Search

Here the statistics concerning X-ray data processing and structure refinement are given, together with the substrate preference analysis for ThBgl1 and ThBgl2. Finally, the analysis of the influence of temperature and pH on the activities of both enzymes are shown.

Plant biomass is a low-cost and abundant source of carbohydrates for production of fuels, "green" chemicals and materials. Currently, biochemical conversion of the biomass into sugars via enzymatic hydrolysis is the most viable technology. Here, the role of carbohydrate binding modules (CBMs) in the disruption of insoluble polysaccharide structures and their capacity to enhance cellulase-promoted lignocellulosic biomass hydrolysis was investigated. We show that CBM addition promotes generation of additional reducing ends in the insoluble substrate by cellulases. On the contrary, bovine serum albumin (BSA), widely used in prevention of a non-specific protein binding, causes an increase in soluble reducing-end production, when applied jointly with cellulases. We demonstrate that binding of CBMs to cellulose is non-homogeneous, irreversible and leads to its amorphisation. Our results also reveal effects of CBM-promoted amorphogenesis on cellulose hydrolysis by cellulases.

The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of β-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general architecture, substrate binding and cleavage. Here, we use a combination of X-ray crystallography, bioinformatics, enzymatic assays, molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure, substrate binding and enzymatic specificity of the GH45 subfamily C endoglucanase from Phanerochaete chrysosporium (PcCel45A). We investigated the role played by different residues in the binding of the enzyme to cellulose oligomers of different lengths and examined the structural characteristics and dynamics of PcCel45A that make subfamily C so dissimilar to other members of the GH45 family. Due to the structural similarity shared between PcCel45A and domain I of expansins, comparative analysis of their substrate binding was also carried out. Our bioinformatics sequence analyses revealed that the hydrolysis mechanisms in GH45 subfamily C is not restricted to use of the imidic asparagine as a general base in the “Newton’s cradle” catalytic mechanism recently proposed for this subfamily.

Trichoderma filamentous fungi have been investigated due to their ability to secrete cellulases which find various biotechnological applications such as biomass hydrolysis and cellulosic ethanol production. Previous studies demonstrated that Trichoderma harzianum IOC-3844 has a high degree of cellulolytic activity and potential for biomass hydrolysis. However, enzymatic, biochemical, and structural studies of cellulases from T. harzianum are scarce. This work reports biochemical characterization of the recombinant endoglucanase I from T. harzianum, ThCel7B, and its catalytic core domain. The constructs display optimum activity at 55 °C and a surprisingly acidic pH optimum of 3.0. The full-length enzyme is able to hydrolyze a variety of substrates, with high specific activity: 75 U/mg for β-glucan, 46 U/mg toward xyloglucan, 39 U/mg for lichenan, 26 U/mg for carboxymethyl cellulose, 18 U/mg for 4-nitrophenyl β-D-cellobioside, 16 U/mg for rye arabinoxylan, and 12 U/mg toward xylan. The enzyme also hydrolyzed filter paper, phosphoric acid swollen cellulose, Sigmacell 20, Avicel PH-101, and cellulose, albeit with lower efficiency. The ThCel7B catalytic domain displays similar substrate diversity. Fluorescence-based thermal shift assays showed that thermal stability is highest at pH 5.0. We determined kinetic parameters and analyzed a pattern of oligosaccharide substrates hydrolysis, revealing cellobiose as a final product of C6 degradation. Finally, we visualized effects of ThCel7B on oat spelt using scanning electron microscopy, demonstrating the morphological changes of the substrate during the hydrolysis. The acidic behavior of ThCel7B and its considerable thermostability hold a promise of its industrial applications and other biotechnological uses under extremely acidic conditions.

Biomass is the most abundant and short-term renewable natural resource on Earth whose recalcitrance toward enzymatic degradation represents significant challenge for a number of biotechnological applications. The not so abundant but critically necessary class of GH45 endoglucanases constitutes an essential component of tailored industrial enzyme cocktails because they randomly and internally cleave cellulose molecules. Moreover, GH45 glucanases are core constituents of major-brand detergent formulations as well as enzymatic aid components in the cotton processing industry, clipping unwanted cellulosic fibers from cotton (cellulosic)-based tissues. Here we report on a recombinant high-yield Neurospora crassa OR74A NcCel45A production system, a single-band GH45 endoglucanase purification, and a complete enzyme functional characterization. NcCel45A is a bimodular endoglucanase showing maximum activity at pH 6.0 and 60 °C, while most active against lichenan and β-glucans and lesser active toward filter paper, carboxymethylcellulose, and phosphoric acid-swollen cellulose. Gluco-oligosaccharide degradation fingerprinting experiments suggest cellopentaose as the minimal length substrate and ThermalFluor studies indicate that NcCel45A displays excellent stability at elevated temperatures up to 70 °C and pHs ranging from 5 to 9. Remarkably, we show that NcCel45A is uniquely resistant to a wide-range of organic solvents and small-angle X-ray scattering show a monkey-wrench molecular shape structure in solution, which indicates, unlike to other known cellulases, a non-fully extended conformation, thus conferring solvent protection. These NcCel45A unique enzymatic properties maybe key for specific industrial applications such as cotton fiber processing and detergent formulations.

Bifidobacterium is an important genus of probiotic bacteria colonizing the human gut. These bacteria can uptake oligosaccharides for the fermentative metabolism of hexoses and pentoses, producing lactate, acetate as well as short-chain fatty acids and propionate. These end-products are known to have important effects on human health. β-glucosidases (EC 3.2.1.21) are pivotal enzymes for the metabolism and homeostasis of Bifidobacterium, since they hydrolyze small and soluble saccharides, typically producing glucose. Here we describe the cloning, expression, biochemical characterization and the first X-ray structure of a GH3 β-glucosidase from the probiotic bacteria Bifidobacterium adolescentis (BaBgl3). The purified BaBgl3 showed a maximal activity at 45 °C and pH 6.5. Under the optimum conditions, BaBgl3 is highly active on 4-nitrophenyl-β- d -glucopyranoside (pNPG) and, at a lesser degree, on 4-nitrophenyl-β- d -xylopyranoside (pNPX, about 32% of the activity observed for pNPG). The 2.4 A resolution crystal structure of BaBgl3 revealed a three-domain structure composed of a TIM barrel domain, which together with α/β sandwich domain accommodate the active site and a third C-terminal fibronectin type III (FnIII) domain with unknown function. Modeling of the substrate in the active site indicates that an aspartate interacts with the hydroxyl group of the C6 present in pNPG but absent in pNPX, which explains the substrate preference. Finally, the enzyme is significantly stabilized by glycerol and galactose, resulting in considerable increase in the enzyme activity and its lifetime. The structural and biochemical studies presented here provide a deeper understanding of the molecular mechanisms of complex carbohydrates degradation utilized by probiotic bacteria as well as for the development of new prebiotic oligosaccharides.

β-glucosidases are glycoside hydrolases able to cleave small and soluble substrates, thus producing monosaccharides. These enzymes are distributed among families GH1, GH2, GH3, GH5, GH9, GH30 and GH116, with GH1 and GH3 being the most relevant families with characterized enzymes to date. A recent transcriptomic analysis of the fungus Trichoderma harzianum, known for its increased β-glucosidase activity as compared to Trichoderma reesei, revealed two enzymes from family GH1 with high expression levels. Here we report the cloning, recombinant expression, purification and crystallization of these enzymes, ThBgl1 and ThBgl2. A close inspection of the enzymatic activity of these enzymes surprisingly revealed a marked difference between them despite the sequence similarity (53%). ThBgl1 has an increased tendency to catalyze transglycosylation reaction while ThBgl2 acts more as a hydrolyzing enzyme. Detailed comparison of their crystal structures and the analysis of the molecular dynamics simulations reveal the presence of an asparagine residue N186 in ThBgl2, which is replaced by the phenylalanine F180 in ThBgl1. This single amino acid substitution seems to be sufficient to create a polar environment that culminates with an increased availability of water molecules in ThBgl2 as compared to ThBgl1, thus conferring stronger hydrolyzing character to the former enzyme.

Made available in DSpace on 2018-11-26T15:29:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-04-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme. Univ Sao Paulo, Sao Carlos Inst Phys, BR-13566590 Sao Paulo, Brazil Univ Estadual Campinas, Inst Chem, BR-13084862 Sao Paulo, Brazil State Univ Sao Paulo, Inst Biosci, BR-18618970 Sao Paulo, Brazil European Synchrotron Radiat Facil, CS40220, Grenoble, France State Univ Sao Paulo, Inst Biosci, BR-18618970 Sao Paulo, Brazil FAPESP: 2008/56255-9 FAPESP: 2009/52840-7 FAPESP: 2010/18773-8 FAPESP: 2013/08293-7 FAPESP: 2013/15582-5 FAPESP: 2014/10448-1 CNPq: 490022/2009-0 CNPq: 301981/2011-6 CNPq: 500091/2014-5 CNPq: 310177/2011-1

Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase fromBifidobacterium bifidumS17 (BbGal43A) are described.BbGal43A was successfully produced and showed activity towards synthetic galactosides.BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences betweenBbGal43A and its characterized homologues.

In a search for better comprehension of β-galactosidase function and specificity, we solved the crystal structures of the GH42 β-galactosidase BbgII from Bifidobacterium bifidum S17, a well-adapted probiotic microorganism from the human digestive tract, and its complex with D-α-galactose. BbgII is a three-domain molecule that forms barrel-shaped trimers in solution. BbgII interactions with D-α-galactose, a competitive inhibitor, showed a number of residues that are involved in the coordination of ligands. A combination of site-directed mutagenesis of these amino acid residues with enzymatic activity measurements confirmed that Glu161 and Glu320 are fundamental for catalysis and their substitution by alanines led to catalytically inactive mutants. Mutation Asn160Ala resulted in a two-orders of magnitude decrease of the enzyme kcat without significant modification in its Km, whereas mutations Tyr289Phe and His371Phe simultaneously decreased kcat and increased Km values. Enzymatic activity of Glu368Ala mutant was too low to be detected. Our docking and molecular dynamics simulations showed that the enzyme recognizes and tightly binds substrates with β1→6 and β1→3 bonds, while binding of the substrates with β1→4 linkages is less favorable. This article is protected by copyright. All rights reserved.

Global gene expression analysis was carried out with Blastocladiella emersonii cells subjected to oxygen deprivation (hypoxia) using cDNA microarrays. In experiments of gradual hypoxia (gradual decrease in dissolved oxygen) and direct hypoxia (direct decrease in dissolved oxygen), about 650 differentially expressed genes were observed. A total of 534 genes were affected directly or indirectly by oxygen availability, as they showed recovery to normal expression levels or a tendency to recover when cells were reoxygenated. In addition to modulating many genes with no putative assigned function, B. emersonii cells respond to hypoxia by readjusting the expression levels of genes responsible for energy production and consumption. At least transcriptionally, this fungus seems to favor anaerobic metabolism through the upregulation of genes encoding glycolytic enzymes and lactate dehydrogenase and the downregulation of most genes coding for tricarboxylic acid (TCA) cycle enzymes. Furthermore, genes involved in energy-costly processes, like protein synthesis, amino acid biosynthesis, protein folding, and transport, had their expression profiles predominantly downregulated during oxygen deprivation, indicating an energy-saving effort. Data also revealed similarities between the transcriptional profiles of cells under hypoxia and under iron(II) deprivation, suggesting that Fe 2+ ion could have a role in oxygen sensing and/or response to hypoxia in B. emersonii . Additionally, treatment of fungal cells prior to hypoxia with the antibiotic geldanamycin, which negatively affects the stability of mammalian hypoxia transcription factor HIF-1α, caused a significant decrease in the levels of certain upregulated hypoxic genes.

Here, we present the draft genome sequence of Thermus filiformis strain ATCC 43280, a thermophile bacterium capable of producing glycosylated carotenoids acylated with branched fatty acids and enzymes of biotechnological potential.

Recent advances in DNA sequencing techniques have led to an explosion in the amount of available genome sequencing data and this provided an inexhaustible source of uncharacterized glycoside hydrolases (GH) to be studied both structurally and enzymatically. Ligation-Independent Cloning (LIC), an interesting alternative to traditional, restriction enzyme-based cloning, and commercial recombinatorial cloning, was adopted and optimized successfully for a high throughput cloning, expression and purification pipeline. Using this platform, 130 genes encoding mainly uncharacterized glycoside hydrolases from 13 different organisms were cloned and submitted to a semi-automated protein expression and solubility screening in Escherichia coli, resulting in 73 soluble targets. The high throughput approach proved to be a powerful tool for production of recombinant glycoside hydrolases for further structural and biochemical characterization and confirmed that thioredoxin fusion tag (TRX) is a better choice to increase solubility of recombinant glycoside hydrolases expressed in E. coli, when compared to His-tag alone.

Superoxide dismutases (SODs; EC 1.15.1.1) are part of the antioxidant system of aerobic organisms and are used as a defense against oxidative injury caused by reactive oxygen species (ROS). The cloning and sequencing of the 788-bp genomic DNA from Trichoderma reesei strain QM9414 (anamorph of Hypocrea jecorina ) revealed an open reading frame encoding a protein of 212 amino acid residues, with 65–90% similarity to manganese superoxide dismutase from other filamentous fungi. The TrMnSOD was purified and shown to be stable from 20 to 90 °C for 1 h at pH from 8 to 11.5, while maintaining its biological activity.

Agrobacterium tumefaciens is widely used for plant DNA transformation and more recently, has also been used to transform yeast, filamentous fungi and even human cells. Using this technique, we developed the first transformation protocol for the saprobic aquatic fungus Blastocladiella emersonii, a Blastocladiomycete localized at the base of fungal phylogenetic tree, which has been shown as a promising and interesting model of study of cellular function and differentiation. We constructed binary T-DNA vectors containing hygromycin phosphotransferase (hph) or enhanced green fluorescent protein (egfp) genes, under the control of Aspergillus nidulans trpC promoter and terminator sequences. 24h of co-cultivation in induction medium (IM) agar plates, followed by transfer to PYG-agar plates containing cefotaxim to kill Agrobacterium tumefsciens and hygromycin to select transformants, resulted in growth and sporulation of resistant transformants. Genomic DNA from the pool o resistant zoospores were shown to contain T-DNA insertion as evidenced by PCR amplification of hph gene. Using a similar protocol we could also evidence the expression of enhanced green fluorescent protein (EGFP) in zoospores derived from transformed cells. This protocol can also open new perspectives for other non-transformable closely related fungi, like the Chytridiomycete class.

Trichoderma reesei is a filamentous fungus which has important biotechnological applications.7 TrMBF1 was identified during the annotation of the EST cDNA library of T. reesei.8 To understand how MBF1 binds to TBP and to other transcription factors enhancing promoter transcription, it is important to have structure information about MBF1 itself, therefore we initiated the study of the three-dimensional structure of TrMBF1 by NMR. As the full-length protein is unstable in solution, we used a shorter construction corresponding to the C-terminal domain (residues 56-155) (Ctd-TrMBF1).

Foi avaliada a influência dos fatores (1) tempo: 10 e 40 minutos; (2) tamanho de partícula: 840 e 420 mm; (3) hidromódulo: 1:50 e 1:100 e (4) temperatura: 40 e 60 °C na extração do 4-nerolidilcatecol, (4-NC) mediante planejamento fatorial "2(4)" em que quatro variáveis foram estudadas em dois níveis (máximo e mínimo). O método de extração foi maceração e a quantificação do 4-nerolidilcatecol foi realizada por cromatografia liquida de alta eficiência (CLAE) com detetor eletroquímico. Os resultados da análise fatorial indicam que o fator principal que favorece a extração do princípio ativo é o tamanho de partícula [efeito (2): 12,2086]. Diminuindo o tamanho de partícula aumenta três vezes a quantidade de 4-nerolidilcatecol extraída, enquanto o tempo de maceração [efeito (1): -0,64198], hidromódulo [efeito (3): 1,069804] e temperatura [efeito (4): -0,64198] não influenciam de forma significativa a extração. As interações de dois fatores: (2:3) tamanho:hidromódulo: 1,181142; (2:1) tamanho:tempo: 0,9435065 e (2:4) tamanho:temperatura: 0,0817575 mostraram que apesar do fator tamanho(2) ter favorecido o processo, quando combinado com os demais fatores, não aumenta a eficiência da extração. A metodologia de otimização mediante análise fatorial aplicada ao processo de extração do 4-nerolidilcatecol demonstra a importância do estudo das interações e não de cada fator isolado. The influence of factors: (1) time, 10 and 40 minutes, (2) particle size, 840 and 420 mm; (3) hydromodule, 1:50 and 1:100, and (4) temperature, 40 and 60 °C, in the extraction of 4-nerolidylcathecol (4-NC) from the roots of P. umbellata using factorial design "2(4)" was studied in two levels (maximal and minimal). The extraction method was maceration and the measurement of 4-NC was by HPLC with electrochemical detection. The results of the factorial analysis indicated that the main factor that increases the extraction of the active principle is particle size [effect (2): 12.2086]. The reduction of the particle size (mesh 60) increases threefold the amount of 4-nerolidylchatecol in the extract, while the time of maceration [effect (1): -0.64198], hydromodule [effect (3): 1.069804] and temperature [effect (4): -0.64198] practically do not influence the extraction. Interaction between two factors (2:3) size-hydromodule 1.181142, (2:1) size-time 0.9435065 and (2:4) size-temperature 0.0817575, showed that although the main factor size (2) increases the efficiency of the process, when one of the other three factors was taken together the amount of 4-NC extracted was not significantly increased. The technique of optimization using factorial analysis to investigate the extraction of 4-nerolylilchatecol showed to be useful to notice the interactions between factors and not only the effect of each isolated factor.

O objetivo do nosso trabalho foi desenvolver um método para avaliação da concentração do ±-tocoferol, considerado o antioxidante lipofílico de maior importância, e do 4-nerolidilcatecol (4-NC), uma substância natural com comprovada ação antioxidante in vitro e in vivo, em matriz biológica (homogeneizado de pele). Utilizamos a cromatografia de alta eficiência acoplada a um detector eletroquímico, sendo que o método apresentou linearidade para as concentrações de 0,025 µg/mL a 0,1 µg/mL para o ±-T (tempo de retenção 3, 4 min) e de 0,15 µg/mL a 2,5 µg/mL para o 4-NC (tempo de retenção 2,06 min), dissolvidos em etanol e etanol:água (1:1). A taxa de recuperação do ±-T adicionado nas concentrações de 0,5; 0,1 e 0,025 µg/mL aos homogeneizados de pele foi de 94,03; 111,2 e 80,7%, respectivamente. A taxa de recuperação de 4-NC adicionado nas concentrações de 2,5; 0,625 e 0,156 µg/mL foi de 103,7; 91,7 e 91,7%. Este método analítico foi e está sendo empregado, com sucesso devido à sua precisão e rapidez, em diversas análises do laboratório. Topical administration of antioxidants, such as ±-tocopherol (±-T), provides an efficient manner of enriching the endogenous cutaneous protection system, and it constitutes a successful strategy for diminishing the ultraviolet radiation-mediated oxidative damage. Besides ±-tocopherol the use of other natural occurring compounds with antioxidant activity has been proposed for the same purpose. The aim of this study was to develop a validated analytical method for the determination of a-tocopherol and 4-nerolidylcathecol (4-NC) concentrations in skin homogenates in a pharmaceutical formulations. We employed liquid chromatography with electrochemical detection. Chromatography was performed on a Supelcosil LC-8, 3 mm, 75x4.6 mm column (Supelco, Bellefonte, PA, USA) with a mobile phase of methanol:water (9:1) for 4-NC and (95:5) for a-T, both containing 20 mM LiClO4 and 2 mM KCl. The flow rate was set at 1.0 ml/min. We established validation parameters including sensitivity, precision, accuracy, stability and found a linear relationship between the concentrations ranges of 0.025 µg/mL to 0.1 µg/mL of ±-T and 0.15 mg/mL to 2.5 mg/mL of 4-NC. The recovery of ±-T from skin homogenates was 94.03, 111.2 and 80.7% for the concentrations of 0.5, 0.1 and 0.025 µg/mL respectively. The recovery for the following concentrations of 4-NC: 2.5, 0.625 and 0.156 µg/mL was 103.7, 91.7 and 91.7%. This analytical procedure has been successfully employed in cutaneous permeation studies, antioxidant activity studies and determinations of 4-NC in Pothomorphe umbellata root extracts.