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[PMID]:28142197
[Au] Autor:Kulkarni TS; Khan S; Villagomez R; Mahmood T; Lindahl S; Logan DT; Linares-Pastén JA; Nordberg Karlsson E
[Ad] Endereço:Biotechnology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden.
[Ti] Título:Crystal structure of ß-glucosidase 1A from Thermotoga neapolitana and comparison of active site mutants for hydrolysis of flavonoid glucosides.
[So] Source:Proteins;85(5):872-884, 2017 May.
[Is] ISSN:1097-0134
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The ß-glucosidase TnBgl1A catalyses hydrolysis of O-linked terminal ß-glycosidic bonds at the nonreducing end of glycosides/oligosaccharides. Enzymes with this specificity have potential in lignocellulose conversion (degrading cellobiose to glucose) and conversion of bioactive flavonoids (modification of glycosylation results in modulation of bioavailability). Previous work has shown TnBgl1A to hydrolyse 3, 4' and 7 glucosylation in flavonoids, and although conversion of 3-glucosylated substrate to aglycone was low, it was improved by mutagenesis of residue N220. To further explore structure-function relationships, the crystal structure of the nucleophile mutant TnBgl1A-E349G was determined at 1.9 Å resolution, and docking studies of flavonoid substrates were made to reveal substrate interacting residues. A series of single amino acid changes were introduced in the aglycone binding region [N220(S/F), N221(S/F), F224(I), F310(L/E), and W322(A)] of the wild type. Activity screening was made on eight glucosylated flavonoids, and kinetic parameters were monitored for the flavonoid quercetin-3-glucoside (Q3), as well as for the model substrate para-nitrophenyl-ß-d-glucopyranoside (pNPGlc). Substitution by Ser at N220 or N221 increased the catalytic efficiency on both pNPGlc and Q3. Residue W322 was proven important for substrate accomodation, as mutagenesis to W322A resulted in a large reduction of hydrolytic activity on 3-glucosylated flavonoids. Flavonoid glucoside hydrolysis was unaffected by mutations at positions 224 and 310. The mutations did not significantly affect thermal stability, and the variants kept an apparent unfolding temperature of 101°C. This work pinpoints positions in the aglycone region of TnBgl1A of importance for specificity on flavonoid-3-glucosides, improving the molecular understanding of activity in GH1 enzymes. Proteins 2017; 85:872-884. © 2016 Wiley Periodicals, Inc.
[Mh] Termos MeSH primário: Aminoácidos/química
Proteínas de Bactérias/química
Isoflavonas/química
Quercetina/análogos & derivados
Thermotoga neapolitana/química
beta-Glucosidase/química
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Aminoácidos/metabolismo
Proteínas de Bactérias/genética
Proteínas de Bactérias/metabolismo
Sítios de Ligação
Biocatálise
Cristalografia por Raios X
Isoflavonas/metabolismo
Cinética
Modelos Moleculares
Simulação de Acoplamento Molecular
Mutagênese Sítio-Dirigida
Mutação
Ligação Proteica
Conformação Proteica em alfa-Hélice
Conformação Proteica em Folha beta
Domínios e Motivos de Interação entre Proteínas
Quercetina/química
Quercetina/metabolismo
Relação Estrutura-Atividade
Especificidade por Substrato
Termodinâmica
Thermotoga neapolitana/enzimologia
beta-Glucosidase/genética
beta-Glucosidase/metabolismo
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0 (Bacterial Proteins); 0 (Isoflavones); 0 (daidzein-7-O-beta-D-glucoside); 0YX10VRV6J (isoquercitrin); 9IKM0I5T1E (Quercetin); EC 3.2.1.21 (beta-Glucosidase)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170728
[Lr] Data última revisão:
170728
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170201
[St] Status:MEDLINE
[do] DOI:10.1002/prot.25256


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[PMID]:27678115
[Au] Autor:Lundemo P; Karlsson EN; Adlercreutz P
[Ad] Endereço:Department of Chemistry, Biotechnology, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
[Ti] Título:Eliminating hydrolytic activity without affecting the transglycosylation of a GH1 ß-glucosidase.
[So] Source:Appl Microbiol Biotechnol;101(3):1121-1131, 2017 Feb.
[Is] ISSN:1432-0614
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Unveiling the determinants for transferase and hydrolase activity in glycoside hydrolases would allow using their vast diversity for creating novel transglycosylases, thereby unlocking an extensive toolbox for carbohydrate chemists. Three different amino acid substitutions at position 220 of a GH1 ß-glucosidase from Thermotoga neapolitana caused an increase of the ratio of transglycosylation to hydrolysis (r /r ) from 0.33 to 1.45-2.71. Further increase in r /r was achieved by modulation of pH of the reaction medium. The wild-type enzyme had a pH optimum for both hydrolysis and transglycosylation around 6 and reduced activity at higher pH. Interestingly, the mutants had constant transglycosylation activity over a broad pH range (5-10), while the hydrolytic activity was largely eliminated at pH 10. The results demonstrate that a combination of protein engineering and medium engineering can be used to eliminate the hydrolytic activity without affecting the transglycosylation activity of a glycoside hydrolase. The underlying factors for this success are pursued, and perturbations of the catalytic acid/base in combination with flexibility are shown to be important factors.
[Mh] Termos MeSH primário: Engenharia de Proteínas
beta-Glucosidase/metabolismo
[Mh] Termos MeSH secundário: Substituição de Aminoácidos
Meios de Cultura/química
Escherichia coli/enzimologia
Glicosilação
Concentração de Íons de Hidrogênio
Hidrólise
Cinética
Simulação de Dinâmica Molecular
Mutação
Especificidade por Substrato
Thermotoga neapolitana/enzimologia
beta-Glucosidase/química
beta-Glucosidase/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Culture Media); EC 3.2.1.21 (beta-Glucosidase)
[Em] Mês de entrada:1701
[Cu] Atualização por classe:170224
[Lr] Data última revisão:
170224
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160929
[St] Status:MEDLINE
[do] DOI:10.1007/s00253-016-7833-9


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[PMID]:27457081
[Au] Autor:Boucher N; Noll KM
[Ad] Endereço:Department of Molecular and Cell Biology, University of Connecticut, Unit 3125, 91 N. Eagleville Rd., Storrs, CT, 06269-3125, USA.
[Ti] Título:Substrate adaptabilities of Thermotogae mannan binding proteins as a function of their evolutionary histories.
[So] Source:Extremophiles;20(5):771-83, 2016 Sep.
[Is] ISSN:1433-4909
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:The Thermotogae possess a large number of ATP-binding cassette (ABC) transporters, including two mannan binding proteins, ManD and CelE (previously called ManE). We show that a gene encoding an ancestor of these was acquired by the Thermotogae from the archaea followed by gene duplication. To address the functional evolution of these proteins as a consequence of their evolutionary histories, we measured the binding affinities of ManD and CelE orthologs from representative Thermotogae. Both proteins bind cellobiose, cellotriose, cellotetraose, ß-1,4-mannotriose, and ß-1,4-mannotetraose. The CelE orthologs additionally bind ß-1,4-mannobiose, laminaribiose, laminaritriose and sophorose while the ManD orthologs additionally only weakly bind ß-1,4-mannobiose. The CelE orthologs have higher unfolding temperatures than the ManD orthologs. An examination of codon sites under positive selection revealed that many of these encode residues located near or in the binding site, suggesting that the proteins experienced selective pressures in regions that might have changed their functions. The gene arrangement, phylogeny, binding properties, and putative regulatory networks suggest that the ancestral mannan binding protein was a CelE ortholog which gave rise to the ManD orthologs. This study provides a window on how one class of proteins adapted to new functions and temperatures to fit the physiologies of their new hosts.
[Mh] Termos MeSH primário: Transportadores de Cassetes de Ligação de ATP/genética
Proteínas de Bactérias/genética
Evolução Molecular
Mananas/metabolismo
Thermotoga maritima/genética
Thermotoga neapolitana/genética
[Mh] Termos MeSH secundário: Transportadores de Cassetes de Ligação de ATP/metabolismo
Proteínas de Bactérias/metabolismo
Sítios de Ligação
Transferência Genética Horizontal
Filogenia
Ligação Proteica
Seleção Genética
Especificidade por Substrato
Thermotoga maritima/enzimologia
Thermotoga neapolitana/enzimologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Mannans)
[Em] Mês de entrada:1702
[Cu] Atualização por classe:171013
[Lr] Data última revisão:
171013
[Sb] Subgrupo de revista:IM; S
[Da] Data de entrada para processamento:160727
[St] Status:MEDLINE
[do] DOI:10.1007/s00792-016-0866-2


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[PMID]:27166592
[Au] Autor:Pradhan N; Dipasquale L; d'Ippolito G; Fontana A; Panico A; Pirozzi F; Lens PNL; Esposito G
[Ad] Endereço:Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio, 43, 03043, Cassino, FR, Italy; Institute of Biomolecular Chemistry, Italian National Council of Research, Via Campi Flegrei 34, 80078, Pozzuoli, Napoli, Italy; Department of Civil, Architectural
[Ti] Título:Model development and experimental validation of capnophilic lactic fermentation and hydrogen synthesis by Thermotoga neapolitana.
[So] Source:Water Res;99:225-234, 2016 Aug 01.
[Is] ISSN:1879-2448
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The aim of the present study was to develop a kinetic model for a recently proposed unique and novel metabolic process called capnophilic (CO2-requiring) lactic fermentation (CLF) pathway in Thermotoga neapolitana. The model was based on Monod kinetics and the mathematical expressions were developed to enable the simulation of biomass growth, substrate consumption and product formation. The calibrated kinetic parameters such as maximum specific uptake rate (k), semi-saturation constant (kS), biomass yield coefficient (Y) and endogenous decay rate (kd) were 1.30 h(-1), 1.42 g/L, 0.1195 and 0.0205 h(-1), respectively. A high correlation (>0.98) was obtained between the experimental data and model predictions for both model validation and cross validation processes. An increase of the lactate production in the range of 40-80% was obtained through CLF pathway compared to the classic dark fermentation model. The proposed kinetic model is the first mechanistically based model for the CLF pathway. This model provides useful information to improve the knowledge about how acetate and CO2 are recycled back by Thermotoga neapolitana to produce lactate without compromising the overall hydrogen yield.
[Mh] Termos MeSH primário: Fermentação
Thermotoga neapolitana
[Mh] Termos MeSH secundário: Biomassa
Reatores Biológicos
Hidrogênio/metabolismo
Cinética
Ácido Láctico/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
33X04XA5AT (Lactic Acid); 7YNJ3PO35Z (Hydrogen)
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170902
[Lr] Data última revisão:
170902
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160512
[St] Status:MEDLINE


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[PMID]:27112133
[Au] Autor:Fatima B; Aftab MN; Haq IU
[Ad] Endereço:Institute of Industrial Biotechnology (IIB), GC University, Lahore, Pakistan. bilqeesravian@gmail.com, fatima_gcu@yahoo.com.
[Ti] Título:Cloning, purification, and characterization of xylose isomerase from Thermotoga naphthophila RKU-10.
[So] Source:J Basic Microbiol;56(9):949-62, 2016 Sep.
[Is] ISSN:1521-4028
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:A 1.3 kb xyl-A gene encoding xylose isomerase from a hyperthermophilic eubacterium Thermotoga naphthophila RKU-10 (TnapXI) was cloned and over-expressed in Escherichia coli to produce the enzyme in mesophilic conditions that work at high temperature. The enzyme was concentrated by lyophilization and purified by heat treatment, fractional precipitation, and UNOsphere Q anion-exchange column chromatography to homogeneity level. The apparent molecular mass was estimated by SDS-PAGE to be 49.5 kDa. The active enzyme showed a clear zone on Native-PAGE when stained with 2, 3, 5-triphenyltetrazolium chloride. The optimum temperature and pH for D-glucose to D-fructose isomerization were 98 °C and 7.0, respectively. Xylose isomerase retains 85% of its activity at 50 °C (t1/2 1732 min) for 4 h and 32.5% at 90 °C (t1/2 58 min) for 2 h. It retains 90-95% of its activity at pH 6.5-7.5 for 30 min. The enzyme was highly activated (350%) with the addition of 0.5 mM Co(2+) and to a lesser extent about 180 and 80% with the addition of 5 and 10 mM Mn(2+) and Mg(2+) , respectively but it was inhibited (54-90%) in the presence of 0.5-10 mM Ca(2+) with respect to apo-enzyme. D-glucose isomerization product was also analyzed by Thin Layer Chromatography (Rf 0.65). The enzyme was very stable at neutral pH and sufficiently high temperature and required only a trace amount of Co(2+) for its optimal activity and stability. Overall, 52.2% conversion of D-glucose to D-fructose was achieved by TnapXI. Thus, it has a great potential for industrial applications.
[Mh] Termos MeSH primário: Aldose-Cetose Isomerases/genética
Clonagem Molecular
Thermotoga neapolitana/enzimologia
Thermotoga neapolitana/metabolismo
Xilose/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Eletroforese em Gel de Poliacrilamida
Estabilidade Enzimática
Escherichia coli/genética
Escherichia coli/metabolismo
Frutose/metabolismo
Glucose/metabolismo
Temperatura Alta
Modelos Moleculares
Simulação de Acoplamento Molecular
Análise de Sequência de DNA
Homologia de Sequência
Thermotoga neapolitana/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
30237-26-4 (Fructose); A1TA934AKO (Xylose); EC 5.3.1.- (Aldose-Ketose Isomerases); EC 5.3.1.5 (xylose isomerase); IY9XDZ35W2 (Glucose)
[Em] Mês de entrada:1702
[Cu] Atualização por classe:170217
[Lr] Data última revisão:
170217
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160427
[St] Status:MEDLINE
[do] DOI:10.1002/jobm.201500589


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[PMID]:26187666
[Au] Autor:Kim JS; Yoon BY; Ahn J; Cha J; Ha NC
[Ad] Endereço:Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul, Republic of Korea.
[Ti] Título:Crystal structure of ß-N-acetylglucosaminidase CbsA from Thermotoga neapolitana.
[So] Source:Biochem Biophys Res Commun;464(3):869-74, 2015 Aug 28.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:CbsA from the thermophilic marine bacteria Thermotoga neapolitana is a chitinolyitc enzyme that can cleave a glycosidic bond of the polymer N-acetylglucosamine at the non-reducing end. This enzyme has particularly high activity on di-N-acetylchitobiose. CbsA consists of a family of 3 glycoside hydrolase (GH3)-type catalytic domains and a unique C-terminal domain. The C-terminal domain distinguishes CbsA from other GH3-type enzymes. Sequence analyses have suggested that CbsA has the Asp-His dyad as a general acid/base with the NagZ of Bacillus subtilis and the Salmonella enterica serovar Typhimurium. Here, we determined the crystal structure of CbsA from T. neapolitana at a resolution of 2.0 Å using the Zn-SAD method, revealing a unique homodimeric assembly facilitated by the C-terminal domains in the dimer. We observed that CbsA is strongly inhibited by ZnCl2, and two zinc ions were consistently bound in the active site. Our results can explain the zinc ion's inhibition mechanism in the subfamily of GH3 enzymes, and provide information on the structural diversity and substrate specificity of this hydrolase family.
[Mh] Termos MeSH primário: Acetilglucosaminidase/química
Acetilglucosaminidase/metabolismo
Thermotoga neapolitana/enzimologia
[Mh] Termos MeSH secundário: Bacillus subtilis/enzimologia
Proteínas de Bactérias/química
Proteínas de Bactérias/metabolismo
Sítios de Ligação
Domínio Catalítico
Cristalografia por Raios X
Modelos Moleculares
Conformação Proteica
Multimerização Proteica
Salmonella typhimurium/enzimologia
Especificidade por Substrato
Zinco/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); EC 3.2.1.52 (Acetylglucosaminidase); J41CSQ7QDS (Zinc)
[Em] Mês de entrada:1511
[Cu] Atualização por classe:150811
[Lr] Data última revisão:
150811
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150719
[St] Status:MEDLINE


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[PMID]:26053393
[Au] Autor:Pradhan N; Dipasquale L; d'Ippolito G; Panico A; Lens PN; Esposito G; Fontana A
[Ad] Endereço:Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio, 43, 03043 Cassino, FR, Italy. nirakar.pradhan@gmail.com.
[Ti] Título:Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana.
[So] Source:Int J Mol Sci;16(6):12578-600, 2015 Jun 04.
[Is] ISSN:1422-0067
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production.
[Mh] Termos MeSH primário: Hidrogênio/metabolismo
Thermotoga neapolitana/metabolismo
[Mh] Termos MeSH secundário: Reatores Biológicos
Carbono/metabolismo
Fermentação
Glucose/metabolismo
Concentração de Íons de Hidrogênio
Especificidade por Substrato
Temperatura Ambiente
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; REVIEW
[Nm] Nome de substância:
7440-44-0 (Carbon); 7YNJ3PO35Z (Hydrogen); IY9XDZ35W2 (Glucose)
[Em] Mês de entrada:1602
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150609
[St] Status:MEDLINE
[do] DOI:10.3390/ijms160612578


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[PMID]:25978307
[Au] Autor:Albertini M; Berto P; Vallese F; Di Valentin M; Costantini P; Carbonera D
[Ad] Endereço:Department of Chemical Sciences, University of Padova , Via F. Marzolo 1, 35131 Padova, Italy.
[Ti] Título:Probing the Solvent Accessibility of the [4Fe-4S] Cluster of the Hydrogenase Maturation Protein HydF from Thermotoga neapolitana by HYSCORE and 3p-ESEEM.
[So] Source:J Phys Chem B;119(43):13680-9, 2015 Oct 29.
[Is] ISSN:1520-5207
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The catalytic site of [FeFe]-hydrogenase, the "H-cluster", composed of a [4Fe-4S] unit connected by a cysteinyl residue to a [2Fe] center coordinated by three CO, two CN(-), and a bridging dithiolate, is assembled in a complex maturation pathway, at present not fully characterized, involving three conserved proteins, HydG, HydE, and HydF. HydF is a complex enzyme, which is thought to act as a scaffold and carrier for the [2Fe] subunit of the H-cluster. This maturase protein contains itself a [4Fe-4S] cluster binding site, with three conserved cysteine residues and a noncysteinyl fourth ligand. In this work, we have exploited 3p-ESEEM and HYSCORE spectroscopies to get insight into the structure and the chemical environment of the [4Fe-4S] cluster of HydF from the hyperthermophilic organism Thermotoga neapolitana. The nature of the fourth ligand and the solvent accessibility of the active site comprising the [4Fe-4S] cluster are discussed on the basis of the spectroscopic results obtained upon H/D exchange. We propose that the noncysteinyl ligated Fe atom of the [4Fe-4S] cluster is the site where the [2Fe] subcluster precursor is anchored and finally processed to be delivered to the hydrogenase (HydA).
[Mh] Termos MeSH primário: Hidrogenase/química
Proteínas com Ferro-Enxofre/química
Thermotoga neapolitana/enzimologia
[Mh] Termos MeSH secundário: Espectroscopia de Ressonância de Spin Eletrônica
Hidrogenase/genética
Hidrogenase/metabolismo
Proteínas com Ferro-Enxofre/metabolismo
Solventes/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Iron-Sulfur Proteins); 0 (Solvents); EC 1.12.7.2 (Hydrogenase)
[Em] Mês de entrada:1605
[Cu] Atualização por classe:151029
[Lr] Data última revisão:
151029
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150516
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jpcb.5b03110


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[PMID]:25711178
[Au] Autor:Rather MY; Nordberg Karlsson E; Adlercreutz P
[Ad] Endereço:Department of Biotechnology, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.
[Ti] Título:Complexation of alkyl glycosides with α-cyclodextrin can have drastically different effects on their conversion by glycoside hydrolases.
[So] Source:J Biotechnol;200:52-8, 2015 Apr 20.
[Is] ISSN:1873-4863
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Substrates present in aggregated forms, such as micelles, are often poorly converted by enzymes. Alkyl glycosides constitute typical examples and the critical micelle concentration (CMC) decreases with increasing length of the alkyl group. In this study, possibilities to hydrolyse alkyl glycosides by glycoside hydrolases were explored, and α-cyclodextrin was used as an agent to form inclusion complexes with the alkyl glycosides, thereby preventing micelle formation. The cyclodextrin complexes were accepted as substrates by the enzymes to variable extent. The ß-glucosidases originating from Thermotoga neapolitana (Tn Bgl3B) and from almond were not at all able to hydrolyse alkyl ß-glucosides in the presence of 100mM α-cyclodextrin. However, Aspergillus niger amyloglucosidase readily accepted the complexes as substrates. In reactions involving decyl and dodecyl maltosides, the presence of 100mM α-cyclodextrin caused an increase in reaction rate in most cases, especially at high substrate concentrations. Surprisingly, the amyloglucosidase-catalyzed hydrolysis of octyl-ß-maltoside to glucose and ß-octylglucoside was faster in the presence of α-cyclodextrin than without, even at substrate concentrations below CMC. A possible explanation of the observed rate enhancement is that binding sites on the carbohydrate binding domain of amyloglucosidase, known to bind cyclodextrins, help to guide the alkyl glycoside-cyclodextrin complex to the active site, and thereby promote its conversion.
[Mh] Termos MeSH primário: Glicosídeo Hidrolases/química
Glicosídeos/química
alfa-Ciclodextrinas/química
[Mh] Termos MeSH secundário: Aspergillus niger/enzimologia
Proteínas de Bactérias/química
Proteínas Fúngicas/química
Hidrólise
Micelas
Proteínas de Plantas/química
Prunus dulcis/enzimologia
Thermotoga neapolitana/enzimologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Fungal Proteins); 0 (Glycosides); 0 (Micelles); 0 (Plant Proteins); 0 (alpha-Cyclodextrins); EC 3.2.1.- (Glycoside Hydrolases); Z1LH97KTRM (alpha-cyclodextrin)
[Em] Mês de entrada:1601
[Cu] Atualização por classe:150403
[Lr] Data última revisão:
150403
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150226
[St] Status:MEDLINE


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[PMID]:25708162
[Au] Autor:Puranik R; Quan G; Werner J; Zhou R; Xu Z
[Ti] Título:A pipeline for completing bacterial genomes using in silico and wet lab approaches.
[So] Source:BMC Genomics;16 Suppl 3:S7, 2015.
[Is] ISSN:1471-2164
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Despite the large volume of genome sequencing data produced by next-generation sequencing technologies and the highly sophisticated software dedicated to handling these types of data, gaps are commonly found in draft genome assemblies. The existence of gaps compromises our ability to take full advantage of the genome data. This study aims to identify a practical approach for biologists to complete their own genome assemblies using commonly available tools and resources. RESULTS: A pipeline was developed to assemble complete genomes primarily from the next generation sequencing (NGS) data. The input of the pipeline is paired-end Illumina sequence reads, and the output is a high quality complete genome sequence. The pipeline alternates the employment of computational and biological methods in seven steps. It combines the strengths of de novo assembly, reference-based assembly, customized programming, public databases utilization, and wet lab experimentation. The application of the pipeline is demonstrated by the completion of a bacterial genome, Thermotoga sp. strain RQ7, a hydrogen-producing strain. CONCLUSIONS: The developed pipeline provides an example of effective integration of computational and biological principles. It highlights the complementary roles that in silico and wet lab methodologies play in bioinformatical studies. The constituting principles and methods are applicable to similar studies on both prokaryotic and eukaryotic genomes.
[Mh] Termos MeSH primário: Genoma Bacteriano
Bacilos Gram-Negativos Anaeróbios Retos, Helicoidais e Curvos/classificação
Bacilos Gram-Negativos Anaeróbios Retos, Helicoidais e Curvos/genética
Sequenciamento de Nucleotídeos em Larga Escala
Análise de Sequência de DNA
Software
[Mh] Termos MeSH secundário: Simulação por Computador
Thermotoga maritima/genética
Thermotoga neapolitana/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1509
[Cu] Atualização por classe:151028
[Lr] Data última revisão:
151028
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150225
[St] Status:MEDLINE
[do] DOI:10.1186/1471-2164-16-S3-S7



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