Role of Organic Acids in the Manganese-Independent Biobleaching System of Bjerkandera sp. Strain BOS55

Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium

BACKGROUND

Lignin peroxidases catalyze a variety of reactions, resulting in cleavage of both β-O-4' ether bonds and C-C bonds in lignin, both of which are essential for depolymerizing lignin into fragments amendable to biological or chemical upgrading to valuable products. Studies of the specificity of lignin peroxidases to catalyze these various reactions and the role reaction conditions such as pH play have been limited by the lack of assays that allow quantification of specific bond-breaking events. The subsequent theoretical understanding of the underlying mechanisms by which pH modulates the activity of lignin peroxidases remains nascent. Here, we report on combined experimental and theoretical studies of the effect of pH on the enzyme-catalyzed cleavage of β-O-4' ether bonds and of C-C bonds by a lignin peroxidase isozyme H8 from Phanerochaete chrysosporium and an acid stabilized variant of the same enzyme.

RESULTS

Using a nanostructure initiator mass spectrometry assay that provides quantification of bond breaking in a phenolic model lignin dimer we found that catalysis of degradation of the dimer to products by an acid-stabilized variant of lignin peroxidase isozyme H8 increased from 38.4% at pH 5 to 92.5% at pH 2.6. At pH 2.6, the observed product distribution resulted from 65.5% β-O-4' ether bond cleavage, 27.0% Cα-C1 carbon bond cleavage, and 3.6% Cα-oxidation as by-product. Using ab initio molecular dynamic simulations and climbing-image Nudge Elastic Band based transition state searches, we suggest the effect of lower pH is via protonation of aliphatic hydroxyl groups under which extremely acidic conditions resulted in lower energetic barriers for bond-cleavages, particularly β-O-4' bonds.

CONCLUSION

These coupled experimental results and theoretical explanations suggest pH is a key driving force for selective and efficient lignin peroxidase isozyme H8 catalyzed depolymerization of the phenolic lignin dimer and further suggest that engineering of lignin peroxidase isozyme H8 and other enzymes involved in lignin depolymerization should include targeting stability at low pH.

Biobleaching of Acacia kraft pulp with extracellular enzymes secreted by Irpex lacteus KB-1.1 and Lentinus tigrinus LP-7 using low-cost media

The white-rot fungi Irpex lacteus KB-1.1 and Lentinus tigrinus LP-7 have been shown in previous studies to have high biobleaching activity in vivo. The aim of this study was to investigate the activities and stabilities of extracellular enzymes, prepared from I. lacteus and L. tigrinus culture grown in three types of economical media of agricultural and forestry wastes, for biobleaching of Acacia oxygen-delignified kraft pulp using kappa number reduction as an indicator of delignification. After 3 days of incubation, the extracellular enzymes preparations from I. lacteus and L. tigrinus cultures in media of Acacia mangium wood powder supplemented with rice bran and addition 1 % glucose (WRBG), resulted in significant decrease of 4.4 and 6.7 %, respectively. A slightly higher kappa number reduction (7.4 %) was achieved with the combine extracellular enzymes from I. lacteus and L. tigrinus. One of the strategies for reducing the cost of enzyme production for treatment processes in the pulp and paper industry is the utilization of agricultural and forestry waste. Thus, WRBG has potential as a culture medium for producing stable lignolytic enzymes simply and economically.

Biological Bleaching of Chemical Pulps

Use of biotechnology in pulp bleaching has attracted considerable attention and achieved interesting results in recent years. Enzymes of the hemicellulolytic type, particularly xylan-attacking enzymes, xylanases are now used commercially in the mills for pulp treatment and subsequent incorporation into bleach sequences. The aims of the enzymatic treatment depend on the actual mill conditions and may be related to environmental demands, reduction of chemical costs or maintenance or even improvement of product quality. The use of oxidative enzymes from white-rot fungi, that can directly attack lignin, is a second-generation approach, which could produce larger chemical savings than xylanase but has not yet been developed to the full scale. It is being studied in several laboratories in Canada, Japan, the U.S.A. and Europe. Certain white-rot fungi can delignify kraft pulps increasing their brightness and their responsiveness to brightening with chemicals. The fungal treatments are too slow but the enzyme manganese peroxidase and laccase can also delignify pulps and enzymatic processes are likely to be easier to optimize and apply than the fungal treatments. Development work on laccase and manganese peroxidase continues. This article presents an overview of developments in the application of hemicellulase enzymes, lignin-oxidizing enzymes and white-rot fungi in bleaching of chemical pulps. The basic enzymology involved and the present knowledge of the mechanisms of the action of enzymes as well as the practical results and advantages obtained on the laboratory and industrial scale are discussed.

Lignolytic enzymes produced by Trametes villosa ccb176 under different culture conditions

The expression of the enzymatic system produced by basidiomycetous fungi, which is involved in the degradation of xenobiotics, mainly depends on culture conditions, especially of the culture medium composition. Trametes villosa is a strain with a proven biotechnological potential for the degradation of organochlorine compounds and for the decolorization of textile dyes. The influence of glucose concentration, addition of a vegetable oil-surfactant emulsion, nature of the surfactant and the presence of manganese and copper on the growth, pH and production of laccase, total peroxidase and manganese-dependent peroxidase activities were evaluated. In general, acidification of the medium was observed, with the pH reaching a value close to 3.5 within the first days of growth. Laccase was the main activity detected under the different conditions and was produced throughout the culture period of the fungus, irrespective of the growth phase. Supplementation of the medium with vegetable oil emulsified with a surfactant induced manganese-dependent peroxidase activity in T. villosa. Higher specific yields of laccase activity were obtained with the addition of copper.

Prokaryotic origins of the non-animal peroxidase superfamily and organelle-mediated transmission to eukaryotes

Members of the superfamily of plant, fungal, and bacterial peroxidases are known to be present in a wide variety of living organisms. Extensive searching within sequencing projects identified organisms containing sequences of this superfamily. Class I peroxidases, cytochrome c peroxidase (CcP), ascorbate peroxidase (APx), and catalase peroxidase (CP), are known to be present in bacteria, fungi, and plants, but have now been found in various protists. CcP sequences were detected in most mitochondria-possessing organisms except for green plants, which possess only ascorbate peroxidases. APx sequences had previously been observed only in green plants but were also found in chloroplastic protists, which acquired chloroplasts by secondary endosymbiosis. CP sequences that are known to be present in prokaryotes and in Ascomycetes were also detected in some Basidiomycetes and occasionally in some protists. Class II peroxidases are involved in lignin biodegradation and are found only in the Homobasidiomycetes. In fact class II peroxidases were identified in only three orders, although degenerate forms were found in different Pezizomycota orders. Class III peroxidases are specific for higher plants, and their evolution is thought to be related to the emergence of the land plants. We have found, however, that class III peroxidases are present in some green algae, which predate land colonization. The presence of peroxidases in all major phyla (except vertebrates) makes them powerful marker genes for understanding the early evolutionary events that led to the appearance of the ancestors of each eukaryotic group.

Determination of lignin by size exclusion chromatography using multi angle laser light scattering

A method was developed using high-performance size exclusion liquid chromatography (HPSEC) with multi-angle laser light scattering (MALLS), quasi-elastic light scattering (QELS), interferometric refractometry (RI) and UV detection to characterize and monitor lignin. The combination proved very effective at tracking changes in molecular conformation of lignin molecules over time; i.e. changes in molecular weight distribution, radius of gyration, and hydrodynamic radius. Until this study, UV detection (280 nm) had been the primary lignin determination method for chromatography. Three different HPLC columns were used to study the effects of pH, flow conditions, and mobile phase compositions (dimethyl sulphoxide, water, 0.1M NaOH, and lithium bromide) on the chromatography of lignin. Since light scattering accuracy is highly dependent on solute concentration, both the UV and RI detectors were calibrated for use as concentration detectors. Shodex Asahipak GS-320 HQ column with 0.1M NaOH (pH 12.0) run at 0.5 ml/min was found to give the highest separation and most consistent recovery. The study also revealed that the lignin aggregated at pH below 8.5. This aggregation was detected only by MALLS and was not observed on UV or RI detectors. It is very important to take this loss in apparent concentration due to aggregation into consideration before collecting reliable depolymerization data.

Conifer root and butt rot caused by Heterobasidion annosum (Fr.) Bref. s.l

SUMMARY The root and butt rot caused by Heterobasidon annosum is one of the most destructive diseases of conifers in the northern temperate regions of the world, particularly in Europe. Economic losses attributable to Heterobasidion infection in Europe are estimated at 800 million euros annually. The fungus has been classified into three separate European intersterile species P (H. annosum), S (H. parviporum) and F (H. abietinum) based on their main host preferences: pine, spruce and fir, respectively. In North America, two intersterile groups are present, P and S/F, but these have not been given scientific names. The ecology of the disease spread has been intensively studied but the genetics, biochemistry and molecular aspects of pathogen virulence have been relatively little examined. Recent advances in transcript profiling, molecular characterization of pathogenicity factors and establishment of DNA-transformation systems have paved the way for future advances in our understanding of this pathosystem.

TAXONOMY

Heterobasidion annosum (Fr.) Bref., H. parviporum Niemelä & Korhonen and H. abietinum Niemelä & Korhonen; kingdom Fungi; class Basidiomycotina; order Aphyllophorales; family Bondarzewiaceae; genus Heterobasidion.

IDENTIFICATION

presence of the fungus fruit bodies, basidiocarps whitish in the margins, upper surface is tan to dark brown, usually irregular shaped, 3.5 (-7) cm thick and up to 40 cm in diameter; pores 5-19, 7-22 and 13-26 mm(2) for the P, F and S groups, respectively. Small brownish non-sporulating postules develop on the outside of infected roots. Asexual spores (conidiospores) are 3.8-6.6 x 2.8-5.0 microm in size. Mating tests are necessary for identification of intersterility groups.

HOST RANGE

The fungus attacks many coniferous tree species. In Europe, particularly trees of the genera Pinus and Juniperus (P), Picea (S), Abies (F) and in North America Pinus (P) and Picea, Tsuga and Abies (S/F). To a lesser extent it causes root rot on some decidous trees (Betula and Quercus). Disease symptoms: symptoms (e.g. exhudation of resin, crown deterioration) due to Heterobasidion root rot in living trees are not particularly characteristic and in most cases cannot be distinguished from those caused by other root pathogens. Heterobasidion annosum s.l. is a white rot fungus. Initial growth in wood causes a stain that varies in colour depending on host tree species. Incipient decay is normally pale yellow and it develops into a light brown decay to become a white pocket rot with black flecks in its advanced stage.

CONTROL

silvicultural methods (e.g. stump removal), chemicals (urea, borates) and biological control agent (Phlebiopsis gigantea, marketed as PG Suspension(R) in the UK, PG IBL(R) in Poland and Rotstop(R) in Fennoscandia) are commonly used approaches for minimizing the disease spread.

Laccase-catalyzed oxidation of Mn(2+) in the presence of natural Mn(3+) chelators as a novel source of extracellular H(2)O(2) production and its impact on manganese peroxidase

A purified and electrophoretically homogeneous blue laccase from the litter-decaying basidiomycete Stropharia rugosoannulata with a molecular mass of approximately 66 kDa oxidized Mn(2+) to Mn(3+), as assessed in the presence of the Mn chelators oxalate, malonate, and pyrophosphate. At rate-saturating concentrations (100 mM) of these chelators and at pH 5.0, Mn(3+) complexes were produced at 0.15, 0.05, and 0.10 micromol/min/mg of protein, respectively. Concomitantly, application of oxalate and malonate, but not pyrophosphate, led to H(2)O(2) formation and tetranitromethane (TNM) reduction indicative for the presence of superoxide anion radical. Employing oxalate, H(2)O(2) production, and TNM reduction significantly exceeded those found for malonate. Evidence is provided that, in the presence of oxalate or malonate, laccase reactions involve enzyme-catalyzed Mn(2+) oxidation and abiotic decomposition of these organic chelators by the resulting Mn(3+), which leads to formation of superoxide and its subsequent reduction to H(2)O(2). A partially purified manganese peroxidase (MnP) from the same organism did not produce Mn(3+) complexes in assays containing 1 mM Mn(2+) and 100 mM oxalate or malonate, but omitting an additional H(2)O(2) source. However, addition of laccase initiated MnP reactions. The results are in support of a physiological role of laccase-catalyzed Mn(2+) oxidation in providing H(2)O(2) for extracellular oxidation reactions and demonstrate a novel type of laccase-MnP cooperation relevant to biodegradation of lignin and xenobiotics.

Laccase-catalyzed oxidation of Mn(2+) in the presence of natural Mn(3+) chelators as a novel source of extracellular H(2)O(2) production and its impact on manganese peroxidase

A purified and electrophoretically homogeneous blue laccase from the litter-decaying basidiomycete Stropharia rugosoannulata with a molecular mass of approximately 66 kDa oxidized Mn(2+) to Mn(3+), as assessed in the presence of the Mn chelators oxalate, malonate, and pyrophosphate. At rate-saturating concentrations (100 mM) of these chelators and at pH 5.0, Mn(3+) complexes were produced at 0.15, 0.05, and 0.10 micromol/min/mg of protein, respectively. Concomitantly, application of oxalate and malonate, but not pyrophosphate, led to H(2)O(2) formation and tetranitromethane (TNM) reduction indicative for the presence of superoxide anion radical. Employing oxalate, H(2)O(2) production, and TNM reduction significantly exceeded those found for malonate. Evidence is provided that, in the presence of oxalate or malonate, laccase reactions involve enzyme-catalyzed Mn(2+) oxidation and abiotic decomposition of these organic chelators by the resulting Mn(3+), which leads to formation of superoxide and its subsequent reduction to H(2)O(2). A partially purified manganese peroxidase (MnP) from the same organism did not produce Mn(3+) complexes in assays containing 1 mM Mn(2+) and 100 mM oxalate or malonate, but omitting an additional H(2)O(2) source. However, addition of laccase initiated MnP reactions. The results are in support of a physiological role of laccase-catalyzed Mn(2+) oxidation in providing H(2)O(2) for extracellular oxidation reactions and demonstrate a novel type of laccase-MnP cooperation relevant to biodegradation of lignin and xenobiotics.

Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily

This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.

Different fungal manganese-oxidizing peroxidases: a comparison between Bjerkandera sp. and Phanerochaete chrysosporium

Two manganese-oxidizing peroxidases differing in glycosylation degree were purified from fermenter cultures of Bjerkandera sp. They were characterized and compared with the three manganese-oxidizing peroxidase isoenzymes obtained from the well-known ligninolytic fungus Phanerochaete chrysosporium. All the enzymes showed similar molecular masses but those from P. chrysosporium had less acidic isoelectric point. Moreover, the latter strictly required Mn2+ to oxidize phenolic substrates whereas the Bjerkandera peroxidases had both Mn-mediated and Mn-independent activity on phenolic and non-phenolic aromatic substrates. Taking into account these results, and those reported for Bjerkandera adusta and different Pleurotus species, we concluded that two different types of Mn(2+)-oxidizing peroxidases are secreted by ligninolytic fungi.