited knowledge of its environmental fate are required concerns. Herein, the biotransformation of C₆₀ by Labrys sp. WJW was investigated. Cell numbers reached 25.76 ± 1.85 folds within 8 days using 100 mg/L C₆₀ as sole carbon source. The biotransformation of C₆₀ by Labrys sp. WJW was analyzed by various characterization methods. Raman spectra indicated that strain WJW broke the soccer ball like structure of C₆₀. After 12 days, over 60% of C₆₀ was degraded evidenced by UV-vis spectrophotometry and liquid chromatography-mass spectrometry. The underlying biotransformation mechanism of C₆₀ through an extracellular Fenton-like reaction was illustrated. In this reaction, the ^•OH production was mediated by reduction of H₂O₂ involving a continuous cycle of Fe(II)/Fe(III). Bacterial transformation of C₆₀ will provide new insights into the understanding of C₆₀ bioremediation process.

Bacteria mediated Fenton-like reaction drives the biotransformation of carbon nanomaterials

Carbon nanomaterials (CNs), which gain heightened attention as novel materials, are increasingly incorporated into daily products and thus are released into the environment. Limited research on CNs environmental fates lags their industry growth, only few bacteria have been confirmed to biotransform CNs and the mechanism behind has not been revealed yet. In this study, four types of commercial CNs, i.e. graphene oxide (GO), reduced graphene oxide (RGO), single walled carbon nanotubes (SWCNTs), and oxidized (carboxylated) SWCNTs, were selected for investigation. The biotransformation of CNs by Labrys sp. WJW, which could grow with these CNs as the sole carbon source, was investigated. The bacterial transformation was proved by qPCR, transmission electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, liquid chromatography/time-of-flight/mass spectrometry, and gas chromatograph-mass spectrometry analyses. The biotransformation resulted in morphology change, defect increase and functional group change of these CNs. Furthermore, the underlying mechanism of CNs biodegradation mediated by extracellular Fenton-like reaction was demonstrated. In this reaction, the OH production was mediated by reduction of H₂O₂ involved a continuous cycle of Fe(II)/Fe(III). These findings reveal a novel degradation mechanism of microorganism towards high molecular weight substrate, which will provide a new insight into the environmental fate of CNs and the guidance for their safer use.

Biological decolorization of Amaranth dye with Trametes polyzona in an airlift reactor under three airflow regimes

In the present work, a strain of the basidiomycete fungus Trametes polyzona was used to decolorize the Amaranth dye. The decolorization was carried out in an Airlift reactor with three flow regimes: 1, 2, and 3 vvm. The results showed that the decolorization was a function of the flow regime. The decolorization times for the regimes of 1, 2, and 3 vvm were 30, 25, and 19 days, respectively. The COD (Chemical Oxygen Demand) decreased from 1600 to 72 mg COD/L. The enzymatic activity kinetics of laccase (Lcc), lignin peroxidase (LiP), and manganese peroxidase (MnP) were determined. In all the treatments, the enzyme LiP was expressed during the first 6 days, at which point 80% decolorization was observed, whereas Lcc and MnP enzymes were produced from day 6 until the end of the decolorization process. The effluent generated showed no inhibitory effects on the growth of the algae Nannochloropsis salina. T. polyzona showed great versatility in the decolorization of synthetic effluents containing the Amaranth dye, and the fungus was able to use this dye as its only carbon source starting at the beginning of the process. LiP was the enzyme that contributed the most to the decolorization process, and on average, 95% decreases in color and the COD were observed.

Ligninolytic Enzyme Production and Decolorization Capacity of Synthetic Dyes by Saprotrophic White Rot, Brown Rot, and Litter Decomposing Basidiomycetes

An extensive screening of saprotrophic Basidiomycetes causing white rot (WR), brown rot (BR), or litter decomposition (LD) for the production of laccase and Mn-peroxidase (MnP) and decolorization of the synthetic dyes Orange G and Remazol Brilliant Blue R (RBBR) was performed. The study considered in total 150 strains belonging to 77 species. The aim of this work was to compare the decolorization and ligninolytic capacity among different ecophysiological and taxonomic groups of Basidiomycetes. WR strains decolorized both dyes most efficiently; high decolorization capacity was also found in some LD fungi. The enzyme production was recorded in all three ecophysiology groups, but to a different extent. All WR and LD fungi produced laccase, and the majority of them also produced MnP. The strains belonging to BR lacked decolorization capabilities. None of them produced MnP and the production of laccase was either very low or absent. The most efficient decolorization of both dyes and the highest laccase production was found among the members of the orders Polyporales and Agaricales. The strains with high MnP activity occurred across almost all fungal orders (Polyporales, Agaricales, Hymenochaetales, and Russulales). Synthetic dye decolorization by fungal strains was clearly related to their production of ligninolytic enzymes and both properties were determined by the interaction of their ecophysiology and taxonomy, with a more relevant role of ecophysiology. Our screening revealed 12 strains with high decolorization capacity (9 WR and 3 LD), which could be promising for further biotechnological utilization.

Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce

BACKGROUND

The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition.

RESULTS

Following a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with auxiliary activities from carbohydrate-active enzyme (CAZy) families AA3 and AA5. In addition, a lytic polysaccharide monooxygenase from family AA9 was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi.

CONCLUSIONS

The inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of specific sequences within large glycoside hydrolase families (e.g., GH5 and GH16), and permitted co-expression analyses that identified new targets for study, including non-catalytic proteins and proteins with unknown function.

Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola

Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed the gene expression levels and RNA editing profiles of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression and RNA editing were observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression and RNA editing encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. There was no overlap between differentially expressed and differentially edited genes, suggesting that these may provide F. pinicola with independent mechanisms for responding to different conditions. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. In contrast, the suites of genes subject to RNA editing were much less affected by culture conditions. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi.IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that enable fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species, aspen, pine, and spruce, under various culture conditions. We examined both gene expression (transcription levels) and RNA editing (posttranscriptional modification of RNA, which can potentially yield different proteins from the same gene). We found that F. pinicola is able to modify both gene expression and RNA editing profiles across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.

Maize Fungal Growth Control with Scopoletin of Cassava Roots Produced in Benin

The chemical contamination of food is among the main public health issues in developing countries. With a view to find new natural bioactive products against fungi responsible for chemical contamination of staple food such as maize, the antifungal activity tests of scopoletin extracted from different components of the cassava root produced in Benin were carried out. The dosage of scopoletin from parts of the root (first skin, second skin, whole root, and flesh) was done by High Performance Liquid Chromatography. The scopoletin extract was used to assess the activity of 12 strains (11 strains of maize and a reference strain). The presence of scopoletin was revealed in all components of the cassava root. Scopoletin extracted from the first skin cassava root was the most active both as inhibition of sporulation (52.29 to 87.91%) and the mycelial growth (36.51-80.41%). Scopoletin extract from the cassava root skins showed significant inhibitory activity on the tested strains with fungicide concentration (MFC) between 0.0125 mg/mL and 0.1 mg/mL. The antifungal scopoletin extracted from the cassava root skins may be well beneficial for the fungal control of the storage of maize.

The Coptotermes gestroi aldo-keto reductase: a multipurpose enzyme for biorefinery applications

BACKGROUND

In nature, termites can be considered as a model biological system for biofuel research based on their remarkable efficiency for lignocellulosic biomass conversion. Redox enzymes are of interest in second-generation ethanol production because they promote synergic enzymatic activity with classical hydrolases for lignocellulose saccharification and inactivate fermentation inhibitory compounds produced after lignocellulose pretreatment steps.

RESULTS

In the present study, the biochemical and structural characteristics of the Coptotermes gestroi aldo-keto reductase (CgAKR-1) were comprehensively investigated. CgAKR-1 displayed major structural differences compared with others AKRs, including the differences in the amino acid composition of the substrate-binding site, providing basis for classification as a founding member of a new AKR subfamily (family AKR1 I). Immunolocalization assays with anti-CgAKR-1 antibodies resulted in strong fluorescence in the salivary gland, proventriculus, and foregut. CgAKR-1 supplementation caused a 32% reduction in phenolic aldehydes, such as furfural, which act as fermentation inhibitors of hemicellulosic hydrolysates, and improved ethanol fermentation by the xylose-fermenting yeast Scheffersomyces stipitis by 45%. We observed synergistic enzymatic interactions between CgAKR-1 and commercial cellulosic cocktail for sugarcane bagasse saccharification, with a maximum synergism degree of 2.17 for sugar release. Our data indicated that additive enzymatic activity could be mediated by reactive oxygen species because CgAKR-1 could produce hydrogen peroxide.

CONCLUSION

In summary, we identified the founding member of an AKRI subfamily with a potential role in the termite digestome. CgAKR-1 was found to be a multipurpose enzyme with potential biotechnological applications. The present work provided a basis for the development and application of integrative and multipurpose enzymes in the bioethanol production chain.

Biogenic Fenton-like Reaction Involvement in Cometabolic Degradation of Tetrabromobisphenol A by Pseudomonas sp. fz

Tetrabromobisphenol A (TBBPA) is a widely used brominated flame retardant (BFR) that has frequently been detected in various environmental compartments. Although TBBPA biotransformation has been observed under both aerobic and anaerobic conditions, knowledge of the detailed mechanism of direct aerobic TBBPA biodegradation still remains limited. In this study, the underlying mechanism of cometabolic degradation of TBBPA by Pseudomonas sp. fz under aerobic conditions was investigated. Two key degradation pathways (beta scission and debromination) were proposed based on triple quadrupole liquid chromatography-mass spectrometry (LC-MS) analysis. TBBPA degradation by strain fz was demonstrated to be an extracellular process associated with the low-molecular-mass component (LMMC). Moreover, LMMC was preliminarily identified as oligopeptides, mainly consisting of glycine, proline, and alanine in a 2:1:1 molar ratio. Quenching studies suggested the involvement of hydroxyl radicals ((•)OH) in extracellular TBBPA degradation. To the best of our knowledge, we provide the first evidence that TBBPA was degraded by a biogenic Fenton-like reaction mediated via extracellular H2O2 and Fe(II)-oligopeptide complexes by the genus Pseudomonas. This study provides a new insight into the fate and biodegradation of TBBPA and other organic pollutants in natural and artificial bioremediation environments.

Transcriptome and Secretome Analyses of the Wood Decay Fungus Wolfiporia cocos Support Alternative Mechanisms of Lignocellulose Conversion

Certain wood decay basidiomycetes, collectively referred to as brown rot fungi, rapidly depolymerize cellulose while leaving behind the bulk of cell wall lignin as a modified residue. The mechanism(s) employed is unclear, but considerable evidence implicates the involvement of diffusible oxidants generated via Fenton-like chemistry. Toward a better understanding of this process, we have examined the transcriptome and secretome of Wolfiporia cocos when cultivated on media containing glucose, purified crystalline cellulose, aspen (Populus grandidentata), or lodgepole pine (Pinus contorta) as the sole carbon source. Compared to the results obtained with glucose, 30, 183, and 207 genes exhibited 4-fold increases in transcript levels in cellulose, aspen, and lodgepole pine, respectively. Mass spectrometry identified peptides corresponding to 64 glycoside hydrolase (GH) proteins, and of these, 17 corresponded to transcripts upregulated on one or both woody substrates. Most of these genes were broadly categorized as hemicellulases or chitinases. Consistent with an important role for hydroxyl radical in cellulose depolymerization, high transcript levels and upregulation were observed for genes involved in iron homeostasis, iron reduction, and extracellular peroxide generation. These patterns of regulation differ markedly from those of the closely related brown rot fungus Postia placenta and expand the number of enzymes potentially involved in the oxidative depolymerization of cellulose.

IMPORTANCE

The decomposition of wood is an essential component of nutrient cycling in forest ecosystems. Few microbes have the capacity to efficiently degrade woody substrates, and the mechanism(s) is poorly understood. Toward a better understanding of these processes, we show that when grown on wood as a sole carbon source the brown rot fungus W. cocos expresses a unique repertoire of genes involved in oxidative and hydrolytic conversions of cell walls.

Presence of extracellular NAD(+) and NADH in cultures of wood-degrading fungi

Our previous studies indicated that extracellular glycoproteins produced by some white-rot and brown-rot basidiomycetous fungi reduce Fe(III) to Fe(II) and O2 to H2O2 and produce hydroxyl radicals. The continuous generation of hydroxyl radicals requires a constant supply of O2 and an electron donor for the reduction of oxidized forms of the glycoproteins to the reduced forms. However, electron donors for this reaction, such as NADH, have not been identified. In this study, the amounts of the extracellular pyridine coenzymes, NAD(＋) and NADH, were measured in agar cultures of four white-rot fungi, one brown-rot fungus, and three soft-rot fungi. The sums of NAD(＋) and NADH detected in wood-containing cultures of all five basidiomycetes were greater than those in glucose cultures. The amounts of NAD(＋) were higher than those of NADH in all wood-containing cultures except that of Irpex lacteus, and NAD(＋) was greater than NADH in all glucose cultures except that of Fomitopsis palustris. Significant amounts of pyridine coenzymes were present in glucose and wood-containing cultures of the three soft-rot fungi. The non-wood-degrading fungus, Penicillium funiculosum, did not produce NAD(＋) or NADH in either glucose or wood-containing cultures. The extracellular pyridine coenzyme levels were relatively high compared to the rates of extracellular hydroxyl radical generation in wood-degrading fungal cultures. Thus, white-, brown-, and soft-rot fungi produce pyridine coenzymes that could serve as electron donors for the production of hydroxyl radicals during wood degradation.

Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis

Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.

Cadmium and lead bioavailability and their effects on polycyclic aromatic hydrocarbons biodegradation by spent mushroom substrate

Bioremediation of mixed metal-organic soil pollution constitutes a difficult task in different ecosystems all around the world. The aims of this work are to determine the capacity of two spent mushroom substrates (Agaricus bisporus and Pleurotus ostreatus) to immobilize Cd and Pb, to assess the effect of these metals on laccase activity, and to determine the potential of spent A. bisporus substrate to biodegrade four polycyclic aromatic hydrocarbons (PAH): fluorene, phenanthrene, anthracene, and pyrene, when those toxic heavy metals Cd and Pb are present. According to adsorption isotherms, spent P. ostreatus and A. bisporus substrates showed a high Pb and Cd adsorption capacity. Pb and Cd interactions with crude laccase enzyme extracts from spent P. ostreatus and A. bisporus substrates showed Cd and Pb enzyme inhibition; however, laccase activity of A. bisporus presented lower inhibition. Spent A. bisporus substrate polluted with PAH and Cd or Pb was able to biodegrade PAH, although both metals decrease the biodegradation rate. Spent A. bisporus substrate contained a microbiological consortium able to oxidize PAH with high ionization potential. Cd and Pb were immobilized during the bioremediation process by spent A. bisporus substrate. Consequently, spent A. bisporus substrate was adequate as a multi-polluted soil bioremediator.

Phenol-oxidizing enzyme expression in Lentinula edodes by the addition of sawdust extract, aromatic compounds, or copper in liquid culture media

This study examined how the addition of a sawdust extract from Castanopsis cuspidata, several aromatic compounds, and copper affected the expression of a phenol-oxidizing enzyme in the white-rot basidiomycete, Lentinula edodes. Compared to liquid media that had not been supplemented with sawdust extract (MYPG), MYPG containing low (MYPG-S100) or high (MYPG-S500) concentrations of sawdust extract had a marked effect on the promotion of mycelial growth. No manganese peroxidase (MnP) production was observed in either MYPG or MYPG-S100 media until 35 days after inoculation. However, MnP production was enhanced by culture in MYPG-S500, with a marked increase observed suddenly at 14 days after inoculation. Northern blot analysis revealed that the transcription of the lemnp2 gene coding extracellular MnP was initially observed at detectable levels at day 10 after the initial inoculation of MYPG-S500, increasing gradually thereafter until days 22-25. However, laccase (Lcc) production was not observed in any of the media until 35 days after inoculation. Addition of 10 mM aromatic compounds - 1,2-benzenediol, 2-methoxyphenol, hydroquinone, and 4-anisidine--into the MYPG-S500 medium completely inhibited MnP production and did not enhance any Lcc production. While the addition of 1 or 2 mM Cu2+ (CuSO4 x 5H2O) to MYPG-S500 medium completely inhibited MnP production, this Cu2+ addition caused a marked increase in Lcc production at 17 and 6 days after the addition, respectively.

Involvement of extracellular and intracellular enzymes of Ceriporia sp. ZLY-2010 for biodegradation of polychlorinated biphenyls (PCBs)

This study examined the interrelation between the biodegradation of polychlorinated biphenyls (PCBs) by Ceriporia sp. ZLY-2010 and its fungal enzyme systems. The degradation rates of Aroclor 1254 and 1260 were 29.01% on day 5 and 36.80% on day 10, respectively. MnP (Manganese dependent peroxidase) and laccase activities showed the greatest increases in the samples containing Aroclors, indicating that extracellular enzymes of Ceriporia sp. ZLY-2010 were affected by the addition of Aroclors. However, the relationship between the biodegradation rate and extracellular enzymes might be obscured by the complexity of the biodegradation process. Cytochrome P450 monooxygenase was inhibited and the biodegradation rate of the Aroclor decreased by adding the inhibitor 1-aminobenzotriazole. Two-dimensional gel electrophoresis showed that intracellular enzymes play a significant role in the biodegradation of Aroclor. Complex extracellular and intracellular enzyme systems in Ceriporia sp. ZLY-2010 play an important role in degrading PCBs. Physiological changes of Ceriporia sp. ZLY-2010 caused by PCBs appeared to affect biodegradation of PCBs. However, it is necessary to further study the unidentified enzymes related to the biodegradation of Aroclor.

Effect of the inducers veratryl alcohol, Xylidine, and ligninosulphonates on activity and thermal stability and inactivation kinetics of laccase from Trametes versicolor

Laccase production from Trametes versicolor was improved in the presence of the inducers ligninosulphonates, veratryl alcohol, and xylidine respectively two-, four-, and eightfold. The thermal inactivation of the produced laccase, after partial purification with ammonium sulfate was kinetically investigated at various temperatures (60-70 °C) and pH values (3.5, 4.5, and 5.5). The inactivation process followed first-order kinetics for all conditions tested, except for veratryl alcohol, for which a constant activity level was observed at the end of the inactivation, also after first-order decay. Enzyme thermostability was affected by the type of inducer used in the culture medium for the production of laccase and also by the pH of incubation mixture. Generally, laccase stability increased with pH increment, being more stable at pH 5.5, except with xylidine. At pHs 4.5 and 5.5, the three inducers significantly increased laccase thermal stability, with the higher effect being observed for pH 5.5 and ligninosulphonates, where increment of half-life times ranged from 3- to 20-fold, depending on the temperature.

Degradation of carbamazepine by Trametes versicolor in an air pulsed fluidized bed bioreactor and identification of intermediates

The paper describes the aerobic degradation of carbamazepine (CBZ), an anti-epileptic drug widely found in aquatic environment, from Erlenmeyer flask to bioreactor by the white-rot fungus Trametes versicolor. In Erlenmeyer flask, CBZ at approximately 9 mg L(-1) was almost completely eliminated (94%) after 6 d, while at near environmentally relevant concentrations of 50 μg L(-1), 61% of the contaminant was degraded in 7 d. Acridone, acridine, 10,11-dihydro-10,11-dihydroxy-CBZ, and 10, 11-epoxy-CBZ were identified as major metabolites, confirming the degradation of CBZ. The degradation process was then carried out in an air pulsed fluidized bioreactor operated in batch and continuous mode. Around 96% of CBZ was removed after 2 days in batch mode operation, and 10,11-dihydro-10,11-epoxycarbamazepine was found as unique metabolite. In bioreactor operated in continuous mode with a hydraulic retention time of 3 d, 54% of the inflow concentration (approx. 200 μg L(-1)) was reduced at the steady state (25 d) with a CBZ degradation rate of 11.9 μg CBZ g(-1) dry weight d(-1). No metabolite was detected in the culture broth. Acute toxicity tests (Microtox) indicated that the final culture broth in both batch and continuous mode operation were non toxic, with 15 min EC50 values of 24% and 77%, respectively.

Secretome of the Coprophilous Fungus Doratomyces stemonitis C8, Isolated from Koala Feces

Coprophilous fungi inhabit herbivore feces, secreting enzymes to degrade the most recalcitrant parts of plant biomass that have resisted the digestive process. Consequently, the secretomes of coprophilous fungi have high potential to contain novel and efficient plant cell wall degrading enzymes of biotechnological interest. We have used one-dimensional and two-dimensional gel electrophoresis, matrix-assisted laser desorption ionization-time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS/MS), and quadrupole time-of-flight liquid chromatography-tandem mass spectrometry (Q-TOF LC-MS/MS) to identify proteins from the secretome of the coprophilous fungus Doratomyces stemonitis C8 (EU551185) isolated from koala feces. As the genome of D. stemonitis has not been sequenced, cross-species identification, de novo sequencing, and zymography formed an integral part of the analysis. A broad range of enzymes involved in the degradation of cellulose, hemicellulose, pectin, lignin, and protein were revealed, dominated by cellobiohydrolase of the glycosyl hydrolase family 7 and endo-1,4-β-xylanase of the glycosyl hydrolase family 10. A high degree of specialization for pectin degradation in the D. stemonitis C8 secretome distinguishes it from the secretomes of some other saprophytic fungi, such as the industrially exploited T. reesei. In the first proteomic analysis of the secretome of a coprophilous fungus reported to date, the identified enzymes provide valuable insight into how coprophilous fungi subsist on herbivore feces, and these findings hold potential for increasing the efficiency of plant biomass degradation in industrial processes such as biofuel production in the future.

Characterization of manganese superoxide dismutase from a marine cyanobacterium Leptolyngbya valderiana BDU20041

Background

Cyanobacteria are recognized as the primordial organisms to grace the earth with molecular oxygen ~3.5 billion years ago as a result of their oxygenic photosynthesis. This laid a selection pressure for the evolution of antioxidative defense mechanisms to alleviate the toxic effect of active oxygen species (AOS) in cyanobacteria. Superoxide dismutases (SODs) are metalloenzymes that are the first arsenal in defense mechanism against oxidative stress followed by an array of antioxidative system. Unlike other living organisms, cyanobacteria possess multiple isoforms of SOD. Hence, an attempt was made to demonstrate the oxidative stress tolerance ability of marine cyanobacterium, Leptolyngbya valderiana BDU 20041 and to PCR amplify and sequence the SOD gene, the central enzyme for alleviating stress.

Result

L. valderiana BDU 20041, a filamentous, non-heterocystous marine cyanobacterium showed tolerance to the tested dye (C.I. Acid Black 1) which is evident by increased in biomass (i.e.) chlorophyll a. The other noticeable change was the total ROS production by culture dosed with dye compared to the control cultures. This prolonged incubation showed sustenance, implying that cyanobacteria maintain their antioxidant levels. The third significant feature was a two-fold increase in SOD activity of dye treated L. valderiana BDU20041 suggesting the role of SOD in alleviating oxidative stress via Asada-Halliwell pathway. Hence, the organism was PCR amplified for SOD gene resulting in an amplicon of 550 bp. The sequence analysis illustrated the presence of first three residues involved in motif; active site residues at H4, 58 and D141 along with highly conserved Mn specific residues. The isolated gene shared 63.8% homology with MnSOD of bacteria confirmed it as Mn isoform. This is the hitherto report on SOD gene from marine cyanobacterium, L. valderiana BDU20041 of Indian subcontinent.

Conclusion

Generation of Reactive Oxygen Species (ROS) coupled with induction of SOD by marine cyanobacterium, L. valderiana BDU20041 was responsible for alleviating stress caused by an azo dye, C. I. Acid Black 1. The partial SOD gene has been sequenced and based on the active site, motif and metal specific residues; it has been identified as Mn metalloform.

Fungal bioconversion of lignocellulosic residues; opportunities & perspectives

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.

Induction of extracellular hydroxyl radical production by white-rot fungi through quinone redox cycling

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.

Function of the iron-binding chelator produced by Coriolus versicolor in lignin biodegradation

An ultrafiltered low-molecular-weight preparation of chelating compounds was isolated from a wood-containing culture of the white-rot basidiomycete Coriolus versicolor. This preparation could chelate Fe3+ and reduce Fe3+ to Fe2+, demonstrating that the substance may serve as a ferric chelator, oxygen-reducing agent, and redox-cycling molecule, which would include functioning as the electron transport carrier in Fenton reaction. Lignin was treated with the iron-binding chelator and the changes in structure were investigated by 1H-NMR, 13C-NMR, difference spectrum caused by ionization under alkaline conditions and nitrobenzene oxidation. The results indicated that the iron-binding chelator could destroy the beta-O-4 bonds in etherified lignin units and insert phenolic hydroxyl groups. The low-molecular-weight chelator secreted by C. versicolor resulted in new phenolic substructures in the lignin polymer, making it susceptible to attack by laccase or manganese peroxidase. Thus, the synergic action of the iron-binding chelator and the lignocellulolytic enzymes made the substrate more accessible to degradation.

Response of Wolfiporia cocos to iron availability: alterations in growth, expression of cellular proteins, Fe3+-reducing activity and Fe3+-chelators production

AIMS

The main objective of this study was to evaluate the behaviour of the brown-rot fungus Wolfiporia cocos under differential iron availability.

METHODS AND RESULTS

W. cocos was grown under three differential iron conditions. Growth, catecholate and hydroxamate production, and mycelial and extracellular Fe3+-reducing activities were determined. Iron starvation slowed fungal growth and accelerated pH decline. Some mycelial proteins of low molecular weight were repressed under iron restriction, whereas others of high molecular weight showed positive iron regulation. Mycelial ferrireductase activity decreased as culture aged, while Fe3+-reducing activity of low molecular reductants constantly increased. Hydroxamates production suffered only limited iron repression, whereas catecholates production showed to be more iron repressible.

CONCLUSIONS

W. cocos seems to possess more than one type of iron acquisition mechanism; one involving secretion of organic acids and ferrireductases and/or extracellular reductants, and another relying on secretion of catecholates and hydroxamates chelators.

SIGNIFICANCE AND IMPACT OF THE STUDY

This paper is the first to report the kinetic study of brown-rot fungus grown under differential iron availability, and the information provided here contributes to address more traditional problems in protecting wood from brown decay, and also makes a contribution in the general area of the physiology of brown-rot fungi.

Biochemical and molecular characterization of a cellobiohydrolase from Trametes versicolor

A cellobiohydrolase-encoding cDNA, Tvcel7a, from Trametes versicolor has been cloned and expressed in Aspergillus niger. The deduced amino acid sequence shows that Tvcel7a encodes a 456-amino acid polypeptide belonging to glycosyl hydrolase family 7. TvCel7a possesses a 19-amino acid secretion signal but does not possess a linker region nor a carbohydrate-binding domain. Two peaks of activity were obtained after TvCel7a was purified to apparent homogeneity by gel-filtration followed by anion-exchange chromatography. Mass spectrometry performed on the purified proteins confirmed that both peaks corresponded to the predicted sequence of the T. versicolor cellulase. The biochemical properties of the purified TvCel7a obtained from both peaks were studied in detail. The pH and temperature optima were 5.0 and 40 degrees C, respectively. The enzyme was stable over a pH range extending from pH 3.0 to 9.0 and at temperatures lower than 50 degrees C. The kinetic parameters with the substrate p-nitrophenyl beta-D: -cellobioside (pNPC) were 0.58 mM and 1.0 micromol/min/mg protein for the purified TvCel7a found in both peaks 1 and 2. TvCel7a catalyzes the hydrolysis of pNPC, filter paper, beta-glucan, and avicel to varying extents, but no detectable hydrolysis was observed when using the substrates carboxymethylcellulose, laminarin and pNPG.

Redox silencing of the Fenton reaction system by an alkylitaconic acid, ceriporic acid B produced by a selective lignin-degrading fungus, Ceriporiopsis subvermispora

The selective lignin-degrading fungus, Ceriporiopsis subvermispora secretes alkylitaconic acids (ceriporic acids) during wood decay. We reported that ceriporic acid B (hexadecylitaconic acid) was protective against the depolymerization of cellulose by the Fenton reaction. To understand the redox silencing effects, we analyzed the physicochemical and redox properties of itaconic, octylitaconic and hexadecylitaconic acids. The initial rate of HO production by the Fenton system with Fe(3+), H(2)O(2) and L-cysteine was suppressed by hexadecylitaconic and octylitaconic acids by 0.04 and 0.16 of the reaction rate without chelators. ESR, O(2) uptake and the assay of Fe(2+) with BPS demonstrated that Fe(3+) reduction by L-cysteine was suppressed by hexadecylitaconic and octylitaconic acids while the reaction of Fe(2+) with H(2)O(2) was not suppressed by the two alkylitaconic acids. Ligand exchange experiments with NTA demonstrated that Fe(3+) chelation by two carboxyl groups of alkylitaconic acids is a critical step in iron redox modulation. In stark contrast, the production of HO* and reduction of Fe(3+) were not suppressed by itaconic acid due to HO*--initiated degradation of the chelator. The strong redox silencing effects by a series of alkylitaconic acids have attracted interest in controlling microbial plant cell wall degradation and chemoprotection against cellular oxidative injury.

Fe(3+)- and Cu(2+)-reduction by phenol derivatives associated with Azure B degradation in Fenton-like reactions

Several phenol derivatives were evaluated regarding their capacities for Fe(3+) and Cu(2+) reduction. Selected compounds were assayed in Fenton-like reactions to degrade Azure B. 3,4-Dihydroxyphenylacetic, 2,5-dihydroxyterephtalic, gallic, chromotropic and 3-hydroxyanthranilic acids were the most efficient reducers of both metallic ions. The reaction system composed of 3-hydroxyanthranilic acid/Fe(3+)/H(2)O(2) was able to degrade Azure B at higher levels than the conventional Fenton reaction (87% and 75% of decolorization after 20min reaction, respectively). Gallic and syringic acids, catechol and vanillin induced Azure B degradations at lower levels as compared with conventional Fenton reaction. Azure B was not degraded in the presence of 10% (v/v) methanol or ethanol, which are OH radical scavengers, confirming the participation of this radical in the degradation reactions. Iron-containing reactions consumed substantially more H(2)O(2) than reactions containing copper. In iron-containing reactions, even the systems that caused a limited degradation of the dye consumed high concentrations of H(2)O(2). On the other hand, the reactions containing Fe(3+), H(2)O(2) and 3-hydroxyanthranilic acid or 3,4-dihydroxyphenylacetic acid were the most efficient on degradation of Azure B and also presented the highest H(2)O(2) consumption. These results indicate that H(2)O(2) consumption occurs even when the dye is not extensively degraded, suggesting that part of the generated OH radicals reacts with the own phenol derivative instead of Azure B.