Technological advances and mechanistic basis for fungal biopulping

Cold-active microbial enzymes and their biotechnological applications

Microorganisms known as psychrophiles/psychrotrophs, which survive in cold climates, constitute majority of the biosphere on Earth. Their capability to produce cold-active enzymes along with other distinguishing characteristics allows them to survive in the cold environments. Due to the relative ease of large-scale production compared to enzymes from plants and animals, commercial uses of microbial enzyme are alluring. The ocean depths, polar, and alpine regions, which make up over 85% of the planet, are inhabited to cold ecosystems. Microbes living in these regions are important for their metabolic contribution to the ecosphere as well as for their enzymes, which may have potential industrial applications. Cold-adapted microorganisms are a possible source of cold-active enzymes that have high catalytic efficacy at low and moderate temperatures at which homologous mesophilic enzymes are not active. Cold-active enzymes can be used in a variety of biotechnological processes, including food processing, additives in the detergent and food industries, textile industry, waste-water treatment, biopulping, environmental bioremediation in cold climates, biotransformation, and molecular biology applications with great potential for energy savings. Genetically manipulated strains that are suitable for producing a particular cold-active enzyme would be crucial in a variety of industrial and biotechnological applications. The potential advantage of cold-adapted enzymes will probably lead to a greater annual market than for thermo-stable enzymes in the near future. This review includes latest updates on various microbial source of cold-active enzymes and their biotechnological applications.

Purification and characterization of two thermostable xylanases from a halotolerant Bacillus sp. Asc6BA isolated from Salar de Ascotán, Atacama Desert

Two extracellular xylanases, denominated X2 and X3, were purified and characterized from the halotolerant bacterium Bacillus sp. Asc6BA isolated from "Salar de Ascotán" in the Atacama Desert. Xylanases were purified by anion exchange, cation exchange and size exclusion liquid chromatography. Xylanase X2 and X3 were purified ~ 690-fold and ~ 629-fold, respectively, compared to the concentrated extracellular fraction with a final specific activity of 169 and 154 u mg^-1, respectively. Optimal conditions of pH and temperature of xylanolytic activity were 6.0 and 60 °C for X2 and 7.0 and 60 °C for X3. Half-life of X2 xylanase was 30 min at 50 °C, while X3 xylanase was remarkably more thermostable, retaining more than 70% of its activity after 32 h of incubation at 50 °C. X2 exhibited K_m, V_max and k_cat values of 7.17 mg mL^-1, 1.28 mM min^-1 mg^-1 and 425.33 s^-1, respectively. X3 exhibited K_m, V_max and k_cat values of 6.00 mg mL^-1, 19.25 mM min^-1 mg^-1 and 82,515 s^-1, respectively. In addition to their thermal stabilities, these enzymes were shown to be resistant to freeze-drying. These stability properties, in addition to the ability of these enzymes to be active in a wide range of temperatures and pHs, make these xylanases good candidates for industrial applications.

Structural Motifs of Wheat Straw Lignin Differ in Susceptibility to Degradation by the White-Rot Fungus Ceriporiopsis subvermispora

The white-rot fungus Ceriporiopsis subvermispora delignifies plant biomass extensively and selectively and, therefore, has great biotechnological potential. We previously demonstrated that after 7 weeks of fungal growth on wheat straw 70% w/w of lignin was removed and established the underlying degradation mechanisms via selectively extracted diagnostic substructures. In this work, we fractionated the residual (more intact) lignin and comprehensively characterized the obtained isolates to determine the susceptibility of wheat straw lignin's structural motifs to fungal degradation. Using 13C IS pyrolysis gas chromatography-mass spectrometry (py-GC-MS), heteronuclear single quantum coherence (HSQC) and 31P NMR spectroscopy, and size-exclusion chromatography (SEC) analyses, it was shown that β-O-4' ethers and the more condensed phenylcoumarans and resinols were equally susceptible to fungal breakdown. Interestingly, for β-O-4' ether substructures, marked cleavage preferences could be observed: β-O-4'-syringyl substructures were degraded more frequently than their β-O-4'-guaiacyl and β-O-4'-tricin analogues. Furthermore, diastereochemistry (threo > erythro) and γ-acylation (γ-OH > γ-acyl) influenced cleavage susceptibility. These results indicate that electron density of the 4'-O-coupled ring and local steric hindrance are important determinants of oxidative β-O-4' ether degradation. Our findings provide novel insight into the delignification mechanisms of C. subvermispora and contribute to improving the valorization of lignocellulosic biomass.

Lignocellulose degradation: An overview of fungi and fungal enzymes involved in lignocellulose degradation

This review aims to present current knowledge of the fungi involved in lignocellulose degradation with an overview of the various classes of lignocellulose-acting enzymes engaged in the pretreatment and saccharification step. Fungi have numerous applications and biotechnological potential for various industries including chemicals, fuel, pulp, and paper. The capability of fungi to degrade lignocellulose containing raw materials is due to their highly effective enzymatic system. Along with the hydrolytic enzymes consisting of cellulases and hemicellulases, responsible for polysaccharide degradation, they have a unique nonenzymatic oxidative system which together with ligninolytic enzymes is responsible for lignin modification and degradation. An overview of the enzymes classification is given by the Carbohydrate-Active enZymes (CAZy) database as the major database for the identification of the lignocellulolytic enzymes by their amino acid sequence similarity. Finally, the recently discovered novel class of recalcitrant polysaccharide degraders-lytic polysaccharide monooxygenases (LPMOs) are presented, because of these enzymes importance in the cellulose degradation process.

Biodegradation of wheat straw by Ochrobactrum oryzae BMP03 and Bacillus sp. BMP01 bacteria to enhance biofuel production by increasing total reducing sugars yield

Pretreatment is a vital step to enhance the yield of total reducing sugars and biofuel production from lignocellulose biomass. An effective new lignin-degrading and polysaccharide-hydrolyzing bacteria, Ochrobactrum oryzae BMP03 and Bacillus sp. BMP01 strains, were isolated and identified from wood-feeding termite's guts. Wheat straw was biodelignified by Ochrobactrum oryzae BMP03 bacteria strains to degrade lignin and to release the trapped cellulose and hemicellulose. The biodelignified wheat straw was hydrolyzed by Bacillus sp. BMP01 strains. Ochrobactrum oryzae BMP03-Bacillus sp. BMP01 consortia were also performed to analyze the effect of the simultaneous system. It was shown that the production of total reducing sugars in a separate hydrolysis system by Bacillus sp. BMP01 strain achieved 439 mg/g at 16 days of hydrolysis time, which is 9.45% higher than the simultaneous system. About 44.47% lignin was degraded by the Ochrobactrum oryzae BMP03 strain after 16 days of biotreatment. This also contributed for increment in cellulose content by 22.38% and hemicellulose content by 18.64%. The simultaneous system converted 368 mg of reducing sugars/g of wheat straw. Separate biodelignification and hydrolysis have an advantage over the simultaneous system in terms of hydrolysis efficiency and vice versa in terms of biotreatment time. Scanning electron microscope, mid-infrared analysis by Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction analysis confirmed the change in composition due to biotreatment. The biotreatment improved hydrolysis efficiency, which reduces the cost of biofuel production and increases the yield of biofuel. These results indicate the possibilities of biofuel production from wheat straw by employing Ochrobactrum oryzae BMP03 and Bacillus sp. BMP01 bacteria strains.

Biological pretreatment of sugarcane bagasse with basidiomycetes producing varied patterns of biodegradation

This work evaluated sugarcane bagasse pretreatment with wood-decay fungi, producing varied patterns of biodegradation. The overall mass balance of sugars released after pretreatment and enzymatic hydrolysis indicated that a selective white-rot was necessary to provide glucose yields similar to the ones observed from leading physico-chemical pretreatment technologies. The selective white-rot Ceriporiopsis subvermispora was selective for lignin degradation in the lignocellulosic material, preserved most of the glucan fraction, and increased the cellulose digestibility of biotreated material. Glucose mass balances indicated that of the potential glucose of untreated bagasse, 47% was recovered as sugar-rich syrup after C. subvermispora biotreatment for 60days followed by enzymatic digestion of the pretreated material.

Exploring glycoside hydrolases and accessory proteins from wood decay fungi to enhance sugarcane bagasse saccharification

BACKGROUND

Glycoside hydrolases (GHs) and accessory proteins are key components for efficient and cost-effective enzymatic hydrolysis of polysaccharides in modern, biochemically based biorefineries. Currently, commercialized GHs and accessory proteins are produced by ascomycetes. However, the role of wood decay basidiomycetes proteins in biomass saccharification has not been extensively pursued. Wood decay fungi degrade polysaccharides in highly lignified tissues in natural environments, and are a promising enzyme source for improving enzymatic cocktails that are designed for in vitro lignocellulose conversion.

RESULTS

GHs and accessory proteins were produced by representative brown- and white-rot fungi, Laetiporus sulphureus and Pleurotus ostreatus, respectively. Concentrated protein extracts were then used to amend commercial enzymatic cocktails for saccharification of alkaline-sulfite pretreated sugarcane bagasse. The main enzymatic activities found in the wood decay fungal protein extracts were attributed to endoglucanases, xylanases and β-glucosidases. Cellobiohydrolase (CBH) activities in the L. sulphureus and P. ostreatus extracts were low and nonexistent, respectively. The initial glucan conversion rates were boosted when the wood decay fungal proteins were used to replace half of the enzymes from the commercial cocktails. L. sulphureus proteins increased the glucan conversion levels, with values above those observed for the full load of commercial enzymes. Wood decay fungal proteins also enhanced the xylan conversion efficiency due to their high xylanase activities. Proteomic studies revealed 104 and 45 different proteins in the P. ostreatus and L. sulphureus extracts, respectively. The enhancement of the saccharification of alkaline-pretreated substrates by the modified enzymatic cocktails was attributed to the following protein families: GH5- and GH45-endoglucanases, GH3-β-glucosidases, and GH10-xylanases.

CONCLUSIONS

The extracellular proteins produced by wood decay fungi provide useful tools to improve commercial enzyme cocktails that are currently used for the saccharification of alkaline-pretreated lignocellulosic substrates. The relevant proteins encompass multiple glycoside hydrolase families, including the GH5- and GH45-endoglucanases, GH3-β-glucosidases, and GH10-xylanases.

Combination of ensiling and fungal delignification as effective wheat straw pretreatment

BACKGROUND

Utilization of lignocellulosic feedstocks for bioenergy production in developing countries demands competitive but low-tech conversion routes. White-rot fungi (WRF) inoculation and ensiling are two methods previously investigated for low-tech pretreatment of biomasses such as wheat straw (WS). This study was undertaken to assess whether a combination of forced ensiling with Lactobacillus buchneri and WRF treatment using a low cellulase fungus, Ceriporiopsis subvermispora, could produce a relevant pretreatment effect on WS for bioethanol and biogas production.

RESULTS

A combination of the ensiling and WRF treatment induced efficient pretreatment of WS by reducing lignin content and increasing enzymatic sugar release, thereby enabling an ethanol yield of 66 % of the theoretical max on the WS glucan, i.e. a yield comparable to yields obtained with high-tech, large-scale pretreatment methods. The pretreatment effect was reached with only a minor total solids loss of 5 % by weight mainly caused by the fungal metabolism. The combination of the biopretreatments did not improve the methane potential of the WS, but improved the initial biogas production rate significantly.

CONCLUSION

The combination of the L. buchneri ensiling and C. subvermispora WRF treatment provided a significant improvement in the pretreatment effect on WS. This combined biopretreatment produced particularly promising results for ethanol production.

A highly diastereoselective oxidant contributes to Ligninolysis by the white rot basidiomycete Ceriporiopsis subvermispora

The white rot basidiomycete Ceriporiopsis subvermispora delignifies wood selectively and has potential biotechnological applications. Its ability to remove lignin before the substrate porosity has increased enough to admit enzymes suggests that small diffusible oxidants contribute to delignification. A key question is whether these unidentified oxidants attack lignin via single-electron transfer (SET), in which case they are expected to cleave its propyl side chains between Cα and Cβ and to oxidize the threo-diastereomer of its predominating β-O-4-linked structures more extensively than the corresponding erythro-diastereomer. We used two-dimensional solution-state nuclear magnetic resonance (NMR) techniques to look for changes in partially biodegraded lignin extracted from spruce wood after white rot caused by C. subvermispora. The results showed that (i) benzoic acid residues indicative of Cα-Cβ cleavage were the major identifiable truncated structures in lignin after decay and (ii) depletion of β-O-4-linked units was markedly diastereoselective with a threo preference. The less selective delignifier Phanerochaete chrysosporium also exhibited this diastereoselectivity on spruce, and a P. chrysosporium lignin peroxidase operating in conjunction with the P. chrysosporium metabolite veratryl alcohol did likewise when cleaving synthetic lignin in vitro. However, C. subvermispora was significantly more diastereoselective than P. chrysosporium or lignin peroxidase-veratryl alcohol. Our results show that the ligninolytic oxidants of C. subvermispora are collectively more diastereoselective than currently known fungal ligninolytic oxidants and suggest that SET oxidation is one of the chemical mechanisms involved.

A first insight into Pycnoporus sanguineus BAFC 2126 transcriptome

Fungi of the genus Pycnoporus are white-rot basidiomycetes widely studied because of their ability to synthesize high added-value compounds and enzymes of industrial interest. Here we report the sequencing, assembly and analysis of the transcriptome of Pycnoporus sanguineus BAFC 2126 grown at stationary phase, in media supplemented with copper sulfate. Using the 454 pyrosequencing platform we obtained a total of 226,336 reads (88,779,843 bases) that were filtered and de novo assembled to generate a reference transcriptome of 7,303 transcripts. Putative functions were assigned for 4,732 transcripts by searching similarities of six-frame translated sequences against a customized protein database and by the presence of conserved protein domains. Through the analysis of translated sequences we identified transcripts encoding 178 putative carbohydrate active enzymes, including representatives of 15 families with roles in lignocellulose degradation. Furthermore, we found many transcripts encoding enzymes related to lignin hydrolysis and modification, including laccases and peroxidases, as well as GMC oxidoreductases, copper radical oxidases and other enzymes involved in the generation of extracellular hydrogen peroxide and iron homeostasis. Finally, we identified the transcripts encoding all of the enzymes involved in terpenoid backbone biosynthesis pathway, various terpene synthases related to the biosynthesis of sesquiterpenoids and triterpenoids precursors, and also cytochrome P450 monooxygenases, glutathione S-transferases and epoxide hydrolases with potential functions in the biodegradation of xenobiotics and the enantioselective biosynthesis of biologically active drugs. To our knowledge this is the first report of a transcriptome of genus Pycnoporus and a resource for future molecular studies in P. sanguineus.

Syringyl-rich lignin renders poplars more resistant to degradation by wood decay fungi

In order to elucidate the effects of lignin composition on the resistance of wood to degradation by decay fungi, wood specimens from two transgenic poplar lines expressing an Arabidopsis gene encoding ferulate 5-hydroxylase (F5H) driven by the cinnimate-4-hydroxylase promoter (C4H::F5H) that increased syringyl/guaiacyl (S/G) monolignol ratios relative to those in the untransformed control wood were incubated with six different wood decay fungi. Alterations in wood weight and chemical composition were monitored over the incubation period. The results showed that transgenic poplar lines extremely rich in syringyl lignin exhibited a drastically improved resistance to degradation by all decay fungi evaluated. Lignin monomer composition and its distribution among cell types and within different cell layers were the sole wood chemistry parameters determining wood durability. Since transgenic poplars with exceedingly high syringyl contents were recalcitrant to degradation, where wood durability is a critical factor, these genotypes may offer improved performance.

Combination of steam explosion and laccase-mediator treatments prior to Eucalyptus globulus kraft pulping

The effect of a pretreatment consisting of steam explosion (SE) followed by a laccase mediator system (LMS) stage on Eucalyptus globulus kraft pulping has been evaluated and compared with fungal pretreatments. Pretreatment with SE and LMS was more efficient than pretreatments using Pycnoporus sanguineus and Trametes sp. I-62. Steam explosion not only improved the enzyme penetration into the wood chips and shortened the pulping process by 60%, but also extracted around 50% of the hemicelluloses which could be converted into value-added products. The optimal conditions for the LMS treatment were 3h, 3UA/g and 40°C. Compared to SE, the SE/LMS treatment yielded an increase in delignification of 13.9% without affecting pulp properties, provided a similar screened kraft yield, and reduced consumption of chemical reagents Na(2)S and NaOH by 11.5% and 6.3%, respectively. Therefore, SE/LMS is a promising pretreatment for converting the pulp mill into a forest bio-refinery.

Lignin peroxidases of some indigenous ligninolytic fungi: secretion and enzymatic characteristics

Secretion and enzymatic characteristics of lignin peroxidases from Gloeophyllum sepiarium MTCC 1170, Cladosporium herbarum MTCC 346, Lenzites betulina MTCC 1183, Daedalea flavida MTCC 145, Hexagonia teruis MTCC 1119 and Coirolopsis floccosa MTCC 1177 ligninolytic fungal strains have been reported. Secretion of lignin peroxidase by these ligninolytic fungal strains have been found to be in the range of 0.86 to 3.0 enzyme unit per ml of the culture medium. The enzymatic characteristics like K(m), pH and temperature optima of all the lignin peroxidases of the above fungal strains have been determined using veratryl alcohol and H(2)O(2) as the variable substrates. The K(m) values using veratryl alcohol as the substrate were found to be 65.0 μM, 58.5 μM, 63.0 μM, 54.5 μM, 54.6 μM and 61.0 μM respectively. The K(m) values using H(2)O(2) as the substrate were found to be 88.0 μM, 86.0 μM, 71.0 μM, 67.0 μM, 80.0 μM and 78.0 μM respectively. The pH optima values for lignin peroxidases of the above ligninolytic fungal strains were found to be 2.5, 2.4, 2.4, 2.25, 2.5 and 2.8 respectively, where as the temperature optima values were 25°C, 24°C, 25°C, 23°C, 24°C and 25°C respectively.

Evaluation of the white-rot fungi Ganoderma australe and Ceriporiopsis subvermispora in biotechnological applications

Ganoderma australe is a white-rot fungus that causes a selective wood biodelignification in some hardwoods found in the Chilean rainforest. Ceriporiopsis subvermispora is also a lignin-degrading fungus used in several biopulping studies. The enzymatic system responsible for lignin degradation in wood can also be used to degrade recalcitrant organic pollutants in liquid effluents. In this work, two strains of G. australe and one strain of C. subvermipora were comparatively evaluated in the biodegradation of ABTS and the dye Poly R-478 in liquid medium, and in the pretreatment of Eucalyptus globulus wood chips for further kraft biopulping. Laccase was detected in liquid and wood cultures with G. australe. Ceriporiopsis subvermispora produce laccase and manganese peroxidase when grown in liquid medium and only manganese peroxidase was detected during wood decay. ABTS was totally depleted by all strains after 8 days of incubation while Poly R-478 was degraded up to 40% with G. australe strains and up to 62% by C. subvermispora after 22 days of incubation. Eucalyptus globulus wood chips decayed for 15 days presented 1-6% of lignin loss and less than 2% of glucan loss. Kraft pulps with kappa number 15 were produced from biotreated wood chips with 2% less active alkali, with up to 3% increase in pulp yield and up to 20% less hexenuronic acids than pulps from undecayed control. Results showed that G. australe strains evaluated were not as efficient as C. subvermispora for dye and wood biodegradation, but could be used as a feasible alternative in biotechnological processes such as bioremediation and biopulping.