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1.
World J Microbiol Biotechnol ; 40(7): 201, 2024 May 13.
Artigo em Inglês | MEDLINE | ID: mdl-38736020

RESUMO

Cariogenic biofilms have a matrix rich in exopolysaccharides (EPS), mutans and dextrans, that contribute to caries development. Although several physical and chemical treatments can be employed to remove oral biofilms, those are only partly efficient and use of biofilm-degrading enzymes represents an exciting opportunity to improve the performance of oral hygiene products. In the present study, a member of a glycosyl hydrolase family 66 from Flavobacterium johnsoniae (FjGH66) was heterologously expressed and biochemically characterized. The recombinant FjGH66 showed a hydrolytic activity against an early EPS-containing S. mutans biofilm, and, when associated with a α-(1,3)-glucosyl hydrolase (mutanase) from GH87 family, displayed outstanding performance, removing more than 80% of the plate-adhered biofilm. The mixture containing FjGH66 and Prevotella melaninogenica GH87 α-1,3-mutanase was added to a commercial mouthwash liquid to synergistically remove the biofilm. Dental floss and polyethylene disks coated with biofilm-degrading enzymes also degraded plate-adhered biofilm with a high efficiency. The results presented in this study might be valuable for future development of novel oral hygiene products.


Assuntos
Biofilmes , Dextranase , Flavobacterium , Glicosídeo Hidrolases , Streptococcus mutans , Biofilmes/crescimento & desenvolvimento , Dextranase/metabolismo , Dextranase/genética , Flavobacterium/enzimologia , Flavobacterium/genética , Streptococcus mutans/enzimologia , Streptococcus mutans/genética , Glicosídeo Hidrolases/metabolismo , Glicosídeo Hidrolases/genética , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/genética , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Hidrólise , Biotecnologia/métodos
2.
World J Microbiol Biotechnol ; 39(12): 357, 2023 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-37882859

RESUMO

Dental biofilms represent a serious oral health problem playing a key role in the development of caries and other oral diseases. In the present work, we cloned and expressed in E. coli two glucanases, Prevotella melaninogenica mutanase (PmGH87) and Capnocytophaga ochracea dextranase (CoGH66), and characterized them biochemically and biophysically. Their three-dimensional structures were elucidated and discussed. Furthermore, we tested the capacity of the enzymes to hydrolyze mutan and dextran to prevent formation of Streptococcus mutans biofilms, as well as to degrade pre- formed biofilms in low and abundant sugar conditions. The percentage of residual biofilm was calculated for each treatment group in relation to the control, as well as the degree of synergism. Our results suggest that both PmGH87 and CoGH66 are capable of inhibiting biofilm formation grown under limited or abundant sucrose conditions. Degradation of pre-formed biofilms experiments reveal a time-dependent effect for the treatment with each enzyme alone. In addition, a synergistic and dose-dependent effects of the combined enzymatic treatment with the enzymes were observed. For instance, the highest biomass degradation was 95.5% after 30 min treatment for the biofilm grown in low sucrose concentration, and 93.8% after 2 h treatment for the biofilm grown in sugar abundant condition. Strong synergistic effects were observed, with calculated degree of synergism of 5.54 and 3.18, respectively and their structural basis was discussed. Jointly, these data can pave the ground for the development of biomedical applications of the enzymes for controlling growth and promoting degradation of established oral biofilms.


Assuntos
Escherichia coli , Prevotella melaninogenica , Escherichia coli/genética , Biofilmes , Sacarose
3.
J Biol Chem ; 296: 100385, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33556371

RESUMO

Glycoside hydrolases (GHs) are involved in the degradation of a wide diversity of carbohydrates and present several biotechnological applications. Many GH families are composed of enzymes with a single well-defined specificity. In contrast, enzymes from the GH16 family can act on a range of different polysaccharides, including ß-glucans and galactans. SCLam, a GH16 member derived from a soil metagenome, an endo-ß-1,3(4)-glucanase (EC 3.2.1.6), can cleave both ß-1,3 and ß-1,4 glycosidic bonds in glucans, such as laminarin, barley ß-glucan, and cello-oligosaccharides. A similar cleavage pattern was previously reported for other GH16 family members. However, the molecular mechanisms for this dual cleavage activity on (1,3)- and (1,4)-ß-D-glycosidic bonds by laminarinases have not been elucidated. In this sense, we determined the X-ray structure of a presumably inactive form of SCLam cocrystallized with different oligosaccharides. The solved structures revealed general bound products that are formed owing to residual activities of hydrolysis and transglycosylation. Biochemical and biophysical analyses and molecular dynamics simulations help to rationalize differences in activity toward different substrates. Our results depicted a bulky aromatic residue near the catalytic site critical to select the preferable configuration of glycosidic bonds in the binding cleft. Altogether, these data contribute to understanding the structural basis of recognition and hydrolysis of ß-1,3 and ß-1,4 glycosidic linkages of the laminarinase enzyme class, which is valuable for future studies on the GH16 family members and applications related to biomass conversion into feedstocks and bioproducts.


Assuntos
Proteínas de Bactérias/metabolismo , Celulases/metabolismo , Glucanos/metabolismo , Proteínas de Bactérias/química , Sequência de Carboidratos , Domínio Catalítico , Celulases/química , Cristalografia por Raios X/métodos , Glucanos/classificação , Glicosídeos/química , Glicosídeos/metabolismo , Hidrólise , Simulação de Dinâmica Molecular , Microbiologia do Solo , Especificidade por Substrato
4.
Biotechnol Bioeng ; 118(10): 4052-4064, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34232504

RESUMO

The heteropolysaccharide xylan is a valuable source of sustainable chemicals and materials from renewable biomass sources. A complete hydrolysis of this major hemicellulose component requires a diverse set of enzymes including endo-ß-1,4-xylanases, ß-xylosidases, acetylxylan esterases, α-l-arabinofuranosidases, and α-glucuronidases. Notably, the most studied xylanases from glycoside hydrolase family 11 (GH11) have exclusively been endo-ß-1,4- and ß-1,3-xylanases. However, a recent analysis of a metatranscriptome library from a microbial lignocellulose community revealed GH11 enzymes capable of releasing solely xylobiose from xylan. Although initial biochemical studies clearly indicated their xylobiohydrolase mode of action, the structural features that drive this new activity still remained unclear. It was also not clear whether the enzymes acted on the reducing or nonreducing end of the substrate. Here, we solved the crystal structure of MetXyn11 in the apo and xylobiose-bound forms. The structure of MetXyn11 revealed the molecular features that explain the observed pattern on xylooligosaccharides released by this nonreducing end xylobiohydrolase.


Assuntos
Compostagem , Dissacarídeos/química , Glicosídeo Hidrolases/química , Lignina/química , Microbiota/genética , Xilanos/química , Glicosídeo Hidrolases/genética
5.
J Chem Inf Model ; 61(9): 4554-4570, 2021 09 27.
Artigo em Inglês | MEDLINE | ID: mdl-34423980

RESUMO

Bacterial glycoside hydrolase 1 (GH1) enzymes with 6-phospho-ß-galactosidase and 6-phospho-ß-glucosidase activities have the important task of releasing phosphorylated and nonphosphorylated monosaccharides into the cytoplasm. Curiously, dual 6-phospho-ß-galactosidase/6-phospho-ß-glucosidase (dual-phospho) enzymes have broad specificity and are able to hydrolyze galacto- and gluco-derived substrates. This study investigates the structure and substrate specificity of a GH family 1 enzyme from Bacillus licheniformis, hereafter known as BlBglC. The enzyme structure has been solved, and sequence analysis, molecular dynamics simulations, and binding free energy calculations offered evidence of dual-phospho activity. Both test ligands p-nitrophenyl-ß-d-galactoside-6-phosphate (PNP6Pgal) and p-nitrophenyl-ß-d-glucoside-6-phosphate (PNP6Pglc) demonstrated strong binding to BlBglC although the pose and interactions of the PNP6Pglc triplicates were slightly more consistent. Interestingly, known specificity-inducing residues, Gln23 and Trp433, bind strongly to the ligand O3 hydroxyl group in the PNP6Pgal-BlBglC complex and to the ligand O4 hydroxyl group in the PNP6Pglc-BlBglC complex. Additionally, the BlBglC-His124 residue is a major contributor of hydrogen bonds to the PNP6Pgal O3 hydroxyl group but does not form any hydrogen bonds with PNP6Pglc. On the other hand, BlBglC residues Tyr173, Tyr301, Gln302, and Thr321 form hydrogen bonds with PNP6Pglc but not PNP6Pgal. These findings provide important details of the broad specificity of dual-phospho activity GH1 enzymes.


Assuntos
Bacillus licheniformis , Glucosidases , Bacillus licheniformis/metabolismo , Galactosidases , Glucosidases/metabolismo , Glicosídeo Hidrolases/metabolismo , Especificidade por Substrato
6.
World J Microbiol Biotechnol ; 37(10): 169, 2021 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-34487266

RESUMO

The majority of lignocellulosic biomass on the planet originates from plant cell walls, which are complex structures build up mainly by cellulose, hemicellulose and lignin. The largest part of hemicellulose, xylan, is a polymer with a ß-(1→4)-linked xylose residues backbone decorated with α-D-glucopyranosyl uronic acids and/or L-arabinofuranose residues. Xylan is the second most abundant biopolymer in nature, which can be sustainably and efficiently degraded into decorated and undecorated xylooligosaccharides (XOS) using combinations of thermochemical pretreatments and enzymatic hydrolyses, that have broad applications in the food, feed, pharmaceutical and cosmetic industries. Endo-xylanases from different complex carbohydrate-active enzyme (CAZyme) families can be used to cleave the backbone of arabino(glucurono)xylans and xylooligosaccharides and degrade them into short XOS. It has been shown that XOS with a low degree of polymerization have enhanced prebiotic effects conferring health benefits to humans and animals. In this review we describe recent advances in the enzymatic production of XOS from lignocellulosic biomass arabino- and glucuronoxylans and their applications as food and feed additives and health-promoting ingredients. Comparative advantages of xylanases from different CAZy families in XOS production are discussed and potential health benefits of different XOS are presented.


Assuntos
Biotecnologia/tendências , Endo-1,4-beta-Xilanases/química , Glucuronatos/química , Oligossacarídeos/química , Xilanos/química , Biocatálise , Hidrólise
7.
Proteins ; 88(1): 106-112, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31299114

RESUMO

Bovine papillomavirus proteins were extensively studied as a prototype for the human papillomavirus. Here, the crystal structure of the extended E2 DNA-binding domain of the dominant transcription regulator from the bovine papillomavirus strain 1 is described in the space group P31 21. We found two protein functional dimers packed in the asymmetric unit. This new protein arrangement inside the crystal led to the reduction of the mobility of a previously unobserved loop directly involved in the protein-DNA interaction, which was then modeled for the first time.


Assuntos
Papillomavirus Bovino 1/química , Proteínas de Ligação a DNA/química , Proteínas Virais/química , Animais , Bovinos/virologia , Doenças dos Bovinos/virologia , Cristalografia por Raios X , Modelos Moleculares , Infecções por Papillomavirus/veterinária , Infecções por Papillomavirus/virologia , Conformação Proteica , Domínios Proteicos , Multimerização Proteica
8.
Biomacromolecules ; 21(12): 5315-5322, 2020 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-33202126

RESUMO

The use of hydrogen peroxide-releasing enzymes as a component to produce alternative and sustainable antimicrobial materials has aroused interest in the scientific community. However, the preparation of such materials requires an effective enzyme binding method that often involves the use of expensive and toxic chemicals. Here, we describe the development of an enzyme-based hydrogen peroxide-producing regenerated cellulose film (RCF) in which a cellobiohydrolase (TrCBHI) and a cellobiose dehydrogenase (MtCDHA) were efficiently adsorbed, 90.38 ± 2.2 and 82.40 ± 5.7%, respectively, without making use of cross-linkers. The enzyme adsorption kinetics and binding isotherm experiments showed high affinity of the proteins possessing cellulose-binding modules for RCF, suggesting that binding on regenerated cellulose via specific interactions can be an alternative method for enzyme immobilization. Resistance to compression and porosity at a micrometer scale were found to be tunable by changing cellulose concentration prior to film regeneration. The self-degradation process, triggered by stacking TrCBHI and MtCDHA (previously immobilized onto separate RCF), produced 0.15 nmol/min·cm2 of H2O2. Moreover, the production of H2O2 was sustained for at least 24 h reaching a concentration of ∼2 mM. The activity of MtCDHA immobilized on RCF was not affected by reuse for at least 3 days (1 cycle/day), suggesting that no significant enzyme leakage occurred in that timeframe. In the material herein designed, cellulose (regenerated from a 1-ethyl-3-methylimidazolium acetate/dimethyl sulfoxide (DMSO) solution) serves both as support and substrate for the immobilized enzymes. The sequential reaction led to the production of H2O2 at a micromolar-millimolar level revealing the potential use of the material as a self-degradable antimicrobial agent.


Assuntos
Celulose , Peróxido de Hidrogênio , Adsorção , Celulose 1,4-beta-Celobiosidase , Enzimas Imobilizadas
9.
Eur Biophys J ; 49(6): 435-447, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32683479

RESUMO

Bacterial esterases are highly versatile enzymes, currently widely used in detergents, biosurfactants, bioemulsifiers and as biocatalysts in paper and food industries. Present work describes heterologous expression, purification, and biophysical and biochemical characterization of a halotolerant esterase from Bacillus licheniformis (BlEstA). BlEstA preferentially cleaves pNP-octanoate and both activity and stability of the enzyme increased in the presence of 2 M NaCl, and also with several organic solvents (ethanol, methanol and DMSO). Furthermore, BlEstA has considerable emulsifying properties, particularly with olive oil as substrate. Our studies also show that the enzyme is monomeric in solution and its small-angle X-ray scattering low-resolution molecular envelope fits well its high-resolution homology model.


Assuntos
Bacillus licheniformis/enzimologia , Emulsificantes/química , Emulsificantes/metabolismo , Esterases/química , Esterases/metabolismo , Biocatálise , Concentração de Íons de Hidrogênio , Modelos Moleculares , Filogenia , Conformação Proteica , Cloreto de Sódio/farmacologia , Especificidade por Substrato , Temperatura
10.
J Chem Inf Model ; 60(12): 6392-6407, 2020 12 28.
Artigo em Inglês | MEDLINE | ID: mdl-33166469

RESUMO

In bacteria, mono- and disaccharides are phosphorylated during the uptake processes through the vastly spread transport system phosphoenolpyruvate-dependent phosphotransferase. As an initial step in the phosphorylated disaccharide metabolism pathway, 6-phospho-ß-glucosidases and 6-phospho-ß-galactosidases play a crucial role by releasing phosphorylated and nonphosphorylated monosaccharides. However, structural determinants for the specificity of these enzymes still need to be clarified. Here, an X-ray structure of a glycoside hydrolase family 1 enzyme from Bacillus licheniformis, hereafter known as BlBglH, was determined at 2.2 Å resolution, and its substrate specificity was investigated. The sequence of BlBglH was compared to the sequences of 58 other GH1 enzymes using sequence alignments, sequence identity calculations, phylogenetic analysis, and motif discovery. Through these various analyses, BlBglH was found to have sequence features characteristic of the 6-phospho-ß-glucosidase activity enzymes. Motif and structural observations highlighted the importance of loop L8 in 6-phospho-ß-glucosidase activity enzymes. To further affirm enzyme specificity, molecular docking and molecular dynamics simulations were performed using the crystallographic structure of BlBglH. Docking was carried out with a 6-phospho-ß-glucosidase enzyme activity positive and negative control ligand, followed by 400 ns of MD simulations. The positive and negative control ligands were PNP6Pglc and PNP6Pgal, respectively. PNP6Pglc maintained favorable interactions within the active site until the end of the MD simulation, while PNP6Pgal exhibited instability. The favorable binding of substrate stabilized the loops that surround the active site. Binding free energy calculations showed that the PNP6Pglc complex had a substantially lower binding energy compared to the PNP6Pgal complex. Altogether, the findings of this study suggest that BlBglH possesses 6-phospho-ß-glucosidase enzymatic activity and revealed sequence and structural differences between bacterial GH1 enzymes of various activities.


Assuntos
Bacillus licheniformis , Bacillus licheniformis/metabolismo , Biologia Computacional , Glucosidases , Glicosídeo Hidrolases/metabolismo , Simulação de Acoplamento Molecular , Filogenia , Especificidade por Substrato , Raios X
11.
Appl Microbiol Biotechnol ; 104(19): 8309-8326, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32813063

RESUMO

Arabinanases from glycoside hydrolase family GH93 are enzymes with exo-activity that hydrolyze the α-1,5 bonds between arabinose residues present on arabinan. Currently, several initiatives aiming to use byproducts rich in arabinan such as pectin and sugar beet pulp as raw material to produce various compounds of interest are being developed. However, it is necessary to use robust enzymes that have an optimal performance under pH and temperature conditions used in the industrial processes. In this work, the first GH93 from the thermophilic fungus Thermothielavioides terrestris (Abn93T) was heterologously expressed in Aspergillus nidulans, purified and biochemically characterized. The enzyme is a thermophilic glycoprotein (optimum activity at 70 °C) with prolonged stability in acid pHs (4.0 to 6.5). The presence of glycosylation affected slightly the hydrolytic capacity of the enzyme, which was further increased by 34% in the presence of 1 mM CoCl2. Small-angle X-ray scattering results show that Abn93T is a globular-like-shaped protein with a slight bulge at one end. The hydrolytic mechanism of the enzyme was elucidated using capillary zone electrophoresis and molecular docking calculations. Abn93T has an ability to produce (in synergism with arabinofuranosidases) arabinose and arabinobiose from sugar beet arabinan, which can be explored as fermentable sugars and prebiotics. KEY POINTS: • Thermophilic exo-arabinanase from family GH93 • Molecular basis of arabinan depolymerization.


Assuntos
Arabinose , Glicosídeo Hidrolases , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/metabolismo , Simulação de Acoplamento Molecular , Sordariales , Especificidade por Substrato
12.
Trends Biochem Sci ; 40(1): 16-24, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25435400

RESUMO

The crystal structures of three nuclear receptor (NR) complexes have emerged to reveal their multidomain architectures on DNA. These pictures provide unprecedented views of interfacial couplings between the DNA-binding domains (DBDs) and ligand-binding domains (LBDs). The detailed pictures contrast with previous interpretations of low-resolution electron microscopy (EM) and small angle X-ray scattering (SAXS) data, which had suggested a common architecture with noninteracting DBDs and LBDs. Revisiting both historical and recent interpretations of NR architecture, we invoke new principles underlying higher-order quaternary organization and the allosteric transmission of signals between domains. We also discuss how NR architectures are being probed in living cells to understand dimerization and DNA-binding events in real time.


Assuntos
Proteínas de Ligação a DNA/química , Conformação Proteica , Estrutura Terciária de Proteína , Receptores Citoplasmáticos e Nucleares/química , Sítios de Ligação , Cristalografia por Raios X , DNA/química , Proteínas de Ligação a DNA/metabolismo , Ligantes , Microscopia Eletrônica , Receptores Citoplasmáticos e Nucleares/metabolismo , Espalhamento a Baixo Ângulo , Relação Estrutura-Atividade
13.
Trends Biochem Sci ; 40(6): 290-2, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25890866

RESUMO

We recently reviewed full-length nuclear receptor (NR) structures in an Opinion article wherein we carefully evaluated a large body of literature. As heads of three separate laboratories working on NR architectures, we expressed our shared insights and critical comments. One group (Moras et al.) has declined to accept our strong concerns about several of their published reports. We comment on their letter.


Assuntos
Proteínas de Ligação a DNA/química , Conformação Proteica , Estrutura Terciária de Proteína , Receptores Citoplasmáticos e Nucleares/química
14.
Appl Microbiol Biotechnol ; 103(3): 1275-1287, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30547217

RESUMO

Lignocellulose feedstock constitutes the most abundant carbon source in the biosphere; however, its recalcitrance remains a challenge for microbial conversion into biofuel and bioproducts. Bacillus licheniformis is a microbial mesophilic bacterium capable of secreting a large number of glycoside hydrolase (GH) enzymes, including a glycoside hydrolase from GH family 9 (BlCel9). Here, we conducted biochemical and biophysical studies of recombinant BlCel9, and its low-resolution molecular shape was retrieved from small angle X-ray scattering (SAXS) data. BlCel9 is an endoglucanase exhibiting maximum catalytic efficiency at pH 7.0 and 60 °C. Furthermore, it retains 80% of catalytic activity within a broad range of pH values (5.5-8.5) and temperatures (up to 50 °C) for extended periods of time (over 48 h). It exhibits the highest hydrolytic activity against phosphoric acid swollen cellulose (PASC), followed by bacterial cellulose (BC), filter paper (FP), and to a lesser extent carboxymethylcellulose (CMC). The HPAEC-PAD analysis of the hydrolytic products demonstrated that the end product of the enzymatic hydrolysis is primarily cellobiose, and also small amounts of glucose, cellotriose, and cellotetraose are produced. SAXS data analysis revealed that the enzyme adopts a monomeric state in solution and has a molecular mass of 65.8 kDa as estimated from SAXS data. The BlCel9 has an elongated shape composed of an N-terminal family 3 carbohydrate-binding module (CBM3c) and a C-terminal GH9 catalytic domain joined together by 20 amino acid residue long linker peptides. The domains are closely juxtaposed in an extended conformation and form a relatively rigid structure in solution, indicating that the interactions between the CBM3c and GH9 catalytic domains might play a key role in cooperative cellulose biomass recognition and hydrolysis.


Assuntos
Bacillus licheniformis/enzimologia , Bacillus licheniformis/metabolismo , Celulase/metabolismo , Glicosídeo Hidrolases/metabolismo , Lignina/metabolismo , Catálise , Celobiose/biossíntese , Celulose/análogos & derivados , Celulose/biossíntese , Glucose/biossíntese , Concentração de Íons de Hidrogênio , Espalhamento a Baixo Ângulo , Tetroses/biossíntese , Trioses/biossíntese , Difração de Raios X
15.
Appl Microbiol Biotechnol ; 103(19): 8035-8049, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31407040

RESUMO

Biotechnologies that aim to produce renewable fuels, chemicals, and bioproducts from residual ligno(hemi)cellulosic biomass mostly rely on enzymatic depolymerization of plant cell walls (PCW). This process requires an arsenal of diverse enzymes, including xylanases, which synergistically act on the hemicellulose, reducing the long and complex xylan chains to oligomers and simple sugars. Thus, xylanases play a crucial role in PCW depolymerization. Until recently, the largest xylanase family, glycoside hydrolase family 11 (GH11) has been exclusively represented by endo-catalytic ß-1,4- and ß-1,3-xylanases. Analysis of a metatranscriptome library from a microbial lignocellulose community resulted in the identification of an unusual exo-acting GH11 ß-1,4-xylanase (MetXyn11). Detailed characterization has been performed on recombinant MetXyn11 including determination of its low-resolution small-angle X-ray scattering (SAXS) molecular envelope in solution. Our results reveal that MetXyn11 is a monomeric globular enzyme that liberates xylobiose from heteroxylans as the only product. MetXyn11 has an optimal activity in a pH range from 6 to 9 and an optimal temperature of 50 °C. The enzyme maintained above 65% of its original activity in the pH range 5 to 6 after being incubated for 72 h at 50 °C. Addition of the enzyme to a commercial enzymatic cocktail (CelicCtec3) promoted a significant increase of enzymatic hydrolysis yields of hydrothermally pretreated sugarcane bagasse (16% after 24 h of hydrolysis).


Assuntos
Endo-1,4-beta-Xilanases/química , Endo-1,4-beta-Xilanases/metabolismo , Consórcios Microbianos , Dissacarídeos/metabolismo , Endo-1,4-beta-Xilanases/isolamento & purificação , Estabilidade Enzimática , Perfilação da Expressão Gênica , Concentração de Íons de Hidrogênio , Metagenômica , Conformação Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Espalhamento a Baixo Ângulo , Temperatura , Xilanos/metabolismo
16.
Can J Microbiol ; 64(12): 992-1003, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30338698

RESUMO

The phylum Chloroflexi is phylogenetically diverse and is a deeply branching lineage of bacteria that express a broad spectrum of physiological and metabolic capabilities. Members of the order Ktedonobacteriales, including the families Ktedonobacteriaceae, Thermosporotrichaceae, and Thermogemmatisporaceae, all have flexible aerobic metabolisms capable of utilizing a wide range of carbohydrates. A number of species within these families are considered cellulolytic and are capable of using cellulose as a sole carbon and energy source. In contrast, Ktedonobacter racemifer, the type strain of the order, does not appear to possess this cellulolytic phenotype. In this study, we confirmed the ability of Thermogemmatispora sp. strain T81 to hydrolyze cellulose, determined the whole-genome sequence of Thermogemmatispora sp. T81, and using comparative bioinformatics analyses, identified genes encoding putative carbohydrate-active enzymes (CAZymes) in the Thermogemmatispora sp. T81, Thermogemmatispora onikobensis, and Ktedonobacter racemifer genomes. Analyses of the Thermogemmatispora sp. T81 genome identified 64 CAZyme gene sequences belonging to 57 glycoside hydrolase families. The genome of Thermogemmatispora sp. T81 encodes 19 genes for putative extracellular CAZymes, similar to the number of putative extracellular CAZymes identified in T. onikobensis (17) and K. racemifer (17), despite K. racemifer not possessing a cellulolytic phenotype. These results suggest that these members of the order Ktedonobacteriales may use a broader range of carbohydrate polymers than currently described.


Assuntos
Metabolismo dos Carboidratos , Chloroflexi/metabolismo , Celulose/metabolismo , Chloroflexi/genética , Biologia Computacional
17.
J Biol Chem ; 291(45): 23734-23743, 2016 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-27621314

RESUMO

Carbohydrate-binding modules (CBMs) are appended to glycoside hydrolases and can contribute to the degradation of complex recalcitrant substrates such as the plant cell wall. For application in bioethanol production, novel enzymes with high catalytic activity against recalcitrant lignocellulosic material are being explored and developed. In this work, we report the functional and structural study of CBM_E1, which was discovered through a metagenomics approach and is the founding member of a novel CBM family, CBM81. CBM_E1, which is linked to an endoglucanase, displayed affinity for mixed linked ß1,3-ß1,4-glucans, xyloglucan, Avicel, and cellooligosaccharides. The crystal structure of CBM_E1 in complex with cellopentaose displayed a canonical ß-sandwich fold comprising two ß-sheets. The planar ligand binding site, observed in a parallel orientation with the ß-strands, is a typical feature of type A CBMs, although the expected affinity for bacterial crystalline cellulose was not detected. Conversely, the binding to soluble glucans was enthalpically driven, which is typical of type B modules. These unique properties of CBM_E1 are at the interface between type A and type B CBMs.


Assuntos
Bactérias/enzimologia , Celulase/metabolismo , Metagenoma , Saccharum/microbiologia , Microbiologia do Solo , Bactérias/química , Bactérias/genética , Bactérias/metabolismo , Sítios de Ligação , Celulase/química , Celulase/genética , Celulose/metabolismo , Cristalografia por Raios X , Glucanos/metabolismo , Modelos Moleculares , Mutagênese Sítio-Dirigida , Mutação , Oligossacarídeos/metabolismo , Conformação Proteica , Termodinâmica , Xilanos/metabolismo
18.
Proteins ; 85(10): 1931-1943, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28677327

RESUMO

Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase, which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here, we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains, the conserved loop verified in family members assumes a closed conformation in either condition. Therefore, the enzymatic mechanism for the target protein might be different of its homologs. Two crystal forms exhibit two monomers whereas the other two show four monomers in the asymmetric unit. While the biological unit has been characterized as a tetramer, differences of their sizes and symmetry are remarkable. Four conformers identified by Small-Angle X-ray Scattering (SAXS) in a ligand-free solution are related to the low frequency normal modes of the crystallographic structures associated with rigid body-like protomer arrangements responsible for the longitudinal and symmetric adjustments between tetramers. When the substrate is present in solution, only two conformers are selected. The most prominent conformer for each case is associated to a normal mode able to elongate the protein by moving apart two dimers. To our knowledge, this work was the first investigation based on the normal modes that analyzed the quaternary structure variability for an enzyme of the SurE family followed by crystallography and SAXS validation. The combined results raise new directions to study allosteric features of XfSurE protein.


Assuntos
Proteínas de Bactérias/química , Plantas/microbiologia , Xylella/química , Cristalografia por Raios X , Espalhamento a Baixo Ângulo , Xylella/patogenicidade
19.
Biochim Biophys Acta Proteins Proteom ; 1865(4): 395-403, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-28088615

RESUMO

The cellulases from Glycoside Hydrolyses family 12 (GH12) play an important role in cellulose degradation and plant cell wall deconstruction being widely used in a number of bioindustrial processes. Aiming to contribute toward better comprehension of these class of the enzymes, here we describe a high-yield secretion of a endoglucanase GH12 from Aspegillus terreus (AtGH12), which was cloned and expressed in Aspergillus nidulans strain A773. The purified protein was used for complete biochemical and functional characterization. The optimal temperature and pH of the enzyme were 55°C and 5.0 respectively, which has high activity against ß-glucan and xyloglucan and also is active toward glucomannan and CMC. The enzyme retained activity up to 60°C. AtGH12 is strongly inhibited by Cu2+, Fe2+, Cd2+, Mn2+, Ca2+, Zn2+ and EDTA, whereas K+, Tween, Cs+, DMSO, Triton X-100 and Mg2+ enhanced the enzyme activity. Furthermore, SAXS data reveal that the enzyme has a globular shape and CD analysis demonstrated a prevalence of a ß-strand structure corroborating with typical ß-sheets fold commonly found for other endoglucanases from GH12 family.


Assuntos
Aspergillus , Celulase , Clonagem Molecular , Proteínas Fúngicas , Expressão Gênica , Aspergillus/enzimologia , Aspergillus/genética , Celulase/biossíntese , Celulase/química , Celulase/genética , Proteínas Fúngicas/biossíntese , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Proteínas Recombinantes
20.
Analyst ; 142(19): 3707-3714, 2017 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-28849810

RESUMO

Cellulose films as well as chitosan-modified cellulose films of approximately 5 µm thickness, reconstituted from ionic liquid media onto a poly(ethylene-terephthalate) (PET, 6 µm thickness) film with a 5, 10, 20, or 40 µm diameter laser-drilled microhole, show significant current rectification in aqueous NaCl. Reconstituted α-cellulose films provide "cationic diodes" (due to predominant cation conductivity) whereas chitosan-doped cellulose shows "anionic diode" effects (due to predominant anion conductivity). The current rectification, or "ionic diode" behaviour, is investigated as a function of NaCl concentration, pH, microhole diameter, and molecular weight of the chitosan dopant. Future applications are envisaged exploiting the surface charge induced switching of diode currents for signal amplification in sensing.

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