Lytic xylan oxidases from wood-decay fungi unlock biomass degradation.

Wood biomass is the most abundant feedstock envisioned for the development of modern biorefineries. However, the cost-effective conversion of this form of biomass into commodity products is limited by its resistance to enzymatic degradation. Here we describe a new family of fungal lytic polysaccharide monooxygenases (LPMOs) prevalent among white-rot and brown-rot basidiomycetes that is active on xylans-a recalcitrant polysaccharide abundant in wood biomass. Two AA14 LPMO members from the white-rot fungus Pycnoporus coccineus substantially increase the efficiency of wood saccharification through oxidative cleavage of highly refractory xylan-coated cellulose fibers. The discovery of this unique enzyme activity advances our knowledge on the degradation of woody biomass in nature and offers an innovative solution for improving enzyme cocktails for biorefinery applications.

Exploitation of genus Rhodosporidium for microbial lipid production.

Oleaginous microorganisms are receiving significant attention worldwide for their utility in biodiesel production and the potentiality to produce some specialty-type lipids. There is an increasing interest in isolation/adaption of robust microbe strains and design of innovative fermentation processes to make microbial lipid production a more efficient and economically feasible bio-process. Currently, the genus Rhodosporidium has been considered an important candidate, for the reason that several strains belonging to this genus have shown excellent capabilities of lipid accumulation, broad adaptabilities to various substrates, and co-production of some carotenoids. This paper reviews the current trends in the exploitation of Rhodosporidium species for microbial lipid production, including the utilization of various (single or mixed, pure or waste-derived) substrates, progress of genetic modification and metabolic engineering, innovations in fermentation mode, lipid characterizations and their potential applications. Finally, the constraints and perspectives of cultivating Rhodosporidium species for lipid production are also discussed.

The discovery of novel LPMO families with a new Hidden Markov model.

BACKGROUND: Renewable biopolymers, such as cellulose, starch and chitin are highly resistance to enzymatic degradation. Therefore, there is a need to upgrade current degradation processes by including novel enzymes. Lytic polysaccharide mono-oxygenases (LPMOs) can disrupt recalcitrant biopolymers, thereby enhancing hydrolysis by conventional enzymes. However, novel LPMO families are difficult to identify using existing methods. Therefore, we developed a novel profile Hidden Markov model (HMM) and used it to mine genomes of ascomycetous fungi for novel LPMOs. RESULTS: We constructed a structural alignment and verified that the alignment was correct. In the alignment we identified several known conserved features, such as the histidine brace and the N/Q/E-X-F/Y motif and previously unidentified conserved proline and glycine residues. These residues are distal from the active site, suggesting a role in structure rather than activity. The multiple protein alignment was subsequently used to build a profile Hidden Markov model. This model was initially tested on manually curated datasets and proved to be both sensitive (no false negatives) and specific (no false positives). In some of the genomes analyzed we identified a yet unknown LPMO family. This new family is mostly confined to the phyla of Ascomycota and Basidiomycota and the class of Oomycota. Genomic clustering indicated that at least some members might be involved in the degradation of ß-glucans, while transcriptomic data suggested that others are possibly involved in the degradation of pectin. CONCLUSIONS: The newly developed profile hidden Markov Model was successfully used to mine fungal genomes for a novel family of LPMOs. However, the model is not limited to bacterial and fungal genomes. This is illustrated by the fact that the model was also able to identify another new LPMO family in Drosophila melanogaster. Furthermore, the Hidden Markov model was used to verify the more distant blast hits from the new fungal family of LPMOs, which belong to the Bivalves, Stony corals and Sea anemones. So this Hidden Markov model (Additional file 3) will help the broader scientific community in identifying other yet unknown LPMOs.

Macaúba (Acrocomia aculeata) cake from biodiesel processing: a low-cost substrate to produce lipases from Moniliella spathulata R25L270 with potential application in the oleochemical industry.

BACKGROUND: Biodiesel industry wastes were evaluated as supplements for lipase production by Moniliella spathulata R25L270, which is newly identified yeast with great lipolytic potential. Macaúba cake (MC), used for the first time in this work as inducer to produce lipases, and residual oil (RO) were mixed to maximise enzyme production. The lipase secreted was biochemically characterised. RESULTS: The best ratio for the mixture (MC:RO) was 0.66:0.34 and the fitted values for lipase activity and total protein concentration were 0.98 U mL(-1) and 0.356 mg mL(-1), respectively. Maximum activity obtained (2.47 U mL(-1)) was achieved at 31.5°C and pH 6.7, and the enzyme was stable in this condition. A novel enzyme was purified and identified for the first time by mass spectrometry. The lipase efficiently hydrolysed different natural oils and exhibited selectivity in the production of eicosapentaenoic acid from fish oil. CONCLUSION: The use of MC and RO as a supplement to produce the new lipase from M. spathulata R25L270 may be one alternative for reducing lipase production costs and simultaneously adding value to biodiesel industry residues. The potential application of the lipase in the oleochemical industry was demonstrated by its pH and temperature stabilities and selective hydrolysis.

In silico and in vitro physicochemical screening of Rigidoporus sp. crude laccase-assisted decolorization of synthetic dyes--approaches for a cost-effective enzyme-based remediation methodology.

The objective of this paper is to compare in silico data with wet lab physicochemical properties of crude laccase enzyme isolated from Rigidoporus sp. using wheat bran as solid substrate support towards dye decolorization. Molecular docking analysis of selected nine textile and non-textile dyes were performed using laccase from Rigidoporus lignosus as reference protein. Enzyme-based remediation methodology using crude enzyme enriched from solid state fermentation was applied to screen the effect of four influencing variables such as pH, temperature, dye concentration, and incubation time toward dye decolorization. The extracellular crude enzyme decolorized 69.8 % Acid Blue 113, 45.07 % Reactive Blue 19, 36.61 % Reactive Orange 122, 30.55 % Acid Red 88, 24.59 % Direct Blue 14, 18.48 % Reactive Black B, 16.49 % Reactive Blue RGB, and 11.66 % Acid Blue 9 at 100 mg/l dye concentration at their optimal pH at room temperature under static and dark conditions after 1 h of incubation without addition of any externally added mediators. Our wet lab studies approach, barring other factors, validate in silico for screening and ranking textile dyes based on their proximity to the T1 site. We are reporting for the first time a combinatorial approach involving in silico methods and wet lab-based crude laccase-mediated dye decolorization without any external mediators.

Industrial and biotechnological applications of ligninolytic enzymes of the basidiomycota: a review

Ligninolytic enzymes of the basidiomycetes play a crucial role in the global carbon cycle. The demand for application of ligninolytic enzymes complexes of white-rot fungi in industry and biotechnology is ever increasing due to their use in a variety of processes. Ligninolytic enzymes have potential applications in a large number of fields, including the chemical, fuel, food, agricultural, paper, textile, cosmetic industrial sectors and more. This ligninolytic system of white-rot fungi is also directly involved in the degradation of various xenobiotic compounds and dyes. Their capacities to remove xenobiotic substances and produce polymeric products make them a useful tool for bioremediation purposes. This paper reviews the applications of ligninolytic enzymes of basidiomycetes within different industrial and biotechnological area.

Assessment of saccharification efficacy in the cellulase system of the brown rot fungus Gloeophyllum trabeum.

Brown rot fungi uniquely degrade wood by creating modifications thought to aid in the selective removal of polysaccharides by an incomplete cellulase suite. This naturally successful mechanism offers potential for current bioprocessing applications. To test the efficacy of brown rot cellulases, southern yellow pine wood blocks were first degraded by the brown rot fungus Gloeophyllum trabeum for 0, 2, 4, and 6 weeks. Characterization of the pine constituents revealed brown rot decay patterns, with selective polysaccharide removal as lignin compositions increased. G. trabeum liquid and solid state cellulase extracts, as well as a commercial Trichoderma reesei extract (Celluclast 1.5 L), were used to saccharify this pretreated material, using beta-glucosidase amendment to remove limitation of cellobiose-to-glucose conversion. Conditions varied according to source and concentration of cellulase extract and to pH (3.0 vs. 4.8). Hydrolysis yields were maximized using solid state G. trabeum extracts at a pH of 4.8. However, the extent of glucose release was low and was not significantly altered when cellulase loading levels were increased threefold. Furthermore, Celluclast 1.5 L continually outperformed G. trabeum cellulase extracts, although extent of glucose release never exceeded 22.0%. Results suggest methodological advances for utilizing crude G. trabeum cellulases and imply that the suboptimal hydrolysis levels obtained with G. trabeum and Celluclast 1.5 L cellulases, even at high loading levels, may be due to brown rot modifications insufficiently distributed throughout the pretreated material.

[Comparative stability assessment of laccases from the basidiomycetes Coriolus hirsutus and Coriolus zonatus in the presence of effectors]. / Sravnitel'noe izuchenie stabil'nosti lakkaz iz bazidiomitsetov Coriolus hirsutus i Coriolus zonatus v prisutstvii éffectorov.

Stability characteristics of the laccases of the basidiomycetes Coriolus hirsutus and Coriolus zonatus were measured comparatively at temperatures 25 and 40 degrees C in the presence of various effectors (proteins, salts, polyalcohols, polyacids, and polyelectrolytes). Stabilization effects of cations on the laccases from C. hirsutus and C. zonatus decreased in the descending series Cu2+ > Mg2+ > Ca2+ and Ca2+ > Mg2+ > Mn2+, respectively. Tween 20 caused insignificant stabilization of the two enzymes. The C. zonatus laccase was also insignificantly stabilized as a result of treatment with bovine serum albumin. The enzymatic activity of the laccase preparations from C. hirsutus and C. zonatus was conserved virtually completely after vacuum drying (84 and 93%, respectively). The most effective stabilizer of the C. hirsutus laccase was found to be dextran (17 kD). Dry preparations treated with this agent conserved up to 95% of the enzymatic activity. The most effective stabilizer of the C. zonatus was polyacrylic acid (102% of the initial activity).

Laccase and other ligninolytic enzyme activities of selected strains of Trametes spp. from different localities and substrates.

Eighty-three strains belonging to three species of the genus Trametes FR. (T. versicolor, T. hirsuta and T. ochracea) collected in different localities and on different substrates were screened for laccase production. The production of other lignin-modifying enzymes--manganese peroxidase (MnP) and lignin peroxidase (LiP)--and the decolorization ability were also determined in 21 of them. Production variability was relatively high and no significant correlation was found between the origin of the strains (locality, substrate) and the enzyme production. Dikaryons of all 3 species (but not of all their strains) exhibited LiP activity, which was not detected in the respective monokaryons.

The 1,4-beta-D-glucan glucanohydrolases from Phanerochaete chrysosporium. Re-assessment of their significance in cellulose degradation mechanisms.

A physico-chemical, functional and structural characterization, including partial sequence data, of three major 1,4-beta-D-glucan glucanohydrolases (EC. 3.2.1.4) isolated from the culture filtrate of the white-rot fungus Phanerochaete chrysosporium, shows that all three enzymes belong to a single family of cellulases. EG44, pI 4.3, (named after its apparent molecular mass in kDa), shows a clear homology with Schizopyllum commune Endoglucanase I (EGI); whereas EG38, pI 4.9, (named in the same manner) is related more closely to Trichoderma reesei (Trichoderma longibrachiatum) Endoglucanase III (EGIII). EG36, pI 5.6-5.7, is probably an EG38 protein lacking its cellulose binding domain. Strong synergistic action is induced by the enzymes acting in concert with cellobiohydrolases (CBHI and CBHII) from the same organism, indicating a highly effective enzymatic system for cellulose degradation. Controlled proteolysis with papain has allowed a so far unique cleavage of endoglucanases EG44 and EG38 into two domains: a core protein, which virtually lacks the capacity to absorb onto microcrystal-line cellulose but retains full catalytic activity against carboxymethyl cellulose and low molecular weight soluble substrates; and a peptide fragment corresponding to the cellulose binding domain. The latter appears to be of paramount significance in the mechanisms involved in the hydrolysis of microcrystalline cellulose.