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1.
J Biol Chem ; 297(5): 101302, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34653507

RESUMO

Cutinases are esterases that release fatty acids from the apoplastic layer in plants. As they accept bulky and hydrophobic substrates, cutinases could be used in many applications, ranging from valorization of bark-rich side streams to plastic recycling. Advancement of these applications, however, requires deeper knowledge of cutinases' biodiversity and structure-function relationships. Here, we mined over 3000 members from carbohydrate esterase family 5 for putative cutinases and condensed it to 151 genes from known or putative lignocellulose-targeting organisms. The 151 genes were subjected to a phylogenetic analysis, which showed that cutinases with available crystal structures were phylogenetically closely related. We then selected nine phylogenic diverse cutinases for recombinant production and characterized their kinetic activity against para-nitrophenol substrates esterified with consecutively longer alkyl chains (pNP-C2 to C16). Each investigated cutinase had a unique activity fingerprint against the tested pNP substrates. The five enzymes with the highest activity on pNP-C12 and C16, indicative of activity on bulky hydrophobic compounds, were selected for in-depth kinetic and structure-function analysis. All five enzymes showed a decrease in kcat values with increasing substrate chain length, whereas KM values and binding energies (calculated from in silico docking analysis) improved. Two cutinases from Fusarium solani and Cryptococcus sp. exhibited outstandingly low KM values, resulting in high catalytic efficiencies toward pNP-C16. Docking analysis suggested that different clades of the phylogenetic tree may harbor enzymes with different modes of substrate interaction, involving a solvent-exposed catalytic triad, a lipase-like lid, or a clamshell-like active site possibly formed by flexible loops.


Assuntos
Hidrolases de Éster Carboxílico , Cryptococcus , Proteínas Fúngicas , Fusarium , Filogenia , Hidrolases de Éster Carboxílico/química , Hidrolases de Éster Carboxílico/genética , Cryptococcus/enzimologia , Cryptococcus/genética , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Fusarium/enzimologia , Fusarium/genética
2.
Appl Biochem Biotechnol ; 193(1): 19-32, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32808247

RESUMO

Cutinase-like enzymes (CLEs) are bi-functional hydrolases, which share the conserved catalytic site of lipase and consensus pentapeptide sequence of cutinase. Here, we have genetically replaced the canonical amino acids (CAA) by their non-canonical fluorinated surrogates to biosynthesize a novel class of congener biocatalyst for esterification of polymeric carbohydrate with long-chain fatty acid. It is a new enzyme-engineering approach used to manipulate industrially relevant biocatalyst through genetic incorporation of new functionally encoded non-canonical amino acids (NCAA). Global fluorination of CLE improved its catalytic, functional, and structural stability. Molecular docking studies confirmed that the fluorinated CLE (FCLE) had developed a binding affinity towards different fatty acids compared with the parent CLE. Importantly, FCLE could catalyze starch oleate synthesis in 24 h with a degree of substitution of 0.3 ± 0.001. Biophysical and microscopic analysis substantiated the efficient synthesis of the ester by FCLE. Our data represent the first step in the generation of an industrially relevant fluorous multifunctional enzyme for facile synthesis of high fatty acid starch esters.


Assuntos
Biocatálise , Hidrolases de Éster Carboxílico/química , Cryptococcus/enzimologia , Proteínas Fúngicas/química , Ácido Oleico/química , Amido/química , Esterificação
3.
Med Mycol ; 58(8): 1138-1148, 2020 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-32246714

RESUMO

Members of the C. neoformans/C. gattiii species complex are an important cause of serious humans infections, including meningoencephalitis. We describe here a 45 kDa extracellular cellulase purified from culture supernatants of C. neoformans var. neoformans. The N-terminal sequence obtained from the purified protein was used to isolate a clone containing the full-length coding sequence from a C. neoformans var. neoformans (strain B-3501A) cDNA library. Bioinformatics analysis indicated that this gene is present, with variable homology, in all sequenced genomes of the C. neoformans/C. gattii species complex. The cDNA clone was used to produce a recombinant 45 kDa protein in E. coli that displayed the ability to convert carboxymethyl cellulose and was therefore designated as NG-Case (standing for Neoformans Gattii Cellulase). To explore its potential use as a vaccine candidate, the recombinant protein was used to immunize mice and was found capable of inducing T helper type 1 responses and delayed-type hypersensitivity reactions, but not immune protection against a highly virulent C. neoformans var grubii strain. These data may be useful to better understand the mechanisms underlying the ability C. neoformans/C. gattii to colonize plant habitats and to interact with the human host during infection.


Assuntos
Celulase/imunologia , Cryptococcus/enzimologia , Proteínas Fúngicas/imunologia , Animais , Carboximetilcelulose Sódica/metabolismo , Celulase/química , Celulase/genética , Celulase/metabolismo , Criptococose/imunologia , Criptococose/microbiologia , Cryptococcus/genética , Cryptococcus/imunologia , Cryptococcus/metabolismo , Cryptococcus neoformans/enzimologia , Cryptococcus neoformans/genética , Cryptococcus neoformans/imunologia , Cryptococcus neoformans/metabolismo , Meios de Cultivo Condicionados , Citocinas/imunologia , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Imunização , Camundongos , Peso Molecular , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/imunologia , Proteínas Recombinantes/metabolismo , Células Th1/imunologia
4.
Biochem Biophys Res Commun ; 506(1): 211-215, 2018 11 17.
Artigo em Inglês | MEDLINE | ID: mdl-30343887

RESUMO

In this study, the combination of two ß-galactosidases to synthesize prebiotic galactooligosaccharides (GOS) was evaluated in terms of total GOS yield as well as GOS structures (chain length). Two different combinations of either Aspergillus oryzae and Cryptococcus laurentii or Aspergillus oryzae and Kluyveromyces lactis were tested to examine the influence of enzyme origin. Neither consecutive nor simultaneous synthesis with A. oryzae and C. laurentii led to an increased GOS yield. However, with the latter, synthesis of higher GOS (≥3 monomer units) was enhanced from 38.5% to 40% with special emphasis of tetra- and pentasaccharides, which increased from 6.7% to 12.8% and from 0.4% to 3.3%, respectively. Additionally, due to the different preferences of the two ß-galactosidases in terms of types of glycosidic linkages, the structural diversity of the final GOS product could be increased. Using K. lactis following the synthesis with A. oryzae increased the yield of total GOS from 24.6% to 33.1%, which was mainly due to the formation of GOS disaccharides. On the other hand, applying A. oryzae as the second enzyme led to a degradation of di- and trisaccharides, and thus total GOS yield was diminished, although the yield of tetrasaccharides could be enhanced. In conclusion, with both studied enzyme combinations it was possible to increase the percentage of higher GOS and reduce the residual lactose content of the final mixture, which is beneficial for subsequent purification processes. Thus, using more than one ß-galactosidase during the synthesis of GOS represents an interesting research area, which should be explored in more detail in the future.


Assuntos
Fungos/enzimologia , Oligossacarídeos/biossíntese , Oligossacarídeos/síntese química , beta-Galactosidase/metabolismo , Aspergillus oryzae/enzimologia , Cryptococcus/enzimologia , Proteínas Fúngicas/metabolismo , Galactose , Kluyveromyces/enzimologia , Estrutura Molecular , Oligossacarídeos/análise , Oligossacarídeos/química , Prebióticos
5.
Appl Biochem Biotechnol ; 184(3): 953-969, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28920164

RESUMO

Naringinase which was extracted from the fermented broth of Cryptococcus albidus was purified about 42-folds with yield 0.7% by sulfate fractionation and chromatography on Toyopearl HW-60, Fractogel DEAE-650-s, and Sepharose 6B columns. Molecular weight of protein determined by gel filtration and SDS-PAGE was 50 kDa. Naringinase of C. albidus includes high content of the dicarbonic and hydrophobic amino acids. Enzyme contains also carbohydrate component, represented by mannose, galactose, rhamnose, ribose, arabinose, xylose, and glucose. The enzyme was optimally active at pH 5.0 and 60 °C. Naringinase was found to exhibit specificity towards p-nitrophenyl-α-L-rhamnose, p-nitrophenyl-ß-D-glucose, naringin, and neohesperidin. Its K m towards naringin was 0.77 mM and the V max was 36 U/mg. Naringinase was inhibited by high concentrations of reaction product-L-rhamnose. Enzyme revealed stability to 20% ethanol and 500 mM glucose in the reaction mixture that makes it possible to forecast its practical use in the food industry in the production of juices and wines.


Assuntos
Cryptococcus/enzimologia , Proteínas Fúngicas , Complexos Multienzimáticos , beta-Glucosidase , Estabilidade Enzimática , Proteínas Fúngicas/química , Proteínas Fúngicas/isolamento & purificação , Temperatura Alta , Concentração de Íons de Hidrogênio , Complexos Multienzimáticos/química , Complexos Multienzimáticos/isolamento & purificação , Especificidade por Substrato , beta-Glucosidase/química , beta-Glucosidase/isolamento & purificação
6.
Appl Microbiol Biotechnol ; 102(2): 743-750, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29159586

RESUMO

Recombinant chimeric α-amylase (AmyP-Cr) was constructed by a catalytic core of α-amylase (AmyP) from a marine metagenomic library and a starch-binding domain (SBDCr) of α-amylase from Cryptococcus sp. S-2. The molecular fusion did not alter optimum pH, optimum temperature, hydrolysis products, and an ability of preferential and rapid degradation towards raw rice starch, but catalytic efficiency and thermostability were remarkably improved compared with those of the wild-type AmyP. AmyP-Cr achieved the final hydrolysis degree of 61.7 ± 1.2% for 10% raw rice starch and 47.3 ± 0.8% for 15% raw rice starch after 4 h at 40 °C with 1.0 U per mg of raw starch. The catalytic efficiency was very high, with 3.6-4.0 times higher than that of AmyP. The enhanced catalytic efficiency was attributed to the better thermostability and the higher adsorption and disruption to raw rice starch caused by SBDCr. The properties of AmyP-Cr open a new way in terms of a new design of raw rice starch processing.


Assuntos
Cryptococcus/enzimologia , Oryza/química , Amido/metabolismo , alfa-Amilases/metabolismo , Catálise , Domínio Catalítico , Cryptococcus/genética , Estabilidade Enzimática , Manipulação de Alimentos , Concentração de Íons de Hidrogênio , Hidrólise , Cinética , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Temperatura , alfa-Amilases/genética
7.
J Biosci Bioeng ; 125(4): 397-406, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29183694

RESUMO

2-Deoxy-scyllo-inosose (DOI) is the first intermediate in the 2-deoxystreptamine-containing aminoglycoside antibiotic biosynthesis pathway and has a six-membered carbocycle structure. DOI is a valuable material because it is easily converted to aromatic compounds and carbasugar derivatives. In this study, we isolated yeast strains capable of assimilating DOI as a carbon source. One of the strains, Cryptococcus podzolicus ND1, mainly converted DOI to scyllo-quercitol and (-)-vibo-quercitol, which is a valuable compound used as an antihypoglycemia agent and as a heat storage material. An NADH-dependent DOI reductase coding gene, DOIR, from C. podzolicus ND1 was cloned and successfully overexpressed in Escherichia coli. The purified protein catalyzed the irreversible reduction of DOI with NADH and converted DOI into (-)-vibo-quercitol. The enzyme had an optimal pH of 8.5 and optimal temperature of 35°C, respectively. The kcat of this enzyme was 9.98 s-1, and the Km values for DOI and NADH were 4.38 and 0.24 mM, respectively. The enzyme showed a strong preference for NADH and showed no activity with NADPH. Multiple-alignment analysis of DOI reductase revealed that it belongs to the GFO_IDH_MocA protein family and is an inositol dehydrogenase homolog in other fungi, such as Cryptococcus gattii, and bacteria, such as Bacillus subtilis. This is the first identification of a DOI-assimilating yeast and a gene involved in DOI metabolism in fungi.


Assuntos
Cryptococcus/genética , Cryptococcus/isolamento & purificação , Inositol/análogos & derivados , Oxirredutases/genética , Oxirredutases/metabolismo , Biocatálise , Clonagem Molecular , Cryptococcus/enzimologia , Escherichia coli/genética , Escherichia coli/metabolismo , Hexosaminas/metabolismo , Inositol/metabolismo , NAD/metabolismo
8.
Int J Biol Macromol ; 104(Pt B): 1682-1691, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28315437

RESUMO

This study provides structural insights into chitin deacetylase, over-expressing under nitrogen limiting condition in Cryptococcus laurentii strain RY1. The enzyme converts chitin, the second most abundant natural biopolymer, to chitosan, which offers tremendous applications in diverse fields. To elucidate the structure-function relationship of this biologically and industrially important enzyme, a homology model of the catalytic domain was constructed. The stability of the structure was assessed by molecular dynamics simulation studies. Tryptophan 151 of the domain was identified to form hydrogen bond and stacking interaction with chitin upon docking. In Silico substitution of Tryptophan (W) to Alanine (A), Phenylalanine (F) and Aspartate (D) corroborated the importance of the Tryptophan residue in interaction with the substrate. This is the first report of unravelling the structural characteristics of chitin deacetylase from Cryptococcus and understanding the approach of the enzyme towards its substrate. Our results would be helpful to perform experimental validations and apply quantum mechanics/molecular mechanics techniques to determine the detailed catalytic mechanism and enhance the industrial potency of the enzyme.


Assuntos
Amidoidrolases/química , Amidoidrolases/metabolismo , Domínio Catalítico , Cryptococcus/enzimologia , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Homologia de Sequência de Aminoácidos , Amidoidrolases/genética , Sequência de Aminoácidos , Quitina/metabolismo , Mutagênese
9.
J Biosci Bioeng ; 122(5): 639-644, 2016 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-27259388

RESUMO

The GAR1 gene, encoding d-galacturonate reductase in Cryptococcus diffluens, was isolated, and the GAR1-expression plasmid was constructed by insertion of GAR1 downstream of the yeast constitutive promoter in the yeast-integrating vector. Recombinant Saccharomyces cerevisiae expressing C. diffluensd-galacturonate reductase from a genome integrated copy of the gene was cultured for use the conversion of d-galacturonic acid to l-galactonic acid. The optimum conditions for l-galactonic acid production were determined in terms of the initial concentration of d-galacturonic acid, fermentation pH, and mixed sugars. The following conditions yielded high efficiency in the conversion of d-galacturonic acid to l-galactonic acid in large-scale cultures: 0.1% initial d-galacturonic acid concentration, pH 3.5, and glucose as additional sugar. The aerobic condition was necessary for the conversion of d-galacturonic acid. Subculture of that recombinant was not showing to decrease of the d-galacturonic acid conversion rate even though it was repeated in ten generations. Culturing in scale-up, the conversion rate of d-galacturonic acid to l-galactonic acid was increased.


Assuntos
Cryptococcus/genética , Fermentação , Álcool Oxidorredutases Dependentes de NAD(+) e NADP(+)/genética , Álcool Oxidorredutases Dependentes de NAD(+) e NADP(+)/metabolismo , Saccharomyces cerevisiae , Açúcares Ácidos/metabolismo , Aerobiose , Cryptococcus/enzimologia , Fermentação/genética , Ácidos Hexurônicos/metabolismo , Organismos Geneticamente Modificados , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo
10.
J Basic Microbiol ; 56(5): 576-9, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-26778162

RESUMO

This study reports the identification of a chitin deacetylase gene in Cryptococcus laurentii strain RY1 over-expressing under nitrogen limitation by differential display. The up-regulation took place in robustly growing cells rather than in starving quiescent autophagic cells. Quantitative Real Time-PCR, enzyme activity in cell lysate and cell wall analysis corroborated the up-regulation of chitin deacetylase under nitrogen limitation. These results suggest chitin deacetylase might play a significant role in nitrogen limiting growth of Cryptococcus laurentii strain RY1.


Assuntos
Amidoidrolases/genética , Cryptococcus/enzimologia , Cryptococcus/crescimento & desenvolvimento , Nitrogênio/deficiência , Amidoidrolases/biossíntese , Cryptococcus/genética , Cryptococcus/metabolismo , Chá de Kombucha/microbiologia , Regulação para Cima
11.
J Biochem ; 159(3): 371-8, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26519738

RESUMO

D-Aspartate oxidase (DDO) catalyzes the oxidative deamination of acidic D-amino acids, whereas neutral and basic D-amino acids are substrates of D-amino acid oxidase (DAO). DDO of the yeast Cryptococcus humicola (ChDDO) has much higher substrate specificity to D-aspartate, but the structural features that confer this specificity have not been elucidated. A three-dimensional model of ChDDO suggested that a histidine residue (His56) in the active site might be involved in the unique substrate specificity, possibly through the interaction with the substrate side chain in the active site. His56 mutants with several different amino acid residues (H56A, H56D, H56F, H56K and H56N) exhibited no significant activity toward acidic D-amino acids, but H56A and H56N mutants gained the ability to utilize neutral D-amino acids as substrates, such as D-methionine, D-phenylalanine and D-glutamine, showing the conversion of ChDDO to DAO by these mutations. This conversion was also demonstrated by the sensitivity of these mutants to competitive inhibitors of DAO. These results and kinetic properties of the mutants show that His56 is involved in the substrate specificity of ChDDO and possibly plays a role in the higher substrate specificity toward D-aspartate.


Assuntos
Cryptococcus/enzimologia , D-Aspartato Oxidase/química , Proteínas Fúngicas/química , Histidina/química , Aminoácidos Neutros/química , Domínio Catalítico , D-Aspartato Oxidase/genética , Ácido D-Aspártico/química , Desaminação , Proteínas Fúngicas/genética , Histidina/genética , Cinética , Modelos Moleculares , Mutagênese Sítio-Dirigida , Especificidade por Substrato/genética
12.
Ukr Biochem J ; 87(3): 23-30, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26502696

RESUMO

Yeast as well as micromycetes α-L-rhamnosidases, currently, are the most promising group of enzymes. Improving of the thermal stability of the enzyme preparation are especially important studies. Increase in stability and efficiency of substrate hydrolysis by α-L-rhamnosidase will improve the production technology of juices and wines. The aim of our study was to investigate the rate of naringin hydrolysis by α-L-rhamnosidase from Cryptococcus albidus, and also some aspects of the thermal denaturation and stabilization of this enzyme. We investigated two forms of α-L-rhamnosidase from C. albidus, which were obtained by cultivation of the producer on two carbon sources--naringin and rhamnose. A comparative study of properties and the process of thermal inactivation of α-L-rhamnosidases showed that the inducer of synthesis had no effect on the efficiency of naringin hydrolysis by the enzyme, but modified thermal stability of the protein molecule. Hydrophobic interactions and the cysteine residues are involved in maintaining of active conformation of the α-L-rhamnosidase molecule. Yeast α-L-rhamnosidase is also stabilized by 0.5% bovine serum albumin and 0.25% glutaraldehyde.


Assuntos
Cryptococcus/enzimologia , Proteínas Fúngicas/química , Glicosídeo Hidrolases/química , Técnicas Bacteriológicas/métodos , Soluções Tampão , Fenômenos Químicos , Cryptococcus/crescimento & desenvolvimento , Estabilidade Enzimática , Indústria Alimentícia , Proteínas Fúngicas/isolamento & purificação , Glicosídeo Hidrolases/isolamento & purificação , Concentração de Íons de Hidrogênio , Temperatura
13.
Braz J Microbiol ; 46(3): 815-23, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26413065

RESUMO

Pectinolytic enzymes are greatly important in winemaking due to their ability to degrade pectic polymers from grape, contributing to enhance process efficiency and wine quality. This study aimed to analyze the occurrence of pectinolytic yeasts during spontaneous fermentation of Argentine Bonarda grape, to select yeasts that produce extracellular pectinases and to characterize their pectinolytic activity under wine-like conditions. Isolated yeasts were grouped using PCR-DGGE and identified by partial sequencing of 26S rRNA gene. Isolates comprised 7 genera, with Aureobasidium pullulans as the most predominant pectinolytic species, followed by Rhodotorula dairenensis and Cryptococcus saitoi. No pectinolytic activity was detected among ascomycetous yeasts isolated on grapes and during fermentation, suggesting a low occurrence of pectinolytic yeast species in wine fermentation ecosystem. This is the first study reporting R. dairenensis and Cr. saitoi species with pectinolytic activity. R. dairenensis GM-15 produced pectinases that proved to be highly active at grape pH, at 12 °C, and under ethanol and SO2 concentrations usually found in vinifications (pectinase activity around 1.1 U/mL). This strain also produced cellulase activity at 12 °C and pH 3.5, but did not produce ß-glucosidase activity under these conditions. The strain showed encouraging enological properties for its potential use in low-temperature winemaking.


Assuntos
Ascomicetos/enzimologia , Cryptococcus/enzimologia , Poligalacturonase/metabolismo , Rhodotorula/enzimologia , Vitis/microbiologia , Vinho/microbiologia , Argentina , Ascomicetos/isolamento & purificação , Cryptococcus/isolamento & purificação , Fermentação/fisiologia , Dados de Sequência Molecular , Tipagem Molecular , Técnicas de Tipagem Micológica , Pectinas/metabolismo , Reação em Cadeia da Polimerase , RNA Ribossômico/genética , Rhodotorula/isolamento & purificação
14.
Braz. j. microbiol ; 46(3): 815-823, July-Sept. 2015. tab, ilus
Artigo em Inglês | LILACS | ID: lil-755801

RESUMO

Pectinolytic enzymes are greatly important in winemaking due to their ability to degrade pectic polymers from grape, contributing to enhance process efficiency and wine quality. This study aimed to analyze the occurrence of pectinolytic yeasts during spontaneous fermentation of Argentine Bonarda grape, to select yeasts that produce extracellular pectinases and to characterize their pectinolytic activity under wine-like conditions. Isolated yeasts were grouped using PCR-DGGE and identified by partial sequencing of 26S rRNA gene. Isolates comprised 7 genera, with Aureobasidium pullulans as the most predominant pectinolytic species, followed by Rhodotorula dairenensis and Cryptococcus saitoi. No pectinolytic activity was detected among ascomycetous yeasts isolated on grapes and during fermentation, suggesting a low occurrence of pectinolytic yeast species in wine fermentation ecosystem. This is the first study reporting R. dairenensis and Cr. saitoi species with pectinolytic activity. R. dairenensis GM-15 produced pectinases that proved to be highly active at grape pH, at 12 °C, and under ethanol and SO2 concentrations usually found in vinifications (pectinase activity around 1.1 U/mL). This strain also produced cellulase activity at 12 °C and pH 3.5, but did not produce β-glucosidase activity under these conditions. The strain showed encouraging enological properties for its potential use in low-temperature winemaking.

.


Assuntos
Ascomicetos/enzimologia , Cryptococcus/enzimologia , Poligalacturonase/metabolismo , Rhodotorula/enzimologia , Vitis/microbiologia , Vinho/microbiologia , Argentina , Ascomicetos/isolamento & purificação , Cryptococcus/isolamento & purificação , Fermentação/fisiologia , Dados de Sequência Molecular , Tipagem Molecular , Técnicas de Tipagem Micológica , Reação em Cadeia da Polimerase , Pectinas/metabolismo , RNA Ribossômico/genética , Rhodotorula/isolamento & purificação
15.
Genome Biol ; 16: 88, 2015 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-25924720

RESUMO

BACKGROUND: Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain atrophy, where protein domains lose a significant number of core structural elements. RESULTS: Here, we implement a new pipeline to systematically identify new cases of domain atrophy across all known protein sequences. The output of this pipeline was carefully checked by hand, which filtered out partial domain instances that were unlikely to represent true domain atrophy due to misannotations or un-annotated sequence fragments. We identify 75 cases of domain atrophy, of which eight cases are found in a three-dimensional protein structure and 67 cases have been inferred based on mapping to a known homologous structure. Domains with structural variations include ancient folds such as the TIM-barrel and Rossmann folds. Most of these domains are observed to show structural loss that does not affect their functional sites. CONCLUSION: Our analysis has significantly increased the known cases of domain atrophy. We discuss specific instances of domain atrophy and see that there has often been a compensatory mechanism that helps to maintain the stability of the partial domain. Our study indicates that although domain atrophy is an extremely rare phenomenon, protein domains under certain circumstances can tolerate extreme mutations giving rise to partial, but functional, domains.


Assuntos
Proteínas de Bactérias/genética , Deleção de Genes , Genes Bacterianos , Luciferases/genética , Oxirredutases/genética , Proteínas de Bactérias/metabolismo , Burkholderia cenocepacia/enzimologia , Burkholderia cenocepacia/genética , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Cryptococcus/enzimologia , Cryptococcus/genética , Escherichia coli/enzimologia , Escherichia coli/genética , Evolução Molecular , Humanos , Lactobacillus/enzimologia , Lactobacillus/genética , Luciferases/metabolismo , Modelos Moleculares , Oxirredutases/metabolismo , Photobacterium/enzimologia , Photobacterium/genética , Filogenia , Estrutura Terciária de Proteína , Pyrococcus furiosus/enzimologia , Pyrococcus furiosus/genética , Staphylococcus aureus/enzimologia , Staphylococcus aureus/genética
16.
Mikrobiol Z ; 76(5): 8-14, 2014.
Artigo em Ucraniano | MEDLINE | ID: mdl-25434209

RESUMO

The component composition of Cryptococcus albidus and Eupenicillium erubescers alpha-L-rhamnosidases have studied. It was shown that enzymes have a monomeric structure. Enzyme preparations of C. albidus and E. erubescens have similar qualitative but differ in quantitative amino acid composition. alpha-L-rhamnosidase of C. albidus characterised by high amount of histidine, proline, cysteine, methionine in compared with alpha-L-rhamnosidase of E. erubescens. alpha-L-Rhamnosidase of E. erubescens, in contrast to the alpha-L-rhamnnosidase of C. albidus, contained higher levels of lysine, arginine, threonine, alanine, isoleucine, leucine, tyrosine, phenylalanine. It is shown that purified preparations of alpha-L-rhamnosidase C. albidus and E. erubescens contained 5 and 1% carbohydrates respectively. Enzyme preparations differ in quantitative monosaccharide composition, which represented by rhanmose, xylose, mannose, galactose and glucose. Furthermore, alpha-L-rhannosidase C. albidus contained fuicose, whereas alpha-L-rhamnosidase E. erubescens--ribose and arabinose. A significant percentage of hydrophobic amino acids, which is 31 and 34% of the total content, and the presence of the carbohydrate component are essential in stabilization of enzymes molecule.


Assuntos
Cryptococcus/enzimologia , Eupenicillium/enzimologia , Glicosídeo Hidrolases/química , Aminoácidos/química , Eletroforese em Gel de Poliacrilamida , Glicosídeo Hidrolases/isolamento & purificação , Peso Molecular , Monossacarídeos/química
17.
Ukr Biochem J ; 86(3): 49-60, 2014.
Artigo em Russo | MEDLINE | ID: mdl-25033554

RESUMO

The influence of cobalt (II, III) coordinative compounds with derivatives of dithiocarbamic acid on Bacillus thuringiensis IMV B-7324 peptidases with elastase and fibrinolytic activity and Eupenicillium erubescens and Cryptococcus albidus alpha-L-rhamnosidases have been studied. Tested coordinative compounds of cobalt (II, III) on the basis of their composition and structure are presented by 6 groups: 1) tetrachlorocobaltates (II) of 3,6-di(R,R')-iminio-1,2,4,5-tetratiane--(RR')2Ditt[CoCl4]; 2) tetrabromocobaltates (II) of 3,6-di(R,R')-iminio-1,2,4,5-tetratiane--(RR')2Ditt[CoBr4]; 3) isothiocyanates of tetra((R,R')-dithiocarbamatoisothiocyanate)cobalt (II)--[Co(RR'Ditc)4](NCS)2]; 4) dithiocarbamates of cobalt (II)--[Co(S2CNRR')2]; 5) dithiocarbamates of cobalt (III)--[Co(S2CNRR')3]; 6) molecular complexes of dithiocarbamates of cobalt (III) with iodine--[Co(S2CNRR')3] x 2I(2). These groups (1-6) are combined by the presence of the same complexing agent (cobalt) and a fragment S2CNRR' in their molecules. Investigated complexes differ by a charge of intrinsic coordination sphere: anionic (1-2), cationic (3) and neutral (4-6). The nature of substituents at nitrogen atoms varies in each group of complexes. It is stated that the studied coordination compounds render both activating and inhibiting effect on enzyme activity, depending on composition, structure, charge of complex, coordination number of complex former and also on the enzyme and strain producer. Maximum effect is achieved by activating of peptidases B. thuringiensis IMV B-7324 with elastase and fibrinolytic activity. So, in order to improve the catalytic properties of peptidase 1, depending on the type of exhibited activity, it is possible to recommend the following compounds: for elastase--coordinately nonsaturated complexes of cobalt (II) (1-4) containing short aliphatic or alicyclic substituents at atoms of nitrogen and increasing activity by 17-100% at an average; for fibrinolytic--neutral dithiocarbamates of cobalt (II, III) (4-5) (by 29-199%). For increasing the fibrinolytic activity of peptidase it is better to use dibenzyl- or ethylphenyldithiocarbamates of cobalt (III), which increase activity by 15-40% at an average. The same complexes, and also compound {(CH2)6}2Ditt[CoCl4] make an activating impact on alpha-L-rhamnosidase C. albidus (by 10-20%).


Assuntos
Proteínas de Bactérias/química , Cobalto/química , Complexos de Coordenação/química , Fibrinolíticos/química , Glicosídeo Hidrolases/química , Elastase Pancreática/química , Peptídeo Hidrolases/química , Tiocarbamatos/química , Bacillus thuringiensis/química , Bacillus thuringiensis/enzimologia , Proteínas de Bactérias/isolamento & purificação , Cryptococcus/química , Cryptococcus/enzimologia , Ativação Enzimática , Eupenicillium/química , Eupenicillium/enzimologia , Fibrinolíticos/isolamento & purificação , Glicosídeo Hidrolases/isolamento & purificação , Concentração de Íons de Hidrogênio , Elastase Pancreática/isolamento & purificação , Peptídeo Hidrolases/isolamento & purificação
18.
Folia Microbiol (Praha) ; 59(1): 9-16, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23722276

RESUMO

The aims of the present study were to isolate new yeasts with high extracellular (exo) invertase activity and to investigate the usability of buffer systems as invertase production media by immobilized yeast cells. Among 70 yeast isolates, Cryptococcus laurentii MT-61 had the highest exo-invertase activity. Immobilization of yeast cells was performed using sodium alginate. Higher exo-invertase activity for immobilized cells was achieved in tris-sucrose buffer system (TSBS) compared to sodium acetate buffer system and potassium phosphate buffer system. TSBS was prepared by dissolving 30 g of sucrose in 1 L of tris buffer solution. The optimum pH, temperature, and incubation time for invertase production with immobilized cells were determined as 8.0, 35 °C and 36 h in TSBS, respectively. Under optimized conditions, maximum exo-invertase activity was found to be 28.4 U/mL in sterile and nonsterile TSBS. Immobilized cells could be reused in 14 and 12 successive cycles in sterile and nonsterile TSBS without any loss in the maximum invertase activity, respectively. This is the first report which showed that immobilized microbial cells could be used as a biocatalyst for exo-invertase production in buffer system. As an additional contribution, a new yeast strain with high invertase activity was isolated.


Assuntos
Células Imobilizadas/enzimologia , Células Imobilizadas/metabolismo , Cryptococcus/enzimologia , Cryptococcus/metabolismo , Meios de Cultura/química , beta-Frutofuranosidase/isolamento & purificação , Biotecnologia/métodos , Soluções Tampão , Concentração de Íons de Hidrogênio , Sacarose , Temperatura , Fatores de Tempo
19.
Mikrobiol Z ; 76(6): 11-8, 2014.
Artigo em Ucraniano | MEDLINE | ID: mdl-25639038

RESUMO

Influence of coordinative compounds of germanium (IV) and stanum (IV) (complexes of germanium (IV) with nicotinamide (Nad) [GeCl2(Nad)4]Cl2 (1) and complexes of stanum (IV) with 2-hydroxybenzoilhydrazone 4-dimetylaminobenzaldehide (2-OH-HBdb) [SnCl4(2-OH-Bdb-H)] (2), 3-hydroxy-2-naphtoilhydrazone 2-hydroxynaphtaldehide (3-OH-H2Lnf) [SnCl3(3-OH-HLnf)] (3) and izonicotinoilhydrazone 2-hydroxyibenzaldehide [SnCl3 (Is·H)] (4) on activity of peptidases 1 and 2 Bacillus thuringiensis, α-L-rhamnosidase Cryptococcus albidus, Eupenicillium erubescens and α-amylase Aspergillus flavus var. oryzae. Results testify that all studied compounds differ on their influence on activity of the enzymes tested: significantly don't change elastolytic activity of peptidases 1 and 2 B. thuringiensis, completely inhibit A. flavus var. oryzae amylase, activate or oppress of α-L-rhamnosidase C. albidus and E. erubescens. Considerable differences in compounds (3, 4) on activity observed in case of the last. It's possible that peculiarity of influence (1) in compare with (2-4) is connected with existence of different central atoms of complexants: germanium (IV) (1) and stanum (IV) (2-4). A certain analogy in oppression of C. albidus α-L-rhamnosidase by compounds (1) and (4) can explain with presence of a pyridinic ring at molecules of their ligands. The less activsty displayed compound (2) with coordinative knot {SnCl4ON}. Nature of compounds (3, 4) activity was absolutely different: essential increase of activity of C. albidus α-L-rhamnosidase and full oppression of E. erubescens α-L-rhamnosidase by compound (3), while the action of compound (4) was feed back. Taking into account identical coordination knot {SnCl3O2N} the major role in this case play change of a hydrazide fragment in molecules of their ligands.


Assuntos
Anti-Infecciosos/farmacologia , Proteínas de Bactérias/metabolismo , Complexos de Coordenação/farmacologia , Proteínas Fúngicas/metabolismo , Germânio/química , Compostos Orgânicos de Estanho/farmacologia , Estanho/química , Anti-Infecciosos/síntese química , Aspergillus flavus/efeitos dos fármacos , Aspergillus flavus/enzimologia , Aspergillus flavus/crescimento & desenvolvimento , Bacillus thuringiensis/efeitos dos fármacos , Bacillus thuringiensis/enzimologia , Bacillus thuringiensis/crescimento & desenvolvimento , Proteínas de Bactérias/antagonistas & inibidores , Benzaldeídos/química , Complexos de Coordenação/síntese química , Cryptococcus/efeitos dos fármacos , Cryptococcus/enzimologia , Cryptococcus/crescimento & desenvolvimento , Eupenicillium/efeitos dos fármacos , Eupenicillium/enzimologia , Eupenicillium/crescimento & desenvolvimento , Proteínas Fúngicas/antagonistas & inibidores , Glicosídeo Hidrolases/antagonistas & inibidores , Glicosídeo Hidrolases/metabolismo , Hidrazonas/química , Testes de Sensibilidade Microbiana , NAD/química , Compostos Orgânicos de Estanho/síntese química , Peptídeo Hidrolases/metabolismo , Relação Estrutura-Atividade
20.
J Microbiol Biotechnol ; 23(10): 1403-12, 2013 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-23851270

RESUMO

Ethanol fuel production from lignocellulosic biomass is emerging as one of the most important technologies for sustainable development. To use this biomass, it is necessary to circumvent the physical and chemical barriers presented by the cohesive combination of the main biomass components, which hinders the hydrolysis of cellulose and hemicellulose into fermentable sugars. This study evaluated the hydrolytic capacity of enzymes produced by yeasts, isolated from the soils of the Brazilian Cerrado biome (savannah) and the Amazon region, on sugarcane bagasse pre-treated with H2SO4. Among the 103 and 214 yeast isolates from the Minas Gerais Cerrado and the Amazon regions, 18 (17.47%) and 11 (5.14%) isolates, respectively, were cellulase-producing. Cryptococcus laurentii was prevalent and produced significant ß- glucosidase levels, which were higher than the endo- and exoglucanase activities. In natura sugarcane bagasse was pre-treated with 2% H2SO4 for 30 min at 150oC. Subsequently, the obtained fibrous residue was subjected to hydrolysis using the Cryptococcus laurentii yeast enzyme extract for 72 h. This enzyme extract promoted the conversion of approximately 32% of the cellulose, of which 2.4% was glucose, after the enzymatic hydrolysis reaction, suggesting that C. laurentii is a good ß-glucosidase producer. The results presented in this study highlight the importance of isolating microbial strains that produce enzymes of biotechnological interest, given their extensive application in biofuel production.


Assuntos
Celulases/metabolismo , Celulose/metabolismo , Cryptococcus/enzimologia , Saccharum/química , Leveduras/enzimologia , Brasil , Celulases/isolamento & purificação , Celulose/isolamento & purificação , Cryptococcus/isolamento & purificação , Hidrólise , Microbiologia do Solo , Leveduras/isolamento & purificação
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